[−] + + List of all items
Structs
- Atom
- AtomMut
- AtomRef
- Error
- FormatMetadata
- Frame
- Match
- PropertiesIter
- Residue
- ResidueRef
- Selection
- Topology
- TopologyRef
- Trajectory
- UnitCell
- UnitCellMut
- UnitCellRef
[−][src]Struct chemfiles::Atom
An Atom is a particle in the current Frame. It stores the following
+atomic properties:
-
+
- atom name; +
- atom type; +
- atom mass; +
- atom charge. +
The atom name is usually an unique identifier (H1, C_a) while the
+atom type will be shared between all particles of the same type: H,
+Ow, CH3.
Implementations
impl Atom[src]
pub fn new<'a>(name: impl Into<&'a str>) -> Atom[src]
Create an atom with the given name, and set the atom type to name.
Example
++let atom = Atom::new("He"); +assert_eq!(atom.name(), "He");
pub fn mass(&self) -> f64[src]
Get the atom mass, in atomic mass units.
+Example
++let atom = Atom::new("He"); +assert_eq!(atom.mass(), 4.002602);
pub fn set_mass(&mut self, mass: f64)[src]
Set the atom mass to mass, in atomic mass units.
Example
++let mut atom = Atom::new("He"); + +atom.set_mass(34.9); +assert_eq!(atom.mass(), 34.9);
pub fn charge(&self) -> f64[src]
Get the atom charge, in number of the electron charge e.
+Example
++let atom = Atom::new("He"); +assert_eq!(atom.charge(), 0.0);
pub fn set_charge(&mut self, charge: f64)[src]
Set the atom charge to charge, in number of the electron charge e.
Example
++let mut atom = Atom::new("He"); + +atom.set_charge(-2.0); +assert_eq!(atom.charge(), -2.0);
pub fn name(&self) -> String[src]
pub fn atomic_type(&self) -> String[src]
pub fn set_name<'a>(&mut self, name: impl Into<&'a str>)[src]
Set the atom name to name.
Example
++let mut atom = Atom::new("He"); + +atom.set_name("Zn3"); +assert_eq!(atom.name(), "Zn3");
pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>)[src]
Set the atom type to atomic_type.
Example
++let mut atom = Atom::new("He"); + +atom.set_atomic_type("F"); +assert_eq!(atom.atomic_type(), "F");
pub fn full_name(&self) -> String[src]
Try to get the full name of the atom from the atomic type. For example, +the full name of "He" is "Helium", and so on. If the name can not be +found, this function returns the empty string.
+Example
++let atom = Atom::new("Zn"); +assert_eq!(atom.full_name(), "Zinc");
pub fn vdw_radius(&self) -> f64[src]
Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").vdw_radius(), 1.4); +assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);
pub fn covalent_radius(&self) -> f64[src]
Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").covalent_radius(), 0.32); +assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);
pub fn atomic_number(&self) -> u64[src]
Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").atomic_number(), 2); +assert_eq!(Atom::new("Xxx").atomic_number(), 0);
pub fn set(&mut self, name: &str, property: impl Into<Property>)[src]
Add a new property with the given name to this atom.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
++let mut atom = Atom::new("He"); +atom.set("a bool", true); +atom.set("a string", "test"); + +assert_eq!(atom.get("a bool"), Some(Property::Bool(true))); +assert_eq!(atom.get("a string"), Some(Property::String("test".into())));
pub fn get(&self, name: &str) -> Option<Property>[src]
Get a property with the given name in this atom, if it exist.
Examples
++let mut atom = Atom::new("He"); +atom.set("foo", Property::Double(22.2)); + +assert_eq!(atom.get("foo"), Some(Property::Double(22.2))); +assert_eq!(atom.get("Bar"), None);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);[src]
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this atom
+Examples
++let mut atom = Atom::new("He"); +atom.set("foo", Property::Double(22.2)); +atom.set("bar", Property::Bool(false)); + +for (name, property) in atom.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(22.2)); + } else if name == "bar" { + assert_eq!(property, Property::Bool(false)); + } +}
Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Atom
impl !Send for Atom
impl !Sync for Atom
impl Unpin for Atom
impl UnwindSafe for Atom
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized, [src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized, [src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized, [src]
T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T[src]
impl<T> From<T> for T[src]
impl<T, U> Into<U> for T where
U: From<T>, [src]
U: From<T>,
impl<T> ToOwned for T where
T: Clone, [src]
T: Clone,
type Owned = T
The resulting type after obtaining ownership.
+pub fn to_owned(&self) -> T[src]
pub fn clone_into(&self, target: &mut T)[src]
impl<T, U> TryFrom<U> for T where
U: Into<T>, [src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
+pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>, [src]
U: TryFrom<T>,
[−][src]Struct chemfiles::AtomMut
An analog to a mutable reference to an atom (&mut Atom)
Methods from Deref<Target = Atom>
pub fn mass(&self) -> f64[src]
Get the atom mass, in atomic mass units.
+Example
++let atom = Atom::new("He"); +assert_eq!(atom.mass(), 4.002602);
pub fn set_mass(&mut self, mass: f64)[src]
Set the atom mass to mass, in atomic mass units.
Example
++let mut atom = Atom::new("He"); + +atom.set_mass(34.9); +assert_eq!(atom.mass(), 34.9);
pub fn charge(&self) -> f64[src]
Get the atom charge, in number of the electron charge e.
+Example
++let atom = Atom::new("He"); +assert_eq!(atom.charge(), 0.0);
pub fn set_charge(&mut self, charge: f64)[src]
Set the atom charge to charge, in number of the electron charge e.
Example
++let mut atom = Atom::new("He"); + +atom.set_charge(-2.0); +assert_eq!(atom.charge(), -2.0);
pub fn name(&self) -> String[src]
pub fn atomic_type(&self) -> String[src]
pub fn set_name<'a>(&mut self, name: impl Into<&'a str>)[src]
Set the atom name to name.
Example
++let mut atom = Atom::new("He"); + +atom.set_name("Zn3"); +assert_eq!(atom.name(), "Zn3");
pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>)[src]
Set the atom type to atomic_type.
Example
++let mut atom = Atom::new("He"); + +atom.set_atomic_type("F"); +assert_eq!(atom.atomic_type(), "F");
pub fn full_name(&self) -> String[src]
Try to get the full name of the atom from the atomic type. For example, +the full name of "He" is "Helium", and so on. If the name can not be +found, this function returns the empty string.
+Example
++let atom = Atom::new("Zn"); +assert_eq!(atom.full_name(), "Zinc");
pub fn vdw_radius(&self) -> f64[src]
Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").vdw_radius(), 1.4); +assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);
pub fn covalent_radius(&self) -> f64[src]
Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").covalent_radius(), 0.32); +assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);
pub fn atomic_number(&self) -> u64[src]
Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").atomic_number(), 2); +assert_eq!(Atom::new("Xxx").atomic_number(), 0);
pub fn set(&mut self, name: &str, property: impl Into<Property>)[src]
Add a new property with the given name to this atom.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
++let mut atom = Atom::new("He"); +atom.set("a bool", true); +atom.set("a string", "test"); + +assert_eq!(atom.get("a bool"), Some(Property::Bool(true))); +assert_eq!(atom.get("a string"), Some(Property::String("test".into())));
pub fn get(&self, name: &str) -> Option<Property>[src]
Get a property with the given name in this atom, if it exist.
Examples
++let mut atom = Atom::new("He"); +atom.set("foo", Property::Double(22.2)); + +assert_eq!(atom.get("foo"), Some(Property::Double(22.2))); +assert_eq!(atom.get("Bar"), None);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);[src]
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this atom
+Examples
++let mut atom = Atom::new("He"); +atom.set("foo", Property::Double(22.2)); +atom.set("bar", Property::Bool(false)); + +for (name, property) in atom.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(22.2)); + } else if name == "bar" { + assert_eq!(property, Property::Bool(false)); + } +}
Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for AtomMut<'a>
impl<'a> !Send for AtomMut<'a>
impl<'a> !Sync for AtomMut<'a>
impl<'a> Unpin for AtomMut<'a>
impl<'a> !UnwindSafe for AtomMut<'a>
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized, [src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized, [src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized, [src]
T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T[src]
impl<T> From<T> for T[src]
impl<T, U> Into<U> for T where
U: From<T>, [src]
U: From<T>,
impl<T, U> TryFrom<U> for T where
U: Into<T>, [src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
+pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>, [src]
U: TryFrom<T>,
[−][src]Struct chemfiles::AtomRef
An analog to a reference to an atom (&Atom)
Methods from Deref<Target = Atom>
pub fn mass(&self) -> f64[src]
Get the atom mass, in atomic mass units.
+Example
++let atom = Atom::new("He"); +assert_eq!(atom.mass(), 4.002602);
pub fn charge(&self) -> f64[src]
Get the atom charge, in number of the electron charge e.
+Example
++let atom = Atom::new("He"); +assert_eq!(atom.charge(), 0.0);
pub fn name(&self) -> String[src]
pub fn atomic_type(&self) -> String[src]
pub fn full_name(&self) -> String[src]
Try to get the full name of the atom from the atomic type. For example, +the full name of "He" is "Helium", and so on. If the name can not be +found, this function returns the empty string.
+Example
++let atom = Atom::new("Zn"); +assert_eq!(atom.full_name(), "Zinc");
pub fn vdw_radius(&self) -> f64[src]
Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").vdw_radius(), 1.4); +assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);
pub fn covalent_radius(&self) -> f64[src]
Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").covalent_radius(), 0.32); +assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);
pub fn atomic_number(&self) -> u64[src]
Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").atomic_number(), 2); +assert_eq!(Atom::new("Xxx").atomic_number(), 0);
pub fn get(&self, name: &str) -> Option<Property>[src]
Get a property with the given name in this atom, if it exist.
Examples
++let mut atom = Atom::new("He"); +atom.set("foo", Property::Double(22.2)); + +assert_eq!(atom.get("foo"), Some(Property::Double(22.2))); +assert_eq!(atom.get("Bar"), None);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);[src]
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this atom
+Examples
++let mut atom = Atom::new("He"); +atom.set("foo", Property::Double(22.2)); +atom.set("bar", Property::Bool(false)); + +for (name, property) in atom.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(22.2)); + } else if name == "bar" { + assert_eq!(property, Property::Bool(false)); + } +}
Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for AtomRef<'a>
impl<'a> !Send for AtomRef<'a>
impl<'a> !Sync for AtomRef<'a>
impl<'a> Unpin for AtomRef<'a>
impl<'a> UnwindSafe for AtomRef<'a>
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized, [src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized, [src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized, [src]
T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T[src]
impl<T> From<T> for T[src]
impl<T, U> Into<U> for T where
U: From<T>, [src]
U: From<T>,
impl<T, U> TryFrom<U> for T where
U: Into<T>, [src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
+pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>, [src]
U: TryFrom<T>,
[−][src]Struct chemfiles::Error
Error type for Chemfiles.
++ Fields
status: StatusThe error status code
+message: StringA message describing the error cause
+Implementations
impl Error[src]
pub fn last_error() -> String[src]
Get the last error message from the C++ library.
+pub fn cleanup()[src]
Clear any error from the C++ library
+Trait Implementations
impl Clone for Error[src]
impl Debug for Error[src]
impl Display for Error[src]
impl Error for Error[src]
fn description(&self) -> &str[src]
fn source(&self) -> Option<&(dyn Error + 'static)>1.30.0[src]
fn backtrace(&self) -> Option<&Backtrace>[src]
fn cause(&self) -> Option<&dyn Error>1.0.0[src]
impl From<chfl_status> for Error[src]
impl PartialEq<Error> for Error[src]
impl StructuralPartialEq for Error[src]
Auto Trait Implementations
impl RefUnwindSafe for Error
impl Send for Error
impl Sync for Error
impl Unpin for Error
impl UnwindSafe for Error
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized, [src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized, [src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized, [src]
T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T[src]
impl<T> From<T> for T[src]
impl<T, U> Into<U> for T where
U: From<T>, [src]
U: From<T>,
impl<T> ToOwned for T where
T: Clone, [src]
T: Clone,
type Owned = T
The resulting type after obtaining ownership.
+pub fn to_owned(&self) -> T[src]
pub fn clone_into(&self, target: &mut T)[src]
impl<T> ToString for T where
T: Display + ?Sized, [src]
T: Display + ?Sized,
impl<T, U> TryFrom<U> for T where
U: Into<T>, [src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
+pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>, [src]
U: TryFrom<T>,
[−][src]Struct chemfiles::FormatMetadata
FormatMetadata contains metdata associated with one format.
+ Fields
name: &'static strName of the format.
+extension: Option<&'static str>Extension associated with the format.
+description: &'static strExtended, user-facing description of the format.
+reference: &'static strURL pointing to the format definition/reference.
+read: boolIs reading files in this format implemented?
+write: boolIs writing files in this format implemented?
+memory: boolDoes this format support in-memory IO?
+positions: boolDoes this format support storing atomic positions?
+velocities: boolDoes this format support storing atomic velocities?
+unit_cell: boolDoes this format support storing unit cell information?
+atoms: boolDoes this format support storing atom names or types?
+bonds: boolDoes this format support storing bonds between atoms?
+residues: boolDoes this format support storing residues?
+Trait Implementations
impl Clone for FormatMetadata[src]
fn clone(&self) -> FormatMetadata[src]
fn clone_from(&mut self, source: &Self)1.0.0[src]
impl Debug for FormatMetadata[src]
impl Eq for FormatMetadata[src]
impl PartialEq<FormatMetadata> for FormatMetadata[src]
fn eq(&self, other: &FormatMetadata) -> bool[src]
fn ne(&self, other: &FormatMetadata) -> bool[src]
impl StructuralEq for FormatMetadata[src]
impl StructuralPartialEq for FormatMetadata[src]
Auto Trait Implementations
impl RefUnwindSafe for FormatMetadata
impl Send for FormatMetadata
impl Sync for FormatMetadata
impl Unpin for FormatMetadata
impl UnwindSafe for FormatMetadata
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized, [src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized, [src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized, [src]
T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T[src]
impl<T> From<T> for T[src]
impl<T, U> Into<U> for T where
U: From<T>, [src]
U: From<T>,
impl<T> ToOwned for T where
T: Clone, [src]
T: Clone,
type Owned = T
The resulting type after obtaining ownership.
+pub fn to_owned(&self) -> T[src]
pub fn clone_into(&self, target: &mut T)[src]
impl<T, U> TryFrom<U> for T where
U: Into<T>, [src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
+pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>, [src]
U: TryFrom<T>,
[−][src]Struct chemfiles::Frame
A Frame contains data from one simulation step: the current unit
+cell, the topology, the positions, and the velocities of the particles in
+the system. If some information is missing (topology or velocity or unit
+cell), the corresponding data is filled with a default value.
Implementations
impl Frame[src]
pub fn new() -> Frame[src]
Create an empty frame. It will be resized by the library as needed.
+Example
++let frame = Frame::new(); + +assert_eq!(frame.size(), 0);
pub fn atom(&self, index: usize) -> AtomRef<'_>[src]
Get a reference to the atom at the given index in this frame.
Panics
+If index is out of bounds.
Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("Zn"), [0.0; 3], None); + +let atom = frame.atom(0); +assert_eq!(atom.name(), "Zn");
pub fn atom_mut(&mut self, index: usize) -> AtomMut<'_>[src]
Get a mutable reference to the atom at the given index in this frame.
Panics
+If index is out of bounds.
Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("Zn"), [0.0; 3], None); + +assert_eq!(frame.atom(0).name(), "Zn"); + +frame.atom_mut(0).set_name("Fe"); +assert_eq!(frame.atom(0).name(), "Fe");
pub fn size(&self) -> usize[src]
Get the current number of atoms in this frame.
+Example
++let mut frame = Frame::new(); +assert_eq!(frame.size(), 0); + +frame.resize(67); +assert_eq!(frame.size(), 67);
pub fn resize(&mut self, natoms: usize)[src]
Resize the positions and the velocities in this frame, to make space for
+natoms atoms. Previous data is conserved, as well as the presence of
+absence of velocities.
Example
++let mut frame = Frame::new(); +frame.resize(67); +assert_eq!(frame.size(), 67);
pub fn add_atom(
&mut self,
atom: &Atom,
position: [f64; 3],
velocity: impl Into<Option<[f64; 3]>>
)[src]
&mut self,
atom: &Atom,
position: [f64; 3],
velocity: impl Into<Option<[f64; 3]>>
)
Add an Atom and the corresponding position and optionally velocity
+data to this frame.
Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("Zn"), [1.0, 1.0, 2.0], None); + +frame.add_velocities(); +frame.add_atom(&Atom::new("Zn"), [-1.0, 1.0, 2.0], [0.2, 0.1, 0.0]);
pub fn remove(&mut self, i: usize)[src]
Remove the atom at index i in this frame.
Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("Zn"), [0.0; 3], None); +frame.add_atom(&Atom::new("Fe"), [0.0; 3], None); +frame.add_atom(&Atom::new("Sn"), [0.0; 3], None); +assert_eq!(frame.size(), 3); + +frame.remove(1); +assert_eq!(frame.size(), 2); +assert_eq!(frame.atom(1).name(), "Sn");
pub fn add_bond(&mut self, i: usize, j: usize)[src]
Add a bond between the atoms at indexes i and j in the frame.
The bond order is set to BondOrder::Unknown.
Example
++let mut frame = Frame::new(); +assert_eq!(frame.topology().bonds_count(), 0); +frame.resize(5); + +frame.add_bond(0, 1); +frame.add_bond(3, 1); +frame.add_bond(2, 4); +assert_eq!(frame.topology().bonds_count(), 3); + +assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown); +assert_eq!(frame.topology().bonds(), vec![[0, 1], [1, 3], [2, 4]]);
pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder)[src]
Add a bond between the atoms at indexes i and j in the frame
+with the given bond order.
Example
++let mut frame = Frame::new(); +assert_eq!(frame.topology().bonds_count(), 0); +frame.resize(2); + +frame.add_bond_with_order(0, 1, BondOrder::Double); +assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Double);
pub fn remove_bond(&mut self, i: usize, j: usize)[src]
Remove any existing bond between the atoms at indexes i and j in
+the frame.
This function does nothing if there is no bond between i and j.
Example
++let mut frame = Frame::new(); +frame.resize(5); + +frame.add_bond(0, 1); +frame.add_bond(3, 1); +frame.add_bond(2, 4); + +let bonds = frame.topology().bonds(); +assert_eq!(bonds, vec![[0, 1], [1, 3], [2, 4]]); + +frame.remove_bond(2, 4); +let bonds = frame.topology().bonds(); +assert_eq!(bonds, vec![[0, 1], [1, 3]]);
pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error>[src]
Add a copy of residue to this frame.
Errors
+This function fails is the residue id is already in this frame's +topology, or if the residue contain atoms that are already in another +residue.
+Example
++let mut frame = Frame::new(); + +let residue = Residue::new("foo"); +frame.add_residue(&residue).unwrap(); + +let topology = frame.topology(); +assert_eq!(topology.residues_count(), 1); +assert_eq!(topology.residue(0).unwrap().name(), "foo");
pub fn distance(&self, i: usize, j: usize) -> f64[src]
Get the distance between the atoms at indexes i and j in this frame,
+accounting for periodic boundary conditions. The result is expressed in
+Angstroms.
Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("B"), [1.0, 2.0, 3.0], None); + +assert_eq!(frame.distance(0, 1), f64::sqrt(14.0));
pub fn angle(&self, i: usize, j: usize, k: usize) -> f64[src]
Get the angle formed by the atoms at indexes i, j and k in this
+frame, accounting for periodic boundary conditions. The result is
+expressed in radians.
Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None); + +assert_eq!(frame.angle(0, 1, 2), f64::consts::PI / 2.0);
pub fn dihedral(&self, i: usize, j: usize, k: usize, m: usize) -> f64[src]
Get the dihedral angle formed by the atoms at indexes i, j, k and
+m in this frame, accounting for periodic boundary conditions. The
+result is expressed in radians.
Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None); +frame.add_atom(&Atom::new("D"), [0.0, 1.0, 1.0], None); + +assert_eq!(frame.dihedral(0, 1, 2, 3), f64::consts::PI / 2.0);
pub fn out_of_plane(&self, i: usize, j: usize, k: usize, m: usize) -> f64[src]
Get the out of plane distance formed by the atoms at indexes i, j,
+k and m in this frame, accounting for periodic boundary conditions.
+The result is expressed in angstroms.
This is the distance between the atom j and the ikm plane. The j atom +is the center of the improper dihedral angle formed by i, j, k and m.
+Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("B"), [0.0, 0.0, 2.0], None); +frame.add_atom(&Atom::new("C"), [1.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("D"), [0.0, 1.0, 0.0], None); + +assert_eq!(frame.out_of_plane(0, 1, 2, 3), 2.0);
pub fn positions(&self) -> &[[f64; 3]][src]
Get a view into the positions of this frame.
+Example
++let mut frame = Frame::new(); +frame.resize(67); + +let positions = frame.positions(); +assert_eq!(positions.len(), 67); +assert_eq!(positions[0], [0.0, 0.0, 0.0]);
pub fn positions_mut(&mut self) -> &mut [[f64; 3]][src]
Get a mutable view into the positions of this frame.
+Example
++let mut frame = Frame::new(); +frame.resize(67); +{ + let positions = frame.positions_mut(); + assert_eq!(positions[0], [0.0, 0.0, 0.0]); + positions[0] = [1.0, 2.0, 3.0]; +} + +let positions = frame.positions(); +assert_eq!(positions[0], [1.0, 2.0, 3.0]);
pub fn velocities(&self) -> &[[f64; 3]][src]
Get a view into the velocities of this frame.
+Example
++let mut frame = Frame::new(); +frame.resize(67); +frame.add_velocities(); + +let velocities = frame.velocities(); +assert_eq!(velocities.len(), 67); +assert_eq!(velocities[0], [0.0, 0.0, 0.0]);
pub fn velocities_mut(&mut self) -> &mut [[f64; 3]][src]
Get a mutable view into the velocities of this frame.
+Example
++let mut frame = Frame::new(); +frame.resize(67); +frame.add_velocities(); +{ + let velocities = frame.velocities_mut(); + assert_eq!(velocities[0], [0.0, 0.0, 0.0]); + velocities[0] = [1.0, 2.0, 3.0]; +} + +let velocities = frame.velocities(); +assert_eq!(velocities[0], [1.0, 2.0, 3.0]);
pub fn has_velocities(&self) -> bool[src]
Check if this frame contains velocity data.
+Example
++let mut frame = Frame::new(); +assert_eq!(frame.has_velocities(), false); + +frame.add_velocities(); +assert_eq!(frame.has_velocities(), true);
pub fn add_velocities(&mut self)[src]
Add velocity data to this frame. If the frame already have velocities, +this does nothing.
+Example
++let mut frame = Frame::new(); +assert_eq!(frame.has_velocities(), false); + +frame.add_velocities(); +assert_eq!(frame.has_velocities(), true);
pub fn cell(&self) -> UnitCellRef<'_>[src]
Get a reference to the UnitCell from this frame.
Example
++let frame = Frame::new(); + +let cell = frame.cell(); +assert_eq!(cell.shape(), CellShape::Infinite);
pub fn cell_mut(&mut self) -> UnitCellMut<'_>[src]
Get a mutable reference to the UnitCell from this frame.
Example
++let mut frame = Frame::new(); + +assert_eq!(frame.cell().shape(), CellShape::Infinite); + +frame.cell_mut().set_shape(CellShape::Triclinic).unwrap(); +assert_eq!(frame.cell().shape(), CellShape::Triclinic);
pub fn set_cell(&mut self, cell: &UnitCell)[src]
Set the UnitCell of this frame to cell.
Example
++let mut frame = Frame::new(); + +frame.set_cell(&UnitCell::new([10.0, 10.0, 10.0])); + +let cell = frame.cell(); +assert_eq!(cell.shape(), CellShape::Orthorhombic); +assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);
pub fn topology(&self) -> TopologyRef<'_>[src]
Get a reference to the Topology of this frame.
Example
++let mut frame = Frame::new(); +frame.resize(42); + +let topology = frame.topology(); +assert_eq!(topology.size(), 42);
pub fn set_topology(&mut self, topology: &Topology) -> Result<(), Error>[src]
Set the Topology of this frame to topology.
Errors
+This function fails if the topology contains a different number of atoms +than this frame.
+Example
++let mut frame = Frame::new(); +frame.resize(2); + +let mut topology = Topology::new(); +topology.add_atom(&Atom::new("Cl")); +topology.add_atom(&Atom::new("Cl")); +topology.add_bond(0, 1); + +frame.set_topology(&topology).unwrap(); +assert_eq!(frame.atom(0).name(), "Cl");
pub fn step(&self) -> usize[src]
Get this frame step, i.e. the frame number in the trajectory
+Example
++let frame = Frame::new(); +assert_eq!(frame.step(), 0);
pub fn set_step(&mut self, step: usize)[src]
Set this frame step to step.
Example
++let mut frame = Frame::new(); +assert_eq!(frame.step(), 0); + +frame.set_step(10); +assert_eq!(frame.step(), 10);
pub fn guess_bonds(&mut self) -> Result<(), Error>[src]
Guess the bonds, angles and dihedrals in this frame.
The bonds are guessed using a distance-based algorithm, and then angles +and dihedrals are guessed from the bonds.
+Errors
+This function can fail if the covalent radius is unknown for some atoms +in the frame.
+Example
++let mut frame = Frame::new(); + +frame.add_atom(&Atom::new("Cl"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("Cl"), [1.5, 0.0, 0.0], None); +assert_eq!(frame.topology().bonds_count(), 0); + +frame.guess_bonds().unwrap(); +assert_eq!(frame.topology().bonds_count(), 1);
pub fn clear_bonds(&mut self)[src]
Remove all existing bonds, angles, dihedral angles and improper +dihedral angles in the topology of the frame.
+Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("H"), [0.0, 1.0, 0.0], None); + +frame.add_bond(0, 1); +frame.add_bond(1, 2); + +assert_eq!(frame.topology().bonds().len(), 2); +assert_eq!(frame.topology().angles().len(), 1); + +frame.clear_bonds(); +assert!(frame.topology().bonds().is_empty()); +assert!(frame.topology().angles().is_empty());
pub fn set(&mut self, name: &str, property: impl Into<Property>)[src]
Add a new property with the given name to this frame.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
++let mut frame = Frame::new(); +frame.set("a string", "hello"); +frame.set("a double", 4.3); + +assert_eq!(frame.get("a string"), Some(Property::String("hello".into()))); +assert_eq!(frame.get("a double"), Some(Property::Double(4.3)));
pub fn get(&self, name: &str) -> Option<Property>[src]
Get a property with the given name in this frame, if it exist.
Examples
++let mut frame = Frame::new(); +frame.set("foo", Property::Double(22.2)); + +assert_eq!(frame.get("foo"), Some(Property::Double(22.2))); +assert_eq!(frame.get("Bar"), None);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);[src]
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this frame
+Examples
++let mut frame = Frame::new(); +frame.set("foo", Property::Double(22.2)); +frame.set("bar", Property::Bool(false)); + +for (name, property) in frame.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(22.2)); + } else if name == "bar" { + assert_eq!(property, Property::Bool(false)); + } +}
Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Frame
impl !Send for Frame
impl !Sync for Frame
impl Unpin for Frame
impl UnwindSafe for Frame
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized, [src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized, [src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized, [src]
T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T[src]
impl<T> From<T> for T[src]
impl<T, U> Into<U> for T where
U: From<T>, [src]
U: From<T>,
impl<T> ToOwned for T where
T: Clone, [src]
T: Clone,
type Owned = T
The resulting type after obtaining ownership.
+pub fn to_owned(&self) -> T[src]
pub fn clone_into(&self, target: &mut T)[src]
impl<T, U> TryFrom<U> for T where
U: Into<T>, [src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
+pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>, [src]
U: TryFrom<T>,
[−][src]Struct chemfiles::Match
A Match is a set of atomic indexes matching a given selection. It can
+mostly be used like a &[usize].
Implementations
impl Match[src]
pub fn len(&self) -> usize[src]
Get the length of the Match.
+Example
++let atomic_match = Match::new(&[3, 4, 5]); +assert_eq!(atomic_match.len(), 3);
pub fn new(atoms: &[usize]) -> Match[src]
Create a new match containing the atoms in the atoms slice.
Panics
+If the slice contains more than 4 elements, which is the maximal size +of a match.
+Example
++let atomic_match = Match::new(&[3, 4, 5]); +assert_eq!(atomic_match.len(), 3); +assert_eq!(atomic_match[0], 3); +assert_eq!(atomic_match[1], 4); +assert_eq!(atomic_match[2], 5);
pub fn iter(&self) -> Iter<'_, usize>[src]
Iterate over the atomic indexes in the match.
+Example
++let atomic_match = Match::new(&[3, 4, 5]); +let mut iter = atomic_match.iter(); + +assert_eq!(iter.next(), Some(&3)); +assert_eq!(iter.next(), Some(&4)); +assert_eq!(iter.next(), Some(&5)); +assert_eq!(iter.next(), None);
Trait Implementations
impl Clone for Match[src]
impl Debug for Match[src]
impl Eq for Match[src]
impl Index<usize> for Match[src]
type Output = usize
The returned type after indexing.
+fn index(&self, i: usize) -> &Self::Output[src]
impl<'a> IntoIterator for &'a Match[src]
type Item = &'a usize
The type of the elements being iterated over.
+type IntoIter = Iter<'a, usize>
Which kind of iterator are we turning this into?
+fn into_iter(self) -> Iter<'a, usize>[src]
impl PartialEq<Match> for Match[src]
impl StructuralEq for Match[src]
impl StructuralPartialEq for Match[src]
Auto Trait Implementations
impl RefUnwindSafe for Match
impl Send for Match
impl Sync for Match
impl Unpin for Match
impl UnwindSafe for Match
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized, [src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized, [src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized, [src]
T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T[src]
impl<T> From<T> for T[src]
impl<T, U> Into<U> for T where
U: From<T>, [src]
U: From<T>,
impl<T> ToOwned for T where
T: Clone, [src]
T: Clone,
type Owned = T
The resulting type after obtaining ownership.
+pub fn to_owned(&self) -> T[src]
pub fn clone_into(&self, target: &mut T)[src]
impl<T, U> TryFrom<U> for T where
U: Into<T>, [src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
+pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>, [src]
U: TryFrom<T>,
[−][src]Struct chemfiles::PropertiesIter
An iterator over the properties in an atom/frame/residue
+Trait Implementations
impl<'a> Iterator for PropertiesIter<'a>[src]
type Item = (String, Property)
The type of the elements being iterated over.
+fn next(&mut self) -> Option<Self::Item>[src]
fn size_hint(&self) -> (usize, Option<usize>)[src]
fn count(self) -> usize[src]
fn last(self) -> Option<Self::Item>1.0.0[src]
fn advance_by(&mut self, n: usize) -> Result<(), usize>[src]
fn nth(&mut self, n: usize) -> Option<Self::Item>1.0.0[src]
fn step_by(self, step: usize) -> StepBy<Self>1.28.0[src]
fn chain<U>(self, other: U) -> Chain<Self, <U as IntoIterator>::IntoIter> where
U: IntoIterator<Item = Self::Item>, 1.0.0[src]
U: IntoIterator<Item = Self::Item>,
fn zip<U>(self, other: U) -> Zip<Self, <U as IntoIterator>::IntoIter> where
U: IntoIterator, 1.0.0[src]
U: IntoIterator,
fn map<B, F>(self, f: F) -> Map<Self, F> where
F: FnMut(Self::Item) -> B, 1.0.0[src]
F: FnMut(Self::Item) -> B,
fn for_each<F>(self, f: F) where
F: FnMut(Self::Item), 1.21.0[src]
F: FnMut(Self::Item),
fn filter<P>(self, predicate: P) -> Filter<Self, P> where
P: FnMut(&Self::Item) -> bool, 1.0.0[src]
P: FnMut(&Self::Item) -> bool,
fn filter_map<B, F>(self, f: F) -> FilterMap<Self, F> where
F: FnMut(Self::Item) -> Option<B>, 1.0.0[src]
F: FnMut(Self::Item) -> Option<B>,
fn enumerate(self) -> Enumerate<Self>1.0.0[src]
fn peekable(self) -> Peekable<Self>1.0.0[src]
fn skip_while<P>(self, predicate: P) -> SkipWhile<Self, P> where
P: FnMut(&Self::Item) -> bool, 1.0.0[src]
P: FnMut(&Self::Item) -> bool,
fn take_while<P>(self, predicate: P) -> TakeWhile<Self, P> where
P: FnMut(&Self::Item) -> bool, 1.0.0[src]
P: FnMut(&Self::Item) -> bool,
fn map_while<B, P>(self, predicate: P) -> MapWhile<Self, P> where
P: FnMut(Self::Item) -> Option<B>, [src]
P: FnMut(Self::Item) -> Option<B>,
fn skip(self, n: usize) -> Skip<Self>1.0.0[src]
fn take(self, n: usize) -> Take<Self>1.0.0[src]
fn scan<St, B, F>(self, initial_state: St, f: F) -> Scan<Self, St, F> where
F: FnMut(&mut St, Self::Item) -> Option<B>, 1.0.0[src]
F: FnMut(&mut St, Self::Item) -> Option<B>,
fn flat_map<U, F>(self, f: F) -> FlatMap<Self, U, F> where
F: FnMut(Self::Item) -> U,
U: IntoIterator, 1.0.0[src]
F: FnMut(Self::Item) -> U,
U: IntoIterator,
fn flatten(self) -> Flatten<Self> where
Self::Item: IntoIterator, 1.29.0[src]
Self::Item: IntoIterator,
fn fuse(self) -> Fuse<Self>1.0.0[src]
fn inspect<F>(self, f: F) -> Inspect<Self, F> where
F: FnMut(&Self::Item), 1.0.0[src]
F: FnMut(&Self::Item),
fn by_ref(&mut self) -> &mut Self1.0.0[src]
#[must_use =
+ "if you really need to exhaust the iterator, consider `.for_each(drop)` instead"]fn collect<B>(self) -> B where
B: FromIterator<Self::Item>, 1.0.0[src]
B: FromIterator<Self::Item>,
fn partition<B, F>(self, f: F) -> (B, B) where
B: Default + Extend<Self::Item>,
F: FnMut(&Self::Item) -> bool, 1.0.0[src]
B: Default + Extend<Self::Item>,
F: FnMut(&Self::Item) -> bool,
fn partition_in_place<'a, T, P>(self, predicate: P) -> usize where
P: FnMut(&T) -> bool,
Self: DoubleEndedIterator<Item = &'a mut T>,
T: 'a, [src]
P: FnMut(&T) -> bool,
Self: DoubleEndedIterator<Item = &'a mut T>,
T: 'a,
fn is_partitioned<P>(self, predicate: P) -> bool where
P: FnMut(Self::Item) -> bool, [src]
P: FnMut(Self::Item) -> bool,
fn try_fold<B, F, R>(&mut self, init: B, f: F) -> R where
F: FnMut(B, Self::Item) -> R,
R: Try<Ok = B>, 1.27.0[src]
F: FnMut(B, Self::Item) -> R,
R: Try<Ok = B>,
fn try_for_each<F, R>(&mut self, f: F) -> R where
F: FnMut(Self::Item) -> R,
R: Try<Ok = ()>, 1.27.0[src]
F: FnMut(Self::Item) -> R,
R: Try<Ok = ()>,
fn fold<B, F>(self, init: B, f: F) -> B where
F: FnMut(B, Self::Item) -> B, 1.0.0[src]
F: FnMut(B, Self::Item) -> B,
fn fold_first<F>(self, f: F) -> Option<Self::Item> where
F: FnMut(Self::Item, Self::Item) -> Self::Item, [src]
F: FnMut(Self::Item, Self::Item) -> Self::Item,
fn all<F>(&mut self, f: F) -> bool where
F: FnMut(Self::Item) -> bool, 1.0.0[src]
F: FnMut(Self::Item) -> bool,
fn any<F>(&mut self, f: F) -> bool where
F: FnMut(Self::Item) -> bool, 1.0.0[src]
F: FnMut(Self::Item) -> bool,
fn find<P>(&mut self, predicate: P) -> Option<Self::Item> where
P: FnMut(&Self::Item) -> bool, 1.0.0[src]
P: FnMut(&Self::Item) -> bool,
fn find_map<B, F>(&mut self, f: F) -> Option<B> where
F: FnMut(Self::Item) -> Option<B>, 1.30.0[src]
F: FnMut(Self::Item) -> Option<B>,
fn try_find<F, R>(
&mut self,
f: F
) -> Result<Option<Self::Item>, <R as Try>::Error> where
F: FnMut(&Self::Item) -> R,
R: Try<Ok = bool>, [src]
&mut self,
f: F
) -> Result<Option<Self::Item>, <R as Try>::Error> where
F: FnMut(&Self::Item) -> R,
R: Try<Ok = bool>,
fn position<P>(&mut self, predicate: P) -> Option<usize> where
P: FnMut(Self::Item) -> bool, 1.0.0[src]
P: FnMut(Self::Item) -> bool,
fn rposition<P>(&mut self, predicate: P) -> Option<usize> where
P: FnMut(Self::Item) -> bool,
Self: ExactSizeIterator + DoubleEndedIterator, 1.0.0[src]
P: FnMut(Self::Item) -> bool,
Self: ExactSizeIterator + DoubleEndedIterator,
fn max(self) -> Option<Self::Item> where
Self::Item: Ord, 1.0.0[src]
Self::Item: Ord,
fn min(self) -> Option<Self::Item> where
Self::Item: Ord, 1.0.0[src]
Self::Item: Ord,
fn max_by_key<B, F>(self, f: F) -> Option<Self::Item> where
B: Ord,
F: FnMut(&Self::Item) -> B, 1.6.0[src]
B: Ord,
F: FnMut(&Self::Item) -> B,
fn max_by<F>(self, compare: F) -> Option<Self::Item> where
F: FnMut(&Self::Item, &Self::Item) -> Ordering, 1.15.0[src]
F: FnMut(&Self::Item, &Self::Item) -> Ordering,
fn min_by_key<B, F>(self, f: F) -> Option<Self::Item> where
B: Ord,
F: FnMut(&Self::Item) -> B, 1.6.0[src]
B: Ord,
F: FnMut(&Self::Item) -> B,
fn min_by<F>(self, compare: F) -> Option<Self::Item> where
F: FnMut(&Self::Item, &Self::Item) -> Ordering, 1.15.0[src]
F: FnMut(&Self::Item, &Self::Item) -> Ordering,
fn rev(self) -> Rev<Self> where
Self: DoubleEndedIterator, 1.0.0[src]
Self: DoubleEndedIterator,
fn unzip<A, B, FromA, FromB>(self) -> (FromA, FromB) where
FromA: Default + Extend<A>,
FromB: Default + Extend<B>,
Self: Iterator<Item = (A, B)>, 1.0.0[src]
FromA: Default + Extend<A>,
FromB: Default + Extend<B>,
Self: Iterator<Item = (A, B)>,
fn copied<'a, T>(self) -> Copied<Self> where
Self: Iterator<Item = &'a T>,
T: 'a + Copy, 1.36.0[src]
Self: Iterator<Item = &'a T>,
T: 'a + Copy,
fn cloned<'a, T>(self) -> Cloned<Self> where
Self: Iterator<Item = &'a T>,
T: 'a + Clone, 1.0.0[src]
Self: Iterator<Item = &'a T>,
T: 'a + Clone,
fn cycle(self) -> Cycle<Self> where
Self: Clone, 1.0.0[src]
Self: Clone,
fn sum<S>(self) -> S where
S: Sum<Self::Item>, 1.11.0[src]
S: Sum<Self::Item>,
fn product<P>(self) -> P where
P: Product<Self::Item>, 1.11.0[src]
P: Product<Self::Item>,
fn cmp<I>(self, other: I) -> Ordering where
I: IntoIterator<Item = Self::Item>,
Self::Item: Ord, 1.5.0[src]
I: IntoIterator<Item = Self::Item>,
Self::Item: Ord,
fn cmp_by<I, F>(self, other: I, cmp: F) -> Ordering where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,
I: IntoIterator, [src]
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,
I: IntoIterator,
fn partial_cmp<I>(self, other: I) -> Option<Ordering> where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>, 1.5.0[src]
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
fn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering> where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,
I: IntoIterator, [src]
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,
I: IntoIterator,
fn eq<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>, 1.5.0[src]
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>,
fn eq_by<I, F>(self, other: I, eq: F) -> bool where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> bool,
I: IntoIterator, [src]
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> bool,
I: IntoIterator,
fn ne<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>, 1.5.0[src]
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>,
fn lt<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>, 1.5.0[src]
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
fn le<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>, 1.5.0[src]
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
fn gt<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>, 1.5.0[src]
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
fn ge<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>, 1.5.0[src]
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
fn is_sorted(self) -> bool where
Self::Item: PartialOrd<Self::Item>, [src]
Self::Item: PartialOrd<Self::Item>,
fn is_sorted_by<F>(self, compare: F) -> bool where
F: FnMut(&Self::Item, &Self::Item) -> Option<Ordering>, [src]
F: FnMut(&Self::Item, &Self::Item) -> Option<Ordering>,
fn is_sorted_by_key<F, K>(self, f: F) -> bool where
F: FnMut(Self::Item) -> K,
K: PartialOrd<K>, [src]
F: FnMut(Self::Item) -> K,
K: PartialOrd<K>,
Auto Trait Implementations
impl<'a> !RefUnwindSafe for PropertiesIter<'a>
impl<'a> !Send for PropertiesIter<'a>
impl<'a> !Sync for PropertiesIter<'a>
impl<'a> Unpin for PropertiesIter<'a>
impl<'a> !UnwindSafe for PropertiesIter<'a>
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized, [src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized, [src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized, [src]
T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T[src]
impl<T> From<T> for T[src]
impl<T, U> Into<U> for T where
U: From<T>, [src]
U: From<T>,
impl<I> IntoIterator for I where
I: Iterator, [src]
I: Iterator,
type Item = <I as Iterator>::Item
The type of the elements being iterated over.
+type IntoIter = I
Which kind of iterator are we turning this into?
+pub fn into_iter(self) -> I[src]
impl<T, U> TryFrom<U> for T where
U: Into<T>, [src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
+pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>, [src]
U: TryFrom<T>,
[−][src]Struct chemfiles::Residue
A Residue is a group of atoms belonging to the same logical unit. They
+can be small molecules, amino-acids in a protein, monomers in polymers,
+etc.
Implementations
impl Residue[src]
pub fn new<'a>(name: impl Into<&'a str>) -> Residue[src]
Create a new residue with the given name
Example
++let residue = Residue::new("ALA"); +assert_eq!(residue.name(), "ALA"); +assert_eq!(residue.id(), None);
pub fn with_id<'a>(name: impl Into<&'a str>, id: i64) -> Residue[src]
Create a new residue with the given name and id as identifier.
Example
++let residue = Residue::with_id("ALA", 67); +assert_eq!(residue.name(), "ALA"); +assert_eq!(residue.id(), Some(67));
pub fn size(&self) -> usize[src]
Get the number of atoms in this residue.
+Example
++let mut residue = Residue::new("water"); +assert_eq!(residue.size(), 0); + +residue.add_atom(0); +residue.add_atom(1); +residue.add_atom(2); +assert_eq!(residue.size(), 3);
pub fn id(&self) -> Option<i64>[src]
Get the identifier of this residue in the initial topology file.
+Example
++let residue = Residue::with_id("", 42); +assert_eq!(residue.id(), Some(42));
pub fn name(&self) -> String[src]
Get the name of this residue.
+Example
++let residue = Residue::new("water"); +assert_eq!(residue.name(), "water");
pub fn add_atom(&mut self, atom: usize)[src]
Add the atom at index atom in this residue.
This will fail if the atom is already in the residue.
+Example
++let mut residue = Residue::new("water"); +assert_eq!(residue.size(), 0); +assert_eq!(residue.contains(56), false); + +residue.add_atom(56); +assert_eq!(residue.size(), 1); +assert_eq!(residue.contains(56), true); + +// Adding the same atom twice is fine +residue.add_atom(56); +assert_eq!(residue.size(), 1);
pub fn contains(&self, atom: usize) -> bool[src]
Check if the atom at index i is in this residue
Example
++let mut residue = Residue::new("water"); +assert_eq!(residue.contains(56), false); + +residue.add_atom(56); +assert_eq!(residue.contains(56), true);
pub fn atoms(&self) -> Vec<usize>[src]
Get the list of atoms of this residue.
+Example
++let mut residue = Residue::new("water"); +assert_eq!(residue.atoms(), vec![]); + +residue.add_atom(56); +assert_eq!(residue.atoms(), vec![56]);
pub fn set(&mut self, name: &str, property: impl Into<Property>)[src]
Add a new property with the given name to this residue.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
++let mut residue = Residue::new("ALA"); +residue.set("a string", "hello"); +residue.set("a double", 3.2); + +assert_eq!(residue.get("a string"), Some(Property::String("hello".into()))); +assert_eq!(residue.get("a double"), Some(Property::Double(3.2)));
pub fn get(&self, name: &str) -> Option<Property>[src]
Get a property with the given name in this frame, if it exist.
Examples
++let mut residue = Residue::new("ALA"); +residue.set("foo", Property::Double(22.2)); + +assert_eq!(residue.get("foo"), Some(Property::Double(22.2))); +assert_eq!(residue.get("Bar"), None);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);[src]
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this frame
+Examples
++let mut residue = Residue::new("ALA"); +residue.set("foo", Property::Double(22.2)); +residue.set("bar", Property::Bool(false)); + +for (name, property) in residue.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(22.2)); + } else if name == "bar" { + assert_eq!(property, Property::Bool(false)); + } +}
Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Residue
impl !Send for Residue
impl !Sync for Residue
impl Unpin for Residue
impl UnwindSafe for Residue
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized, [src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized, [src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized, [src]
T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T[src]
impl<T> From<T> for T[src]
impl<T, U> Into<U> for T where
U: From<T>, [src]
U: From<T>,
impl<T> ToOwned for T where
T: Clone, [src]
T: Clone,
type Owned = T
The resulting type after obtaining ownership.
+pub fn to_owned(&self) -> T[src]
pub fn clone_into(&self, target: &mut T)[src]
impl<T, U> TryFrom<U> for T where
U: Into<T>, [src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
+pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>, [src]
U: TryFrom<T>,
[−][src]Struct chemfiles::ResidueRef
An analog to a reference to a residue (&Residue)
Methods from Deref<Target = Residue>
pub fn size(&self) -> usize[src]
Get the number of atoms in this residue.
+Example
++let mut residue = Residue::new("water"); +assert_eq!(residue.size(), 0); + +residue.add_atom(0); +residue.add_atom(1); +residue.add_atom(2); +assert_eq!(residue.size(), 3);
pub fn id(&self) -> Option<i64>[src]
Get the identifier of this residue in the initial topology file.
+Example
++let residue = Residue::with_id("", 42); +assert_eq!(residue.id(), Some(42));
pub fn name(&self) -> String[src]
Get the name of this residue.
+Example
++let residue = Residue::new("water"); +assert_eq!(residue.name(), "water");
pub fn contains(&self, atom: usize) -> bool[src]
Check if the atom at index i is in this residue
Example
++let mut residue = Residue::new("water"); +assert_eq!(residue.contains(56), false); + +residue.add_atom(56); +assert_eq!(residue.contains(56), true);
pub fn atoms(&self) -> Vec<usize>[src]
Get the list of atoms of this residue.
+Example
++let mut residue = Residue::new("water"); +assert_eq!(residue.atoms(), vec![]); + +residue.add_atom(56); +assert_eq!(residue.atoms(), vec![56]);
pub fn get(&self, name: &str) -> Option<Property>[src]
Get a property with the given name in this frame, if it exist.
Examples
++let mut residue = Residue::new("ALA"); +residue.set("foo", Property::Double(22.2)); + +assert_eq!(residue.get("foo"), Some(Property::Double(22.2))); +assert_eq!(residue.get("Bar"), None);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);[src]
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this frame
+Examples
++let mut residue = Residue::new("ALA"); +residue.set("foo", Property::Double(22.2)); +residue.set("bar", Property::Bool(false)); + +for (name, property) in residue.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(22.2)); + } else if name == "bar" { + assert_eq!(property, Property::Bool(false)); + } +}
Trait Implementations
impl<'a> Deref for ResidueRef<'a>[src]
Auto Trait Implementations
impl<'a> RefUnwindSafe for ResidueRef<'a>
impl<'a> !Send for ResidueRef<'a>
impl<'a> !Sync for ResidueRef<'a>
impl<'a> Unpin for ResidueRef<'a>
impl<'a> UnwindSafe for ResidueRef<'a>
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized, [src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized, [src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized, [src]
T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T[src]
impl<T> From<T> for T[src]
impl<T, U> Into<U> for T where
U: From<T>, [src]
U: From<T>,
impl<T, U> TryFrom<U> for T where
U: Into<T>, [src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
+pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>, [src]
U: TryFrom<T>,
[−][src]Struct chemfiles::Selection
A Selection allow to select atoms in a Frame, from a selection
+language. The selection language is built by combining basic operations.
+Each basic operation follows the <selector>[(<variable>)] <operator> <value> structure, where <operator> is a comparison operator in
+== != < <= > >=.
Implementations
impl Selection[src]
pub fn new<'a, S: Into<&'a str>>(selection: S) -> Result<Selection, Error>[src]
Create a new selection from the given selection string.
+Errors
+This function fails if the selection string is invalid.
+Example
++let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
pub fn size(&self) -> usize[src]
Get the size of the selection, i.e. the number of atoms we are selecting +together.
+This value is 1 for the 'atom' context, 2 for the 'pair' and 'bond' +context, 3 for the 'three' and 'angles' context and 4 for the 'four' +and 'dihedral' context.
+Example
++let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap(); +assert_eq!(selection.size(), 2);
pub fn string(&self) -> String[src]
Get the selection string used to create this selection.
+Example
++let selection = Selection::new("name H").unwrap(); +assert_eq!(selection.string(), "name H");
pub fn evaluate(&mut self, frame: &Frame) -> Vec<Match>[src]
Evaluate a selection for a given frame, and return the corresponding +matches.
+Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None); + +let mut selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap(); +let matches = selection.evaluate(&frame); + +assert_eq!(matches.len(), 2); + +assert_eq!(matches[0].len(), 2); +assert_eq!(matches[0][0], 0); +assert_eq!(matches[0][1], 1); + +assert_eq!(matches[1].len(), 2); +assert_eq!(matches[1][0], 2); +assert_eq!(matches[1][1], 1);
pub fn list(&mut self, frame: &Frame) -> Vec<usize>[src]
Evaluates a selection of size 1 on a given frame. This function
+returns the list of atomic indexes in the frame matching this selection.
Panics
+If the selection size is not 1
+Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None); + +let mut selection = Selection::new("name H").unwrap(); +let matches = selection.list(&frame); + +assert_eq!(matches.len(), 2); +assert_eq!(matches[0], 0); +assert_eq!(matches[1], 2);
Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Selection
impl !Send for Selection
impl !Sync for Selection
impl Unpin for Selection
impl UnwindSafe for Selection
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized, [src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized, [src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized, [src]
T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T[src]
impl<T> From<T> for T[src]
impl<T, U> Into<U> for T where
U: From<T>, [src]
U: From<T>,
impl<T> ToOwned for T where
T: Clone, [src]
T: Clone,
type Owned = T
The resulting type after obtaining ownership.
+pub fn to_owned(&self) -> T[src]
pub fn clone_into(&self, target: &mut T)[src]
impl<T, U> TryFrom<U> for T where
U: Into<T>, [src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
+pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>, [src]
U: TryFrom<T>,
[−][src]Struct chemfiles::Topology
A Topology contains the definition of all the atoms in the system, and
+the liaisons between the atoms (bonds, angles, dihedrals, ...). It will
+also contain all the residues information if it is available.
Implementations
impl Topology[src]
pub fn new() -> Topology[src]
Create a new empty topology.
+Example
++let topology = Topology::new(); +assert_eq!(topology.size(), 0);
pub fn atom(&self, index: usize) -> AtomRef<'_>[src]
Get a reference of the atom at the given index in this topology.
Panics
+If index is out of bounds.
Example
++let mut topology = Topology::new(); +topology.resize(6); + +let atom = topology.atom(4); +assert_eq!(atom.name(), "");
pub fn atom_mut(&mut self, index: usize) -> AtomMut<'_>[src]
Get a mutable reference to the atom at the given index in this topology.
Panics
+If index is out of bounds.
Example
++let mut topology = Topology::new(); +topology.resize(6); + +assert_eq!(topology.atom(4).name(), ""); + +topology.atom_mut(4).set_name("Fe"); +assert_eq!(topology.atom(4).name(), "Fe");
pub fn size(&self) -> usize[src]
Get the current number of atoms in this topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.size(), 0); + +topology.resize(6); +assert_eq!(topology.size(), 6);
pub fn resize(&mut self, natoms: usize)[src]
Resize this topology to hold natoms atoms, inserting dummy atoms if
+the new size if bigger than the old one.
Example
++let mut topology = Topology::new(); +assert_eq!(topology.size(), 0); + +topology.resize(6); +assert_eq!(topology.size(), 6);
pub fn add_atom(&mut self, atom: &Atom)[src]
Add an Atom at the end of this topology
Example
++let mut topology = Topology::new(); +topology.add_atom(&Atom::new("Mg")); + +let atom = topology.atom(0); +assert_eq!(atom.name(), "Mg");
pub fn remove(&mut self, index: usize)[src]
Remove an Atom from this topology by index. This modify all the
+other atoms indexes.
Panics
+If the index is out of bounds
Example
++let mut topology = Topology::new(); +topology.resize(9); +assert_eq!(topology.size(), 9); + +topology.remove(7); +assert_eq!(topology.size(), 8);
pub fn bonds_count(&self) -> usize[src]
Get the number of bonds in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.bonds_count(), 3);
pub fn angles_count(&self) -> usize[src]
Get the number of angles in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.angles_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.angles_count(), 2);
pub fn dihedrals_count(&self) -> usize[src]
Get the number of dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.dihedrals_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.dihedrals_count(), 1);
pub fn impropers_count(&self) -> usize[src]
Get the number of improper dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.dihedrals_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(0, 2); +topology.add_bond(0, 3); +assert_eq!(topology.impropers_count(), 1);
pub fn bonds(&self) -> Vec<[usize; 2]>[src]
Get the list of bonds in the topology.
+Example
++let mut topology = Topology::new(); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);
pub fn angles(&self) -> Vec<[usize; 3]>[src]
Get the list of angles in the topology.
+Example
++let mut topology = Topology::new(); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);
pub fn dihedrals(&self) -> Vec<[usize; 4]>[src]
Get the list of dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); + +assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);
pub fn impropers(&self) -> Vec<[usize; 4]>[src]
Get the list of improper dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(0, 2); +topology.add_bond(0, 3); + +assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);
pub fn clear_bonds(&mut self)[src]
Remove all existing bonds, angles, dihedral angles and improper +dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(4); +topology.add_bond(0, 1); +topology.add_bond(0, 2); +assert_eq!(topology.bonds_count(), 2); +assert_eq!(topology.angles().len(), 1); + +topology.clear_bonds(); +assert!(topology.bonds().is_empty()); +assert!(topology.angles().is_empty());
pub fn add_bond(&mut self, i: usize, j: usize)[src]
Add a bond between the atoms at indexes i and j in the topology.
The bond order is set to BondOrder::Unknown.
Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(0, 2); +assert_eq!(topology.bonds_count(), 2); + +assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);
pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder)[src]
Add a bond between the atoms at indexes i and j in the topology
+with the given bond order.
Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(2); + +topology.add_bond_with_order(0, 1, BondOrder::Double); +assert_eq!(topology.bond_order(0, 1), BondOrder::Double);
pub fn bond_order(&self, i: usize, j: usize) -> BondOrder[src]
Get the bond order for the bond between the atoms at indexes i and
+j.
Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(2); + +topology.add_bond_with_order(0, 1, BondOrder::Double); +assert_eq!(topology.bond_order(0, 1), BondOrder::Double);
pub fn bond_orders(&self) -> Vec<BondOrder>[src]
Get the bond order for all the bonds in the topology
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(3); + +topology.add_bond_with_order(0, 1, BondOrder::Double); +topology.add_bond_with_order(0, 2, BondOrder::Single); + +assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);
pub fn remove_bond(&mut self, i: usize, j: usize)[src]
Remove any existing bond between the atoms at indexes i and j in
+this topology.
This function does nothing if there is no bond between i and j.
Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(1, 2); +assert_eq!(topology.bonds_count(), 2); + +topology.remove_bond(0, 1); +assert_eq!(topology.bonds_count(), 1); + +// Removing a bond that does not exists is fine +topology.remove_bond(0, 2); +assert_eq!(topology.bonds_count(), 1);
pub fn residue(&self, index: u64) -> Option<ResidueRef<'_>>[src]
Get a reference to the residue at index index from this topology.
The residue index in the topology is not always the same as the residue
+id.
Example
++let mut topology = Topology::new(); +topology.add_residue(&Residue::new("water")).unwrap(); + +let residue = topology.residue(0).unwrap(); +assert_eq!(residue.name(), "water");
pub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef<'_>>[src]
Get a copy of the residue containing the atom at index index in this
+topology, if any.
Example
++let mut topology = Topology::new(); +topology.resize(8); + +let mut residue = Residue::new("water"); +residue.add_atom(0); +residue.add_atom(1); +residue.add_atom(2); +topology.add_residue(&residue).unwrap(); + +let residue = topology.residue_for_atom(0).unwrap(); +assert_eq!(residue.name(), "water"); + +assert!(topology.residue_for_atom(6).is_none());
pub fn residues_count(&self) -> u64[src]
Get the number of residues in this topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.residues_count(), 0); + +topology.add_residue(&Residue::with_id("water", 0)).unwrap(); +topology.add_residue(&Residue::with_id("protein", 1)).unwrap(); +assert_eq!(topology.residues_count(), 2);
pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error>[src]
Add a residue to this topology.
+Errors
+This function fails is the residue id is not already in the topology,
+or if the residue contains atoms that are already in another residue.
Example
++let mut topology = Topology::new(); +topology.add_residue(&Residue::new("water")).unwrap(); + +let residue = topology.residue(0).unwrap(); +assert_eq!(residue.name(), "water");
pub fn are_linked(&self, first: &Residue, second: &Residue) -> bool[src]
Check if the two residues first and second from the topology are
+linked together, i.e. if there is a bond between one atom in the
+first residue and one atom in the second one.
Example
++let mut topology = Topology::new(); + +topology.add_residue(&Residue::with_id("water", 0)).unwrap(); +topology.add_residue(&Residue::with_id("protein", 1)).unwrap(); + +let first = topology.residue(0).unwrap(); +let second = topology.residue(1).unwrap(); +assert_eq!(topology.are_linked(&first, &second), false);
Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Topology
impl !Send for Topology
impl !Sync for Topology
impl Unpin for Topology
impl UnwindSafe for Topology
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized, [src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized, [src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized, [src]
T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T[src]
impl<T> From<T> for T[src]
impl<T, U> Into<U> for T where
U: From<T>, [src]
U: From<T>,
impl<T> ToOwned for T where
T: Clone, [src]
T: Clone,
type Owned = T
The resulting type after obtaining ownership.
+pub fn to_owned(&self) -> T[src]
pub fn clone_into(&self, target: &mut T)[src]
impl<T, U> TryFrom<U> for T where
U: Into<T>, [src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
+pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>, [src]
U: TryFrom<T>,
[−][src]Struct chemfiles::TopologyRef
An analog to a reference to a topology (&Topology)
Methods from Deref<Target = Topology>
pub fn atom(&self, index: usize) -> AtomRef<'_>[src]
Get a reference of the atom at the given index in this topology.
Panics
+If index is out of bounds.
Example
++let mut topology = Topology::new(); +topology.resize(6); + +let atom = topology.atom(4); +assert_eq!(atom.name(), "");
pub fn size(&self) -> usize[src]
Get the current number of atoms in this topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.size(), 0); + +topology.resize(6); +assert_eq!(topology.size(), 6);
pub fn bonds_count(&self) -> usize[src]
Get the number of bonds in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.bonds_count(), 3);
pub fn angles_count(&self) -> usize[src]
Get the number of angles in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.angles_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.angles_count(), 2);
pub fn dihedrals_count(&self) -> usize[src]
Get the number of dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.dihedrals_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.dihedrals_count(), 1);
pub fn impropers_count(&self) -> usize[src]
Get the number of improper dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.dihedrals_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(0, 2); +topology.add_bond(0, 3); +assert_eq!(topology.impropers_count(), 1);
pub fn bonds(&self) -> Vec<[usize; 2]>[src]
Get the list of bonds in the topology.
+Example
++let mut topology = Topology::new(); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);
pub fn angles(&self) -> Vec<[usize; 3]>[src]
Get the list of angles in the topology.
+Example
++let mut topology = Topology::new(); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);
pub fn dihedrals(&self) -> Vec<[usize; 4]>[src]
Get the list of dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); + +assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);
pub fn impropers(&self) -> Vec<[usize; 4]>[src]
Get the list of improper dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(0, 2); +topology.add_bond(0, 3); + +assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);
pub fn bond_order(&self, i: usize, j: usize) -> BondOrder[src]
Get the bond order for the bond between the atoms at indexes i and
+j.
Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(2); + +topology.add_bond_with_order(0, 1, BondOrder::Double); +assert_eq!(topology.bond_order(0, 1), BondOrder::Double);
pub fn bond_orders(&self) -> Vec<BondOrder>[src]
Get the bond order for all the bonds in the topology
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(3); + +topology.add_bond_with_order(0, 1, BondOrder::Double); +topology.add_bond_with_order(0, 2, BondOrder::Single); + +assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);
pub fn residue(&self, index: u64) -> Option<ResidueRef<'_>>[src]
Get a reference to the residue at index index from this topology.
The residue index in the topology is not always the same as the residue
+id.
Example
++let mut topology = Topology::new(); +topology.add_residue(&Residue::new("water")).unwrap(); + +let residue = topology.residue(0).unwrap(); +assert_eq!(residue.name(), "water");
pub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef<'_>>[src]
Get a copy of the residue containing the atom at index index in this
+topology, if any.
Example
++let mut topology = Topology::new(); +topology.resize(8); + +let mut residue = Residue::new("water"); +residue.add_atom(0); +residue.add_atom(1); +residue.add_atom(2); +topology.add_residue(&residue).unwrap(); + +let residue = topology.residue_for_atom(0).unwrap(); +assert_eq!(residue.name(), "water"); + +assert!(topology.residue_for_atom(6).is_none());
pub fn residues_count(&self) -> u64[src]
Get the number of residues in this topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.residues_count(), 0); + +topology.add_residue(&Residue::with_id("water", 0)).unwrap(); +topology.add_residue(&Residue::with_id("protein", 1)).unwrap(); +assert_eq!(topology.residues_count(), 2);
pub fn are_linked(&self, first: &Residue, second: &Residue) -> bool[src]
Check if the two residues first and second from the topology are
+linked together, i.e. if there is a bond between one atom in the
+first residue and one atom in the second one.
Example
++let mut topology = Topology::new(); + +topology.add_residue(&Residue::with_id("water", 0)).unwrap(); +topology.add_residue(&Residue::with_id("protein", 1)).unwrap(); + +let first = topology.residue(0).unwrap(); +let second = topology.residue(1).unwrap(); +assert_eq!(topology.are_linked(&first, &second), false);
Trait Implementations
impl<'a> Deref for TopologyRef<'a>[src]
Auto Trait Implementations
impl<'a> RefUnwindSafe for TopologyRef<'a>
impl<'a> !Send for TopologyRef<'a>
impl<'a> !Sync for TopologyRef<'a>
impl<'a> Unpin for TopologyRef<'a>
impl<'a> UnwindSafe for TopologyRef<'a>
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized, [src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized, [src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized, [src]
T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T[src]
impl<T> From<T> for T[src]
impl<T, U> Into<U> for T where
U: From<T>, [src]
U: From<T>,
impl<T, U> TryFrom<U> for T where
U: Into<T>, [src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
+pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>, [src]
U: TryFrom<T>,
[−][src]Struct chemfiles::Trajectory
The Trajectory type is the main entry point when using chemfiles. A
+Trajectory behave a bit like a file, allowing to read and/or write
+Frame.
Implementations
impl Trajectory[src]
pub fn open<P>(path: P, mode: char) -> Result<Trajectory, Error> where
P: AsRef<Path>, [src]
P: AsRef<Path>,
Open the file at the given path in the given mode.
Valid modes are 'r' for read, 'w' for write and 'a' for append.
Errors
+This function fails if the file is not accessible for the given mode, if +it is incorrectly formatted for the corresponding format, or in case of +I/O errors from the OS.
+Example
++let trajectory = Trajectory::open("water.xyz", 'r').unwrap();
pub fn open_with_format<'a, P, S>(
filename: P,
mode: char,
format: S
) -> Result<Trajectory, Error> where
P: AsRef<Path>,
S: Into<&'a str>, [src]
filename: P,
mode: char,
format: S
) -> Result<Trajectory, Error> where
P: AsRef<Path>,
S: Into<&'a str>,
Open the file at the given path using a specific file format and the
+given mode.
Valid modes are 'r' for read, 'w' for write and 'a' for append.
Specifying a format is needed when the file format does not match the
+extension, or when there is not standard extension for this format. If
+format is an empty string, the format will be guessed from the
+extension.
Errors
+This function fails if the file is not accessible for the given mode, if +it is incorrectly formatted for the corresponding format, or in case of +I/O errors from the OS.
+Example
++let trajectory = Trajectory::open_with_format("water.zeo", 'r', "XYZ").unwrap();
pub fn memory_reader<'a, S>(data: S, format: S) -> Result<Trajectory, Error> where
S: Into<&'a str>, [src]
S: Into<&'a str>,
Read a memory buffer as though it was a formatted file.
+The memory buffer used to store the file is given using the data
+argument. The format parameter is required and should follow the same
+rules as in the main Trajectory constructor.
Errors
+This function fails if the data is incorrectly formatted for the +corresponding format, or if the format do not support in-memory readers.
+Example
++let aromatics = "c1ccccc1\nc1ccco1\nc1ccccn1\n"; +let mut trajectory = Trajectory::memory_reader(aromatics, "SMI").unwrap(); +let mut frame = Frame::new(); +trajectory.read(&mut frame).unwrap(); +assert_eq!(frame.size(), 6);
pub fn memory_writer<'a, S>(format: S) -> Result<Trajectory, Error> where
S: Into<&'a str>, [src]
S: Into<&'a str>,
Write to a memory buffer as though it was a formatted file.
+The format parameter should follow the same rules as in the main
+Trajectory constructor, except that compression specification
+is not supported.
The memory_buffer function can be used to retrieve the data written
+to memory of the Trajectory.
Errors
+This function fails if the format do not support in-memory writers.
+Example
++let trajectory_memory = Trajectory::memory_writer("SMI"); + +// Binary formats typically do not support this feature +assert!(Trajectory::memory_writer("XTC").is_err());
pub fn read(&mut self, frame: &mut Frame) -> Result<(), Error>[src]
Read the next step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of atom +in the next step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format, or in case of I/O errors from the OS.
+Example
++let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); +let mut frame = Frame::new(); + +trajectory.read(&mut frame).unwrap();
pub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error>[src]
Read a specific step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of +atom at this step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format.
+Example
++let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); +let mut frame = Frame::new(); + +trajectory.read_step(10, &mut frame).unwrap();
pub fn write(&mut self, frame: &Frame) -> Result<(), Error>[src]
Write a frame to this trajectory.
Errors
+This function fails if the data is incorrectly formatted for the +corresponding format.
+Example
++let mut trajectory = Trajectory::open("water.pdb", 'w').unwrap(); +let mut frame = Frame::new(); + +trajectory.write(&mut frame).unwrap();
pub fn set_topology(&mut self, topology: &Topology)[src]
Set the topology associated with this trajectory. This topology will
+be used when reading and writing the files, replacing any topology in
+the frames or files.
Example
++let mut topology = Topology::new(); +topology.add_atom(&Atom::new("H")); +topology.add_atom(&Atom::new("O")); +topology.add_atom(&Atom::new("H")); +topology.add_bond(0, 1); +topology.add_bond(1, 2); + +let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); +trajectory.set_topology(&topology);
pub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error> where
P: AsRef<Path>, [src]
P: AsRef<Path>,
Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in format;
+and extracting the topology of this frame.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
++let mut trajectory = Trajectory::open("water.nc", 'r').unwrap(); +trajectory.set_topology_file("topology.pdb").unwrap();
pub fn set_topology_with_format<'a, P, S>(
&mut self,
path: P,
format: S
) -> Result<(), Error> where
P: AsRef<Path>,
S: Into<&'a str>, [src]
&mut self,
path: P,
format: S
) -> Result<(), Error> where
P: AsRef<Path>,
S: Into<&'a str>,
Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in
+format; and extracting the topology of this frame.
If format is an empty string, the format will be guessed from the
+path extension.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
++let mut trajectory = Trajectory::open("water.nc", 'r').unwrap(); +trajectory.set_topology_with_format("topology.mol", "PDB").unwrap();
pub fn set_cell(&mut self, cell: &UnitCell)[src]
Set the unit cell associated with a trajectory. This cell will be
+used when reading and writing the files, replacing any unit cell in the
+frames or files.
Example
++let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); +trajectory.set_cell(&UnitCell::new([10.0, 11.0, 12.5]));
pub fn nsteps(&mut self) -> usize[src]
Get the number of steps (the number of frames) in a trajectory.
+Example
++let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + +println!("This trajectory contains {} steps", trajectory.nsteps());
pub fn memory_buffer(&self) -> Result<&str, Error>[src]
Obtain the memory buffer written to by the trajectory.
+Errors
+This fails if the trajectory was not opened with
+Trajectory::memory_writer.
Example
++let mut trajectory_memory = Trajectory::memory_writer("SMI").unwrap(); + +let mut frame = Frame::new(); +frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None); +frame.add_bond_with_order(0, 1, BondOrder::Single); + +trajectory_memory.write(&frame).unwrap(); + +let result = trajectory_memory.memory_buffer(); +assert_eq!(result.unwrap(), "CC\n");
pub fn path(&self) -> String[src]
Get file path for this trajectory.
+Example
++let trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + +assert_eq!(trajectory.path(), "water.xyz");
Trait Implementations
impl Drop for Trajectory[src]
Auto Trait Implementations
impl RefUnwindSafe for Trajectory
impl !Send for Trajectory
impl !Sync for Trajectory
impl Unpin for Trajectory
impl UnwindSafe for Trajectory
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized, [src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized, [src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized, [src]
T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T[src]
impl<T> From<T> for T[src]
impl<T, U> Into<U> for T where
U: From<T>, [src]
U: From<T>,
impl<T, U> TryFrom<U> for T where
U: Into<T>, [src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
+pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>, [src]
U: TryFrom<T>,
[−][src]Struct chemfiles::UnitCell
An UnitCell represent the box containing the atoms, and its periodicity.
An unit cell is fully represented by three lengths (a, b, c); and three +angles (alpha, beta, gamma). The angles are stored in degrees, and the +lengths in Angstroms.
+A cell also has a matricial representation, by projecting the three base +vector into an orthonormal base. We choose to represent such matrix as an +upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |
+Implementations
impl UnitCell[src]
pub fn new(lengths: [f64; 3]) -> UnitCell[src]
Create an Orthorhombic UnitCell from the three lengths, in Angstroms.
Example
++let cell = UnitCell::new([30.0, 30.0, 23.0]); + +assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]); +assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); +assert_eq!(cell.shape(), CellShape::Orthorhombic);
pub fn infinite() -> UnitCell[src]
Create an Infinite UnitCell.
Example
++let cell = UnitCell::infinite(); + +assert_eq!(cell.lengths(), [0.0, 0.0, 0.0]); +assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); +assert_eq!(cell.shape(), CellShape::Infinite);
pub fn triclinic(lengths: [f64; 3], angles: [f64; 3]) -> UnitCell[src]
Create an Triclinic UnitCell from the three lengths (in Angstroms)
+and three angles (in degree). alpha is the angle between the vectors
+b and c; beta is the between the vectors a and c and gamma
+is the angle between the vectors a and b.
Example
++let cell = UnitCell::triclinic([10.0, 10.0, 10.0], [98.0, 99.0, 90.0]); + +assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]); +assert_eq!(cell.angles()[0], 98.0); +// Rounding errors might occur due to internal representation +assert!((cell.angles()[1] - 99.0).abs() < 1e-12); +assert_eq!(cell.angles()[2], 90.0); +assert_eq!(cell.shape(), CellShape::Triclinic);
pub fn from_matrix(matrix: [[f64; 3]; 3]) -> UnitCell[src]
Create an UnitCell from a cell matrix. If matrix contains only
+zeros, then an Infinite cell is created. If only the diagonal of the
+matrix is non-zero, then the cell is Orthorhombic. Else a
+Triclinic cell is created. The matrix entries should be in Angstroms.
Panics
+If the matrix has a negative determinant, or more generally is not +representing a unit cell.
+Example
++let cell = UnitCell::from_matrix([ + [1.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0] +]); + +assert_eq!(cell.lengths(), [1.0, 2.0, 3.0]); +assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); +assert_eq!(cell.shape(), CellShape::Orthorhombic);
pub fn lengths(&self) -> [f64; 3][src]
Get the three lengths of the cell, in Angstroms.
+Example
++let cell = UnitCell::new([30.0, 30.0, 23.0]); +assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
pub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error>[src]
Set the three lengths of the cell, in Angstroms.
+Errors
+This function fails if the unit cell is infinite, or if one of the +lengths is negative.
+Example
++let mut cell = UnitCell::new([30.0, 30.0, 23.0]); + +cell.set_lengths([10.0, 30.0, 42.0]).unwrap(); +assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]); + +assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());
pub fn angles(&self) -> [f64; 3][src]
Get the three angles of the cell, in degrees.
+Example
++let cell = UnitCell::new([20.0, 20.0, 20.0]); +assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); + +let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]); +assert_eq!(cell.angles()[0], 100.0); +// Rounding errors might occur due to internal representation +assert!((cell.angles()[1] - 120.0).abs() < 1e-12); +assert_eq!(cell.angles()[2], 90.0);
pub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error>[src]
Set the three angles of the cell, in degrees.
+Errors
+This function fails if the unit cell is not Triclinic.
Example
++let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]); +assert_eq!(cell.angles()[0], 100.0); +// Rounding errors might occur due to internal representation +assert!((cell.angles()[1] - 120.0).abs() < 1e-12); +assert_eq!(cell.angles()[2], 90.0); + +cell.set_angles([90.0, 90.0, 90.0]).unwrap(); +assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
pub fn matrix(&self) -> [[f64; 3]; 3][src]
Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); + +let matrix = cell.matrix(); + +assert_eq!(matrix[0][0], 10.0); +assert_eq!(matrix[1][1], 20.0); +assert_eq!(matrix[2][2], 30.0); + +assert!(matrix[1][2].abs() < 1e-9);
pub fn shape(&self) -> CellShape[src]
Get the shape of the unit cell.
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); +assert_eq!(cell.shape(), CellShape::Orthorhombic);
pub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error>[src]
Set the shape of the unit cell to shape.
Errors
+This can fail if the cell length or angles are incompatible with the +new shape.
+Example
++let mut cell = UnitCell::new([10.0, 20.0, 30.0]); +assert_eq!(cell.shape(), CellShape::Orthorhombic); + +cell.set_shape(CellShape::Triclinic).unwrap(); +assert_eq!(cell.shape(), CellShape::Triclinic);
pub fn volume(&self) -> f64[src]
Get the volume of the unit cell.
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); +assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0);
pub fn wrap(&self, vector: &mut [f64; 3])[src]
Wrap a vector in this unit cell.
Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); + +let mut vector = [12.0, 5.2, -45.3]; +cell.wrap(&mut vector); +assert_eq!(vector, [2.0, 5.2, 14.700000000000003]);
Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for UnitCell
impl !Send for UnitCell
impl !Sync for UnitCell
impl Unpin for UnitCell
impl UnwindSafe for UnitCell
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized, [src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized, [src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized, [src]
T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T[src]
impl<T> From<T> for T[src]
impl<T, U> Into<U> for T where
U: From<T>, [src]
U: From<T>,
impl<T> ToOwned for T where
T: Clone, [src]
T: Clone,
type Owned = T
The resulting type after obtaining ownership.
+pub fn to_owned(&self) -> T[src]
pub fn clone_into(&self, target: &mut T)[src]
impl<T, U> TryFrom<U> for T where
U: Into<T>, [src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
+pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>, [src]
U: TryFrom<T>,
[−][src]Struct chemfiles::UnitCellMut
An analog to a mutable reference to an unit cell (&mut UnitCell)
Methods from Deref<Target = UnitCell>
pub fn lengths(&self) -> [f64; 3][src]
Get the three lengths of the cell, in Angstroms.
+Example
++let cell = UnitCell::new([30.0, 30.0, 23.0]); +assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
pub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error>[src]
Set the three lengths of the cell, in Angstroms.
+Errors
+This function fails if the unit cell is infinite, or if one of the +lengths is negative.
+Example
++let mut cell = UnitCell::new([30.0, 30.0, 23.0]); + +cell.set_lengths([10.0, 30.0, 42.0]).unwrap(); +assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]); + +assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());
pub fn angles(&self) -> [f64; 3][src]
Get the three angles of the cell, in degrees.
+Example
++let cell = UnitCell::new([20.0, 20.0, 20.0]); +assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); + +let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]); +assert_eq!(cell.angles()[0], 100.0); +// Rounding errors might occur due to internal representation +assert!((cell.angles()[1] - 120.0).abs() < 1e-12); +assert_eq!(cell.angles()[2], 90.0);
pub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error>[src]
Set the three angles of the cell, in degrees.
+Errors
+This function fails if the unit cell is not Triclinic.
Example
++let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]); +assert_eq!(cell.angles()[0], 100.0); +// Rounding errors might occur due to internal representation +assert!((cell.angles()[1] - 120.0).abs() < 1e-12); +assert_eq!(cell.angles()[2], 90.0); + +cell.set_angles([90.0, 90.0, 90.0]).unwrap(); +assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
pub fn matrix(&self) -> [[f64; 3]; 3][src]
Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); + +let matrix = cell.matrix(); + +assert_eq!(matrix[0][0], 10.0); +assert_eq!(matrix[1][1], 20.0); +assert_eq!(matrix[2][2], 30.0); + +assert!(matrix[1][2].abs() < 1e-9);
pub fn shape(&self) -> CellShape[src]
Get the shape of the unit cell.
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); +assert_eq!(cell.shape(), CellShape::Orthorhombic);
pub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error>[src]
Set the shape of the unit cell to shape.
Errors
+This can fail if the cell length or angles are incompatible with the +new shape.
+Example
++let mut cell = UnitCell::new([10.0, 20.0, 30.0]); +assert_eq!(cell.shape(), CellShape::Orthorhombic); + +cell.set_shape(CellShape::Triclinic).unwrap(); +assert_eq!(cell.shape(), CellShape::Triclinic);
pub fn volume(&self) -> f64[src]
Get the volume of the unit cell.
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); +assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0);
pub fn wrap(&self, vector: &mut [f64; 3])[src]
Wrap a vector in this unit cell.
Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); + +let mut vector = [12.0, 5.2, -45.3]; +cell.wrap(&mut vector); +assert_eq!(vector, [2.0, 5.2, 14.700000000000003]);
Trait Implementations
impl<'a> Deref for UnitCellMut<'a>[src]
impl<'a> DerefMut for UnitCellMut<'a>[src]
Auto Trait Implementations
impl<'a> RefUnwindSafe for UnitCellMut<'a>
impl<'a> !Send for UnitCellMut<'a>
impl<'a> !Sync for UnitCellMut<'a>
impl<'a> Unpin for UnitCellMut<'a>
impl<'a> !UnwindSafe for UnitCellMut<'a>
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized, [src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized, [src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized, [src]
T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T[src]
impl<T> From<T> for T[src]
impl<T, U> Into<U> for T where
U: From<T>, [src]
U: From<T>,
impl<T, U> TryFrom<U> for T where
U: Into<T>, [src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
+pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>, [src]
U: TryFrom<T>,
[−][src]Struct chemfiles::UnitCellRef
An analog to a reference to an unit cell (&UnitCell)
Methods from Deref<Target = UnitCell>
pub fn lengths(&self) -> [f64; 3][src]
Get the three lengths of the cell, in Angstroms.
+Example
++let cell = UnitCell::new([30.0, 30.0, 23.0]); +assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
pub fn angles(&self) -> [f64; 3][src]
Get the three angles of the cell, in degrees.
+Example
++let cell = UnitCell::new([20.0, 20.0, 20.0]); +assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); + +let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]); +assert_eq!(cell.angles()[0], 100.0); +// Rounding errors might occur due to internal representation +assert!((cell.angles()[1] - 120.0).abs() < 1e-12); +assert_eq!(cell.angles()[2], 90.0);
pub fn matrix(&self) -> [[f64; 3]; 3][src]
Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); + +let matrix = cell.matrix(); + +assert_eq!(matrix[0][0], 10.0); +assert_eq!(matrix[1][1], 20.0); +assert_eq!(matrix[2][2], 30.0); + +assert!(matrix[1][2].abs() < 1e-9);
pub fn shape(&self) -> CellShape[src]
Get the shape of the unit cell.
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); +assert_eq!(cell.shape(), CellShape::Orthorhombic);
pub fn volume(&self) -> f64[src]
Get the volume of the unit cell.
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); +assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0);
pub fn wrap(&self, vector: &mut [f64; 3])[src]
Wrap a vector in this unit cell.
Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); + +let mut vector = [12.0, 5.2, -45.3]; +cell.wrap(&mut vector); +assert_eq!(vector, [2.0, 5.2, 14.700000000000003]);
Trait Implementations
impl<'a> Deref for UnitCellRef<'a>[src]
Auto Trait Implementations
impl<'a> RefUnwindSafe for UnitCellRef<'a>
impl<'a> !Send for UnitCellRef<'a>
impl<'a> !Sync for UnitCellRef<'a>
impl<'a> Unpin for UnitCellRef<'a>
impl<'a> UnwindSafe for UnitCellRef<'a>
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized, [src]
T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized, [src]
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized, [src]
T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T[src]
impl<T> From<T> for T[src]
impl<T, U> Into<U> for T where
U: From<T>, [src]
U: From<T>,
impl<T, U> TryFrom<U> for T where
U: Into<T>, [src]
U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
+pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>[src]
impl<T, U> TryInto<U> for T where
U: TryFrom<T>, [src]
U: TryFrom<T>,
Redirecting to ../../chemfiles/enum.BondOrder.html...
+ + + \ No newline at end of file diff --git a/0.10.0/chemfiles/topology/struct.Topology.html b/0.10.0/chemfiles/topology/struct.Topology.html new file mode 100644 index 000000000..53c3a8234 --- /dev/null +++ b/0.10.0/chemfiles/topology/struct.Topology.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.Topology.html...
+ + + \ No newline at end of file diff --git a/0.10.0/chemfiles/topology/struct.TopologyRef.html b/0.10.0/chemfiles/topology/struct.TopologyRef.html new file mode 100644 index 000000000..1a31a3219 --- /dev/null +++ b/0.10.0/chemfiles/topology/struct.TopologyRef.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.TopologyRef.html...
+ + + \ No newline at end of file diff --git a/0.10.0/chemfiles/trajectory/struct.Trajectory.html b/0.10.0/chemfiles/trajectory/struct.Trajectory.html new file mode 100644 index 000000000..8d4845dd3 --- /dev/null +++ b/0.10.0/chemfiles/trajectory/struct.Trajectory.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.Trajectory.html...
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FormatMetadata","synthetic":false,"types":[]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.0/implementors/core/cmp/trait.Ord.js b/0.10.0/implementors/core/cmp/trait.Ord.js new file mode 100644 index 000000000..001aa85dd --- /dev/null +++ b/0.10.0/implementors/core/cmp/trait.Ord.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Ord for BondOrder","synthetic":false,"types":[]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.0/implementors/core/cmp/trait.PartialEq.js b/0.10.0/implementors/core/cmp/trait.PartialEq.js new file mode 100644 index 000000000..5cbf507d3 --- /dev/null +++ b/0.10.0/implementors/core/cmp/trait.PartialEq.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl PartialEq<Error> for Error","synthetic":false,"types":[]},{"text":"impl PartialEq<Status> for Status","synthetic":false,"types":[]},{"text":"impl PartialEq<CellShape> for CellShape","synthetic":false,"types":[]},{"text":"impl PartialEq<BondOrder> for BondOrder","synthetic":false,"types":[]},{"text":"impl PartialEq<Match> for Match","synthetic":false,"types":[]},{"text":"impl PartialEq<Property> for Property","synthetic":false,"types":[]},{"text":"impl PartialEq<FormatMetadata> for FormatMetadata","synthetic":false,"types":[]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.0/implementors/core/cmp/trait.PartialOrd.js b/0.10.0/implementors/core/cmp/trait.PartialOrd.js new file mode 100644 index 000000000..0162431e1 --- /dev/null +++ b/0.10.0/implementors/core/cmp/trait.PartialOrd.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl PartialOrd<BondOrder> for BondOrder","synthetic":false,"types":[]},{"text":"impl PartialOrd<Property> for Property","synthetic":false,"types":[]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.0/implementors/core/convert/trait.From.js b/0.10.0/implementors/core/convert/trait.From.js new file mode 100644 index 000000000..5a5be08a1 --- /dev/null +++ b/0.10.0/implementors/core/convert/trait.From.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl From<chfl_status> for Error","synthetic":false,"types":[]},{"text":"impl From<chfl_cellshape> for CellShape","synthetic":false,"types":[]},{"text":"impl From<CellShape> for chfl_cellshape","synthetic":false,"types":[]},{"text":"impl From<chfl_bond_order> for 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Debug for CellShape","synthetic":false,"types":[]},{"text":"impl Debug for BondOrder","synthetic":false,"types":[]},{"text":"impl Debug for Match","synthetic":false,"types":[]},{"text":"impl Debug for Property","synthetic":false,"types":[]},{"text":"impl Debug for FormatMetadata","synthetic":false,"types":[]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.0/implementors/core/fmt/trait.Display.js b/0.10.0/implementors/core/fmt/trait.Display.js new file mode 100644 index 000000000..a6cc0e7e2 --- /dev/null +++ b/0.10.0/implementors/core/fmt/trait.Display.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Display for Error","synthetic":false,"types":[]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.0/implementors/core/iter/traits/collect/trait.IntoIterator.js b/0.10.0/implementors/core/iter/traits/collect/trait.IntoIterator.js new file mode 100644 index 000000000..6ac05f02d --- /dev/null +++ b/0.10.0/implementors/core/iter/traits/collect/trait.IntoIterator.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl<'a> IntoIterator for &'a Match","synthetic":false,"types":[]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.0/implementors/core/iter/traits/iterator/trait.Iterator.js b/0.10.0/implementors/core/iter/traits/iterator/trait.Iterator.js new file mode 100644 index 000000000..651919888 --- /dev/null +++ b/0.10.0/implementors/core/iter/traits/iterator/trait.Iterator.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl<'a> Iterator for PropertiesIter<'a>","synthetic":false,"types":[]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.0/implementors/core/marker/trait.Copy.js b/0.10.0/implementors/core/marker/trait.Copy.js new file mode 100644 index 000000000..5d6ec7218 --- /dev/null +++ b/0.10.0/implementors/core/marker/trait.Copy.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Copy for BondOrder","synthetic":false,"types":[]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.0/implementors/core/marker/trait.Freeze.js b/0.10.0/implementors/core/marker/trait.Freeze.js new file mode 100644 index 000000000..ac053b07f --- /dev/null +++ b/0.10.0/implementors/core/marker/trait.Freeze.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Freeze for Error","synthetic":true,"types":[]},{"text":"impl Freeze for Atom","synthetic":true,"types":[]},{"text":"impl<'a> Freeze for AtomRef<'a>","synthetic":true,"types":[]},{"text":"impl<'a> Freeze for AtomMut<'a>","synthetic":true,"types":[]},{"text":"impl Freeze for UnitCell","synthetic":true,"types":[]},{"text":"impl<'a> Freeze for UnitCellRef<'a>","synthetic":true,"types":[]},{"text":"impl<'a> Freeze for UnitCellMut<'a>","synthetic":true,"types":[]},{"text":"impl Freeze for Residue","synthetic":true,"types":[]},{"text":"impl<'a> Freeze for ResidueRef<'a>","synthetic":true,"types":[]},{"text":"impl Freeze for Topology","synthetic":true,"types":[]},{"text":"impl<'a> Freeze for TopologyRef<'a>","synthetic":true,"types":[]},{"text":"impl Freeze for Frame","synthetic":true,"types":[]},{"text":"impl Freeze for Trajectory","synthetic":true,"types":[]},{"text":"impl Freeze for 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Error","synthetic":true,"types":[]},{"text":"impl !Send for Atom","synthetic":true,"types":[]},{"text":"impl<'a> !Send for AtomRef<'a>","synthetic":true,"types":[]},{"text":"impl<'a> !Send for AtomMut<'a>","synthetic":true,"types":[]},{"text":"impl !Send for UnitCell","synthetic":true,"types":[]},{"text":"impl<'a> !Send for UnitCellRef<'a>","synthetic":true,"types":[]},{"text":"impl<'a> !Send for UnitCellMut<'a>","synthetic":true,"types":[]},{"text":"impl !Send for Residue","synthetic":true,"types":[]},{"text":"impl<'a> !Send for ResidueRef<'a>","synthetic":true,"types":[]},{"text":"impl !Send for Topology","synthetic":true,"types":[]},{"text":"impl<'a> !Send for TopologyRef<'a>","synthetic":true,"types":[]},{"text":"impl !Send for Frame","synthetic":true,"types":[]},{"text":"impl !Send for Trajectory","synthetic":true,"types":[]},{"text":"impl Send for Match","synthetic":true,"types":[]},{"text":"impl !Send for Selection","synthetic":true,"types":[]},{"text":"impl<'a> !Send for PropertiesIter<'a>","synthetic":true,"types":[]},{"text":"impl Send for FormatMetadata","synthetic":true,"types":[]},{"text":"impl Send for Status","synthetic":true,"types":[]},{"text":"impl Send for CellShape","synthetic":true,"types":[]},{"text":"impl Send for BondOrder","synthetic":true,"types":[]},{"text":"impl Send for Property","synthetic":true,"types":[]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.0/implementors/core/marker/trait.StructuralEq.js b/0.10.0/implementors/core/marker/trait.StructuralEq.js new file mode 100644 index 000000000..09f9179b4 --- /dev/null +++ b/0.10.0/implementors/core/marker/trait.StructuralEq.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl StructuralEq for CellShape","synthetic":false,"types":[]},{"text":"impl StructuralEq for BondOrder","synthetic":false,"types":[]},{"text":"impl StructuralEq for Match","synthetic":false,"types":[]},{"text":"impl StructuralEq for FormatMetadata","synthetic":false,"types":[]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.0/implementors/core/marker/trait.StructuralPartialEq.js b/0.10.0/implementors/core/marker/trait.StructuralPartialEq.js new file mode 100644 index 000000000..6beecb325 --- /dev/null +++ b/0.10.0/implementors/core/marker/trait.StructuralPartialEq.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl StructuralPartialEq for Error","synthetic":false,"types":[]},{"text":"impl StructuralPartialEq for Status","synthetic":false,"types":[]},{"text":"impl StructuralPartialEq for CellShape","synthetic":false,"types":[]},{"text":"impl StructuralPartialEq for BondOrder","synthetic":false,"types":[]},{"text":"impl StructuralPartialEq for Match","synthetic":false,"types":[]},{"text":"impl StructuralPartialEq for Property","synthetic":false,"types":[]},{"text":"impl StructuralPartialEq for FormatMetadata","synthetic":false,"types":[]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.0/implementors/core/marker/trait.Sync.js b/0.10.0/implementors/core/marker/trait.Sync.js new file mode 100644 index 000000000..cdb1108cd --- /dev/null +++ b/0.10.0/implementors/core/marker/trait.Sync.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Sync for Error","synthetic":true,"types":[]},{"text":"impl !Sync for Atom","synthetic":true,"types":[]},{"text":"impl<'a> !Sync for AtomRef<'a>","synthetic":true,"types":[]},{"text":"impl<'a> !Sync for 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CellShape","synthetic":true,"types":[]},{"text":"impl Sync for BondOrder","synthetic":true,"types":[]},{"text":"impl Sync for Property","synthetic":true,"types":[]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.0/implementors/core/marker/trait.Unpin.js b/0.10.0/implementors/core/marker/trait.Unpin.js new file mode 100644 index 000000000..e29f42985 --- /dev/null +++ b/0.10.0/implementors/core/marker/trait.Unpin.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Unpin for Error","synthetic":true,"types":[]},{"text":"impl Unpin for Atom","synthetic":true,"types":[]},{"text":"impl<'a> Unpin for AtomRef<'a>","synthetic":true,"types":[]},{"text":"impl<'a> Unpin for AtomMut<'a>","synthetic":true,"types":[]},{"text":"impl Unpin for UnitCell","synthetic":true,"types":[]},{"text":"impl<'a> Unpin for 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Property","synthetic":true,"types":[]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.0/implementors/core/ops/deref/trait.Deref.js b/0.10.0/implementors/core/ops/deref/trait.Deref.js new file mode 100644 index 000000000..90859c88d --- /dev/null +++ b/0.10.0/implementors/core/ops/deref/trait.Deref.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl<'a> Deref for AtomRef<'a>","synthetic":false,"types":[]},{"text":"impl<'a> Deref for AtomMut<'a>","synthetic":false,"types":[]},{"text":"impl<'a> Deref for UnitCellRef<'a>","synthetic":false,"types":[]},{"text":"impl<'a> Deref for UnitCellMut<'a>","synthetic":false,"types":[]},{"text":"impl<'a> Deref for ResidueRef<'a>","synthetic":false,"types":[]},{"text":"impl<'a> Deref for TopologyRef<'a>","synthetic":false,"types":[]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.0/implementors/core/ops/deref/trait.DerefMut.js b/0.10.0/implementors/core/ops/deref/trait.DerefMut.js new file mode 100644 index 000000000..e410cbf42 --- /dev/null +++ b/0.10.0/implementors/core/ops/deref/trait.DerefMut.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl<'a> DerefMut for AtomMut<'a>","synthetic":false,"types":[]},{"text":"impl<'a> DerefMut for UnitCellMut<'a>","synthetic":false,"types":[]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.0/implementors/core/ops/drop/trait.Drop.js b/0.10.0/implementors/core/ops/drop/trait.Drop.js new file mode 100644 index 000000000..8514fd8c0 --- /dev/null +++ b/0.10.0/implementors/core/ops/drop/trait.Drop.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Drop for Atom","synthetic":false,"types":[]},{"text":"impl Drop for UnitCell","synthetic":false,"types":[]},{"text":"impl Drop for Residue","synthetic":false,"types":[]},{"text":"impl Drop for Topology","synthetic":false,"types":[]},{"text":"impl Drop for Frame","synthetic":false,"types":[]},{"text":"impl Drop for Trajectory","synthetic":false,"types":[]},{"text":"impl Drop for Selection","synthetic":false,"types":[]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.0/implementors/core/ops/index/trait.Index.js b/0.10.0/implementors/core/ops/index/trait.Index.js new file mode 100644 index 000000000..44943a284 --- /dev/null +++ b/0.10.0/implementors/core/ops/index/trait.Index.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = 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-0,0 +1,4 @@ +var searchIndex = JSON.parse('{\ +"chemfiles":{"doc":"Chemfiles is a multi-language library written in modern…","i":[[3,"Error","chemfiles","Error type for Chemfiles.",null,null],[12,"status","","The error status code",0,null],[12,"message","","A message describing the error cause",0,null],[3,"Atom","","An `Atom` is a particle in the current `Frame`. It stores…",null,null],[3,"AtomRef","","An analog to a reference to an atom (`&Atom`)",null,null],[3,"AtomMut","","An analog to a mutable reference to an atom (`&mut Atom`)",null,null],[3,"UnitCell","","An `UnitCell` represent the box containing the atoms, and…",null,null],[3,"UnitCellRef","","An analog to a reference to an unit cell (`&UnitCell`)",null,null],[3,"UnitCellMut","","An analog to a mutable reference to an unit cell (`&mut…",null,null],[3,"Residue","","A `Residue` is a group of atoms belonging to the same…",null,null],[3,"ResidueRef","","An analog to a reference to a residue (`&Residue`)",null,null],[3,"Topology","","A `Topology` contains the definition of all the atoms in…",null,null],[3,"TopologyRef","","An analog to a reference to a topology (`&Topology`)",null,null],[3,"Frame","","A `Frame` contains data from one simulation step: the…",null,null],[3,"Trajectory","","The `Trajectory` type is the main entry point when using…",null,null],[3,"Match","","A `Match` is a set of atomic indexes matching a given…",null,null],[3,"Selection","","A `Selection` allow to select atoms in a `Frame`, from a…",null,null],[3,"PropertiesIter","","An iterator over the properties in an atom/frame/residue",null,null],[3,"FormatMetadata","","`FormatMetadata` contains metdata associated with one…",null,null],[12,"name","","Name of the format.",1,null],[12,"extension","","Extension associated with the format.",1,null],[12,"description","","Extended, user-facing description of the format.",1,null],[12,"reference","","URL pointing to the format definition/reference.",1,null],[12,"read","","Is reading files in this format implemented?",1,null],[12,"write","","Is writing files in this format implemented?",1,null],[12,"memory","","Does this format support in-memory IO?",1,null],[12,"positions","","Does this format support storing atomic positions?",1,null],[12,"velocities","","Does this format support storing atomic velocities?",1,null],[12,"unit_cell","","Does this format support storing unit cell information?",1,null],[12,"atoms","","Does this format support storing atom names or types?",1,null],[12,"bonds","","Does this format support storing bonds between atoms?",1,null],[12,"residues","","Does this format support storing residues?",1,null],[4,"Status","","Possible causes of error in chemfiles",null,null],[13,"Success","","No error",2,null],[13,"MemoryError","","Error in memory allocations",2,null],[13,"FileError","","Error while reading or writing a file",2,null],[13,"FormatError","","Error in file formatting, i.e. the file is invalid",2,null],[13,"SelectionError","","Error in selection string syntax",2,null],[13,"ConfigurationError","","Error in configuration files syntax",2,null],[13,"OutOfBounds","","Error for out of bounds indexing",2,null],[13,"PropertyError","","Error related to properties",2,null],[13,"ChemfilesError","","Exception in the C++ chemfiles library",2,null],[13,"StdCppError","","Exception in the C++ standard library",2,null],[13,"UTF8PathError","","The given path is not valid UTF8",2,null],[4,"CellShape","","Available unit cell shapes.",null,null],[13,"Orthorhombic","","Orthorhombic cell, with the three angles equals to 90°.",3,null],[13,"Triclinic","","Triclinic cell, with any values for the angles.",3,null],[13,"Infinite","","Infinite cell, to use when there is no cell.",3,null],[4,"BondOrder","","Possible bond order associated with bonds",null,null],[13,"Unknown","","Unknown or unspecified bond order",4,null],[13,"Single","","Single bond",4,null],[13,"Double","","Double bond",4,null],[13,"Triple","","Triple bond",4,null],[13,"Quadruple","","Quadruple bond (present in some metals)",4,null],[13,"Quintuplet","","Quintuplet bond (present in some metals)",4,null],[13,"Amide","","Amide bond (required by some file formats)",4,null],[13,"Aromatic","","Aromatic bond (required by some file formats)",4,null],[4,"Property","","A `Property` is a piece of data that can be associated…",null,null],[13,"Bool","","Boolean property",5,null],[13,"Double","","Floating point property",5,null],[13,"String","","String property",5,null],[13,"Vector3D","","3-dimensional vector property",5,null],[5,"set_warning_callback","","Use `callback` for every chemfiles warning. The callback…",null,[[]]],[5,"formats_list","","Get the list of formats known by chemfiles, as well as all…",null,[[],[["vec",3],["formatmetadata",3]]]],[5,"version","","Get the version of the chemfiles library.",null,[[],["string",3]]],[5,"add_configuration","","Read configuration data from the file at `path`.",null,[[],[["result",4],["error",3]]]],[11,"last_error","","Get the last error message from the C++ library.",0,[[],["string",3]]],[11,"cleanup","","Clear any error from the C++ library",0,[[]]],[11,"new","","Create an atom with the given `name`, and set the atom…",6,[[],["atom",3]]],[11,"mass","","Get the atom mass, in atomic mass units.",6,[[]]],[11,"set_mass","","Set the atom mass to `mass`, in atomic mass units.",6,[[]]],[11,"charge","","Get the atom charge, in number of the electron charge e.",6,[[]]],[11,"set_charge","","Set the atom charge to `charge`, in number of the electron…",6,[[]]],[11,"name","","Get the atom name.",6,[[],["string",3]]],[11,"atomic_type","","Get the atom type.",6,[[],["string",3]]],[11,"set_name","","Set the atom name to `name`.",6,[[]]],[11,"set_atomic_type","","Set the atom type to `atomic_type`.",6,[[]]],[11,"full_name","","Try to get the full name of the atom from the atomic type.…",6,[[],["string",3]]],[11,"vdw_radius","","Try to get the Van der Waals radius of the atom from the…",6,[[]]],[11,"covalent_radius","","Try to get the covalent radius of the atom from the atomic…",6,[[]]],[11,"atomic_number","","Try to get the atomic number of the atom from the atomic…",6,[[]]],[11,"set","","Add a new `property` with the given `name` to this atom.",6,[[]]],[11,"get","","Get a property with the given `name` in this atom, if it…",6,[[],[["option",4],["property",4]]]],[11,"properties","","Get an iterator over all (name, property) pairs for this…",6,[[],["propertiesiter",3]]],[11,"new","","Create an `Orthorhombic` `UnitCell` from the three…",7,[[],["unitcell",3]]],[11,"infinite","","Create an `Infinite` `UnitCell`.",7,[[],["unitcell",3]]],[11,"triclinic","","Create an `Triclinic` `UnitCell` from the three lengths…",7,[[],["unitcell",3]]],[11,"from_matrix","","Create an `UnitCell` from a cell matrix. If `matrix`…",7,[[],["unitcell",3]]],[11,"lengths","","Get the three lengths of the cell, in Angstroms.",7,[[]]],[11,"set_lengths","","Set the three lengths of the cell, in Angstroms.",7,[[],[["result",4],["error",3]]]],[11,"angles","","Get the three angles of the cell, in degrees.",7,[[]]],[11,"set_angles","","Set the three angles of the cell, in degrees.",7,[[],[["result",4],["error",3]]]],[11,"matrix","","Get the unit cell matricial representation.",7,[[]]],[11,"shape","","Get the shape of the unit cell.",7,[[],["cellshape",4]]],[11,"set_shape","","Set the shape of the unit cell to `shape`.",7,[[["cellshape",4]],[["result",4],["error",3]]]],[11,"volume","","Get the volume of the unit cell.",7,[[]]],[11,"wrap","","Wrap a `vector` in this unit cell.",7,[[]]],[11,"new","","Create a new residue with the given `name`",8,[[],["residue",3]]],[11,"with_id","","Create a new residue with the given `name` and `id` as…",8,[[],["residue",3]]],[11,"size","","Get the number of atoms in this residue.",8,[[]]],[11,"id","","Get the identifier of this residue in the initial topology…",8,[[],["option",4]]],[11,"name","","Get the name of this residue.",8,[[],["string",3]]],[11,"add_atom","","Add the atom at index `atom` in this residue.",8,[[]]],[11,"contains","","Check if the atom at index `i` is in this residue",8,[[]]],[11,"atoms","","Get the list of atoms of this residue.",8,[[],["vec",3]]],[11,"set","","Add a new `property` with the given `name` to this residue.",8,[[]]],[11,"get","","Get a property with the given `name` in this frame, if it…",8,[[],[["option",4],["property",4]]]],[11,"properties","","Get an iterator over all (name, property) pairs for this…",8,[[],["propertiesiter",3]]],[11,"new","","Create a new empty topology.",9,[[],["topology",3]]],[11,"atom","","Get a reference of the atom at the given `index` in this…",9,[[],["atomref",3]]],[11,"atom_mut","","Get a mutable reference to the atom at the given `index`…",9,[[],["atommut",3]]],[11,"size","","Get the current number of atoms in this topology.",9,[[]]],[11,"resize","","Resize this topology to hold `natoms` atoms, inserting…",9,[[]]],[11,"add_atom","","Add an `Atom` at the end of this topology",9,[[["atom",3]]]],[11,"remove","","Remove an `Atom` from this topology by `index`. This…",9,[[]]],[11,"bonds_count","","Get the number of bonds in the topology.",9,[[]]],[11,"angles_count","","Get the number of angles in the topology.",9,[[]]],[11,"dihedrals_count","","Get the number of dihedral angles in the topology.",9,[[]]],[11,"impropers_count","","Get the number of improper dihedral angles in the topology.",9,[[]]],[11,"bonds","","Get the list of bonds in the topology.",9,[[],["vec",3]]],[11,"angles","","Get the list of angles in the topology.",9,[[],["vec",3]]],[11,"dihedrals","","Get the list of dihedral angles in the topology.",9,[[],["vec",3]]],[11,"impropers","","Get the list of improper dihedral angles in the topology.",9,[[],["vec",3]]],[11,"clear_bonds","","Remove all existing bonds, angles, dihedral angles and…",9,[[]]],[11,"add_bond","","Add a bond between the atoms at indexes `i` and `j` in the…",9,[[]]],[11,"add_bond_with_order","","Add a bond between the atoms at indexes `i` and `j` in the…",9,[[["bondorder",4]]]],[11,"bond_order","","Get the bond order for the bond between the atoms at…",9,[[],["bondorder",4]]],[11,"bond_orders","","Get the bond order for all the bonds in the topology",9,[[],[["vec",3],["bondorder",4]]]],[11,"remove_bond","","Remove any existing bond between the atoms at indexes `i`…",9,[[]]],[11,"residue","","Get a reference to the residue at index `index` from this…",9,[[],[["option",4],["residueref",3]]]],[11,"residue_for_atom","","Get a copy of the residue containing the atom at index…",9,[[],[["option",4],["residueref",3]]]],[11,"residues_count","","Get the number of residues in this topology.",9,[[]]],[11,"add_residue","","Add a residue to this topology.",9,[[["residue",3]],[["result",4],["error",3]]]],[11,"are_linked","","Check if the two residues `first` and `second` from the…",9,[[["residue",3]]]],[11,"new","","Create an empty frame. It will be resized by the library…",10,[[],["frame",3]]],[11,"atom","","Get a reference to the atom at the given `index` in this…",10,[[],["atomref",3]]],[11,"atom_mut","","Get a mutable reference to the atom at the given `index`…",10,[[],["atommut",3]]],[11,"size","","Get the current number of atoms in this frame.",10,[[]]],[11,"resize","","Resize the positions and the velocities in this frame, to…",10,[[]]],[11,"add_atom","","Add an `Atom` and the corresponding position and…",10,[[["atom",3]]]],[11,"remove","","Remove the atom at index `i` in this frame.",10,[[]]],[11,"add_bond","","Add a bond between the atoms at indexes `i` and `j` in the…",10,[[]]],[11,"add_bond_with_order","","Add a bond between the atoms at indexes `i` and `j` in the…",10,[[["bondorder",4]]]],[11,"remove_bond","","Remove any existing bond between the atoms at indexes `i`…",10,[[]]],[11,"add_residue","","Add a copy of `residue` to this frame.",10,[[["residue",3]],[["result",4],["error",3]]]],[11,"distance","","Get the distance between the atoms at indexes `i` and `j`…",10,[[]]],[11,"angle","","Get the angle formed by the atoms at indexes `i`, `j` and…",10,[[]]],[11,"dihedral","","Get the dihedral angle formed by the atoms at indexes `i`,…",10,[[]]],[11,"out_of_plane","","Get the out of plane distance formed by the atoms at…",10,[[]]],[11,"positions","","Get a view into the positions of this frame.",10,[[]]],[11,"positions_mut","","Get a mutable view into the positions of this frame.",10,[[]]],[11,"velocities","","Get a view into the velocities of this frame.",10,[[]]],[11,"velocities_mut","","Get a mutable view into the velocities of this frame.",10,[[]]],[11,"has_velocities","","Check if this frame contains velocity data.",10,[[]]],[11,"add_velocities","","Add velocity data to this frame. If the frame already have…",10,[[]]],[11,"cell","","Get a reference to the `UnitCell` from this frame.",10,[[],["unitcellref",3]]],[11,"cell_mut","","Get a mutable reference to the `UnitCell` from this frame.",10,[[],["unitcellmut",3]]],[11,"set_cell","","Set the `UnitCell` of this frame to `cell`.",10,[[["unitcell",3]]]],[11,"topology","","Get a reference to the `Topology` of this frame.",10,[[],["topologyref",3]]],[11,"set_topology","","Set the `Topology` of this frame to `topology`.",10,[[["topology",3]],[["result",4],["error",3]]]],[11,"step","","Get this frame step, i.e. the frame number in the trajectory",10,[[]]],[11,"set_step","","Set this frame step to `step`.",10,[[]]],[11,"guess_bonds","","Guess the bonds, angles and dihedrals in this `frame`.",10,[[],[["result",4],["error",3]]]],[11,"clear_bonds","","Remove all existing bonds, angles, dihedral angles and…",10,[[]]],[11,"set","","Add a new `property` with the given `name` to this frame.",10,[[]]],[11,"get","","Get a property with the given `name` in this frame, if it…",10,[[],[["option",4],["property",4]]]],[11,"properties","","Get an iterator over all (name, property) pairs for this…",10,[[],["propertiesiter",3]]],[11,"open","","Open the file at the given `path` in the given `mode`.",11,[[],[["trajectory",3],["error",3],["result",4]]]],[11,"open_with_format","","Open the file at the given `path` using a specific file…",11,[[],[["trajectory",3],["error",3],["result",4]]]],[11,"memory_reader","","Read a memory buffer as though it was a formatted file.",11,[[],[["trajectory",3],["error",3],["result",4]]]],[11,"memory_writer","","Write to a memory buffer as though it was a formatted file.",11,[[],[["trajectory",3],["error",3],["result",4]]]],[11,"read","","Read the next step of this trajectory into a `frame`.",11,[[["frame",3]],[["result",4],["error",3]]]],[11,"read_step","","Read a specific `step` of this trajectory into a `frame`.",11,[[["frame",3]],[["result",4],["error",3]]]],[11,"write","","Write a `frame` to this trajectory.",11,[[["frame",3]],[["result",4],["error",3]]]],[11,"set_topology","","Set the `topology` associated with this trajectory. 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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +use std::ops::{Drop, Deref, DerefMut}; +use std::marker::PhantomData; +use std::ptr; + +use chemfiles_sys::*; +use errors::{check_success, check_not_null}; +use strings; + +use property::{Property, RawProperty, PropertiesIter}; + +/// An `Atom` is a particle in the current `Frame`. It stores the following +/// atomic properties: +/// +/// - atom name; +/// - atom type; +/// - atom mass; +/// - atom charge. +/// +/// The atom name is usually an unique identifier (`H1`, `C_a`) while the +/// atom type will be shared between all particles of the same type: `H`, +/// `Ow`, `CH3`. +pub struct Atom { + handle: *mut CHFL_ATOM, +} + +/// An analog to a reference to an atom (`&Atom`) +pub struct AtomRef<'a> { + inner: Atom, + marker: PhantomData<&'a Atom> +} + +impl<'a> Deref for AtomRef<'a> { + type Target = Atom; + fn deref(&self) -> &Atom { + &self.inner + } +} + +/// An analog to a mutable reference to an atom (`&mut Atom`) +pub struct AtomMut<'a> { + inner: Atom, + marker: PhantomData<&'a mut Atom> +} + +impl<'a> Deref for AtomMut<'a> { + type Target = Atom; + fn deref(&self) -> &Atom { + &self.inner + } +} + +impl<'a> DerefMut for AtomMut<'a> { + fn deref_mut(&mut self) -> &mut Atom { + &mut self.inner + } +} + +impl Clone for Atom { + fn clone(&self) -> Atom { + unsafe { + let new_handle = chfl_atom_copy(self.as_ptr()); + Atom::from_ptr(new_handle) + } + } +} + +impl Atom { + /// Create an owned `Atom` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the + /// pointer. + #[inline] + pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_ATOM) -> Atom { + check_not_null(ptr); + Atom { + handle: ptr + } + } + + /// Create a borrowed `Atom` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the + /// pointer, and the caller is responsible for setting the right lifetime + #[inline] + pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_ATOM) -> AtomRef<'a> { + AtomRef { + inner: Atom::from_ptr(ptr as *mut CHFL_ATOM), + marker: PhantomData, + } + } + + /// Create a mutably borrowed `Atom` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the + /// pointer, and the caller is responsible for setting the right lifetime + #[inline] + pub(crate) unsafe fn ref_mut_from_ptr<'a>(ptr: *mut CHFL_ATOM) -> AtomMut<'a> { + AtomMut { + inner: Atom::from_ptr(ptr), + marker: PhantomData, + } + } + + /// Get the underlying C pointer as a const pointer. + #[inline] + pub(crate) fn as_ptr(&self) -> *const CHFL_ATOM { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer. + #[inline] + pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_ATOM { + self.handle + } + + /// Create an atom with the given `name`, and set the atom type to `name`. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let atom = Atom::new("He"); + /// assert_eq!(atom.name(), "He"); + /// ``` + pub fn new<'a>(name: impl Into<&'a str>) -> Atom { + let buffer = strings::to_c(name.into()); + unsafe { + let handle = chfl_atom(buffer.as_ptr()); + Atom::from_ptr(handle) + } + } + + /// Get the atom mass, in atomic mass units. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let atom = Atom::new("He"); + /// assert_eq!(atom.mass(), 4.002602); + /// ``` + pub fn mass(&self) -> f64 { + let mut mass = 0.0; + unsafe { + check_success(chfl_atom_mass(self.as_ptr(), &mut mass)); + } + return mass; + } + + /// Set the atom mass to `mass`, in atomic mass units. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let mut atom = Atom::new("He"); + /// + /// atom.set_mass(34.9); + /// assert_eq!(atom.mass(), 34.9); + /// ``` + pub fn set_mass(&mut self, mass: f64) { + unsafe { + check_success(chfl_atom_set_mass(self.as_mut_ptr(), mass)); + } + } + + /// Get the atom charge, in number of the electron charge *e*. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let atom = Atom::new("He"); + /// assert_eq!(atom.charge(), 0.0); + /// ``` + pub fn charge(&self) -> f64 { + let mut charge = 0.0; + unsafe { + check_success(chfl_atom_charge(self.as_ptr(), &mut charge)); + } + return charge; + } + + /// Set the atom charge to `charge`, in number of the electron charge *e*. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let mut atom = Atom::new("He"); + /// + /// atom.set_charge(-2.0); + /// assert_eq!(atom.charge(), -2.0); + /// ``` + pub fn set_charge(&mut self, charge: f64) { + unsafe { + check_success(chfl_atom_set_charge(self.as_mut_ptr(), charge)); + } + } + + /// Get the atom name. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let atom = Atom::new("He"); + /// assert_eq!(atom.name(), "He"); + /// ``` + pub fn name(&self) -> String { + let get_name = |ptr, len| unsafe { chfl_atom_name(self.as_ptr(), ptr, len) }; + let name = strings::call_autogrow_buffer(10, get_name).expect("getting name failed"); + return strings::from_c(name.as_ptr()); + } + + /// Get the atom type. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let atom = Atom::new("He"); + /// assert_eq!(atom.atomic_type(), "He"); + /// ``` + pub fn atomic_type(&self) -> String { + let get_type = |ptr, len| unsafe { chfl_atom_type(self.as_ptr(), ptr, len) }; + let buffer = strings::call_autogrow_buffer(10, get_type).expect("getting type failed"); + return strings::from_c(buffer.as_ptr()); + } + + /// Set the atom name to `name`. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let mut atom = Atom::new("He"); + /// + /// atom.set_name("Zn3"); + /// assert_eq!(atom.name(), "Zn3"); + /// ``` + pub fn set_name<'a>(&mut self, name: impl Into<&'a str>) { + let buffer = strings::to_c(name.into()); + unsafe { + check_success(chfl_atom_set_name(self.as_mut_ptr(), buffer.as_ptr())); + } + } + + /// Set the atom type to `atomic_type`. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let mut atom = Atom::new("He"); + /// + /// atom.set_atomic_type("F"); + /// assert_eq!(atom.atomic_type(), "F"); + /// ``` + pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>) { + let buffer = strings::to_c(atomic_type.into()); + unsafe { + check_success(chfl_atom_set_type(self.as_mut_ptr(), buffer.as_ptr())); + } + } + + /// Try to get the full name of the atom from the atomic type. For example, + /// the full name of "He" is "Helium", and so on. If the name can not be + /// found, this function returns the empty string. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let atom = Atom::new("Zn"); + /// assert_eq!(atom.full_name(), "Zinc"); + /// ``` + pub fn full_name(&self) -> String { + let get_full_name = |ptr, len| unsafe { chfl_atom_full_name(self.as_ptr(), ptr, len) }; + let name = strings::call_autogrow_buffer(10, get_full_name).expect("getting full name failed"); + return strings::from_c(name.as_ptr()); + } + + /// Try to get the Van der Waals radius of the atom from the atomic type. + /// If the radius can not be found, returns 0. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// assert_eq!(Atom::new("He").vdw_radius(), 1.4); + /// assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0); + /// ``` + pub fn vdw_radius(&self) -> f64 { + let mut radius: f64 = 0.0; + unsafe { + check_success(chfl_atom_vdw_radius(self.as_ptr(), &mut radius)); + } + return radius; + } + + /// Try to get the covalent radius of the atom from the atomic type. If the + /// radius can not be found, returns 0. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// assert_eq!(Atom::new("He").covalent_radius(), 0.32); + /// assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0); + /// ``` + pub fn covalent_radius(&self) -> f64 { + let mut radius: f64 = 0.0; + unsafe { + check_success(chfl_atom_covalent_radius(self.as_ptr(), &mut radius)); + } + return radius; + } + + /// Try to get the atomic number of the atom from the atomic type. If the + /// number can not be found, returns 0. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// assert_eq!(Atom::new("He").atomic_number(), 2); + /// assert_eq!(Atom::new("Xxx").atomic_number(), 0); + /// ``` + pub fn atomic_number(&self) -> u64 { + let mut number = 0; + unsafe { + check_success(chfl_atom_atomic_number(self.as_ptr(), &mut number)); + } + return number; + } + + /// Add a new `property` with the given `name` to this atom. + /// + /// If a property with the same name already exists, this function override + /// the existing property with the new one. + /// + /// # Examples + /// ``` + /// # use chemfiles::{Atom, Property}; + /// let mut atom = Atom::new("He"); + /// atom.set("a bool", true); + /// atom.set("a string", "test"); + /// + /// assert_eq!(atom.get("a bool"), Some(Property::Bool(true))); + /// assert_eq!(atom.get("a string"), Some(Property::String("test".into()))); + /// ``` + pub fn set(&mut self, name: &str, property: impl Into<Property>) { + let buffer = strings::to_c(name); + let property = property.into().as_raw(); + unsafe { + check_success(chfl_atom_set_property( + self.as_mut_ptr(), buffer.as_ptr(), property.as_ptr() + )); + } + } + + + /// Get a property with the given `name` in this atom, if it exist. + /// + /// # Examples + /// ``` + /// # use chemfiles::{Atom, Property}; + /// let mut atom = Atom::new("He"); + /// atom.set("foo", Property::Double(22.2)); + /// + /// assert_eq!(atom.get("foo"), Some(Property::Double(22.2))); + /// assert_eq!(atom.get("Bar"), None); + /// ``` + pub fn get(&self, name: &str) -> Option<Property> { + let buffer = strings::to_c(name); + unsafe { + let handle = chfl_atom_get_property(self.as_ptr(), buffer.as_ptr()); + if handle.is_null() { + None + } else { + let raw = RawProperty::from_ptr(handle); + let property = Property::from_raw(raw); + Some(property) + } + } + } + + /// Get an iterator over all (name, property) pairs for this atom + /// + /// # Examples + /// ``` + /// # use chemfiles::{Atom, Property}; + /// let mut atom = Atom::new("He"); + /// atom.set("foo", Property::Double(22.2)); + /// atom.set("bar", Property::Bool(false)); + /// + /// for (name, property) in atom.properties() { + /// if name == "foo" { + /// assert_eq!(property, Property::Double(22.2)); + /// } else if name == "bar" { + /// assert_eq!(property, Property::Bool(false)); + /// } + /// } + /// ``` + pub fn properties(&self) -> PropertiesIter { + let mut count = 0; + unsafe { + check_success(chfl_atom_properties_count(self.as_ptr(), &mut count)); + } + + #[allow(clippy::cast_possible_truncation)] + let size = count as usize; + let mut c_names = vec![ptr::null_mut(); size]; + unsafe { + check_success(chfl_atom_list_properties(self.as_ptr(), c_names.as_mut_ptr(), count)); + } + + let mut names = Vec::new(); + for ptr in c_names { + names.push(strings::from_c(ptr)); + } + + PropertiesIter { + names: names.into_iter(), + getter: Box::new(move |name| self.get(&*name).expect("failed to get property")) + } + } +} + +impl Drop for Atom { + fn drop(&mut self) { + unsafe { + let _ = chfl_free(self.as_ptr() as *const _); + } + } +} + +#[cfg(test)] +mod test { + use super::*; + + #[test] + fn clone() { + let mut atom = Atom::new("He"); + assert_eq!(atom.name(), "He"); + + let copy = atom.clone(); + assert_eq!(copy.name(), "He"); + + atom.set_name("Na"); + assert_eq!(atom.name(), "Na"); + assert_eq!(copy.name(), "He"); + } + + #[test] + fn mass() { + let mut atom = Atom::new("He"); + assert_ulps_eq!(atom.mass(), 4.002602); + atom.set_mass(15.0); + assert_eq!(atom.mass(), 15.0); + } + + #[test] + fn charge() { + let mut atom = Atom::new("He"); + assert_eq!(atom.charge(), 0.0); + atom.set_charge(-1.5); + assert_eq!(atom.charge(), -1.5); + } + + #[test] + fn name() { + let mut atom = Atom::new("He"); + assert_eq!(atom.name(), "He"); + atom.set_name("Zn-12"); + assert_eq!(atom.name(), "Zn-12"); + } + + #[test] + fn atomic_type() { + let mut atom = Atom::new("He"); + assert_eq!(atom.atomic_type(), "He"); + atom.set_atomic_type("Zn"); + assert_eq!(atom.atomic_type(), "Zn"); + } + + #[test] + fn full_name() { + let mut atom = Atom::new("He"); + assert_eq!(atom.full_name(), "Helium"); + + atom.set_atomic_type("Zn"); + assert_eq!(atom.full_name(), "Zinc"); + + let atom = Atom::new("Unknown"); + assert_eq!(atom.full_name(), ""); + } + + #[test] + fn radii() { + let atom = Atom::new("He"); + assert_ulps_eq!(atom.vdw_radius(), 1.4); + assert_ulps_eq!(atom.covalent_radius(), 0.32); + + let atom = Atom::new("Unknown"); + assert_eq!(atom.vdw_radius(), 0.0); + assert_eq!(atom.covalent_radius(), 0.0); + } + + #[test] + fn atomic_number() { + let atom = Atom::new("He"); + assert_eq!(atom.atomic_number(), 2); + + let atom = Atom::new("Unknown"); + assert_eq!(atom.atomic_number(), 0); + } + + #[test] + fn property() { + let mut atom = Atom::new("F"); + + atom.set("foo", -22.0); + assert_eq!(atom.get("foo"), Some(Property::Double(-22.0))); + assert_eq!(atom.get("bar"), None); + + atom.set("bar", Property::String("here".into())); + for (name, property) in atom.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(-22.0)); + } else if name == "bar" { + assert_eq!(property, Property::String("here".into())); + } + } + } +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +use std::ops::{Drop, Deref, DerefMut}; +use std::marker::PhantomData; +use std::ptr; + +use chemfiles_sys::*; +use errors::{check_success, check_not_null, check, Error}; + +/// Available unit cell shapes. +#[derive(Clone, Debug, PartialEq, Eq)] +pub enum CellShape { + /// Orthorhombic cell, with the three angles equals to 90°. + Orthorhombic, + /// Triclinic cell, with any values for the angles. + Triclinic, + /// Infinite cell, to use when there is no cell. + Infinite, +} + +impl From<chfl_cellshape> for CellShape { + fn from(celltype: chfl_cellshape) -> CellShape { + match celltype { + chfl_cellshape::CHFL_CELL_ORTHORHOMBIC => CellShape::Orthorhombic, + chfl_cellshape::CHFL_CELL_TRICLINIC => CellShape::Triclinic, + chfl_cellshape::CHFL_CELL_INFINITE => CellShape::Infinite, + } + } +} + +impl From<CellShape> for chfl_cellshape { + fn from(celltype: CellShape) -> chfl_cellshape { + match celltype { + CellShape::Orthorhombic => chfl_cellshape::CHFL_CELL_ORTHORHOMBIC, + CellShape::Triclinic => chfl_cellshape::CHFL_CELL_TRICLINIC, + CellShape::Infinite => chfl_cellshape::CHFL_CELL_INFINITE, + } + } +} + +/// An `UnitCell` represent the box containing the atoms, and its periodicity. +/// +/// An unit cell is fully represented by three lengths (a, b, c); and three +/// angles (alpha, beta, gamma). The angles are stored in degrees, and the +/// lengths in Angstroms. +/// +/// A cell also has a matricial representation, by projecting the three base +/// vector into an orthonormal base. We choose to represent such matrix as an +/// upper triangular matrix: +/// +/// ```text +/// | a_x b_x c_x | +/// | 0 b_y c_y | +/// | 0 0 c_z | +/// ``` +pub struct UnitCell { + handle: *mut CHFL_CELL, +} + +/// An analog to a reference to an unit cell (`&UnitCell`) +pub struct UnitCellRef<'a> { + inner: UnitCell, + marker: PhantomData<&'a UnitCell> +} + +impl<'a> Deref for UnitCellRef<'a> { + type Target = UnitCell; + fn deref(&self) -> &UnitCell { + &self.inner + } +} + +/// An analog to a mutable reference to an unit cell (`&mut UnitCell`) +pub struct UnitCellMut<'a> { + inner: UnitCell, + marker: PhantomData<&'a mut UnitCell> +} + +impl<'a> Deref for UnitCellMut<'a> { + type Target = UnitCell; + fn deref(&self) -> &UnitCell { + &self.inner + } +} + +impl<'a> DerefMut for UnitCellMut<'a> { + fn deref_mut(&mut self) -> &mut UnitCell { + &mut self.inner + } +} + +impl Clone for UnitCell { + fn clone(&self) -> UnitCell { + unsafe { + let new_handle = chfl_cell_copy(self.as_ptr()); + UnitCell::from_ptr(new_handle) + } + } +} + +impl UnitCell { + /// Create an owned `UnitCell` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the pointer. + #[inline] + pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_CELL) -> UnitCell { + check_not_null(ptr); + UnitCell { + handle: ptr + } + } + + /// Create a borrowed `UnitCell` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the + /// pointer, and the caller is responsible for setting the right lifetime. + #[inline] + pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_CELL) -> UnitCellRef<'a> { + UnitCellRef { + inner: UnitCell::from_ptr(ptr as *mut CHFL_CELL), + marker: PhantomData, + } + } + + /// Create a borrowed `UnitCell` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the + /// pointer, except for it being non-null, and the caller is responsible for + /// setting the right lifetime + #[inline] + pub(crate) unsafe fn ref_mut_from_ptr<'a>(ptr: *mut CHFL_CELL) -> UnitCellMut<'a> { + UnitCellMut { + inner: UnitCell::from_ptr(ptr), + marker: PhantomData, + } + } + + /// Get the underlying C pointer as a const pointer. + #[inline] + pub(crate) fn as_ptr(&self) -> *const CHFL_CELL { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer. + #[inline] + pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_CELL { + self.handle + } + + /// Create an `Orthorhombic` `UnitCell` from the three lengths, in Angstroms. + /// + /// # Example + /// ``` + /// # use chemfiles::{UnitCell, CellShape}; + /// let cell = UnitCell::new([30.0, 30.0, 23.0]); + /// + /// assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]); + /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); + /// assert_eq!(cell.shape(), CellShape::Orthorhombic); + /// ``` + pub fn new(lengths: [f64; 3]) -> UnitCell { + unsafe { + let handle = chfl_cell(lengths.as_ptr(), ptr::null()); + UnitCell::from_ptr(handle) + } + } + + /// Create an `Infinite` `UnitCell`. + /// + /// # Example + /// ``` + /// # use chemfiles::{UnitCell, CellShape}; + /// let cell = UnitCell::infinite(); + /// + /// assert_eq!(cell.lengths(), [0.0, 0.0, 0.0]); + /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); + /// assert_eq!(cell.shape(), CellShape::Infinite); + /// ``` + pub fn infinite() -> UnitCell { + let mut cell = UnitCell::new([0.0, 0.0, 0.0]); + cell.set_shape(CellShape::Infinite).expect("could not set cell shape"); + return cell; + } + + /// Create an `Triclinic` `UnitCell` from the three lengths (in Angstroms) + /// and three angles (in degree). `alpha` is the angle between the vectors + /// `b` and `c`; `beta` is the between the vectors `a` and `c` and `gamma` + /// is the angle between the vectors `a` and `b`. + /// + /// # Example + /// ``` + /// # use chemfiles::{UnitCell, CellShape}; + /// let cell = UnitCell::triclinic([10.0, 10.0, 10.0], [98.0, 99.0, 90.0]); + /// + /// assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]); + /// assert_eq!(cell.angles()[0], 98.0); + /// // Rounding errors might occur due to internal representation + /// assert!((cell.angles()[1] - 99.0).abs() < 1e-12); + /// assert_eq!(cell.angles()[2], 90.0); + /// assert_eq!(cell.shape(), CellShape::Triclinic); + /// ``` + pub fn triclinic(lengths: [f64; 3], angles: [f64; 3]) -> UnitCell { + unsafe { + let handle = chfl_cell(lengths.as_ptr(), angles.as_ptr()); + UnitCell::from_ptr(handle) + } + } + + /// Create an `UnitCell` from a cell matrix. If `matrix` contains only + /// zeros, then an `Infinite` cell is created. If only the diagonal of the + /// matrix is non-zero, then the cell is `Orthorhombic`. Else a + /// `Triclinic` cell is created. The matrix entries should be in Angstroms. + /// + /// # Panics + /// + /// If the matrix has a negative determinant, or more generally is not + /// representing a unit cell. + /// + /// # Example + /// ``` + /// # use chemfiles::{UnitCell, CellShape}; + /// let cell = UnitCell::from_matrix([ + /// [1.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0] + /// ]); + /// + /// assert_eq!(cell.lengths(), [1.0, 2.0, 3.0]); + /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); + /// assert_eq!(cell.shape(), CellShape::Orthorhombic); + /// ``` + pub fn from_matrix(mut matrix: [[f64; 3]; 3]) -> UnitCell { + unsafe { + let handle = chfl_cell_from_matrix(matrix.as_mut_ptr()); + UnitCell::from_ptr(handle) + } + } + + /// Get the three lengths of the cell, in Angstroms. + /// + /// # Example + /// ``` + /// # use chemfiles::UnitCell; + /// let cell = UnitCell::new([30.0, 30.0, 23.0]); + /// assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]); + /// ``` + pub fn lengths(&self) -> [f64; 3] { + let mut lengths = [0.0; 3]; + unsafe { + check_success(chfl_cell_lengths(self.as_ptr(), lengths.as_mut_ptr())); + } + return lengths; + } + + /// Set the three lengths of the cell, in Angstroms. + /// + /// # Errors + /// + /// This function fails if the unit cell is infinite, or if one of the + /// lengths is negative. + /// + /// # Example + /// ``` + /// # use chemfiles::UnitCell; + /// let mut cell = UnitCell::new([30.0, 30.0, 23.0]); + /// + /// cell.set_lengths([10.0, 30.0, 42.0]).unwrap(); + /// assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]); + /// + /// assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err()); + /// ``` + pub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error> { + unsafe { + check(chfl_cell_set_lengths(self.as_mut_ptr(), lengths.as_ptr())) + } + } + + /// Get the three angles of the cell, in degrees. + /// + /// # Example + /// ``` + /// # use chemfiles::UnitCell; + /// let cell = UnitCell::new([20.0, 20.0, 20.0]); + /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); + /// + /// let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]); + /// assert_eq!(cell.angles()[0], 100.0); + /// // Rounding errors might occur due to internal representation + /// assert!((cell.angles()[1] - 120.0).abs() < 1e-12); + /// assert_eq!(cell.angles()[2], 90.0); + /// ``` + pub fn angles(&self) -> [f64; 3] { + let mut angles = [0.0; 3]; + unsafe { + check_success(chfl_cell_angles(self.as_ptr(), angles.as_mut_ptr())); + } + return angles; + } + + /// Set the three angles of the cell, in degrees. + /// + /// # Errors + /// + /// This function fails if the unit cell is not `Triclinic`. + /// + /// # Example + /// ``` + /// # use chemfiles::UnitCell; + /// let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]); + /// assert_eq!(cell.angles()[0], 100.0); + /// // Rounding errors might occur due to internal representation + /// assert!((cell.angles()[1] - 120.0).abs() < 1e-12); + /// assert_eq!(cell.angles()[2], 90.0); + /// + /// cell.set_angles([90.0, 90.0, 90.0]).unwrap(); + /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); + /// ``` + pub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error> { + unsafe { + check(chfl_cell_set_angles(self.as_mut_ptr(), angles.as_ptr())) + } + } + + /// Get the unit cell matricial representation. + /// + /// The unit cell representation is obtained by aligning the a vector along + /// the *x* axis and putting the b vector in the *xy* plane. This make the + /// matrix an upper triangular matrix: + /// + /// ```text + /// | a_x b_x c_x | + /// | 0 b_y c_y | + /// | 0 0 c_z | + /// ``` + /// + /// # Example + /// ``` + /// # use chemfiles::UnitCell; + /// let cell = UnitCell::new([10.0, 20.0, 30.0]); + /// + /// let matrix = cell.matrix(); + /// + /// assert_eq!(matrix[0][0], 10.0); + /// assert_eq!(matrix[1][1], 20.0); + /// assert_eq!(matrix[2][2], 30.0); + /// + /// assert!(matrix[1][2].abs() < 1e-9); + /// ``` + pub fn matrix(&self) -> [[f64; 3]; 3] { + let mut matrix = [[0.0; 3]; 3]; + unsafe { + check_success(chfl_cell_matrix(self.as_ptr(), matrix.as_mut_ptr())); + } + return matrix; + } + + /// Get the shape of the unit cell. + /// + /// # Example + /// ``` + /// # use chemfiles::{UnitCell, CellShape}; + /// let cell = UnitCell::new([10.0, 20.0, 30.0]); + /// assert_eq!(cell.shape(), CellShape::Orthorhombic); + /// ``` + pub fn shape(&self) -> CellShape { + let mut shape = chfl_cellshape::CHFL_CELL_INFINITE; + unsafe { + check_success(chfl_cell_shape(self.as_ptr(), &mut shape)); + } + return CellShape::from(shape); + } + + /// Set the shape of the unit cell to `shape`. + /// + /// # Errors + /// + /// This can fail if the cell length or angles are incompatible with the + /// new shape. + /// + /// # Example + /// ``` + /// # use chemfiles::{UnitCell, CellShape}; + /// let mut cell = UnitCell::new([10.0, 20.0, 30.0]); + /// assert_eq!(cell.shape(), CellShape::Orthorhombic); + /// + /// cell.set_shape(CellShape::Triclinic).unwrap(); + /// assert_eq!(cell.shape(), CellShape::Triclinic); + /// ``` + pub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error> { + unsafe { + check(chfl_cell_set_shape(self.as_mut_ptr(), shape.into())) + } + } + + /// Get the volume of the unit cell. + /// + /// # Example + /// ``` + /// # use chemfiles::UnitCell; + /// let cell = UnitCell::new([10.0, 20.0, 30.0]); + /// assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0); + /// ``` + pub fn volume(&self) -> f64 { + let mut volume = 0.0; + unsafe { + check_success(chfl_cell_volume(self.as_ptr(), &mut volume)); + } + return volume; + } + + /// Wrap a `vector` in this unit cell. + /// + /// # Example + /// ``` + /// # use chemfiles::UnitCell; + /// let cell = UnitCell::new([10.0, 20.0, 30.0]); + /// + /// let mut vector = [12.0, 5.2, -45.3]; + /// cell.wrap(&mut vector); + /// assert_eq!(vector, [2.0, 5.2, 14.700000000000003]); + /// ``` + pub fn wrap(&self, vector: &mut [f64; 3]) { + unsafe { + check_success(chfl_cell_wrap(self.as_ptr(), vector.as_mut_ptr())) + } + } +} + +impl Drop for UnitCell { + fn drop(&mut self) { + unsafe { + let _ = chfl_free(self.as_ptr() as *const _); + } + } +} + + +#[cfg(test)] +mod test { + use super::*; + + #[test] + fn clone() { + let mut cell = UnitCell::new([2.0, 3.0, 4.0]); + assert_eq!(cell.lengths(), [2.0, 3.0, 4.0]); + + let copy = cell.clone(); + assert_eq!(copy.lengths(), [2.0, 3.0, 4.0]); + + cell.set_lengths([10.0, 12.0, 11.0]).unwrap(); + assert_eq!(cell.lengths(), [10.0, 12.0, 11.0]); + assert_eq!(copy.lengths(), [2.0, 3.0, 4.0]); + } + + #[test] + fn lengths() { + let mut cell = UnitCell::new([2.0, 3.0, 4.0]); + assert_eq!(cell.lengths(), [2.0, 3.0, 4.0]); + cell.set_lengths([10.0, 12.0, 11.0]).unwrap(); + assert_eq!(cell.lengths(), [10.0, 12.0, 11.0]); + } + + #[test] + fn angles() { + let mut cell = UnitCell::new([2.0, 3.0, 4.0]); + crate::assert_vector3d_eq(&cell.angles(), &[90.0, 90.0, 90.0], 1e-6); + + cell.set_shape(CellShape::Triclinic).unwrap(); + cell.set_angles([80.0, 89.0, 100.0]).unwrap(); + + crate::assert_vector3d_eq(&cell.angles(), &[80.0, 89.0, 100.0], 1e-6); + + let cell = UnitCell::triclinic([1., 2., 3.], [80., 90., 100.]); + crate::assert_vector3d_eq(&cell.angles(), &[80.0, 90.0, 100.0], 1e-6); + } + + #[test] + fn volume() { + let cell = UnitCell::new([2.0, 3.0, 4.0]); + assert_eq!(cell.volume(), 2.0 * 3.0 * 4.0); + } + + #[test] + fn wrap() { + let cell = UnitCell::new([10.0, 20.0, 30.0]); + let mut vector = [12.0, 5.2, -45.3]; + cell.wrap(&mut vector); + crate::assert_vector3d_eq(&vector, &[2.0, 5.2, 14.7], 1e-6); + } + + #[test] + fn matrix() { + let cell = UnitCell::new([2.0, 3.0, 4.0]); + + let matrix = cell.matrix(); + let result = [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]]; + + for i in 0..3 { + for j in 0..3 { + assert_ulps_eq!(matrix[i][j], result[i][j], epsilon = 1e-12); + } + } + } + + #[test] + fn from_matrix() { + let cell = UnitCell::from_matrix([[10.0, 0.0, 0.0], [0.0, 21.0, 0.0], [0.0, 0.0, 32.0]]); + assert_eq!(cell.shape(), CellShape::Orthorhombic); + assert_eq!(cell.lengths(), [10.0, 21.0, 32.0]); + + let result_matrix = [ + [123.0, 4.08386, 71.7295], + [0.0, 233.964, 133.571], + [0.0, 0.0, 309.901], + ]; + let cell = UnitCell::from_matrix(result_matrix); + + assert_eq!(cell.shape(), CellShape::Triclinic); + for i in 0..3 { + assert_ulps_eq!( + cell.lengths()[i], + [123.0, 234.0, 345.0][i], + epsilon = 1e-3 + ); + assert_ulps_eq!(cell.angles()[i], [67.0, 78.0, 89.0][i], epsilon = 1e-3); + } + + let matrix = cell.matrix(); + for i in 0..3 { + for j in 0..3 { + assert_ulps_eq!(matrix[i][j], result_matrix[i][j], epsilon = 1e-12); + } + } + } + + #[test] + fn shape() { + let cell = UnitCell::new([2.0, 3.0, 4.0]); + assert_eq!(cell.shape(), CellShape::Orthorhombic); + + let cell = UnitCell::infinite(); + assert_eq!(cell.shape(), CellShape::Infinite); + + let cell = UnitCell::triclinic([1.0, 2.0, 3.0], [80.0, 90.0, 100.0]); + assert_eq!(cell.shape(), CellShape::Triclinic); + + let mut cell = UnitCell::new([10.0, 10.0, 10.0]); + assert_eq!(cell.shape(), CellShape::Orthorhombic); + cell.set_shape(CellShape::Triclinic).unwrap(); + assert_eq!(cell.shape(), CellShape::Triclinic); + } +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +extern crate libc; + +use std::error; +use std::fmt; +use std::panic::{self, RefUnwindSafe}; +use std::path::Path; + +use self::libc::c_char; + +use chemfiles_sys::*; +use strings; + +#[derive(Clone, Debug, PartialEq)] +/// Error type for Chemfiles. +pub struct Error { + /// The error status code + pub status: Status, + /// A message describing the error cause + pub message: String, +} + +#[repr(C)] +#[non_exhaustive] +#[derive(Clone, Debug, PartialEq)] +/// Possible causes of error in chemfiles +pub enum Status { + /// No error + Success = chfl_status::CHFL_SUCCESS as isize, + /// Error in memory allocations + MemoryError = chfl_status::CHFL_MEMORY_ERROR as isize, + /// Error while reading or writing a file + FileError = chfl_status::CHFL_FILE_ERROR as isize, + /// Error in file formatting, *i.e.* the file is invalid + FormatError = chfl_status::CHFL_FORMAT_ERROR as isize, + /// Error in selection string syntax + SelectionError = chfl_status::CHFL_SELECTION_ERROR as isize, + /// Error in configuration files syntax + ConfigurationError = chfl_status::CHFL_CONFIGURATION_ERROR as isize, + /// Error for out of bounds indexing + OutOfBounds = chfl_status::CHFL_OUT_OF_BOUNDS as isize, + /// Error related to properties + PropertyError = chfl_status::CHFL_PROPERTY_ERROR as isize, + /// Exception in the C++ chemfiles library + ChemfilesError = chfl_status::CHFL_GENERIC_ERROR as isize, + /// Exception in the C++ standard library + StdCppError = chfl_status::CHFL_CXX_ERROR as isize, + /// The given path is not valid UTF8 + UTF8PathError, +} + +impl From<chfl_status> for Error { + fn from(status: chfl_status) -> Error { + let status = match status { + chfl_status::CHFL_SUCCESS => Status::Success, + chfl_status::CHFL_CXX_ERROR => Status::StdCppError, + chfl_status::CHFL_GENERIC_ERROR => Status::ChemfilesError, + chfl_status::CHFL_MEMORY_ERROR => Status::MemoryError, + chfl_status::CHFL_FILE_ERROR => Status::FileError, + chfl_status::CHFL_FORMAT_ERROR => Status::FormatError, + chfl_status::CHFL_SELECTION_ERROR => Status::SelectionError, + chfl_status::CHFL_CONFIGURATION_ERROR => Status::ConfigurationError, + chfl_status::CHFL_OUT_OF_BOUNDS => Status::OutOfBounds, + chfl_status::CHFL_PROPERTY_ERROR => Status::PropertyError, + }; + + let message = Error::last_error(); + Error { + status, + message, + } + } +} + +impl Error { + /// Create a new error because the given `path` is invalid UTF-8 data + pub(crate) fn utf8_path_error(path: &Path) -> Error { + Error { + status: Status::UTF8PathError, + message: format!("Could not convert '{}' to UTF8", path.display()), + } + } + + /// Get the last error message from the C++ library. + pub fn last_error() -> String { + unsafe { strings::from_c(chfl_last_error()) } + } + + /// Clear any error from the C++ library + pub fn cleanup() { + unsafe { + check(chfl_clear_errors()).expect("error in chfl_clear_errors. Things went very bad"); + } + } +} + +/// Check return value of a C function, and get the error if needed. +pub(crate) fn check(status: chfl_status) -> Result<(), Error> { + if status == chfl_status::CHFL_SUCCESS { + Ok(()) + } else { + Err(Error::from(status)) + } +} + +/// Check return value of a C function, panic if it failed. +pub(crate) fn check_success(status: chfl_status) { + if status != chfl_status::CHFL_SUCCESS { + panic!("unexpected failure: {}", Error::last_error()); + } +} + +/// Check a pointer for null. +pub(crate) fn check_not_null<T>(ptr: *const T) { + if ptr.is_null() { + panic!("unexpected null pointer: {}", Error::last_error()); + } +} + +pub trait WarningCallback: RefUnwindSafe + Fn(&str) {} +impl<T> WarningCallback for T +where + T: RefUnwindSafe + Fn(&str), +{ +} + +static mut LOGGING_CALLBACK: Option<*mut dyn WarningCallback<Output = ()>> = None; + +extern "C" fn warning_callback(message: *const c_char) { + unsafe { + let callback = &*LOGGING_CALLBACK.expect("No callback provided, this is an internal bug"); + // ignore result. If a panic happened, everything is going badly anyway + let _ = panic::catch_unwind(|| { + callback(&strings::from_c(message)); + }); + } +} + +/// Use `callback` for every chemfiles warning. The callback will be passed +/// the warning message. This will drop any previous warning callback. +pub fn set_warning_callback<F>(callback: F) where F: WarningCallback + 'static { + // box callback to ensure it stays accessible + let callback = Box::into_raw(Box::new(callback)); + unsafe { + if let Some(previous) = LOGGING_CALLBACK { + // set the LOGGING_CALLBACK to the new one + LOGGING_CALLBACK = Some(callback); + // drop the previous callback + let _ = Box::from_raw(previous); + } else { + // set the LOGGING_CALLBACK + LOGGING_CALLBACK = Some(callback); + // Tell C code to use Rust-provided callback + check_success(chfl_set_warning_callback(warning_callback)); + } + } +} + + +impl fmt::Display for Error { + fn fmt(&self, fmt: &mut fmt::Formatter) -> Result<(), fmt::Error> { + write!(fmt, "{}", self.message) + } +} + +impl error::Error for Error { + fn description(&self) -> &str { + match self.status { + Status::Success => "Success", + Status::StdCppError => "Exception from the C++ standard library", + Status::ChemfilesError => "Exception from the chemfiles library", + Status::MemoryError => "Error in memory allocations", + Status::FileError => "Error while reading or writing a file", + Status::FormatError => "Error in file formatting, i.e. the file is invalid", + Status::SelectionError => "Error in selection string syntax", + Status::UTF8PathError => "The given path is not valid UTF8", + Status::ConfigurationError => "Error in configuration files", + Status::OutOfBounds => "Out of bounds indexing", + Status::PropertyError => "Error in property", + } + } +} + + +#[cfg(test)] +mod test { + use super::*; + use Trajectory; + + #[test] + fn errors() { + Error::cleanup(); + assert_eq!(Error::last_error(), ""); + assert!(Trajectory::open("nope", 'r').is_err()); + assert_eq!( + Error::last_error(), + "file at \'nope\' does not have an extension, provide a format name to read it" + ); + Error::cleanup(); + assert_eq!(Error::last_error(), ""); + } + + #[test] + fn codes() { + assert_eq!(Error::from(chfl_status::CHFL_SUCCESS).status, Status::Success); + assert_eq!(Error::from(chfl_status::CHFL_CXX_ERROR).status, Status::StdCppError); + assert_eq!(Error::from(chfl_status::CHFL_GENERIC_ERROR).status, Status::ChemfilesError); + assert_eq!(Error::from(chfl_status::CHFL_MEMORY_ERROR).status, Status::MemoryError); + assert_eq!(Error::from(chfl_status::CHFL_FILE_ERROR).status, Status::FileError); + assert_eq!(Error::from(chfl_status::CHFL_FORMAT_ERROR).status, Status::FormatError); + assert_eq!(Error::from(chfl_status::CHFL_SELECTION_ERROR).status, Status::SelectionError); + assert_eq!(Error::from(chfl_status::CHFL_OUT_OF_BOUNDS).status, Status::OutOfBounds); + assert_eq!(Error::from(chfl_status::CHFL_PROPERTY_ERROR).status, Status::PropertyError); + } +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +use std::ops::Drop; +use std::ptr; +use std::slice; + +use chemfiles_sys::*; +use strings; +use errors::{check_not_null, check_success, check, Error}; +use super::{Atom, AtomRef, AtomMut}; +use super::{Topology, TopologyRef, Residue, BondOrder}; +use super::{UnitCell, UnitCellRef, UnitCellMut}; +use property::{Property, RawProperty, PropertiesIter}; + +/// A `Frame` contains data from one simulation step: the current unit +/// cell, the topology, the positions, and the velocities of the particles in +/// the system. If some information is missing (topology or velocity or unit +/// cell), the corresponding data is filled with a default value. +pub struct Frame { + handle: *mut CHFL_FRAME, +} + +impl Clone for Frame { + fn clone(&self) -> Frame { + unsafe { + let new_handle = chfl_frame_copy(self.as_ptr()); + Frame::from_ptr(new_handle) + } + } +} + +impl Frame { + /// Create a `Frame` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the pointer, + /// except for it being non-null. + #[inline] + pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_FRAME) -> Frame { + check_not_null(ptr); + Frame { + handle: ptr + } + } + + /// Get the underlying C pointer as a const pointer. + #[inline] + pub(crate) fn as_ptr(&self) -> *const CHFL_FRAME { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer. + #[inline] + pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_FRAME { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer FROM A SHARED REFERENCE. + /// + /// For uses with functions of the C API using mut pointers for both read + /// and write access. Users should check that this does not lead to multiple + /// mutable borrows + #[inline] + #[allow(non_snake_case)] + pub(crate) fn as_mut_ptr_MANUALLY_CHECKING_BORROW(&self) -> *mut CHFL_FRAME { + self.handle + } + + /// Create an empty frame. It will be resized by the library as needed. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let frame = Frame::new(); + /// + /// assert_eq!(frame.size(), 0); + /// ``` + pub fn new() -> Frame { + unsafe { + Frame::from_ptr(chfl_frame()) + } + } + + /// Get a reference to the atom at the given `index` in this frame. + /// + /// # Panics + /// + /// If `index` is out of bounds. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None); + /// + /// let atom = frame.atom(0); + /// assert_eq!(atom.name(), "Zn"); + /// ``` + pub fn atom(&self, index: usize) -> AtomRef { + unsafe { + let handle = chfl_atom_from_frame( + self.as_mut_ptr_MANUALLY_CHECKING_BORROW(), + index as u64 + ); + Atom::ref_from_ptr(handle) + } + } + + /// Get a mutable reference to the atom at the given `index` in this frame. + /// + /// # Panics + /// + /// If `index` is out of bounds. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None); + /// + /// assert_eq!(frame.atom(0).name(), "Zn"); + /// + /// frame.atom_mut(0).set_name("Fe"); + /// assert_eq!(frame.atom(0).name(), "Fe"); + /// ``` + pub fn atom_mut(&mut self, index: usize) -> AtomMut { + unsafe { + let handle = chfl_atom_from_frame(self.as_mut_ptr(), index as u64); + Atom::ref_mut_from_ptr(handle) + } + } + + /// Get the current number of atoms in this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// assert_eq!(frame.size(), 0); + /// + /// frame.resize(67); + /// assert_eq!(frame.size(), 67); + /// ``` + pub fn size(&self) -> usize { + let mut size = 0; + unsafe { + check_success(chfl_frame_atoms_count(self.as_ptr(), &mut size)); + } + #[allow(clippy::cast_possible_truncation)] + return size as usize; + } + + /// Resize the positions and the velocities in this frame, to make space for + /// `natoms` atoms. Previous data is conserved, as well as the presence of + /// absence of velocities. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// frame.resize(67); + /// assert_eq!(frame.size(), 67); + /// ``` + pub fn resize(&mut self, natoms: usize) { + unsafe { + check_success(chfl_frame_resize(self.as_mut_ptr(), natoms as u64)); + } + } + + /// Add an `Atom` and the corresponding position and optionally velocity + /// data to this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("Zn"), [1.0, 1.0, 2.0], None); + /// + /// frame.add_velocities(); + /// frame.add_atom(&Atom::new("Zn"), [-1.0, 1.0, 2.0], [0.2, 0.1, 0.0]); + /// ``` + pub fn add_atom( + &mut self, + atom: &Atom, + position: [f64; 3], + velocity: impl Into<Option<[f64; 3]>>, + ) + { + let velocity = velocity.into(); + let velocity_ptr = match velocity { + Some(ref data) => data.as_ptr(), + None => ptr::null(), + }; + + unsafe { + check_success(chfl_frame_add_atom( + self.as_mut_ptr(), + atom.as_ptr(), + position.as_ptr(), + velocity_ptr + )); + } + + } + + /// Remove the atom at index `i` in this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None); + /// frame.add_atom(&Atom::new("Fe"), [0.0; 3], None); + /// frame.add_atom(&Atom::new("Sn"), [0.0; 3], None); + /// assert_eq!(frame.size(), 3); + /// + /// frame.remove(1); + /// assert_eq!(frame.size(), 2); + /// assert_eq!(frame.atom(1).name(), "Sn"); + /// ``` + pub fn remove(&mut self, i: usize) { + unsafe { + check_success(chfl_frame_remove(self.as_mut_ptr(), i as u64)); + } + } + + /// Add a bond between the atoms at indexes `i` and `j` in the frame. + /// + /// The bond order is set to `BondOrder::Unknown`. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, BondOrder}; + /// let mut frame = Frame::new(); + /// assert_eq!(frame.topology().bonds_count(), 0); + /// frame.resize(5); + /// + /// frame.add_bond(0, 1); + /// frame.add_bond(3, 1); + /// frame.add_bond(2, 4); + /// assert_eq!(frame.topology().bonds_count(), 3); + /// + /// assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown); + /// assert_eq!(frame.topology().bonds(), vec![[0, 1], [1, 3], [2, 4]]); + /// ``` + pub fn add_bond(&mut self, i: usize, j: usize) { + unsafe { + check_success(chfl_frame_add_bond(self.as_mut_ptr(), i as u64, j as u64)); + } + } + + /// Add a bond between the atoms at indexes `i` and `j` in the frame + /// with the given bond `order`. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, BondOrder}; + /// let mut frame = Frame::new(); + /// assert_eq!(frame.topology().bonds_count(), 0); + /// frame.resize(2); + /// + /// frame.add_bond_with_order(0, 1, BondOrder::Double); + /// assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Double); + /// ``` + pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder) { + unsafe { + check_success(chfl_frame_bond_with_order( + self.as_mut_ptr(), + i as u64, + j as u64, + order.as_raw(), + )); + } + } + + /// Remove any existing bond between the atoms at indexes `i` and `j` in + /// the frame. + /// + /// This function does nothing if there is no bond between `i` and `j`. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// frame.resize(5); + /// + /// frame.add_bond(0, 1); + /// frame.add_bond(3, 1); + /// frame.add_bond(2, 4); + /// + /// let bonds = frame.topology().bonds(); + /// assert_eq!(bonds, vec![[0, 1], [1, 3], [2, 4]]); + /// + /// frame.remove_bond(2, 4); + /// let bonds = frame.topology().bonds(); + /// assert_eq!(bonds, vec![[0, 1], [1, 3]]); + /// ``` + pub fn remove_bond(&mut self, i: usize, j: usize) { + unsafe { + check_success(chfl_frame_remove_bond( + self.as_mut_ptr(), + i as u64, + j as u64, + )); + } + } + + /// Add a copy of `residue` to this frame. + /// + /// # Errors + /// + /// This function fails is the residue id is already in this frame's + /// topology, or if the residue contain atoms that are already in another + /// residue. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Residue}; + /// let mut frame = Frame::new(); + /// + /// let residue = Residue::new("foo"); + /// frame.add_residue(&residue).unwrap(); + /// + /// let topology = frame.topology(); + /// assert_eq!(topology.residues_count(), 1); + /// assert_eq!(topology.residue(0).unwrap().name(), "foo"); + /// ``` + pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error> { + unsafe { + check(chfl_frame_add_residue(self.as_mut_ptr(), residue.as_ptr())) + } + } + + /// Get the distance between the atoms at indexes `i` and `j` in this frame, + /// accounting for periodic boundary conditions. The result is expressed in + /// Angstroms. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("B"), [1.0, 2.0, 3.0], None); + /// + /// assert_eq!(frame.distance(0, 1), f64::sqrt(14.0)); + /// ``` + pub fn distance(&self, i: usize, j: usize) -> f64 { + let mut distance = 0.0; + unsafe { + check_success(chfl_frame_distance( + self.as_ptr(), + i as u64, + j as u64, + &mut distance, + )); + } + return distance; + } + + /// Get the angle formed by the atoms at indexes `i`, `j` and `k` in this + /// frame, accounting for periodic boundary conditions. The result is + /// expressed in radians. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// # use std::f64; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None); + /// + /// assert_eq!(frame.angle(0, 1, 2), f64::consts::PI / 2.0); + /// ``` + pub fn angle(&self, i: usize, j: usize, k: usize) -> f64 { + let mut angle = 0.0; + unsafe { + check_success(chfl_frame_angle( + self.as_ptr(), + i as u64, + j as u64, + k as u64, + &mut angle, + )); + } + return angle; + } + + /// Get the dihedral angle formed by the atoms at indexes `i`, `j`, `k` and + /// `m` in this frame, accounting for periodic boundary conditions. The + /// result is expressed in radians. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// # use std::f64; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None); + /// frame.add_atom(&Atom::new("D"), [0.0, 1.0, 1.0], None); + /// + /// assert_eq!(frame.dihedral(0, 1, 2, 3), f64::consts::PI / 2.0); + /// ``` + pub fn dihedral(&self, i: usize, j: usize, k: usize, m: usize) -> f64 { + let mut dihedral = 0.0; + unsafe { + check_success(chfl_frame_dihedral( + self.as_ptr(), + i as u64, + j as u64, + k as u64, + m as u64, + &mut dihedral, + )); + } + return dihedral; + } + + /// Get the out of plane distance formed by the atoms at indexes `i`, `j`, + /// `k` and `m` in this frame, accounting for periodic boundary conditions. + /// The result is expressed in angstroms. + /// + /// This is the distance between the atom j and the ikm plane. The j atom + /// is the center of the improper dihedral angle formed by i, j, k and m. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 2.0], None); + /// frame.add_atom(&Atom::new("C"), [1.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("D"), [0.0, 1.0, 0.0], None); + /// + /// assert_eq!(frame.out_of_plane(0, 1, 2, 3), 2.0); + /// ``` + pub fn out_of_plane(&self, i: usize, j: usize, k: usize, m: usize) -> f64 { + let mut distance = 0.0; + unsafe { + check_success(chfl_frame_out_of_plane( + self.as_ptr(), + i as u64, + j as u64, + k as u64, + m as u64, + &mut distance, + )); + } + return distance; + } + + /// Get a view into the positions of this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// frame.resize(67); + /// + /// let positions = frame.positions(); + /// assert_eq!(positions.len(), 67); + /// assert_eq!(positions[0], [0.0, 0.0, 0.0]); + /// ``` + pub fn positions(&self) -> &[[f64; 3]] { + let mut ptr = ptr::null_mut(); + let mut natoms = 0; + unsafe { + check_success(chfl_frame_positions( + self.as_mut_ptr_MANUALLY_CHECKING_BORROW(), + &mut ptr, + &mut natoms + )); + } + + #[allow(clippy::cast_possible_truncation)] + let size = natoms as usize; + unsafe { + return slice::from_raw_parts(ptr, size); + } + } + + /// Get a mutable view into the positions of this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// frame.resize(67); + /// { + /// let positions = frame.positions_mut(); + /// assert_eq!(positions[0], [0.0, 0.0, 0.0]); + /// positions[0] = [1.0, 2.0, 3.0]; + /// } + /// + /// let positions = frame.positions(); + /// assert_eq!(positions[0], [1.0, 2.0, 3.0]); + /// ``` + pub fn positions_mut(&mut self) -> &mut [[f64; 3]] { + let mut ptr = ptr::null_mut(); + let mut natoms = 0; + unsafe { + check_success(chfl_frame_positions(self.as_mut_ptr(), &mut ptr, &mut natoms)); + } + #[allow(clippy::cast_possible_truncation)] + let size = natoms as usize; + unsafe { + return slice::from_raw_parts_mut(ptr, size); + } + } + + /// Get a view into the velocities of this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// frame.resize(67); + /// frame.add_velocities(); + /// + /// let velocities = frame.velocities(); + /// assert_eq!(velocities.len(), 67); + /// assert_eq!(velocities[0], [0.0, 0.0, 0.0]); + /// ``` + pub fn velocities(&self) -> &[[f64; 3]] { + let mut ptr = ptr::null_mut(); + let mut natoms = 0; + unsafe { + check_success(chfl_frame_velocities( + self.as_mut_ptr_MANUALLY_CHECKING_BORROW(), + &mut ptr, + &mut natoms + )); + } + #[allow(clippy::cast_possible_truncation)] + let size = natoms as usize; + unsafe { + return slice::from_raw_parts(ptr, size); + } + } + + /// Get a mutable view into the velocities of this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// frame.resize(67); + /// frame.add_velocities(); + /// { + /// let velocities = frame.velocities_mut(); + /// assert_eq!(velocities[0], [0.0, 0.0, 0.0]); + /// velocities[0] = [1.0, 2.0, 3.0]; + /// } + /// + /// let velocities = frame.velocities(); + /// assert_eq!(velocities[0], [1.0, 2.0, 3.0]); + /// ``` + pub fn velocities_mut(&mut self) -> &mut [[f64; 3]] { + let mut ptr = ptr::null_mut(); + let mut natoms = 0; + unsafe { + check_success(chfl_frame_velocities(self.as_mut_ptr(), &mut ptr, &mut natoms)); + } + #[allow(clippy::cast_possible_truncation)] + let size = natoms as usize; + unsafe { + return slice::from_raw_parts_mut(ptr, size); + } + } + + /// Check if this frame contains velocity data. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// assert_eq!(frame.has_velocities(), false); + /// + /// frame.add_velocities(); + /// assert_eq!(frame.has_velocities(), true); + /// ``` + pub fn has_velocities(&self) -> bool { + let mut res = 0; + unsafe { + check_success(chfl_frame_has_velocities(self.as_ptr(), &mut res)); + } + return res != 0; + } + + /// Add velocity data to this frame. If the frame already have velocities, + /// this does nothing. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// assert_eq!(frame.has_velocities(), false); + /// + /// frame.add_velocities(); + /// assert_eq!(frame.has_velocities(), true); + /// ``` + pub fn add_velocities(&mut self) { + unsafe { + check_success(chfl_frame_add_velocities(self.as_mut_ptr())); + } + } + + /// Get a reference to the `UnitCell` from this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, CellShape}; + /// let frame = Frame::new(); + /// + /// let cell = frame.cell(); + /// assert_eq!(cell.shape(), CellShape::Infinite); + /// ``` + pub fn cell(&self) -> UnitCellRef { + unsafe { + let handle = chfl_cell_from_frame(self.as_mut_ptr_MANUALLY_CHECKING_BORROW()); + UnitCell::ref_from_ptr(handle) + } + } + + /// Get a mutable reference to the `UnitCell` from this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, CellShape}; + /// let mut frame = Frame::new(); + /// + /// assert_eq!(frame.cell().shape(), CellShape::Infinite); + /// + /// frame.cell_mut().set_shape(CellShape::Triclinic).unwrap(); + /// assert_eq!(frame.cell().shape(), CellShape::Triclinic); + /// ``` + pub fn cell_mut(&mut self) -> UnitCellMut { + unsafe { + let handle = chfl_cell_from_frame(self.as_mut_ptr()); + UnitCell::ref_mut_from_ptr(handle) + } + } + + /// Set the `UnitCell` of this frame to `cell`. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, UnitCell, CellShape}; + /// let mut frame = Frame::new(); + /// + /// frame.set_cell(&UnitCell::new([10.0, 10.0, 10.0])); + /// + /// let cell = frame.cell(); + /// assert_eq!(cell.shape(), CellShape::Orthorhombic); + /// assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]); + /// ``` + pub fn set_cell(&mut self, cell: &UnitCell) { + unsafe { + check_success(chfl_frame_set_cell(self.as_mut_ptr(), cell.as_ptr())); + } + } + + /// Get a reference to the `Topology` of this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// frame.resize(42); + /// + /// let topology = frame.topology(); + /// assert_eq!(topology.size(), 42); + /// ``` + pub fn topology(&self) -> TopologyRef { + unsafe { + let handle = chfl_topology_from_frame(self.as_ptr()); + Topology::ref_from_ptr(handle) + } + } + + /// Set the `Topology` of this frame to `topology`. + /// + /// # Errors + /// + /// This function fails if the topology contains a different number of atoms + /// than this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Topology, Atom}; + /// let mut frame = Frame::new(); + /// frame.resize(2); + /// + /// let mut topology = Topology::new(); + /// topology.add_atom(&Atom::new("Cl")); + /// topology.add_atom(&Atom::new("Cl")); + /// topology.add_bond(0, 1); + /// + /// frame.set_topology(&topology).unwrap(); + /// assert_eq!(frame.atom(0).name(), "Cl"); + /// ``` + pub fn set_topology(&mut self, topology: &Topology) -> Result<(), Error> { + unsafe { + check(chfl_frame_set_topology(self.as_mut_ptr(), topology.as_ptr())) + } + } + + /// Get this frame step, i.e. the frame number in the trajectory + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let frame = Frame::new(); + /// assert_eq!(frame.step(), 0); + /// ``` + pub fn step(&self) -> usize { + let mut step = 0; + unsafe { + check_success(chfl_frame_step(self.as_ptr(), &mut step)); + } + #[allow(clippy::cast_possible_truncation)] + return step as usize; + } + + /// Set this frame step to `step`. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// assert_eq!(frame.step(), 0); + /// + /// frame.set_step(10); + /// assert_eq!(frame.step(), 10); + /// ``` + pub fn set_step(&mut self, step: usize) { + unsafe { + check_success(chfl_frame_set_step(self.as_mut_ptr(), step as u64)); + } + } + + /// Guess the bonds, angles and dihedrals in this `frame`. + /// + /// The bonds are guessed using a distance-based algorithm, and then angles + /// and dihedrals are guessed from the bonds. + /// + /// # Errors + //// + /// This function can fail if the covalent radius is unknown for some atoms + /// in the frame. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// let mut frame = Frame::new(); + /// + /// frame.add_atom(&Atom::new("Cl"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("Cl"), [1.5, 0.0, 0.0], None); + /// assert_eq!(frame.topology().bonds_count(), 0); + /// + /// frame.guess_bonds().unwrap(); + /// assert_eq!(frame.topology().bonds_count(), 1); + /// ``` + pub fn guess_bonds(&mut self) -> Result<(), Error> { + unsafe { + check(chfl_frame_guess_bonds(self.as_mut_ptr())) + } + } + + /// Remove all existing bonds, angles, dihedral angles and improper + /// dihedral angles in the topology of the frame. + /// + /// # Example + /// ``` + /// # use chemfiles::{Atom, Frame}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("H"), [0.0, 1.0, 0.0], None); + /// + /// frame.add_bond(0, 1); + /// frame.add_bond(1, 2); + /// + /// assert_eq!(frame.topology().bonds().len(), 2); + /// assert_eq!(frame.topology().angles().len(), 1); + /// + /// frame.clear_bonds(); + /// assert!(frame.topology().bonds().is_empty()); + /// assert!(frame.topology().angles().is_empty()); + /// ``` + pub fn clear_bonds(&mut self) { + unsafe { + check_success(chfl_frame_clear_bonds(self.as_mut_ptr())); + } + } + + /// Add a new `property` with the given `name` to this frame. + /// + /// If a property with the same name already exists, this function override + /// the existing property with the new one. + /// + /// # Examples + /// ``` + /// # use chemfiles::{Frame, Property}; + /// let mut frame = Frame::new(); + /// frame.set("a string", "hello"); + /// frame.set("a double", 4.3); + /// + /// assert_eq!(frame.get("a string"), Some(Property::String("hello".into()))); + /// assert_eq!(frame.get("a double"), Some(Property::Double(4.3))); + /// ``` + pub fn set(&mut self, name: &str, property: impl Into<Property>) { + let buffer = strings::to_c(name); + let property = property.into().as_raw(); + unsafe { + check_success(chfl_frame_set_property( + self.as_mut_ptr(), buffer.as_ptr(), property.as_ptr() + )); + } + } + + /// Get a property with the given `name` in this frame, if it exist. + /// + /// # Examples + /// ``` + /// # use chemfiles::{Frame, Property}; + /// let mut frame = Frame::new(); + /// frame.set("foo", Property::Double(22.2)); + /// + /// assert_eq!(frame.get("foo"), Some(Property::Double(22.2))); + /// assert_eq!(frame.get("Bar"), None); + /// ``` + pub fn get(&self, name: &str) -> Option<Property> { + let buffer = strings::to_c(name); + unsafe { + let handle = chfl_frame_get_property(self.as_ptr(), buffer.as_ptr()); + if handle.is_null() { + None + } else { + let raw = RawProperty::from_ptr(handle); + Some(Property::from_raw(raw)) + } + } + } + + /// Get an iterator over all (name, property) pairs for this frame + /// + /// # Examples + /// ``` + /// # use chemfiles::{Frame, Property}; + /// let mut frame = Frame::new(); + /// frame.set("foo", Property::Double(22.2)); + /// frame.set("bar", Property::Bool(false)); + /// + /// for (name, property) in frame.properties() { + /// if name == "foo" { + /// assert_eq!(property, Property::Double(22.2)); + /// } else if name == "bar" { + /// assert_eq!(property, Property::Bool(false)); + /// } + /// } + /// ``` + pub fn properties(&self) -> PropertiesIter { + let mut count = 0; + unsafe { + check_success(chfl_frame_properties_count(self.as_ptr(), &mut count)); + } + + #[allow(clippy::cast_possible_truncation)] + let size = count as usize; + let mut c_names = vec![ptr::null_mut(); size]; + unsafe { + check_success(chfl_frame_list_properties(self.as_ptr(), c_names.as_mut_ptr(), count)); + } + + let mut names = Vec::new(); + for ptr in c_names { + names.push(strings::from_c(ptr)); + } + + PropertiesIter { + names: names.into_iter(), + getter: Box::new(move |name| self.get(&*name).expect("failed to get property")) + } + } +} + +impl Drop for Frame { + fn drop(&mut self) { + unsafe { + let _ = chfl_free(self.as_ptr() as *const _); + } + } +} + +#[cfg(test)] +mod test { + use super::*; + use {Atom, Topology, UnitCell}; + + #[test] + fn clone() { + let mut frame = Frame::new(); + assert_eq!(frame.size(), 0); + let copy = frame.clone(); + assert_eq!(copy.size(), 0); + + frame.resize(42); + assert_eq!(frame.size(), 42); + assert_eq!(copy.size(), 0); + } + + #[test] + fn size() { + let mut frame = Frame::new(); + assert_eq!(frame.size(), 0); + + frame.resize(12); + assert_eq!(frame.size(), 12); + } + + #[test] + fn add_atom() { + let mut frame = Frame::new(); + + frame.add_atom(&Atom::new("U"), [1.0, 1.0, 2.0], None); + assert_eq!(frame.size(), 1); + assert_eq!(frame.atom(0).name(), "U"); + + let positions = &[[1.0, 1.0, 2.0]]; + assert_eq!(frame.positions(), positions); + + frame.add_velocities(); + frame.add_atom(&Atom::new("F"), [1.0, 1.0, 2.0], [4.0, 3.0, 2.0]); + assert_eq!(frame.size(), 2); + assert_eq!(frame.atom(0).name(), "U"); + assert_eq!(frame.atom(1).name(), "F"); + + let positions = &[[1.0, 1.0, 2.0], [1.0, 1.0, 2.0]]; + assert_eq!(frame.positions(), positions); + + let velocities = &[[0.0, 0.0, 0.0], [4.0, 3.0, 2.0]]; + assert_eq!(frame.velocities(), velocities); + } + + #[test] + #[should_panic] + fn out_of_bounds_atom() { + let mut frame = Frame::new(); + frame.resize(22); + let _ = frame.atom(23); + } + + #[test] + fn remove_atom() { + let mut frame = Frame::new(); + frame.add_atom(&Atom::new("U"), [1.0, 1.0, 2.0], None); + frame.add_atom(&Atom::new("F"), [1.0, 1.0, 2.0], None); + + assert_eq!(frame.size(), 2); + assert_eq!(frame.atom(0).name(), "U"); + + frame.remove(0); + assert_eq!(frame.size(), 1); + assert_eq!(frame.atom(0).name(), "F"); + } + + #[test] + #[should_panic] + fn remove_out_of_bounds() { + let mut frame = Frame::new(); + frame.resize(32); + + frame.remove(100); + } + + #[test] + fn positions() { + let mut frame = Frame::new(); + frame.resize(4); + let expected = &[ + [1.0, 2.0, 3.0], + [4.0, 5.0, 6.0], + [7.0, 8.0, 9.0], + [10.0, 11.0, 12.0], + ]; + + frame.positions_mut().clone_from_slice(expected); + assert_eq!(frame.positions(), expected); + } + + #[test] + fn velocities() { + let mut frame = Frame::new(); + frame.resize(4); + assert_eq!(frame.has_velocities(), false); + frame.add_velocities(); + assert_eq!(frame.has_velocities(), true); + + let expected = &[ + [1.0, 2.0, 3.0], + [4.0, 5.0, 6.0], + [7.0, 8.0, 9.0], + [10.0, 11.0, 12.0], + ]; + + frame.velocities_mut().clone_from_slice(expected); + assert_eq!(frame.velocities(), expected); + } + + #[test] + fn cell() { + let mut frame = Frame::new(); + frame.set_cell(&UnitCell::new([3.0, 4.0, 5.0])); + let cell = frame.cell(); + assert_eq!(cell.lengths(), [3.0, 4.0, 5.0]); + } + + #[test] + fn topology() { + let mut frame = Frame::new(); + frame.resize(2); + let mut topology = Topology::new(); + + topology.add_atom(&Atom::new("Zn")); + topology.add_atom(&Atom::new("Ar")); + + assert!(frame.set_topology(&topology).is_ok()); + + let topology = frame.topology(); + + assert_eq!(topology.atom(0).name(), "Zn"); + assert_eq!(topology.atom(1).name(), "Ar"); + + assert_eq!(frame.atom(0).name(), "Zn"); + assert_eq!(frame.atom(1).name(), "Ar"); + } + + #[test] + fn bonds() { + let mut frame = Frame::new(); + frame.resize(12); + assert_eq!(frame.topology().bonds_count(), 0); + + frame.add_bond(0, 1); + frame.add_bond(9, 2); + frame.add_bond_with_order(3, 7, BondOrder::Aromatic); + assert_eq!(frame.topology().bonds_count(), 3); + + assert_eq!(frame.topology().bonds(), vec![[0, 1], [2, 9], [3, 7]]); + let expected = vec![BondOrder::Unknown, BondOrder::Unknown, BondOrder::Aromatic]; + assert_eq!(frame.topology().bond_orders(), expected); + + assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown); + assert_eq!(frame.topology().bond_order(3, 7), BondOrder::Aromatic); + + frame.remove_bond(3, 7); + // Removing unexisting bond is OK if both indexes are in bounds + frame.remove_bond(8, 7); + assert_eq!(frame.topology().bonds_count(), 2); + + frame.clear_bonds(); + assert_eq!(frame.topology().bonds_count(), 0); + } + + #[test] + #[should_panic] + fn out_of_bounds_bonds() { + let mut frame = Frame::new(); + frame.resize(12); + frame.add_bond(300, 7); + } + + #[test] + #[should_panic] + fn out_of_bounds_remove_bond() { + let mut frame = Frame::new(); + frame.resize(12); + frame.remove_bond(300, 7); + } + + #[test] + #[should_panic] + fn out_of_bounds_bonds_with_order() { + let mut frame = Frame::new(); + frame.resize(12); + frame.add_bond_with_order(300, 7, BondOrder::Unknown); + } + + #[test] + fn residues() { + let mut frame = Frame::new(); + assert_eq!(frame.topology().residues_count(), 0); + + let residue = &Residue::new("foobar"); + frame.add_residue(residue).unwrap(); + frame.add_residue(residue).unwrap(); + frame.add_residue(residue).unwrap(); + + assert_eq!(frame.topology().residues_count(), 3); + assert_eq!(frame.topology().residue(0).unwrap().name(), "foobar"); + } + + #[test] + fn step() { + let mut frame = Frame::new(); + assert_eq!(frame.step(), 0); + frame.set_step(42); + assert_eq!(frame.step(), 42); + } + + #[test] + fn property() { + let mut frame = Frame::new(); + frame.set("foo", -22.0); + assert_eq!(frame.get("foo"), Some(Property::Double(-22.0))); + assert_eq!(frame.get("bar"), None); + + frame.set("bar", Property::String("here".into())); + for (name, property) in frame.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(-22.0)); + } else if name == "bar" { + assert_eq!(property, Property::String("here".into())); + } + } + } + + #[test] + fn pbc_geometry() { + use std::f64::consts::PI; + + let mut frame = Frame::new(); + let atom = &Atom::new(""); + + frame.add_atom(atom, [1.0, 0.0, 0.0], None); + frame.add_atom(atom, [0.0, 0.0, 0.0], None); + frame.add_atom(atom, [0.0, 1.0, 0.0], None); + frame.add_atom(atom, [0.0, 1.0, 1.0], None); + frame.add_atom(atom, [0.0, 0.0, 2.0], None); + + assert_eq!(frame.distance(0, 2), f64::sqrt(2.0)); + assert_eq!(frame.angle(0, 1, 2), PI / 2.0); + assert_eq!(frame.dihedral(0, 1, 2, 3), PI / 2.0); + assert_eq!(frame.out_of_plane(1, 4, 0, 2), 2.0); + } +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed + +//! Chemfiles is a multi-language library written in modern C++ for reading and +//! writing from and to molecular trajectory files. These files are created by +//! your favorite theoretical chemistry program, and contains information about +//! atomic or residues names and positions. Some format also have additional +//! information, such as velocities, forces, energy, … +//! +//! This crate expose the C API of chemfiles to Rust, and make all the +//! functionalities accessible. For more information on the C++ library, +//! please see its [documentation][cxx_doc]. Specifically, the following pages +//! are worth reading: +//! +//! - The [overview][overview] of the classes organization; +//! - The list of [supported formats][formats]; +//! - The documentation for the [selection language][selections]; +//! +//! [cxx_doc]: https://chemfiles.org/chemfiles +//! [overview]: https://chemfiles.org/chemfiles/latest/overview.html +//! [formats]: https://chemfiles.org/chemfiles/latest/formats.html +//! [selections]: https://chemfiles.org/chemfiles/latest/selections.html + +#![deny(missing_docs)] +#![warn(trivial_casts, unused_import_braces, variant_size_differences)] +#![warn(unused_qualifications, unused_results)] +// Configuration for clippy lints +#![warn(clippy::all, clippy::pedantic)] +#![allow(clippy::needless_return, clippy::module_name_repetitions)] +#![allow(clippy::must_use_candidate, clippy::wildcard_imports)] + +// Allow a few more clippy lints in test mode +#![cfg_attr(test, allow(clippy::float_cmp, clippy::unreadable_literal, clippy::shadow_unrelated))] + +// deny(warnings) in doc tests +#![doc(test(attr(deny(warnings))))] +#![doc(test(attr(allow(unused_variables))))] + +#[cfg(test)] +#[macro_use] +extern crate approx; + +extern crate chemfiles_sys; +use chemfiles_sys::{chfl_add_configuration, chfl_version}; + +mod strings; + +mod errors; +pub use errors::{Error, Status}; +pub use errors::set_warning_callback; + +mod atom; +pub use atom::Atom; +pub use atom::AtomRef; +pub use atom::AtomMut; + +mod cell; +pub use cell::UnitCell; +pub use cell::UnitCellRef; +pub use cell::UnitCellMut; +pub use cell::CellShape; + +mod residue; +pub use residue::Residue; +pub use residue::ResidueRef; + +mod topology; +pub use topology::Topology; +pub use topology::TopologyRef; +pub use topology::BondOrder; + +mod frame; +pub use frame::Frame; + +mod trajectory; +pub use trajectory::Trajectory; + +mod selection; +pub use selection::{Match, Selection}; + +mod property; +pub use property::Property; +pub use property::PropertiesIter; + +mod metadata; +pub use metadata::{FormatMetadata, formats_list}; + +/// Get the version of the chemfiles library. +/// +/// # Example +/// ``` +/// let version = chemfiles::version(); +/// assert!(version.starts_with("0.10")); +/// ``` +pub fn version() -> String { + unsafe { strings::from_c(chfl_version()) } +} + +/// Read configuration data from the file at `path`. +/// +/// By default, chemfiles reads configuration from any file named +/// `.chemfiles.toml` in the current directory or any parent directory. This +/// function can be used to add data from another configuration file. Data from +/// the new configuration file will overwrite any existing data. +/// +/// # Errors +/// +/// This function will fail if there is no file at `path`, or if the file is +/// incorrectly formatted. +/// +/// # Example +/// ```no_run +/// chemfiles::add_configuration("local-config.toml").unwrap(); +/// // from now on, the data from "local-config.toml" will be used +/// ``` +pub fn add_configuration<S>(path: S) -> Result<(), Error> +where + S: AsRef<str>, +{ + let buffer = strings::to_c(path.as_ref()); + unsafe { + errors::check(chfl_add_configuration(buffer.as_ptr())) + } +} + +#[cfg(test)] +mod tests { + #[test] + fn version() { + assert!(!crate::version().is_empty()); + assert!(crate::version().starts_with("0.10")); + } +} + +#[cfg(test)] +fn assert_vector3d_eq(lhs: &[f64; 3], rhs: &[f64; 3], eps: f64) { + lhs.iter() + .zip(rhs) + .for_each(|(l, r)| assert_ulps_eq!(l, r, epsilon = eps)); +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2020 Guillaume Fraux -- BSD licensed + +use std::convert::TryInto; +use std::ffi::CStr; + +use chemfiles_sys::{chfl_format_metadata, chfl_formats_list, chfl_free}; +use errors::check_success; + +/// `FormatMetadata` contains metdata associated with one format. +#[allow(clippy::struct_excessive_bools)] +#[derive(Debug, Clone, PartialEq, Eq)] +pub struct FormatMetadata { + /// Name of the format. + pub name: &'static str, + /// Extension associated with the format. + pub extension: Option<&'static str>, + /// Extended, user-facing description of the format. + pub description: &'static str, + /// URL pointing to the format definition/reference. + pub reference: &'static str, + /// Is reading files in this format implemented? + pub read: bool, + /// Is writing files in this format implemented? + pub write: bool, + /// Does this format support in-memory IO? + pub memory: bool, + /// Does this format support storing atomic positions? + pub positions: bool, + /// Does this format support storing atomic velocities? + pub velocities: bool, + /// Does this format support storing unit cell information? + pub unit_cell: bool, + /// Does this format support storing atom names or types? + pub atoms: bool, + /// Does this format support storing bonds between atoms? + pub bonds: bool, + /// Does this format support storing residues? + pub residues: bool, +} + +impl FormatMetadata { + pub(crate) fn from_raw(raw: &chfl_format_metadata) -> Self { + let str_from_ptr = |ptr| unsafe { + CStr::from_ptr(ptr) + .to_str() + .expect("Invalid Rust str from C") + }; + let extension = if raw.extension.is_null() { + None + } else { + Some(str_from_ptr(raw.extension)) + }; + Self { + name: str_from_ptr(raw.name), + extension, + description: str_from_ptr(raw.description), + reference: str_from_ptr(raw.reference), + read: raw.read, + write: raw.write, + memory: raw.memory, + positions: raw.positions, + velocities: raw.velocities, + unit_cell: raw.unit_cell, + atoms: raw.atoms, + bonds: raw.bonds, + residues: raw.residues, + } + } +} + +/// Get the list of formats known by chemfiles, as well as all associated metadata. +/// +/// # Example +/// ``` +/// let formats = chemfiles::formats_list(); +/// println!("chemfiles supports {} formats:", formats.len()); +/// for format in &formats { +/// println!( +/// " {:<15} {}", +/// format.name, +/// format.extension.as_deref().unwrap_or("") +/// ); +/// } +/// ``` +#[must_use] +pub fn formats_list() -> Vec<FormatMetadata> { + let mut formats = std::ptr::null_mut(); + let mut count: u64 = 0; + let formats_slice = unsafe { + check_success(chfl_formats_list(&mut formats, &mut count)); + std::slice::from_raw_parts(formats, count.try_into().unwrap()) + }; + let formats_vec = formats_slice + .iter() + .map(|fm| FormatMetadata::from_raw(fm)) + .collect(); + unsafe { + let _ = chfl_free(formats as *const _); + } + return formats_vec; +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +use std::ops::Drop; +use std::vec::IntoIter; + +use chemfiles_sys::*; +use errors::{check, check_not_null, check_success, Error}; +use strings; + +/// A thin wrapper around `CHFL_PROPERTY` +pub(crate) struct RawProperty { + handle: *mut CHFL_PROPERTY, +} + +impl RawProperty { + /// Create a `RawProperty` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the pointer. + pub unsafe fn from_ptr(ptr: *mut CHFL_PROPERTY) -> RawProperty { + check_not_null(ptr); + RawProperty { + handle: ptr + } + } + + /// Get the underlying C pointer as a const pointer. + pub fn as_ptr(&self) -> *const CHFL_PROPERTY { + self.handle + } + + fn double(value: f64) -> RawProperty { + unsafe { + let handle = chfl_property_double(value); + RawProperty::from_ptr(handle) + } + } + + fn bool(value: bool) -> RawProperty { + let value = if value { 1 } else { 0 }; + unsafe { + let handle = chfl_property_bool(value); + RawProperty::from_ptr(handle) + } + } + + fn vector3d(value: [f64; 3]) -> RawProperty { + unsafe { + let handle = chfl_property_vector3d(value.as_ptr()); + RawProperty::from_ptr(handle) + } + } + + fn string(value: &str) -> RawProperty { + let buffer = strings::to_c(value); + unsafe { + let handle = chfl_property_string(buffer.as_ptr()); + RawProperty::from_ptr(handle) + } + } + + fn get_kind(&self) -> chfl_property_kind { + let mut kind = chfl_property_kind::CHFL_PROPERTY_BOOL; + unsafe { + check_success(chfl_property_get_kind(self.as_ptr(), &mut kind)); + } + return kind; + } + + fn get_bool(&self) -> Result<bool, Error> { + let mut value = 0; + unsafe { + check(chfl_property_get_bool(self.as_ptr(), &mut value))?; + } + return Ok(value != 0); + } + + fn get_double(&self) -> Result<f64, Error> { + let mut value = 0.0; + unsafe { + check(chfl_property_get_double(self.as_ptr(), &mut value))?; + } + return Ok(value); + } + + fn get_string(&self) -> Result<String, Error> { + let get_string = |ptr, len| unsafe { chfl_property_get_string(self.as_ptr(), ptr, len) }; + let value = strings::call_autogrow_buffer(64, get_string)?; + return Ok(strings::from_c(value.as_ptr())); + } + + fn get_vector3d(&self) -> Result<[f64; 3], Error> { + let mut value = [0.0; 3]; + unsafe { + check(chfl_property_get_vector3d(self.as_ptr(), value.as_mut_ptr()))?; + } + return Ok(value); + } +} + +impl Drop for RawProperty { + fn drop(&mut self) { + unsafe { + let _ = chfl_free(self.as_ptr() as *const _); + } + } +} + +/// A `Property` is a piece of data that can be associated with an `Atom` or a +/// `Frame`. +#[derive(Debug, Clone, PartialEq, PartialOrd)] +pub enum Property { + /// Boolean property + Bool(bool), + /// Floating point property + Double(f64), + /// String property + String(String), + /// 3-dimensional vector property + Vector3D([f64; 3]), +} + +impl From<bool> for Property { + fn from(value: bool) -> Self { + Property::Bool(value) + } +} + +impl From<f64> for Property { + fn from(value: f64) -> Self { + Property::Double(value) + } +} + +impl From<String> for Property { + fn from(value: String) -> Self { + Property::String(value) + } +} + +impl<'a> From<&'a str> for Property { + fn from(value: &'a str) -> Self { + Property::String(value.into()) + } +} + +impl From<[f64; 3]> for Property { + fn from(value: [f64; 3]) -> Self { + Property::Vector3D(value) + } +} + +impl Property { + pub(crate) fn as_raw(&self) -> RawProperty { + match *self { + Property::Bool(value) => RawProperty::bool(value), + Property::Double(value) => RawProperty::double(value), + Property::String(ref value) => RawProperty::string(value), + Property::Vector3D(value) => RawProperty::vector3d(value), + } + } + + #[allow(clippy::needless_pass_by_value)] // raw property + pub(crate) fn from_raw(raw: RawProperty) -> Property { + match raw.get_kind() { + chfl_property_kind::CHFL_PROPERTY_BOOL => { + Property::Bool(raw.get_bool().expect("shoudl be a bool")) + } + chfl_property_kind::CHFL_PROPERTY_DOUBLE => { + Property::Double(raw.get_double().expect("should be a double")) + } + chfl_property_kind::CHFL_PROPERTY_STRING => { + Property::String(raw.get_string().expect("should be a string")) + } + chfl_property_kind::CHFL_PROPERTY_VECTOR3D => { + Property::Vector3D(raw.get_vector3d().expect("should be a vector3d")) + } + } + } +} + +/// An iterator over the properties in an atom/frame/residue +pub struct PropertiesIter<'a> where { + pub(crate) names: IntoIter<String>, + pub(crate) getter: Box<dyn Fn(&str) -> Property + 'a>, +} + +impl<'a> Iterator for PropertiesIter<'a> { + type Item = (String, Property); + fn next(&mut self) -> Option<Self::Item> { + self.names.next().map(|name| { + let property = (self.getter)(&*name); + (name, property) + }) + } + + fn size_hint(&self) -> (usize, Option<usize>) { + self.names.size_hint() + } + + fn count(self) -> usize { + self.names.count() + } +} + +#[cfg(test)] +mod tests { + mod raw { + use super::super::*; + + #[test] + fn bool() { + let property = RawProperty::bool(false); + assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_BOOL); + assert_eq!(property.get_bool(), Ok(false)); + } + + #[test] + fn double() { + let property = RawProperty::double(45.0); + assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_DOUBLE); + assert_eq!(property.get_double(), Ok(45.0)); + } + + #[test] + fn string() { + let property = RawProperty::string("test"); + assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_STRING); + assert_eq!(property.get_string(), Ok("test".into())); + } + + #[test] + fn vector3d() { + let property = RawProperty::vector3d([1.2, 3.4, 5.6]); + assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_VECTOR3D); + assert_eq!(property.get_vector3d(), Ok([1.2, 3.4, 5.6])); + } + } + + mod rust { + use super::super::*; + + #[test] + fn bool() { + let property = Property::Bool(false); + + let raw = property.as_raw(); + assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_BOOL); + assert_eq!(raw.get_bool(), Ok(false)); + + assert_eq!(Property::from_raw(raw), property); + } + + #[test] + fn double() { + let property = Property::Double(45.0); + + let raw = property.as_raw(); + assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_DOUBLE); + assert_eq!(raw.get_double(), Ok(45.0)); + + assert_eq!(Property::from_raw(raw), property); + } + + #[test] + fn string() { + let property = Property::String("test".into()); + + let raw = property.as_raw(); + assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_STRING); + assert_eq!(raw.get_string(), Ok("test".into())); + + assert_eq!(Property::from_raw(raw), property); + + let property = Property::String("long string ".repeat(128)); + let raw = property.as_raw(); + assert_eq!(raw.get_string(), Ok("long string ".repeat(128))); + } + + #[test] + fn vector3d() { + let property = Property::Vector3D([1.2, 3.4, 5.6]); + + let raw = property.as_raw(); + assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_VECTOR3D); + assert_eq!(raw.get_vector3d(), Ok([1.2, 3.4, 5.6])); + + assert_eq!(Property::from_raw(raw), property); + } + } +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +use std::ops::{Drop, Deref}; +use std::marker::PhantomData; +use std::ptr; + +use chemfiles_sys::*; +use errors::{check_not_null, check_success, Error}; +use property::{Property, RawProperty, PropertiesIter}; +use strings; + +/// A `Residue` is a group of atoms belonging to the same logical unit. They +/// can be small molecules, amino-acids in a protein, monomers in polymers, +/// *etc.* +pub struct Residue { + handle: *mut CHFL_RESIDUE, +} + +/// An analog to a reference to a residue (`&Residue`) +pub struct ResidueRef<'a> { + inner: Residue, + marker: PhantomData<&'a Residue> +} + +impl<'a> Deref for ResidueRef<'a> { + type Target = Residue; + fn deref(&self) -> &Residue { + &self.inner + } +} + +impl Clone for Residue { + fn clone(&self) -> Residue { + unsafe { + let new_handle = chfl_residue_copy(self.as_ptr()); + Residue::from_ptr(new_handle) + } + } +} + +impl Residue { + /// Create a `Residue` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the pointer. + #[inline] + pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_RESIDUE) -> Residue { + check_not_null(ptr); + Residue { + handle: ptr + } + } + + /// Create a borrowed `Residue` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the + /// pointer, except for it being non-null, and the caller is responsible + /// for setting the right lifetime + #[inline] + pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_RESIDUE) -> ResidueRef<'a> { + ResidueRef { + inner: Residue::from_ptr(ptr as *mut CHFL_RESIDUE), + marker: PhantomData, + } + } + + /// Get the underlying C pointer as a const pointer. + #[inline] + pub(crate) fn as_ptr(&self) -> *const CHFL_RESIDUE { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer. + #[inline] + pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_RESIDUE { + self.handle + } + + /// Create a new residue with the given `name` + /// + /// # Example + /// ``` + /// # use chemfiles::Residue; + /// let residue = Residue::new("ALA"); + /// assert_eq!(residue.name(), "ALA"); + /// assert_eq!(residue.id(), None); + /// ``` + pub fn new<'a>(name: impl Into<&'a str>) -> Residue { + let buffer = strings::to_c(name.into()); + unsafe { + let handle = chfl_residue(buffer.as_ptr()); + Residue::from_ptr(handle) + } + } + + /// Create a new residue with the given `name` and `id` as identifier. + /// + /// # Example + /// ``` + /// # use chemfiles::Residue; + /// let residue = Residue::with_id("ALA", 67); + /// assert_eq!(residue.name(), "ALA"); + /// assert_eq!(residue.id(), Some(67)); + /// ``` + pub fn with_id<'a>(name: impl Into<&'a str>, id: i64) -> Residue { + let buffer = strings::to_c(name.into()); + unsafe { + let handle = chfl_residue_with_id(buffer.as_ptr(), id); + Residue::from_ptr(handle) + } + } + + /// Get the number of atoms in this residue. + /// + /// # Example + /// ``` + /// # use chemfiles::Residue; + /// let mut residue = Residue::new("water"); + /// assert_eq!(residue.size(), 0); + /// + /// residue.add_atom(0); + /// residue.add_atom(1); + /// residue.add_atom(2); + /// assert_eq!(residue.size(), 3); + /// ``` + pub fn size(&self) -> usize { + let mut size = 0; + unsafe { + check_success(chfl_residue_atoms_count(self.as_ptr(), &mut size)); + } + #[allow(clippy::cast_possible_truncation)] + return size as usize; + } + + /// Get the identifier of this residue in the initial topology file. + /// + /// # Example + /// ``` + /// # use chemfiles::Residue; + /// let residue = Residue::with_id("", 42); + /// assert_eq!(residue.id(), Some(42)); + /// ``` + pub fn id(&self) -> Option<i64> { + let mut resid = 0; + let status = unsafe { + chfl_residue_id(self.as_ptr(), &mut resid) + }; + + if status == chfl_status::CHFL_SUCCESS { + return Some(resid); + } else if status == chfl_status::CHFL_GENERIC_ERROR { + return None; + } else { + panic!("unexpected failure: {}", Error::last_error()); + } + } + + /// Get the name of this residue. + /// + /// # Example + /// ``` + /// # use chemfiles::Residue; + /// let residue = Residue::new("water"); + /// assert_eq!(residue.name(), "water"); + /// ``` + pub fn name(&self) -> String { + let get_name = |ptr, len| unsafe { chfl_residue_name(self.as_ptr(), ptr, len) }; + let name = strings::call_autogrow_buffer(64, get_name).expect("getting residue name failed"); + return strings::from_c(name.as_ptr()); + } + + /// Add the atom at index `atom` in this residue. + /// + /// This will fail if the atom is already in the residue. + /// + /// # Example + /// ``` + /// # use chemfiles::Residue; + /// let mut residue = Residue::new("water"); + /// assert_eq!(residue.size(), 0); + /// assert_eq!(residue.contains(56), false); + /// + /// residue.add_atom(56); + /// assert_eq!(residue.size(), 1); + /// assert_eq!(residue.contains(56), true); + /// + /// // Adding the same atom twice is fine + /// residue.add_atom(56); + /// assert_eq!(residue.size(), 1); + /// ``` + pub fn add_atom(&mut self, atom: usize) { + unsafe { + check_success(chfl_residue_add_atom(self.as_mut_ptr(), atom as u64)); + } + } + + /// Check if the atom at index `i` is in this residue + /// + /// # Example + /// ``` + /// # use chemfiles::Residue; + /// let mut residue = Residue::new("water"); + /// assert_eq!(residue.contains(56), false); + /// + /// residue.add_atom(56); + /// assert_eq!(residue.contains(56), true); + /// ``` + pub fn contains(&self, atom: usize) -> bool { + let mut inside = 0; + unsafe { + check_success(chfl_residue_contains(self.as_ptr(), atom as u64, &mut inside)); + } + return inside != 0; + } + + /// Get the list of atoms of this residue. + /// + /// # Example + /// ``` + /// # use chemfiles::Residue; + /// let mut residue = Residue::new("water"); + /// assert_eq!(residue.atoms(), vec![]); + /// + /// residue.add_atom(56); + /// assert_eq!(residue.atoms(), vec![56]); + /// ``` + pub fn atoms(&self) -> Vec<usize> { + let size = self.size(); + let count = size as u64; + let mut indices = vec![u64::max_value(); size]; + unsafe { + check_success(chfl_residue_atoms( + self.as_ptr(), + indices.as_mut_ptr(), + count, + )); + } + #[allow(clippy::cast_possible_truncation)] + return indices.into_iter().map(|idx| idx as usize).collect(); + } + + /// Add a new `property` with the given `name` to this residue. + /// + /// If a property with the same name already exists, this function override + /// the existing property with the new one. + /// + /// # Examples + /// ``` + /// # use chemfiles::{Residue, Property}; + /// let mut residue = Residue::new("ALA"); + /// residue.set("a string", "hello"); + /// residue.set("a double", 3.2); + /// + /// assert_eq!(residue.get("a string"), Some(Property::String("hello".into()))); + /// assert_eq!(residue.get("a double"), Some(Property::Double(3.2))); + /// ``` + pub fn set(&mut self, name: &str, property: impl Into<Property>) { + let buffer = strings::to_c(name); + let property = property.into().as_raw(); + unsafe { + check_success(chfl_residue_set_property( + self.as_mut_ptr(), buffer.as_ptr(), property.as_ptr() + )); + } + } + + /// Get a property with the given `name` in this frame, if it exist. + /// + /// # Examples + /// ``` + /// # use chemfiles::{Residue, Property}; + /// let mut residue = Residue::new("ALA"); + /// residue.set("foo", Property::Double(22.2)); + /// + /// assert_eq!(residue.get("foo"), Some(Property::Double(22.2))); + /// assert_eq!(residue.get("Bar"), None); + /// ``` + pub fn get(&self, name: &str) -> Option<Property> { + let buffer = strings::to_c(name); + unsafe { + let handle = chfl_residue_get_property(self.as_ptr(), buffer.as_ptr()); + if handle.is_null() { + None + } else { + let raw = RawProperty::from_ptr(handle); + Some(Property::from_raw(raw)) + } + } + } + + /// Get an iterator over all (name, property) pairs for this frame + /// + /// # Examples + /// ``` + /// # use chemfiles::{Residue, Property}; + /// let mut residue = Residue::new("ALA"); + /// residue.set("foo", Property::Double(22.2)); + /// residue.set("bar", Property::Bool(false)); + /// + /// for (name, property) in residue.properties() { + /// if name == "foo" { + /// assert_eq!(property, Property::Double(22.2)); + /// } else if name == "bar" { + /// assert_eq!(property, Property::Bool(false)); + /// } + /// } + /// ``` + pub fn properties(&self) -> PropertiesIter { + let mut count = 0; + unsafe { + check_success(chfl_residue_properties_count(self.as_ptr(), &mut count)); + } + + #[allow(clippy::cast_possible_truncation)] + let size = count as usize; + let mut c_names = vec![ptr::null_mut(); size]; + unsafe { + check_success(chfl_residue_list_properties(self.as_ptr(), c_names.as_mut_ptr(), count)); + } + + let mut names = Vec::new(); + for ptr in c_names { + names.push(strings::from_c(ptr)); + } + + PropertiesIter { + names: names.into_iter(), + getter: Box::new(move |name| self.get(&*name).expect("failed to get property")) + } + } +} + +impl Drop for Residue { + fn drop(&mut self) { + unsafe { + let _ = chfl_free(self.as_ptr() as *const _); + } + } +} + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + fn clone() { + let mut residue = Residue::new("A"); + assert_eq!(residue.size(), 0); + + let copy = residue.clone(); + assert_eq!(copy.size(), 0); + + residue.add_atom(3); + residue.add_atom(7); + assert_eq!(residue.size(), 2); + assert_eq!(copy.size(), 0); + } + + #[test] + fn name() { + let residue = Residue::new("A"); + assert_eq!(residue.name(), "A"); + } + + #[test] + fn id() { + let residue = Residue::new("A"); + assert_eq!(residue.id(), None); + + let residue = Residue::with_id("A", 42); + assert_eq!(residue.id(), Some(42)); + + let residue = Residue::with_id("A", -3); + assert_eq!(residue.id(), Some(-3)); + } + + #[test] + fn atoms() { + let mut residue = Residue::new("A"); + assert_eq!(residue.size(), 0); + + residue.add_atom(0); + residue.add_atom(3); + residue.add_atom(45); + assert_eq!(residue.size(), 3); + + assert_eq!(residue.contains(3), true); + assert_eq!(residue.contains(5), false); + + assert_eq!(residue.atoms(), vec![0, 3, 45]); + } + + #[test] + fn property() { + let mut residue = Residue::new("ALA"); + + residue.set("foo", -22.0); + assert_eq!(residue.get("foo"), Some(Property::Double(-22.0))); + assert_eq!(residue.get("bar"), None); + + residue.set("bar", Property::String("here".into())); + for (name, property) in residue.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(-22.0)); + } else if name == "bar" { + assert_eq!(property, Property::String("here".into())); + } + } + } +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +use std::ops::{Drop, Index}; +use std::iter::IntoIterator; +use std::slice::Iter; + +use chemfiles_sys::*; +use errors::{check, check_not_null, check_success, Error, Status}; +use strings; +use frame::Frame; + +#[derive(Debug, Clone, PartialEq, Eq)] +/// A `Match` is a set of atomic indexes matching a given selection. It can +/// mostly be used like a `&[usize]`. +pub struct Match { + size: usize, + atoms: [usize; 4], +} + +#[allow(clippy::len_without_is_empty)] +impl Match { + /// Get the length of the Match. + /// + /// # Example + /// + /// ``` + /// # use chemfiles::Match; + /// let atomic_match = Match::new(&[3, 4, 5]); + /// assert_eq!(atomic_match.len(), 3); + /// ``` + pub fn len(&self) -> usize { + self.size + } + + /// Create a new match containing the atoms in the `atoms` slice. + /// + /// # Panics + /// + /// If the slice contains more than 4 elements, which is the maximal size + /// of a match. + /// + /// # Example + /// + /// ``` + /// # use chemfiles::Match; + /// let atomic_match = Match::new(&[3, 4, 5]); + /// assert_eq!(atomic_match.len(), 3); + /// assert_eq!(atomic_match[0], 3); + /// assert_eq!(atomic_match[1], 4); + /// assert_eq!(atomic_match[2], 5); + /// ``` + pub fn new(atoms: &[usize]) -> Match { + assert!(atoms.len() <= 4); + let size = atoms.len(); + let mut matches = [usize::max_value(); 4]; + for (i, atom) in atoms.iter().enumerate() { + matches[i] = *atom; + } + Match { + size, + atoms: matches, + } + } + + /// Iterate over the atomic indexes in the match. + /// + /// # Example + /// + /// ``` + /// # use chemfiles::Match; + /// let atomic_match = Match::new(&[3, 4, 5]); + /// let mut iter = atomic_match.iter(); + /// + /// assert_eq!(iter.next(), Some(&3)); + /// assert_eq!(iter.next(), Some(&4)); + /// assert_eq!(iter.next(), Some(&5)); + /// assert_eq!(iter.next(), None); + /// ``` + pub fn iter(&self) -> Iter<usize> { + self.atoms[..self.len()].iter() + } +} + +impl Index<usize> for Match { + type Output = usize; + fn index(&self, i: usize) -> &Self::Output { + assert!(i < self.len()); + &self.atoms[i] + } +} + +impl<'a> IntoIterator for &'a Match { + type Item = &'a usize; + type IntoIter = Iter<'a, usize>; + fn into_iter(self) -> Iter<'a, usize> { + self.atoms[..self.len()].iter() + } +} + +/// A `Selection` allow to select atoms in a `Frame`, from a selection +/// language. The selection language is built by combining basic operations. +/// Each basic operation follows the `<selector>[(<variable>)] <operator> +/// <value>` structure, where `<operator>` is a comparison operator in +/// `== != < <= > >=`. +pub struct Selection { + handle: *mut CHFL_SELECTION, +} + +impl Clone for Selection { + fn clone(&self) -> Selection { + unsafe { + let new_handle = chfl_selection_copy(self.as_ptr()); + Selection::from_ptr(new_handle) + } + } +} + +impl Drop for Selection { + fn drop(&mut self) { + unsafe { + let _ = chfl_free(self.as_ptr() as *const _); + } + } +} + +impl Selection { + /// Create a `Selection` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the pointer. + #[inline] + pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_SELECTION) -> Selection { + check_not_null(ptr); + Selection { + handle: ptr + } + } + + /// Get the underlying C pointer as a const pointer. + #[inline] + pub(crate) fn as_ptr(&self) -> *const CHFL_SELECTION { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer. + #[inline] + pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_SELECTION { + self.handle + } + + /// Create a new selection from the given selection string. + /// + /// # Errors + /// + /// This function fails if the selection string is invalid. + /// + /// # Example + /// ``` + /// # use chemfiles::Selection; + /// let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap(); + /// ``` + pub fn new<'a, S: Into<&'a str>>(selection: S) -> Result<Selection, Error> { + let buffer = strings::to_c(selection.into()); + unsafe { + let handle = chfl_selection(buffer.as_ptr()); + if handle.is_null() { + Err(Error { + status: Status::SelectionError, + message: Error::last_error() + }) + } else { + Ok(Selection::from_ptr(handle)) + } + } + } + + /// Get the size of the selection, i.e. the number of atoms we are selecting + /// together. + /// + /// This value is 1 for the 'atom' context, 2 for the 'pair' and 'bond' + /// context, 3 for the 'three' and 'angles' context and 4 for the 'four' + /// and 'dihedral' context. + /// + /// # Example + /// ``` + /// # use chemfiles::Selection; + /// let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap(); + /// assert_eq!(selection.size(), 2); + /// ``` + pub fn size(&self) -> usize { + let mut size = 0; + unsafe { + check_success(chfl_selection_size(self.as_ptr(), &mut size)); + } + #[allow(clippy::cast_possible_truncation)] + return size as usize; + } + + /// Get the selection string used to create this selection. + /// + /// # Example + /// ``` + /// # use chemfiles::Selection; + /// let selection = Selection::new("name H").unwrap(); + /// assert_eq!(selection.string(), "name H"); + /// ``` + pub fn string(&self) -> String { + let get_string = |ptr, len| unsafe { chfl_selection_string(self.as_ptr(), ptr, len) }; + let selection = strings::call_autogrow_buffer(1024, get_string).expect("failed to get selection string"); + return strings::from_c(selection.as_ptr()); + } + + /// Evaluate a selection for a given frame, and return the corresponding + /// matches. + /// + /// # Example + /// ``` + /// # use chemfiles::{Selection, Frame, Atom}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None); + /// + /// let mut selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap(); + /// let matches = selection.evaluate(&frame); + /// + /// assert_eq!(matches.len(), 2); + /// + /// assert_eq!(matches[0].len(), 2); + /// assert_eq!(matches[0][0], 0); + /// assert_eq!(matches[0][1], 1); + /// + /// assert_eq!(matches[1].len(), 2); + /// assert_eq!(matches[1][0], 2); + /// assert_eq!(matches[1][1], 1); + /// ``` + pub fn evaluate(&mut self, frame: &Frame) -> Vec<Match> { + #![allow(clippy::cast_possible_truncation)] + let mut count = 0; + unsafe { + check(chfl_selection_evaluate( + self.as_mut_ptr(), frame.as_ptr(), &mut count + )).expect("failed to evaluate selection"); + } + + let size = count as usize; + let mut chfl_matches = vec![chfl_match { size: 0, atoms: [0; 4] }; size]; + unsafe { + check(chfl_selection_matches( + self.handle, + chfl_matches.as_mut_ptr(), + count + )).expect("failed to extract matches"); + } + + return chfl_matches.into_iter() + .map(|chfl_match| Match { + size: chfl_match.size as usize, + atoms: [ + chfl_match.atoms[0] as usize, + chfl_match.atoms[1] as usize, + chfl_match.atoms[2] as usize, + chfl_match.atoms[3] as usize, + ], + }) + .collect(); + } + + /// Evaluates a selection of size 1 on a given `frame`. This function + /// returns the list of atomic indexes in the frame matching this selection. + /// + /// # Panics + /// + /// If the selection size is not 1 + /// + /// # Example + /// ``` + /// # use chemfiles::{Selection, Frame, Atom}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None); + /// + /// let mut selection = Selection::new("name H").unwrap(); + /// let matches = selection.list(&frame); + /// + /// assert_eq!(matches.len(), 2); + /// assert_eq!(matches[0], 0); + /// assert_eq!(matches[1], 2); + /// ``` + pub fn list(&mut self, frame: &Frame) -> Vec<usize> { + if self.size() != 1 { + panic!("can not call `Selection::list` on a multiple selection") + } + return self.evaluate(frame) + .into_iter() + .map(|m| m[0] as usize) + .collect(); + } +} + +#[cfg(test)] +mod tests { + use super::*; + use Frame; + use Topology; + use Atom; + + #[test] + fn clone() { + let selection = Selection::new("name H").unwrap(); + + let copy = selection.clone(); + assert_eq!(selection.size(), 1); + assert_eq!(copy.size(), 1); + } + + fn testing_frame() -> Frame { + let mut topology = Topology::new(); + + topology.add_atom(&Atom::new("H")); + topology.add_atom(&Atom::new("O")); + topology.add_atom(&Atom::new("O")); + topology.add_atom(&Atom::new("H")); + + topology.add_bond(0, 1); + topology.add_bond(1, 2); + topology.add_bond(2, 3); + + let mut frame = Frame::new(); + frame.resize(4); + frame.set_topology(&topology).unwrap(); + return frame; + } + + mod matches { + use super::*; + + #[test] + fn index() { + let m = Match::new(&[1, 2, 3, 4]); + assert_eq!(m[0], 1); + assert_eq!(m[1], 2); + assert_eq!(m[2], 3); + assert_eq!(m[3], 4); + + let m = Match::new(&[1, 2]); + assert_eq!(m[0], 1); + assert_eq!(m[1], 2); + } + + #[test] + fn iter() { + let match_ = Match::new(&[1, 2, 3, 4]); + assert_eq!(match_.iter().cloned().collect::<Vec<usize>>(), vec![1, 2, 3, 4]); + + let v = vec![1, 2, 3, 4]; + for (i, &m) in match_.iter().enumerate() { + assert_eq!(v[i], m); + } + } + + #[test] + #[should_panic] + fn out_of_bound() { + let m = Match::new(&[1, 2]); + let _ = m[2]; + } + + #[test] + #[should_panic] + fn too_big() { + let _ = Match::new(&[1, 2, 3, 5, 4]); + } + } + + #[test] + fn size() { + let selection = Selection::new("name H").unwrap(); + assert_eq!(selection.size(), 1); + + let selection = Selection::new("angles: name(#1) H").unwrap(); + assert_eq!(selection.size(), 3); + + let selection = Selection::new("four: name(#1) H").unwrap(); + assert_eq!(selection.size(), 4); + } + + #[test] + fn string() { + let selection = Selection::new("name H").unwrap(); + assert_eq!(selection.string(), "name H"); + + let selection = Selection::new("angles: name(#1) H").unwrap(); + assert_eq!(selection.string(), "angles: name(#1) H"); + } + + #[test] + fn evaluate() { + let frame = testing_frame(); + + let mut selection = Selection::new("name H").unwrap(); + let res = selection.evaluate(&frame); + assert_eq!(res, &[Match::new(&[0]), Match::new(&[3])]); + + let mut selection = Selection::new("angles: all").unwrap(); + let res = selection.evaluate(&frame); + for m in &[Match::new(&[0, 1, 2]), Match::new(&[1, 2, 3])] { + assert!(res.iter().any(|r| r == m)) + } + } + + #[test] + fn list() { + let frame = testing_frame(); + + let mut selection = Selection::new("name H").unwrap(); + let res = selection.list(&frame); + assert_eq!(res, vec![0, 3]); + } + + #[test] + #[should_panic = "can not call `Selection::list` on a multiple selection"] + fn list_on_size_1_selection() { + let frame = testing_frame(); + let mut selection = Selection::new("pairs: name(#1) H").unwrap(); + let _ = selection.list(&frame); + } +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed + +//! String conversions between C and Rust +use std::ffi::{CStr, CString}; + +use chemfiles_sys::chfl_status; +use errors::{check, Error}; + +/// Create a Rust string from a C string. Clones all characters in `buffer`. +pub fn from_c(buffer: *const i8) -> String { + unsafe { + let rust_str = CStr::from_ptr(buffer) + .to_str() + .expect("Invalid Rust string from C"); + return String::from(rust_str); + } +} + +/// Create a C string from a Rust string. +pub fn to_c(string: &str) -> CString { + CString::new(string).expect("Invalid C string from Rust") +} + +/// Check if a string buffer was big enough when passed to a C function +fn buffer_was_big_enough(buffer: &[i8]) -> bool { + let len = buffer.len(); + if len < 2 { + false + } else { + // The C code should always set the last element to 0 + debug_assert_eq!(buffer[len - 1], 0); + buffer[len - 2] == 0 + } +} + +/// Call `callback` C function with a string buffer and it length, using +/// `initial` as the buffer initial size. If the buffer was filled and the +/// result truncated by the C library, grow the buffer and try again until we +/// get all the data. Then return the filled buffer to the caller. +pub fn call_autogrow_buffer<F>(initial: usize, callback: F) -> Result<Vec<i8>, Error> +where + F: Fn(*mut i8, u64) -> chfl_status, +{ + let mut size = initial; + let mut buffer = vec![0; size]; + check(callback(buffer.as_mut_ptr(), buffer.len() as u64))?; + + while !buffer_was_big_enough(&buffer) { + // Grow the buffer and retry + size *= 2; + buffer.resize(size, 0); + check(callback(buffer.as_mut_ptr(), buffer.len() as u64))?; + } + + Ok(buffer) +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +use std::ops::{Drop, Deref}; +use std::marker::PhantomData; + +use chemfiles_sys::*; +use errors::{check, check_not_null, check_success, Error}; +use super::{Atom, AtomRef, AtomMut}; +use super::{Residue, ResidueRef}; + +/// Possible bond order associated with bonds +#[repr(C)] +#[non_exhaustive] +#[derive(Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord)] +pub enum BondOrder { + /// Unknown or unspecified bond order + Unknown = chfl_bond_order::CHFL_BOND_UNKNOWN as isize, + /// Single bond + Single = chfl_bond_order::CHFL_BOND_SINGLE as isize, + /// Double bond + Double = chfl_bond_order::CHFL_BOND_DOUBLE as isize, + /// Triple bond + Triple = chfl_bond_order::CHFL_BOND_TRIPLE as isize, + /// Quadruple bond (present in some metals) + Quadruple = chfl_bond_order::CHFL_BOND_QUADRUPLE as isize, + /// Quintuplet bond (present in some metals) + Quintuplet = chfl_bond_order::CHFL_BOND_QUINTUPLET as isize, + /// Amide bond (required by some file formats) + Amide = chfl_bond_order::CHFL_BOND_AMIDE as isize, + /// Aromatic bond (required by some file formats) + Aromatic = chfl_bond_order::CHFL_BOND_AROMATIC as isize, +} + +impl BondOrder { + pub(crate) fn as_raw(self) -> chfl_bond_order { + match self { + BondOrder::Unknown => chfl_bond_order::CHFL_BOND_UNKNOWN, + BondOrder::Single => chfl_bond_order::CHFL_BOND_SINGLE, + BondOrder::Double => chfl_bond_order::CHFL_BOND_DOUBLE, + BondOrder::Triple => chfl_bond_order::CHFL_BOND_TRIPLE, + BondOrder::Quadruple => chfl_bond_order::CHFL_BOND_QUADRUPLE, + BondOrder::Quintuplet => chfl_bond_order::CHFL_BOND_QUINTUPLET, + BondOrder::Amide => chfl_bond_order::CHFL_BOND_AMIDE, + BondOrder::Aromatic => chfl_bond_order::CHFL_BOND_AROMATIC, + } + } +} + +impl From<chfl_bond_order> for BondOrder { + fn from(order: chfl_bond_order) -> BondOrder { + match order { + chfl_bond_order::CHFL_BOND_UNKNOWN => BondOrder::Unknown, + chfl_bond_order::CHFL_BOND_SINGLE => BondOrder::Single, + chfl_bond_order::CHFL_BOND_DOUBLE => BondOrder::Double, + chfl_bond_order::CHFL_BOND_TRIPLE => BondOrder::Triple, + chfl_bond_order::CHFL_BOND_QUADRUPLE => BondOrder::Quadruple, + chfl_bond_order::CHFL_BOND_QUINTUPLET => BondOrder::Quintuplet, + chfl_bond_order::CHFL_BOND_AMIDE => BondOrder::Amide, + chfl_bond_order::CHFL_BOND_AROMATIC => BondOrder::Aromatic, + } + } +} + +/// A `Topology` contains the definition of all the atoms in the system, and +/// the liaisons between the atoms (bonds, angles, dihedrals, ...). It will +/// also contain all the residues information if it is available. +pub struct Topology { + handle: *mut CHFL_TOPOLOGY, +} + +/// An analog to a reference to a topology (`&Topology`) +pub struct TopologyRef<'a> { + inner: Topology, + marker: PhantomData<&'a Topology> +} + +impl<'a> Deref for TopologyRef<'a> { + type Target = Topology; + fn deref(&self) -> &Topology { + &self.inner + } +} + +impl Clone for Topology { + fn clone(&self) -> Topology { + unsafe { + let new_handle = chfl_topology_copy(self.as_ptr()); + Topology::from_ptr(new_handle) + } + } +} + +impl Topology { + /// Create a `Topology` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the pointer, + /// except for it being non-null. + #[inline] + pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_TOPOLOGY) -> Topology { + check_not_null(ptr); + Topology { + handle: ptr + } + } + + /// Create a borrowed `Topology` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the + /// pointer, except for it being non-null, and the caller is responsible + /// for setting the right lifetime + #[inline] + pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_TOPOLOGY) -> TopologyRef<'a> { + TopologyRef { + inner: Topology::from_ptr(ptr as *mut CHFL_TOPOLOGY), + marker: PhantomData, + } + } + + /// Get the underlying C pointer as a const pointer. + #[inline] + pub(crate) fn as_ptr(&self) -> *const CHFL_TOPOLOGY { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer. + #[inline] + pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_TOPOLOGY { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer FROM A SHARED REFERENCE. + /// + /// For uses with functions of the C API using mut pointers for both read + /// and write access. Users should check that this does not lead to multiple + /// mutable borrows + #[inline] + #[allow(non_snake_case)] + pub(crate) fn as_mut_ptr_MANUALLY_CHECKING_BORROW(&self) -> *mut CHFL_TOPOLOGY { + self.handle + } + + /// Create a new empty topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let topology = Topology::new(); + /// assert_eq!(topology.size(), 0); + /// ``` + pub fn new() -> Topology { + unsafe { + Topology::from_ptr(chfl_topology()) + } + } + + /// Get a reference of the atom at the given `index` in this topology. + /// + /// # Panics + /// + /// If `index` is out of bounds. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// topology.resize(6); + /// + /// let atom = topology.atom(4); + /// assert_eq!(atom.name(), ""); + /// ``` + pub fn atom(&self, index: usize) -> AtomRef { + unsafe { + let handle = chfl_atom_from_topology( + self.as_mut_ptr_MANUALLY_CHECKING_BORROW(), index as u64 + ); + Atom::ref_from_ptr(handle) + } + } + + /// Get a mutable reference to the atom at the given `index` in this topology. + /// + /// # Panics + /// + /// If `index` is out of bounds. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// topology.resize(6); + /// + /// assert_eq!(topology.atom(4).name(), ""); + /// + /// topology.atom_mut(4).set_name("Fe"); + /// assert_eq!(topology.atom(4).name(), "Fe"); + /// ``` + pub fn atom_mut(&mut self, index: usize) -> AtomMut { + unsafe { + let handle = chfl_atom_from_topology( + self.as_mut_ptr(), index as u64 + ); + Atom::ref_mut_from_ptr(handle) + } + } + + /// Get the current number of atoms in this topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.size(), 0); + /// + /// topology.resize(6); + /// assert_eq!(topology.size(), 6); + /// ``` + pub fn size(&self) -> usize { + let mut size = 0; + unsafe { + check_success(chfl_topology_atoms_count(self.as_ptr(), &mut size)); + } + #[allow(clippy::cast_possible_truncation)] + return size as usize; + } + + /// Resize this topology to hold `natoms` atoms, inserting dummy atoms if + /// the new size if bigger than the old one. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.size(), 0); + /// + /// topology.resize(6); + /// assert_eq!(topology.size(), 6); + /// ``` + pub fn resize(&mut self, natoms: usize) { + unsafe { + check_success(chfl_topology_resize(self.as_mut_ptr(), natoms as u64)); + } + } + + /// Add an `Atom` at the end of this topology + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, Atom}; + /// let mut topology = Topology::new(); + /// topology.add_atom(&Atom::new("Mg")); + /// + /// let atom = topology.atom(0); + /// assert_eq!(atom.name(), "Mg"); + /// ``` + pub fn add_atom(&mut self, atom: &Atom) { + unsafe { + check_success(chfl_topology_add_atom(self.as_mut_ptr(), atom.as_ptr())); + } + } + + /// Remove an `Atom` from this topology by `index`. This modify all the + /// other atoms indexes. + /// + /// # Panics + /// + /// If the `index` is out of bounds + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// topology.resize(9); + /// assert_eq!(topology.size(), 9); + /// + /// topology.remove(7); + /// assert_eq!(topology.size(), 8); + /// ``` + pub fn remove(&mut self, index: usize) { + unsafe { + check_success(chfl_topology_remove(self.as_mut_ptr(), index as u64)); + } + } + + /// Get the number of bonds in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.bonds_count(), 0); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(2, 1); + /// topology.add_bond(2, 3); + /// assert_eq!(topology.bonds_count(), 3); + /// ``` + pub fn bonds_count(&self) -> usize { + let mut count = 0; + unsafe { + check_success(chfl_topology_bonds_count(self.as_ptr(), &mut count)); + } + #[allow(clippy::cast_possible_truncation)] + return count as usize; + } + + /// Get the number of angles in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.angles_count(), 0); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(2, 1); + /// topology.add_bond(2, 3); + /// assert_eq!(topology.angles_count(), 2); + /// ``` + pub fn angles_count(&self) -> usize { + let mut count = 0; + unsafe { + check_success(chfl_topology_angles_count(self.as_ptr(), &mut count)); + } + #[allow(clippy::cast_possible_truncation)] + return count as usize; + } + + /// Get the number of dihedral angles in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.dihedrals_count(), 0); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(2, 1); + /// topology.add_bond(2, 3); + /// assert_eq!(topology.dihedrals_count(), 1); + /// ``` + pub fn dihedrals_count(&self) -> usize { + let mut count = 0; + unsafe { + check_success(chfl_topology_dihedrals_count(self.as_ptr(), &mut count)); + } + #[allow(clippy::cast_possible_truncation)] + return count as usize; + } + + /// Get the number of improper dihedral angles in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.dihedrals_count(), 0); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(0, 2); + /// topology.add_bond(0, 3); + /// assert_eq!(topology.impropers_count(), 1); + /// ``` + pub fn impropers_count(&self) -> usize { + let mut count = 0; + unsafe { + check_success(chfl_topology_impropers_count(self.as_ptr(), &mut count)); + } + #[allow(clippy::cast_possible_truncation)] + return count as usize; + } + + /// Get the list of bonds in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(2, 1); + /// topology.add_bond(2, 3); + /// assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]); + /// ``` + pub fn bonds(&self) -> Vec<[usize; 2]> { + let size = self.bonds_count(); + let count = size as u64; + let mut bonds = vec![[u64::max_value(); 2]; size]; + unsafe { + check_success(chfl_topology_bonds(self.as_ptr(), bonds.as_mut_ptr(), count)); + } + #[allow(clippy::cast_possible_truncation)] + return bonds + .into_iter() + .map(|bond| [bond[0] as usize, bond[1] as usize]) + .collect(); + } + + /// Get the list of angles in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(2, 1); + /// topology.add_bond(2, 3); + /// assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]); + /// ``` + pub fn angles(&self) -> Vec<[usize; 3]> { + let size = self.angles_count(); + let count = size as u64; + let mut angles = vec![[u64::max_value(); 3]; size]; + unsafe { + check_success(chfl_topology_angles(self.as_ptr(), angles.as_mut_ptr(), count)); + } + #[allow(clippy::cast_possible_truncation)] + return angles + .into_iter() + .map(|angle| [angle[0] as usize, angle[1] as usize, angle[2] as usize]) + .collect(); + } + + /// Get the list of dihedral angles in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(2, 1); + /// topology.add_bond(2, 3); + /// + /// assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]); + /// ``` + pub fn dihedrals(&self) -> Vec<[usize; 4]> { + let size = self.dihedrals_count(); + let count = size as u64; + let mut dihedrals = vec![[u64::max_value(); 4]; size]; + unsafe { + check_success(chfl_topology_dihedrals( + self.as_ptr(), dihedrals.as_mut_ptr(), count + )); + } + #[allow(clippy::cast_possible_truncation)] + return dihedrals + .into_iter() + .map(|dihedral| { + [ + dihedral[0] as usize, + dihedral[1] as usize, + dihedral[2] as usize, + dihedral[3] as usize, + ] + }) + .collect(); + } + + /// Get the list of improper dihedral angles in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(0, 2); + /// topology.add_bond(0, 3); + /// + /// assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]); + /// ``` + pub fn impropers(&self) -> Vec<[usize; 4]> { + let size = self.impropers_count(); + let count = size as u64; + let mut impropers = vec![[u64::max_value(); 4]; size]; + unsafe { + check_success(chfl_topology_impropers( + self.as_ptr(), impropers.as_mut_ptr(), count + )); + } + #[allow(clippy::cast_possible_truncation)] + return impropers + .into_iter() + .map(|improper| { + [ + improper[0] as usize, + improper[1] as usize, + improper[2] as usize, + improper[3] as usize, + ] + }) + .collect(); + } + + /// Remove all existing bonds, angles, dihedral angles and improper + /// dihedral angles in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.bonds_count(), 0); + /// topology.resize(4); + /// topology.add_bond(0, 1); + /// topology.add_bond(0, 2); + /// assert_eq!(topology.bonds_count(), 2); + /// assert_eq!(topology.angles().len(), 1); + /// + /// topology.clear_bonds(); + /// assert!(topology.bonds().is_empty()); + /// assert!(topology.angles().is_empty()); + /// ``` + pub fn clear_bonds(&mut self) { + unsafe { + check_success(chfl_topology_clear_bonds(self.as_mut_ptr())); + } + } + + /// Add a bond between the atoms at indexes `i` and `j` in the topology. + /// + /// The bond order is set to `BondOrder::Unknown`. + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, BondOrder}; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.bonds_count(), 0); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(0, 2); + /// assert_eq!(topology.bonds_count(), 2); + /// + /// assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown); + /// ``` + pub fn add_bond(&mut self, i: usize, j: usize) { + unsafe { + check_success(chfl_topology_add_bond(self.as_mut_ptr(), i as u64, j as u64)); + } + } + + /// Add a bond between the atoms at indexes `i` and `j` in the topology + /// with the given bond `order`. + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, BondOrder}; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.bonds_count(), 0); + /// topology.resize(2); + /// + /// topology.add_bond_with_order(0, 1, BondOrder::Double); + /// assert_eq!(topology.bond_order(0, 1), BondOrder::Double); + /// ``` + pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder) { + unsafe { + check_success(chfl_topology_bond_with_order( + self.as_mut_ptr(), i as u64, j as u64, order.as_raw() + )); + } + } + + /// Get the bond order for the bond between the atoms at indexes `i` and + /// `j`. + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, BondOrder}; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.bonds_count(), 0); + /// topology.resize(2); + /// + /// topology.add_bond_with_order(0, 1, BondOrder::Double); + /// assert_eq!(topology.bond_order(0, 1), BondOrder::Double); + /// ``` + pub fn bond_order(&self, i: usize, j: usize) -> BondOrder { + let mut order = chfl_bond_order::CHFL_BOND_UNKNOWN; + unsafe { + check_success(chfl_topology_bond_order( + self.as_ptr(), i as u64, j as u64, &mut order + )); + } + return order.into() + } + + /// Get the bond order for all the bonds in the topology + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, BondOrder}; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.bonds_count(), 0); + /// topology.resize(3); + /// + /// topology.add_bond_with_order(0, 1, BondOrder::Double); + /// topology.add_bond_with_order(0, 2, BondOrder::Single); + /// + /// assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]); + /// ``` + pub fn bond_orders(&self) -> Vec<BondOrder> { + let size = self.bonds_count(); + let count = size as u64; + let mut bonds = vec![BondOrder::Unknown; size]; + unsafe { + check_success(chfl_topology_bond_orders( + self.as_ptr(), + // Casting BondOrder to chfl_bond_order is safe, as they are + // both `repr(C)` enums with the same values. + bonds.as_mut_ptr() as *mut _, + count + )); + } + return bonds; + } + + /// Remove any existing bond between the atoms at indexes `i` and `j` in + /// this topology. + /// + /// This function does nothing if there is no bond between `i` and `j`. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.bonds_count(), 0); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(1, 2); + /// assert_eq!(topology.bonds_count(), 2); + /// + /// topology.remove_bond(0, 1); + /// assert_eq!(topology.bonds_count(), 1); + /// + /// // Removing a bond that does not exists is fine + /// topology.remove_bond(0, 2); + /// assert_eq!(topology.bonds_count(), 1); + /// ``` + pub fn remove_bond(&mut self, i: usize, j: usize) { + unsafe { + check_success(chfl_topology_remove_bond(self.as_mut_ptr(), i as u64, j as u64)); + } + } + + /// Get a reference to the residue at index `index` from this topology. + /// + /// The residue index in the topology is not always the same as the residue + /// `id`. + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, Residue}; + /// let mut topology = Topology::new(); + /// topology.add_residue(&Residue::new("water")).unwrap(); + /// + /// let residue = topology.residue(0).unwrap(); + /// assert_eq!(residue.name(), "water"); + /// ``` + pub fn residue(&self, index: u64) -> Option<ResidueRef> { + unsafe { + let handle = chfl_residue_from_topology(self.as_ptr(), index as u64); + if handle.is_null() { + None + } else { + Some(Residue::ref_from_ptr(handle)) + } + } + } + + /// Get a copy of the residue containing the atom at index `index` in this + /// topology, if any. + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, Residue}; + /// let mut topology = Topology::new(); + /// topology.resize(8); + /// + /// let mut residue = Residue::new("water"); + /// residue.add_atom(0); + /// residue.add_atom(1); + /// residue.add_atom(2); + /// topology.add_residue(&residue).unwrap(); + /// + /// let residue = topology.residue_for_atom(0).unwrap(); + /// assert_eq!(residue.name(), "water"); + /// + /// assert!(topology.residue_for_atom(6).is_none()); + /// ``` + pub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef> { + let handle = unsafe { + chfl_residue_for_atom(self.as_ptr(), index as u64) + }; + if handle.is_null() { + None + } else { + unsafe { + Some(Residue::ref_from_ptr(handle)) + } + } + } + + /// Get the number of residues in this topology. + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, Residue}; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.residues_count(), 0); + /// + /// topology.add_residue(&Residue::with_id("water", 0)).unwrap(); + /// topology.add_residue(&Residue::with_id("protein", 1)).unwrap(); + /// assert_eq!(topology.residues_count(), 2); + /// ``` + pub fn residues_count(&self) -> u64 { + let mut count = 0; + unsafe { + check_success(chfl_topology_residues_count(self.as_ptr(), &mut count)); + } + return count; + } + + /// Add a residue to this topology. + /// + /// # Errors + /// + /// This function fails is the residue `id` is not already in the topology, + /// or if the residue contains atoms that are already in another residue. + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, Residue}; + /// let mut topology = Topology::new(); + /// topology.add_residue(&Residue::new("water")).unwrap(); + /// + /// let residue = topology.residue(0).unwrap(); + /// assert_eq!(residue.name(), "water"); + /// ``` + pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error> { + unsafe { + check(chfl_topology_add_residue(self.as_mut_ptr(), residue.as_ptr())) + } + } + + /// Check if the two residues `first` and `second` from the `topology` are + /// linked together, *i.e.* if there is a bond between one atom in the + /// first residue and one atom in the second one. + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, Residue}; + /// let mut topology = Topology::new(); + /// + /// topology.add_residue(&Residue::with_id("water", 0)).unwrap(); + /// topology.add_residue(&Residue::with_id("protein", 1)).unwrap(); + /// + /// let first = topology.residue(0).unwrap(); + /// let second = topology.residue(1).unwrap(); + /// assert_eq!(topology.are_linked(&first, &second), false); + /// ``` + pub fn are_linked(&self, first: &Residue, second: &Residue) -> bool { + let mut linked = 0; + unsafe { + check_success(chfl_topology_residues_linked( + self.as_ptr(), + first.as_ptr(), + second.as_ptr(), + &mut linked + )); + } + return linked != 0; + } +} + +impl Drop for Topology { + fn drop(&mut self) { + unsafe { + let _ = chfl_free(self.as_ptr() as *const _); + } + } +} + +#[cfg(test)] +mod test { + use super::*; + use {Atom, Residue}; + + #[test] + fn clone() { + let mut topology = Topology::new(); + assert_eq!(topology.size(), 0); + + let copy = topology.clone(); + assert_eq!(copy.size(), 0); + + topology.resize(10); + assert_eq!(topology.size(), 10); + assert_eq!(copy.size(), 0); + } + + #[test] + fn size() { + let mut topology = Topology::new(); + assert_eq!(topology.size(), 0); + + topology.resize(10); + assert_eq!(topology.size(), 10); + + topology.remove(7); + assert_eq!(topology.size(), 9); + + topology.add_atom(&Atom::new("Hg")); + assert_eq!(topology.size(), 10); + } + + #[test] + fn atoms() { + let mut topology = Topology::new(); + + topology.add_atom(&Atom::new("Hg")); + topology.add_atom(&Atom::new("Mn")); + topology.add_atom(&Atom::new("W")); + topology.add_atom(&Atom::new("Fe")); + + assert_eq!(topology.atom(0).name(), "Hg"); + assert_eq!(topology.atom(3).name(), "Fe"); + } + + #[test] + fn remove() { + let mut topology = Topology::new(); + topology.add_atom(&Atom::new("Hg")); + topology.add_atom(&Atom::new("Mn")); + topology.add_atom(&Atom::new("W")); + topology.add_atom(&Atom::new("Fe")); + + assert_eq!(topology.atom(0).name(), "Hg"); + assert_eq!(topology.atom(2).name(), "W"); + + topology.remove(1); + assert_eq!(topology.atom(0).name(), "Hg"); + assert_eq!(topology.atom(2).name(), "Fe"); + } + + #[test] + #[should_panic] + fn out_of_bounds_remove() { + let mut topology = Topology::new(); + topology.resize(18); + topology.remove(33); + } + + + #[test] + fn bonds() { + let mut topology = Topology::new(); + topology.resize(12); + assert_eq!(topology.bonds_count(), 0); + + topology.add_bond(0, 1); + topology.add_bond(9, 2); + topology.add_bond_with_order(3, 7, BondOrder::Aromatic); + assert_eq!(topology.bonds_count(), 3); + + assert_eq!(topology.bonds(), vec![[0, 1], [2, 9], [3, 7]]); + let expected = vec![BondOrder::Unknown, BondOrder::Unknown, BondOrder::Aromatic]; + assert_eq!(topology.bond_orders(), expected); + + assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown); + assert_eq!(topology.bond_order(3, 7), BondOrder::Aromatic); + + topology.remove_bond(3, 7); + // Removing unexisting bond is OK if both indexes are in bounds + topology.remove_bond(8, 7); + assert_eq!(topology.bonds_count(), 2); + + topology.clear_bonds(); + assert_eq!(topology.bonds_count(), 0); + } + + #[test] + #[should_panic] + fn out_of_bounds_bonds() { + let mut topology = Topology::new(); + topology.resize(12); + topology.add_bond(300, 7); + } + + #[test] + #[should_panic] + fn out_of_bounds_remove_bond() { + let mut topology = Topology::new(); + topology.resize(12); + topology.remove_bond(300, 7); + } + + #[test] + #[should_panic] + fn out_of_bounds_bonds_with_order() { + let mut topology = Topology::new(); + topology.resize(12); + topology.add_bond_with_order(300, 7, BondOrder::Unknown); + } + + #[test] + fn angles() { + let mut topology = Topology::new(); + topology.resize(12); + assert_eq!(topology.angles_count(), 0); + + topology.add_bond(0, 1); + topology.add_bond(1, 2); + topology.add_bond(3, 7); + topology.add_bond(3, 5); + assert_eq!(topology.angles_count(), 2); + + assert_eq!(topology.angles(), vec![[0, 1, 2], [5, 3, 7]]); + + topology.clear_bonds(); + assert_eq!(topology.angles_count(), 0); + } + + #[test] + fn dihedrals() { + let mut topology = Topology::new(); + topology.resize(12); + assert_eq!(topology.dihedrals_count(), 0); + + topology.add_bond(0, 1); + topology.add_bond(1, 2); + topology.add_bond(3, 2); + topology.add_bond(4, 7); + topology.add_bond(4, 5); + topology.add_bond(7, 10); + assert_eq!(topology.dihedrals_count(), 2); + + assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3], [5, 4, 7, 10]]); + + topology.clear_bonds(); + assert_eq!(topology.dihedrals_count(), 0); + } + + #[test] + fn impropers() { + let mut topology = Topology::new(); + topology.resize(12); + assert_eq!(topology.impropers_count(), 0); + + topology.add_bond(0, 1); + topology.add_bond(0, 2); + topology.add_bond(0, 3); + topology.add_bond(4, 7); + topology.add_bond(4, 5); + topology.add_bond(4, 8); + assert_eq!(topology.impropers_count(), 2); + + assert_eq!(topology.impropers(), vec![[1, 0, 2, 3], [5, 4, 7, 8]]); + + topology.clear_bonds(); + assert_eq!(topology.impropers_count(), 0); + } + + #[test] + fn residues() { + let mut topology = Topology::new(); + topology.resize(4); + assert_eq!(topology.residues_count(), 0); + + let mut residue = Residue::new("Foo"); + residue.add_atom(0); + residue.add_atom(2); + + topology.add_residue(&residue).unwrap(); + assert_eq!(topology.residues_count(), 1); + + assert_eq!(topology.residue(0).unwrap().name(), "Foo"); + { + let residue = topology.residue_for_atom(2).unwrap(); + assert_eq!(residue.name(), "Foo"); + } + + let mut residue = Residue::new("Bar"); + residue.add_atom(3); + topology.add_residue(&residue).unwrap(); + assert_eq!(topology.residues_count(), 2); + + let first = topology.residue(0).unwrap(); + let second = topology.residue(0).unwrap(); + assert_eq!(topology.are_linked(&first, &second), true); + + // missing residue + assert!(topology.residue_for_atom(1).is_none()); + // out of bounds + assert!(topology.residue_for_atom(67).is_none()); + } +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +use std::ops::Drop; +use std::path::Path; +use std::ptr; + +use chemfiles_sys::*; +use errors::{check, check_success, Error, Status}; +use strings; + +use {Frame, Topology, UnitCell}; + +/// The `Trajectory` type is the main entry point when using chemfiles. A +/// `Trajectory` behave a bit like a file, allowing to read and/or write +/// `Frame`. +pub struct Trajectory { + handle: *mut CHFL_TRAJECTORY, +} + +impl Trajectory { + /// Create a `Trajectory` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the pointer. + #[inline] + pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_TRAJECTORY) -> Result<Trajectory, Error> { + if ptr.is_null() { + Err(Error { + status: Status::FileError, + message: Error::last_error() + }) + } else { + Ok(Trajectory { + handle: ptr + }) + } + } + + /// Get the underlying C pointer as a pointer. + #[inline] + pub(crate) fn as_ptr(&self) -> *const CHFL_TRAJECTORY { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer. + #[inline] + pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_TRAJECTORY { + self.handle + } + + /// Open the file at the given `path` in the given `mode`. + /// + /// Valid modes are `'r'` for read, `'w'` for write and `'a'` for append. + /// + /// # Errors + /// + /// This function fails if the file is not accessible for the given mode, if + /// it is incorrectly formatted for the corresponding format, or in case of + /// I/O errors from the OS. + /// + /// # Example + /// ```no_run + /// # use chemfiles::Trajectory; + /// let trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + /// ``` + pub fn open<P>(path: P, mode: char) -> Result<Trajectory, Error> + where + P: AsRef<Path>, + { + let path = path.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(path.as_ref()))?; + + let path = strings::to_c(path); + unsafe { + #[allow(clippy::cast_possible_wrap)] + let handle = chfl_trajectory_open(path.as_ptr(), mode as i8); + Trajectory::from_ptr(handle) + } + } + + /// Open the file at the given `path` using a specific file `format` and the + /// given `mode`. + /// + /// Valid modes are `'r'` for read, `'w'` for write and `'a'` for append. + /// + /// Specifying a format is needed when the file format does not match the + /// extension, or when there is not standard extension for this format. If + /// `format` is an empty string, the format will be guessed from the + /// extension. + /// + /// # Errors + /// + /// This function fails if the file is not accessible for the given mode, if + /// it is incorrectly formatted for the corresponding format, or in case of + /// I/O errors from the OS. + /// + /// # Example + /// ```no_run + /// # use chemfiles::Trajectory; + /// let trajectory = Trajectory::open_with_format("water.zeo", 'r', "XYZ").unwrap(); + /// ``` + pub fn open_with_format<'a, P, S>(filename: P, mode: char, format: S) -> Result<Trajectory, Error> + where + P: AsRef<Path>, + S: Into<&'a str>, + { + let filename = + filename.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(filename.as_ref()))?; + + let filename = strings::to_c(filename); + let format = strings::to_c(format.into()); + unsafe { + #[allow(clippy::cast_possible_wrap)] + let handle = chfl_trajectory_with_format( + filename.as_ptr(), mode as i8, format.as_ptr() + ); + Trajectory::from_ptr(handle) + } + } + + /// Read a memory buffer as though it was a formatted file. + /// + /// The memory buffer used to store the file is given using the `data` + /// argument. The `format` parameter is required and should follow the same + /// rules as in the main `Trajectory` constructor. + /// + /// # Errors + /// + /// This function fails if the data is incorrectly formatted for the + /// corresponding format, or if the format do not support in-memory readers. + /// + /// # Example + /// ``` + /// # use chemfiles::{Trajectory, Frame}; + /// let aromatics = "c1ccccc1\nc1ccco1\nc1ccccn1\n"; + /// let mut trajectory = Trajectory::memory_reader(aromatics, "SMI").unwrap(); + /// let mut frame = Frame::new(); + /// trajectory.read(&mut frame).unwrap(); + /// assert_eq!(frame.size(), 6); + /// ``` + pub fn memory_reader<'a, S>(data: S, format: S) -> Result<Trajectory, Error> + where S: Into<&'a str>, + { + let data = strings::to_c(data.into()); + let format = strings::to_c(format.into()); + unsafe { + let handle = chfl_trajectory_memory_reader( + data.as_ptr(), data.as_bytes().len() as u64, format.as_ptr() + ); + Trajectory::from_ptr(handle) + } + } + + /// Write to a memory buffer as though it was a formatted file. + /// + /// The `format` parameter should follow the same rules as in the main + /// `Trajectory` constructor, except that compression specification + /// is not supported. + /// + /// The `memory_buffer` function can be used to retrieve the data written + /// to memory of the `Trajectory`. + /// + /// # Errors + /// + /// This function fails if the format do not support in-memory writers. + /// + /// # Example + /// ``` + /// # use chemfiles::Trajectory; + /// let trajectory_memory = Trajectory::memory_writer("SMI"); + /// + /// // Binary formats typically do not support this feature + /// assert!(Trajectory::memory_writer("XTC").is_err()); + /// ``` + pub fn memory_writer<'a, S>(format: S) -> Result<Trajectory, Error> + where S: Into<&'a str>, + { + let format = strings::to_c(format.into()); + unsafe { + let handle = chfl_trajectory_memory_writer(format.as_ptr()); + Trajectory::from_ptr(handle) + } + } + + /// Read the next step of this trajectory into a `frame`. + /// + /// If the number of atoms in frame does not correspond to the number of atom + /// in the next step, the frame is resized. + /// + /// # Errors + /// + /// This function fails if the data is incorrectly formatted for the + /// corresponding format, or in case of I/O errors from the OS. + /// + /// # Example + /// ```no_run + /// # use chemfiles::{Trajectory, Frame}; + /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + /// let mut frame = Frame::new(); + /// + /// trajectory.read(&mut frame).unwrap(); + /// ``` + pub fn read(&mut self, frame: &mut Frame) -> Result<(), Error> { + unsafe { + check(chfl_trajectory_read(self.as_mut_ptr(), frame.as_mut_ptr())) + } + } + + /// Read a specific `step` of this trajectory into a `frame`. + /// + /// If the number of atoms in frame does not correspond to the number of + /// atom at this step, the frame is resized. + /// + /// # Errors + /// + /// This function fails if the data is incorrectly formatted for the + /// corresponding format. + /// + /// # Example + /// ```no_run + /// # use chemfiles::{Trajectory, Frame}; + /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + /// let mut frame = Frame::new(); + /// + /// trajectory.read_step(10, &mut frame).unwrap(); + /// ``` + pub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error> { + unsafe { + check(chfl_trajectory_read_step(self.as_mut_ptr(), step as u64, frame.as_mut_ptr())) + } + } + + /// Write a `frame` to this trajectory. + /// + /// # Errors + /// + /// This function fails if the data is incorrectly formatted for the + /// corresponding format. + /// + /// # Example + /// ```no_run + /// # use chemfiles::{Trajectory, Frame}; + /// let mut trajectory = Trajectory::open("water.pdb", 'w').unwrap(); + /// let mut frame = Frame::new(); + /// + /// trajectory.write(&mut frame).unwrap(); + /// ``` + pub fn write(&mut self, frame: &Frame) -> Result<(), Error> { + unsafe { + check(chfl_trajectory_write(self.as_mut_ptr(), frame.as_ptr())) + } + } + + /// Set the `topology` associated with this trajectory. This topology will + /// be used when reading and writing the files, replacing any topology in + /// the frames or files. + /// + /// # Example + /// ```no_run + /// # use chemfiles::{Trajectory, Atom, Topology}; + /// let mut topology = Topology::new(); + /// topology.add_atom(&Atom::new("H")); + /// topology.add_atom(&Atom::new("O")); + /// topology.add_atom(&Atom::new("H")); + /// topology.add_bond(0, 1); + /// topology.add_bond(1, 2); + /// + /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + /// trajectory.set_topology(&topology); + /// ``` + pub fn set_topology(&mut self, topology: &Topology) { + unsafe { + check_success(chfl_trajectory_set_topology(self.as_mut_ptr(), topology.as_ptr())); + } + } + + /// Set the topology associated with this trajectory by reading the first + /// frame of the file at the given `path` using the file format in `format`; + /// and extracting the topology of this frame. + /// + /// # Errors + /// + /// This function fails if the topology file is incorrectly formatted for + /// the corresponding format, or in case of I/O errors from the OS. + /// + /// # Example + /// ```no_run + /// # use chemfiles::Trajectory; + /// let mut trajectory = Trajectory::open("water.nc", 'r').unwrap(); + /// trajectory.set_topology_file("topology.pdb").unwrap(); + /// ``` + pub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error> + where + P: AsRef<Path>, + { + let path = path.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(path.as_ref()))?; + + let path = strings::to_c(path); + unsafe { + check(chfl_trajectory_topology_file(self.as_mut_ptr(), path.as_ptr(), ptr::null())) + } + } + + /// Set the topology associated with this trajectory by reading the first + /// frame of the file at the given `path` using the file format in + /// `format`; and extracting the topology of this frame. + /// + /// If `format` is an empty string, the format will be guessed from the + /// `path` extension. + /// + /// # Errors + /// + /// This function fails if the topology file is incorrectly formatted for + /// the corresponding format, or in case of I/O errors from the OS. + /// + /// # Example + /// ```no_run + /// # use chemfiles::Trajectory; + /// let mut trajectory = Trajectory::open("water.nc", 'r').unwrap(); + /// trajectory.set_topology_with_format("topology.mol", "PDB").unwrap(); + /// ``` + pub fn set_topology_with_format<'a, P, S>(&mut self, path: P, format: S) -> Result<(), Error> + where + P: AsRef<Path>, + S: Into<&'a str>, + { + let path = path.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(path.as_ref()))?; + + let format = strings::to_c(format.into()); + let path = strings::to_c(path); + unsafe { + check(chfl_trajectory_topology_file(self.as_mut_ptr(), path.as_ptr(), format.as_ptr())) + } + } + + /// Set the unit `cell` associated with a trajectory. This cell will be + /// used when reading and writing the files, replacing any unit cell in the + /// frames or files. + /// + /// # Example + /// ```no_run + /// # use chemfiles::{Trajectory, UnitCell}; + /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + /// trajectory.set_cell(&UnitCell::new([10.0, 11.0, 12.5])); + /// ``` + pub fn set_cell(&mut self, cell: &UnitCell) { + unsafe { + check_success(chfl_trajectory_set_cell(self.as_mut_ptr(), cell.as_ptr())); + } + } + + /// Get the number of steps (the number of frames) in a trajectory. + /// + /// # Example + /// ```no_run + /// # use chemfiles::Trajectory; + /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + /// + /// println!("This trajectory contains {} steps", trajectory.nsteps()); + /// ``` + // FIXME should this take &self instead? The file can be modified by this + // function, but the format should reset the state. + pub fn nsteps(&mut self) -> usize { + let mut res = 0; + unsafe { + check(chfl_trajectory_nsteps(self.as_mut_ptr(), &mut res)).expect( + "failed to get the number of steps in this trajectory" + ); + } + #[allow(clippy::cast_possible_truncation)] + return res as usize; + } + + /// Obtain the memory buffer written to by the trajectory. + /// + /// # Errors + /// + /// This fails if the trajectory was not opened with + /// `Trajectory::memory_writer`. + /// + /// # Example + /// ``` + /// # use chemfiles::{Atom, BondOrder, Frame, Trajectory}; + /// let mut trajectory_memory = Trajectory::memory_writer("SMI").unwrap(); + /// + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None); + /// frame.add_bond_with_order(0, 1, BondOrder::Single); + /// + /// trajectory_memory.write(&frame).unwrap(); + /// + /// let result = trajectory_memory.memory_buffer(); + /// assert_eq!(result.unwrap(), "CC\n"); + /// ``` + #[allow(clippy::cast_possible_truncation)] + pub fn memory_buffer(&self) -> Result<&str, Error> { + let mut raw_str: *const i8 = std::ptr::null(); + let mut strlen: u64 = 0; + unsafe { + check(chfl_trajectory_memory_buffer(self.as_ptr(), &mut raw_str, &mut strlen))?; + let mem_buf = std::ffi::CStr::from_ptr(raw_str); + assert_eq!(mem_buf.to_bytes().len(), strlen as usize); + Ok(mem_buf.to_str().unwrap()) + } + } + + /// Get file path for this trajectory. + /// + /// # Example + /// ```no_run + /// # use chemfiles::Trajectory; + /// let trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + /// + /// assert_eq!(trajectory.path(), "water.xyz"); + /// ``` + pub fn path(&self) -> String { + let get_string = |ptr, len| unsafe { chfl_trajectory_path(self.as_ptr(), ptr, len) }; + let path = strings::call_autogrow_buffer(1024, get_string).expect("failed to get path string"); + return strings::from_c(path.as_ptr()); + } +} + +impl Drop for Trajectory { + fn drop(&mut self) { + unsafe { + let _ = chfl_trajectory_close(self.as_ptr()); + } + } +} + +#[cfg(test)] +mod test { + use super::*; + + use std::fs; + use std::path::Path; + use std::io::Read; + + use approx::assert_ulps_eq; + + use {Atom, CellShape, Frame, Topology, UnitCell}; + + #[test] + fn read() { + let root = Path::new(file!()).parent().unwrap().join(".."); + let filename = root.join("data").join("water.xyz"); + let mut file = Trajectory::open(filename.to_str().unwrap(), 'r').unwrap(); + + if cfg!(target_family = "unix") { + assert_eq!(file.path(), "src/../data/water.xyz"); + } else if cfg!(target_family = "windows") { + assert_eq!(file.path(), "src\\..\\data\\water.xyz"); + } else { + panic!("please add test for this OS!"); + } + + assert_eq!(file.nsteps(), 100); + + let mut frame = Frame::new(); + assert!(file.read(&mut frame).is_ok()); + + assert_eq!(frame.size(), 297); + assert_ulps_eq!(frame.positions()[0][0], 0.417219); + assert_ulps_eq!(frame.positions()[0][1], 8.303366); + assert_ulps_eq!(frame.positions()[0][2], 11.737172); + assert_ulps_eq!(frame.positions()[124][0], 5.099554); + assert_ulps_eq!(frame.positions()[124][1], -0.045104); + assert_ulps_eq!(frame.positions()[124][2], 14.153846); + + assert_eq!(frame.atom(0).name(), "O"); + + file.set_cell(&UnitCell::new([30.0, 30.0, 30.0])); + assert!(file.read_step(41, &mut frame).is_ok()); + let cell = frame.cell().clone(); + assert_eq!(cell.lengths(), [30.0, 30.0, 30.0]); + + + assert_ulps_eq!(frame.positions()[0][0], 0.761277); + assert_ulps_eq!(frame.positions()[0][1], 8.106125); + assert_ulps_eq!(frame.positions()[0][2], 10.622949); + assert_ulps_eq!(frame.positions()[124][0], 5.13242); + assert_ulps_eq!(frame.positions()[124][1], 0.079862); + assert_ulps_eq!(frame.positions()[124][2], 14.194161); + + { + let topology = frame.topology(); + assert_eq!(topology.size(), 297); + assert_eq!(topology.bonds_count(), 0); + } + + assert!(frame.guess_bonds().is_ok()); + { + let topology = frame.topology(); + assert_eq!(topology.size(), 297); + assert_eq!(topology.bonds_count(), 180); + assert_eq!(topology.angles_count(), 84); + } + + let mut topology = Topology::new(); + let atom = Atom::new("Cs"); + for _ in 0..297 { + topology.add_atom(&atom); + } + + file.set_topology(&topology); + assert!(file.read_step(10, &mut frame).is_ok()); + assert_eq!(frame.atom(42).name(), "Cs"); + + let filename = root.join("data").join("topology.xyz"); + assert!(file.set_topology_file(filename.to_str().unwrap()).is_ok()); + assert!(file.read(&mut frame).is_ok()); + assert_eq!(frame.atom(100).name(), "Rd"); + + let filename = root.join("data").join("helium.xyz.but.not.really"); + let filename = filename.to_str().unwrap(); + let mut file = Trajectory::open_with_format(filename, 'r', "XYZ").unwrap(); + assert!(file.read(&mut frame).is_ok()); + assert_eq!(frame.size(), 125); + } + + fn write_file(path: &str) { + let mut file = Trajectory::open(path, 'w').unwrap(); + let mut frame = Frame::new(); + frame.resize(4); + + for position in frame.positions_mut() { + *position = [1.0, 2.0, 3.0]; + } + + let mut topology = Topology::new(); + let atom = Atom::new("X"); + for _ in 0..4 { + topology.add_atom(&atom); + } + frame.set_topology(&topology).unwrap(); + assert!(file.write(&frame).is_ok()); + } + + #[test] + fn write() { + let filename = "test-tmp.xyz"; + write_file(filename); + + let expected_content = "4 +Properties=species:S:1:pos:R:3 +X 1 2 3 +X 1 2 3 +X 1 2 3 +X 1 2 3".lines().collect::<Vec<_>>(); + + let mut file = fs::File::open(filename).unwrap(); + let mut content = String::new(); + let _ = file.read_to_string(&mut content).unwrap(); + + assert_eq!(expected_content, content.lines().collect::<Vec<_>>()); + fs::remove_file(filename).unwrap(); + } + + #[test] + fn memory() { + // formats in decreasing order of their memory buffer length to check null termination + for format in &["CSSR", "GRO", "XYZ"] { + let mut frame_write = Frame::new(); + frame_write.add_atom(&Atom::new("H"), [1.5, 3.0, -10.0], None); + frame_write.add_atom(&Atom::new("O"), [2.3, -1.4, 50.0], None); + frame_write.add_atom(&Atom::new("H"), [-1.5, 10.0, 0.0], None); + let cell = UnitCell::new([10.0, 11.0, 12.5]); + + let mut trajectory_write = Trajectory::memory_writer(*format).unwrap(); + trajectory_write.set_cell(&cell); + trajectory_write.write(&frame_write).unwrap(); + + let buffer = trajectory_write.memory_buffer().unwrap(); + let mut trajectory_read = Trajectory::memory_reader(buffer, *format).unwrap(); + let mut frame_read = Frame::new(); + trajectory_read.read(&mut frame_read).unwrap(); + + assert_eq!(trajectory_read.nsteps(), 1); + assert_eq!(frame_read.cell().shape(), CellShape::Orthorhombic); + assert_eq!(frame_read.size(), 3); + assert_eq!(frame_read.atom(1).name(), "O"); + crate::assert_vector3d_eq(&frame_read.positions()[2], &[-1.5, 10.0, 0.0], 1e-4); + } + } +} +
List of all items[−] + +
Structs
- Atom
- AtomMut
- AtomRef
- Error
- FormatMetadata
- Frame
- Match
- PropertiesIter
- Residue
- ResidueRef
- Selection
- Topology
- TopologyRef
- Trajectory
- UnitCell
- UnitCellMut
- UnitCellRef
Enums
Functions
Redirecting to ../../chemfiles/struct.Atom.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/atom/struct.AtomMut.html b/0.10.1/chemfiles/atom/struct.AtomMut.html new file mode 100644 index 000000000..a62923670 --- /dev/null +++ b/0.10.1/chemfiles/atom/struct.AtomMut.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.AtomMut.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/atom/struct.AtomRef.html b/0.10.1/chemfiles/atom/struct.AtomRef.html new file mode 100644 index 000000000..042ac5995 --- /dev/null +++ b/0.10.1/chemfiles/atom/struct.AtomRef.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.AtomRef.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/cell/enum.CellShape.html b/0.10.1/chemfiles/cell/enum.CellShape.html new file mode 100644 index 000000000..e1c2cc748 --- /dev/null +++ b/0.10.1/chemfiles/cell/enum.CellShape.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/enum.CellShape.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/cell/struct.UnitCell.html b/0.10.1/chemfiles/cell/struct.UnitCell.html new file mode 100644 index 000000000..cddcfc6bf --- /dev/null +++ b/0.10.1/chemfiles/cell/struct.UnitCell.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.UnitCell.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/cell/struct.UnitCellMut.html b/0.10.1/chemfiles/cell/struct.UnitCellMut.html new file mode 100644 index 000000000..c6b7d5aee --- /dev/null +++ b/0.10.1/chemfiles/cell/struct.UnitCellMut.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.UnitCellMut.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/cell/struct.UnitCellRef.html b/0.10.1/chemfiles/cell/struct.UnitCellRef.html new file mode 100644 index 000000000..0b0ac3556 --- /dev/null +++ b/0.10.1/chemfiles/cell/struct.UnitCellRef.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.UnitCellRef.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/enum.BondOrder.html b/0.10.1/chemfiles/enum.BondOrder.html new file mode 100644 index 000000000..dd83d7ba8 --- /dev/null +++ b/0.10.1/chemfiles/enum.BondOrder.html @@ -0,0 +1,58 @@ +Enum chemfiles::BondOrder [−][src]
#[repr(C)]
+#[non_exhaustive]
+pub enum BondOrder {
+ Unknown,
+ Single,
+ Double,
+ Triple,
+ Quadruple,
+ Quintuplet,
+ Amide,
+ Aromatic,
+}Possible bond order associated with bonds
++ Variants (Non-exhaustive)
+Non-exhaustive enums could have additional variants added in future. Therefore, when matching against variants of non-exhaustive enums, an extra wildcard arm must be added to account for any future variants.
Unknown or unspecified bond order
+Single bond
+Double bond
+Triple bond
+Quadruple bond (present in some metals)
+Quintuplet bond (present in some metals)
+Amide bond (required by some file formats)
+Aromatic bond (required by some file formats)
+Trait Implementations
impl PartialOrd<BondOrder> for BondOrder[src]
impl PartialOrd<BondOrder> for BondOrder[src]impl Copy for BondOrder[src]
impl Eq for BondOrder[src]
impl StructuralEq for BondOrder[src]
impl StructuralPartialEq for BondOrder[src]
Auto Trait Implementations
impl RefUnwindSafe for BondOrder
impl Send for BondOrder
impl Sync for BondOrder
impl Unpin for BondOrder
impl UnwindSafe for BondOrder
Blanket Implementations
Enum chemfiles::CellShape [−][src]
pub enum CellShape {
+ Orthorhombic,
+ Triclinic,
+ Infinite,
+}Available unit cell shapes.
++ Variants
+Orthorhombic cell, with the three angles equals to 90°.
+Triclinic cell, with any values for the angles.
+Infinite cell, to use when there is no cell.
+Trait Implementations
impl Eq for CellShape[src]
impl StructuralEq for CellShape[src]
impl StructuralPartialEq for CellShape[src]
Auto Trait Implementations
impl RefUnwindSafe for CellShape
impl Send for CellShape
impl Sync for CellShape
impl Unpin for CellShape
impl UnwindSafe for CellShape
Blanket Implementations
Enum chemfiles::Property [−][src]
A Property is a piece of data that can be associated with an Atom or a
+Frame.
+ Variants
+Bool(bool)Boolean property
+Double(f64)Floating point property
+String(String)String property
+3-dimensional vector property
+Trait Implementations
impl PartialOrd<Property> for Property[src]
impl PartialOrd<Property> for Property[src]impl StructuralPartialEq for Property[src]
Auto Trait Implementations
impl RefUnwindSafe for Property
impl Send for Property
impl Sync for Property
impl Unpin for Property
impl UnwindSafe for Property
Blanket Implementations
Enum chemfiles::Status [−][src]
#[repr(C)]
+#[non_exhaustive]
+pub enum Status {
+ Success,
+ MemoryError,
+ FileError,
+ FormatError,
+ SelectionError,
+ ConfigurationError,
+ OutOfBounds,
+ PropertyError,
+ ChemfilesError,
+ StdCppError,
+ UTF8PathError,
+}Possible causes of error in chemfiles
++ Variants (Non-exhaustive)
+Non-exhaustive enums could have additional variants added in future. Therefore, when matching against variants of non-exhaustive enums, an extra wildcard arm must be added to account for any future variants.
No error
+Error in memory allocations
+Error while reading or writing a file
+Error in file formatting, i.e. the file is invalid
+Error in selection string syntax
+Error in configuration files syntax
+Error for out of bounds indexing
+Error related to properties
+Exception in the C++ chemfiles library
+Exception in the C++ standard library
+The given path is not valid UTF8
+Trait Implementations
impl StructuralPartialEq for Status[src]
Auto Trait Implementations
impl RefUnwindSafe for Status
impl Send for Status
impl Sync for Status
impl Unpin for Status
impl UnwindSafe for Status
Blanket Implementations
Redirecting to ../../chemfiles/enum.Status.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/errors/fn.set_warning_callback.html b/0.10.1/chemfiles/errors/fn.set_warning_callback.html new file mode 100644 index 000000000..bf8004830 --- /dev/null +++ b/0.10.1/chemfiles/errors/fn.set_warning_callback.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/fn.set_warning_callback.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/errors/struct.Error.html b/0.10.1/chemfiles/errors/struct.Error.html new file mode 100644 index 000000000..413e6df25 --- /dev/null +++ b/0.10.1/chemfiles/errors/struct.Error.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.Error.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/fn.add_configuration.html b/0.10.1/chemfiles/fn.add_configuration.html new file mode 100644 index 000000000..3741d3989 --- /dev/null +++ b/0.10.1/chemfiles/fn.add_configuration.html @@ -0,0 +1,17 @@ +Function chemfiles::add_configuration [−][src]
pub fn add_configuration<S>(path: S) -> Result<(), Error> where
S: AsRef<str>,
Read configuration data from the file at path.
By default, chemfiles reads configuration from any file named
+.chemfiles.toml in the current directory or any parent directory. This
+function can be used to add data from another configuration file. Data from
+the new configuration file will overwrite any existing data.
Errors
+This function will fail if there is no file at path, or if the file is
+incorrectly formatted.
Example
++chemfiles::add_configuration("local-config.toml").unwrap(); +// from now on, the data from "local-config.toml" will be used
Function chemfiles::formats_list [−][src]
#[must_use] +pub fn formats_list() -> Vec<FormatMetadata>
Get the list of formats known by chemfiles, as well as all associated metadata.
+Example
++let formats = chemfiles::formats_list(); +println!("chemfiles supports {} formats:", formats.len()); +for format in &formats { + println!( + " {:<15} {}", + format.name, + format.extension.as_deref().unwrap_or("") + ); +}
Function chemfiles::guess_format [−][src]
pub fn guess_format(path: &str) -> String
Get the format that chemfiles would use to read a file at the given
+path.
The format is mostly guessed from the path extension, chemfiles only tries
+to read the file to distinguish between CIF and mmCIF files. Opening the
+file using the returned format string might still fail. For example, it will
+fail if the file is not actually formatted according to the guessed format;
+or the format/compression combination is not supported (e.g. XTC / GZ will
+not work since the XTC reader does not support compressed files).
The returned format is represented in a way compatible with the various
+Trajectory constructors, i.e. "<format name> [/ <compression>]", where
+compression is optional.
Examples
++let format = chemfiles::guess_format("trajectory.xyz.xz"); +assert_eq!(format, "XYZ / XZ"); + +let format = chemfiles::guess_format("trajectory.nc"); +assert_eq!(format, "Amber NetCDF");
Function chemfiles::set_warning_callback [−][src]
pub fn set_warning_callback<F>(callback: F) where
F: WarningCallback + 'static, Use callback for every chemfiles warning. The callback will be passed
+the warning message. This will drop any previous warning callback.
Function chemfiles::version [−][src]
pub fn version() -> String
Get the version of the chemfiles library.
+Example
++let version = chemfiles::version(); +assert!(version.starts_with("0.10"));
Redirecting to ../../chemfiles/struct.Frame.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/index.html b/0.10.1/chemfiles/index.html new file mode 100644 index 000000000..6c84d4dbf --- /dev/null +++ b/0.10.1/chemfiles/index.html @@ -0,0 +1,65 @@ +Crate chemfiles[−][src]
Chemfiles is a multi-language library written in modern C++ for reading and +writing from and to molecular trajectory files. These files are created by +your favorite theoretical chemistry program, and contains information about +atomic or residues names and positions. Some format also have additional +information, such as velocities, forces, energy, …
+This crate expose the C API of chemfiles to Rust, and make all the +functionalities accessible. For more information on the C++ library, +please see its documentation. Specifically, the following pages +are worth reading:
+-
+
- The overview of the classes organization; +
- The list of supported formats; +
- The documentation for the selection language; +
Structs
+| Atom | An |
| AtomMut | An analog to a mutable reference to an atom ( |
| AtomRef | An analog to a reference to an atom ( |
| Error | Error type for Chemfiles. + |
| FormatMetadata |
|
| Frame | A |
| Match | A |
| PropertiesIter | An iterator over the properties in an atom/frame/residue + |
| Residue | A |
| ResidueRef | An analog to a reference to a residue ( |
| Selection | A |
| Topology | A |
| TopologyRef | An analog to a reference to a topology ( |
| Trajectory | The |
| UnitCell | An |
| UnitCellMut | An analog to a mutable reference to an unit cell ( |
| UnitCellRef | An analog to a reference to an unit cell ( |
Enums
+| BondOrder | Possible bond order associated with bonds + |
| CellShape | Available unit cell shapes. + |
| Property | A |
| Status | Possible causes of error in chemfiles + |
Functions
+| add_configuration | Read configuration data from the file at |
| formats_list | Get the list of formats known by chemfiles, as well as all associated metadata. + |
| guess_format | Get the format that chemfiles would use to read a file at the given
+ |
| set_warning_callback | Use |
| version | Get the version of the chemfiles library. + |
Redirecting to ../../chemfiles/fn.formats_list.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/misc/fn.guess_format.html b/0.10.1/chemfiles/misc/fn.guess_format.html new file mode 100644 index 000000000..f4741431e --- /dev/null +++ b/0.10.1/chemfiles/misc/fn.guess_format.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/fn.guess_format.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/misc/struct.FormatMetadata.html b/0.10.1/chemfiles/misc/struct.FormatMetadata.html new file mode 100644 index 000000000..f380c5718 --- /dev/null +++ b/0.10.1/chemfiles/misc/struct.FormatMetadata.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.FormatMetadata.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/property/enum.Property.html b/0.10.1/chemfiles/property/enum.Property.html new file mode 100644 index 000000000..b3727aac1 --- /dev/null +++ b/0.10.1/chemfiles/property/enum.Property.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/enum.Property.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/property/struct.PropertiesIter.html b/0.10.1/chemfiles/property/struct.PropertiesIter.html new file mode 100644 index 000000000..815bc6c1c --- /dev/null +++ b/0.10.1/chemfiles/property/struct.PropertiesIter.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.PropertiesIter.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/residue/struct.Residue.html b/0.10.1/chemfiles/residue/struct.Residue.html new file mode 100644 index 000000000..d9b75c1b0 --- /dev/null +++ b/0.10.1/chemfiles/residue/struct.Residue.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.Residue.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/residue/struct.ResidueRef.html b/0.10.1/chemfiles/residue/struct.ResidueRef.html new file mode 100644 index 000000000..7219dbf27 --- /dev/null +++ b/0.10.1/chemfiles/residue/struct.ResidueRef.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.ResidueRef.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/selection/struct.Match.html b/0.10.1/chemfiles/selection/struct.Match.html new file mode 100644 index 000000000..848ab37f8 --- /dev/null +++ b/0.10.1/chemfiles/selection/struct.Match.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.Match.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/selection/struct.Selection.html b/0.10.1/chemfiles/selection/struct.Selection.html new file mode 100644 index 000000000..2268a4ddb --- /dev/null +++ b/0.10.1/chemfiles/selection/struct.Selection.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.Selection.html...
+ + + \ No newline at end of file diff --git a/0.10.1/chemfiles/sidebar-items.js b/0.10.1/chemfiles/sidebar-items.js new file mode 100644 index 000000000..dc3572b15 --- /dev/null +++ b/0.10.1/chemfiles/sidebar-items.js @@ -0,0 +1 @@ +initSidebarItems({"enum":[["BondOrder","Possible bond order associated with bonds"],["CellShape","Available unit cell shapes."],["Property","A `Property` is a piece of data that can be associated with an `Atom` or a `Frame`."],["Status","Possible causes of error in chemfiles"]],"fn":[["add_configuration","Read configuration data from the file at `path`."],["formats_list","Get the list of formats known by chemfiles, as well as all associated metadata."],["guess_format","Get the format that chemfiles would use to read a file at the given `path`."],["set_warning_callback","Use `callback` for every chemfiles warning. The callback will be passed the warning message. This will drop any previous warning callback."],["version","Get the version of the chemfiles library."]],"struct":[["Atom","An `Atom` is a particle in the current `Frame`. It stores the following atomic properties:"],["AtomMut","An analog to a mutable reference to an atom (`&mut Atom`)"],["AtomRef","An analog to a reference to an atom (`&Atom`)"],["Error","Error type for Chemfiles."],["FormatMetadata","`FormatMetadata` contains metadata associated with one format."],["Frame","A `Frame` contains data from one simulation step: the current unit cell, the topology, the positions, and the velocities of the particles in the system. If some information is missing (topology or velocity or unit cell), the corresponding data is filled with a default value."],["Match","A `Match` is a set of atomic indexes matching a given selection. It can mostly be used like a `&[usize]`."],["PropertiesIter","An iterator over the properties in an atom/frame/residue"],["Residue","A `Residue` is a group of atoms belonging to the same logical unit. They can be small molecules, amino-acids in a protein, monomers in polymers, etc."],["ResidueRef","An analog to a reference to a residue (`&Residue`)"],["Selection","A `Selection` allow to select atoms in a `Frame`, from a selection language. The selection language is built by combining basic operations. Each basic operation follows the `Struct chemfiles::Atom [−][src]
pub struct Atom { /* fields omitted */ }An Atom is a particle in the current Frame. It stores the following
+atomic properties:
-
+
- atom name; +
- atom type; +
- atom mass; +
- atom charge. +
The atom name is usually an unique identifier (H1, C_a) while the
+atom type will be shared between all particles of the same type: H,
+Ow, CH3.
Implementations
impl Atom[src]
impl Atom[src]pub fn new<'a>(name: impl Into<&'a str>) -> Atom[src]
Create an atom with the given name, and set the atom type to name.
Example
++let atom = Atom::new("He"); +assert_eq!(atom.name(), "He");
pub fn mass(&self) -> f64[src]
Get the atom mass, in atomic mass units.
+Example
++let atom = Atom::new("He"); +assert_eq!(atom.mass(), 4.002602);
pub fn set_mass(&mut self, mass: f64)[src]
Set the atom mass to mass, in atomic mass units.
Example
++let mut atom = Atom::new("He"); + +atom.set_mass(34.9); +assert_eq!(atom.mass(), 34.9);
pub fn charge(&self) -> f64[src]
Get the atom charge, in number of the electron charge e.
+Example
++let atom = Atom::new("He"); +assert_eq!(atom.charge(), 0.0);
pub fn set_charge(&mut self, charge: f64)[src]
Set the atom charge to charge, in number of the electron charge e.
Example
++let mut atom = Atom::new("He"); + +atom.set_charge(-2.0); +assert_eq!(atom.charge(), -2.0);
pub fn name(&self) -> String[src]
pub fn atomic_type(&self) -> String[src]
pub fn set_name<'a>(&mut self, name: impl Into<&'a str>)[src]
Set the atom name to name.
Example
++let mut atom = Atom::new("He"); + +atom.set_name("Zn3"); +assert_eq!(atom.name(), "Zn3");
pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>)[src]
Set the atom type to atomic_type.
Example
++let mut atom = Atom::new("He"); + +atom.set_atomic_type("F"); +assert_eq!(atom.atomic_type(), "F");
pub fn full_name(&self) -> String[src]
Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
++let atom = Atom::new("Zn"); +assert_eq!(atom.full_name(), "Zinc");
pub fn vdw_radius(&self) -> f64[src]
Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").vdw_radius(), 1.4); +assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);
pub fn covalent_radius(&self) -> f64[src]
Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").covalent_radius(), 0.32); +assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);
pub fn atomic_number(&self) -> u64[src]
Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").atomic_number(), 2); +assert_eq!(Atom::new("Xxx").atomic_number(), 0);
pub fn set(&mut self, name: &str, property: impl Into<Property>)[src]
Add a new property with the given name to this atom.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
++let mut atom = Atom::new("He"); +atom.set("a bool", true); +atom.set("a string", "test"); + +assert_eq!(atom.get("a bool"), Some(Property::Bool(true))); +assert_eq!(atom.get("a string"), Some(Property::String("test".into())));
pub fn get(&self, name: &str) -> Option<Property>[src]
Get a property with the given name in this atom, if it exist.
Examples
++let mut atom = Atom::new("He"); +atom.set("foo", Property::Double(22.2)); + +assert_eq!(atom.get("foo"), Some(Property::Double(22.2))); +assert_eq!(atom.get("Bar"), None);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);[src]
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this atom
+Examples
++let mut atom = Atom::new("He"); +atom.set("foo", Property::Double(22.2)); +atom.set("bar", Property::Bool(false)); + +for (name, property) in atom.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(22.2)); + } else if name == "bar" { + assert_eq!(property, Property::Bool(false)); + } +}
Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Atom
impl !Send for Atom
impl !Sync for Atom
impl Unpin for Atom
impl UnwindSafe for Atom
Blanket Implementations
Struct chemfiles::AtomMut [−][src]
pub struct AtomMut<'a> { /* fields omitted */ }An analog to a mutable reference to an atom (&mut Atom)
Methods from Deref<Target = Atom>
pub fn mass(&self) -> f64[src]
Get the atom mass, in atomic mass units.
+Example
++let atom = Atom::new("He"); +assert_eq!(atom.mass(), 4.002602);
pub fn set_mass(&mut self, mass: f64)[src]
Set the atom mass to mass, in atomic mass units.
Example
++let mut atom = Atom::new("He"); + +atom.set_mass(34.9); +assert_eq!(atom.mass(), 34.9);
pub fn charge(&self) -> f64[src]
Get the atom charge, in number of the electron charge e.
+Example
++let atom = Atom::new("He"); +assert_eq!(atom.charge(), 0.0);
pub fn set_charge(&mut self, charge: f64)[src]
Set the atom charge to charge, in number of the electron charge e.
Example
++let mut atom = Atom::new("He"); + +atom.set_charge(-2.0); +assert_eq!(atom.charge(), -2.0);
pub fn name(&self) -> String[src]
pub fn atomic_type(&self) -> String[src]
pub fn set_name<'a>(&mut self, name: impl Into<&'a str>)[src]
Set the atom name to name.
Example
++let mut atom = Atom::new("He"); + +atom.set_name("Zn3"); +assert_eq!(atom.name(), "Zn3");
pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>)[src]
Set the atom type to atomic_type.
Example
++let mut atom = Atom::new("He"); + +atom.set_atomic_type("F"); +assert_eq!(atom.atomic_type(), "F");
pub fn full_name(&self) -> String[src]
Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
++let atom = Atom::new("Zn"); +assert_eq!(atom.full_name(), "Zinc");
pub fn vdw_radius(&self) -> f64[src]
Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").vdw_radius(), 1.4); +assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);
pub fn covalent_radius(&self) -> f64[src]
Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").covalent_radius(), 0.32); +assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);
pub fn atomic_number(&self) -> u64[src]
Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").atomic_number(), 2); +assert_eq!(Atom::new("Xxx").atomic_number(), 0);
pub fn set(&mut self, name: &str, property: impl Into<Property>)[src]
Add a new property with the given name to this atom.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
++let mut atom = Atom::new("He"); +atom.set("a bool", true); +atom.set("a string", "test"); + +assert_eq!(atom.get("a bool"), Some(Property::Bool(true))); +assert_eq!(atom.get("a string"), Some(Property::String("test".into())));
pub fn get(&self, name: &str) -> Option<Property>[src]
Get a property with the given name in this atom, if it exist.
Examples
++let mut atom = Atom::new("He"); +atom.set("foo", Property::Double(22.2)); + +assert_eq!(atom.get("foo"), Some(Property::Double(22.2))); +assert_eq!(atom.get("Bar"), None);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);[src]
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this atom
+Examples
++let mut atom = Atom::new("He"); +atom.set("foo", Property::Double(22.2)); +atom.set("bar", Property::Bool(false)); + +for (name, property) in atom.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(22.2)); + } else if name == "bar" { + assert_eq!(property, Property::Bool(false)); + } +}
Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for AtomMut<'a>
impl<'a> !Send for AtomMut<'a>
impl<'a> !Sync for AtomMut<'a>
impl<'a> Unpin for AtomMut<'a>
impl<'a> !UnwindSafe for AtomMut<'a>
Blanket Implementations
Struct chemfiles::AtomRef [−][src]
pub struct AtomRef<'a> { /* fields omitted */ }An analog to a reference to an atom (&Atom)
Methods from Deref<Target = Atom>
pub fn mass(&self) -> f64[src]
Get the atom mass, in atomic mass units.
+Example
++let atom = Atom::new("He"); +assert_eq!(atom.mass(), 4.002602);
pub fn charge(&self) -> f64[src]
Get the atom charge, in number of the electron charge e.
+Example
++let atom = Atom::new("He"); +assert_eq!(atom.charge(), 0.0);
pub fn name(&self) -> String[src]
pub fn atomic_type(&self) -> String[src]
pub fn full_name(&self) -> String[src]
Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
++let atom = Atom::new("Zn"); +assert_eq!(atom.full_name(), "Zinc");
pub fn vdw_radius(&self) -> f64[src]
Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").vdw_radius(), 1.4); +assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);
pub fn covalent_radius(&self) -> f64[src]
Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").covalent_radius(), 0.32); +assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);
pub fn atomic_number(&self) -> u64[src]
Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
++assert_eq!(Atom::new("He").atomic_number(), 2); +assert_eq!(Atom::new("Xxx").atomic_number(), 0);
pub fn get(&self, name: &str) -> Option<Property>[src]
Get a property with the given name in this atom, if it exist.
Examples
++let mut atom = Atom::new("He"); +atom.set("foo", Property::Double(22.2)); + +assert_eq!(atom.get("foo"), Some(Property::Double(22.2))); +assert_eq!(atom.get("Bar"), None);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);[src]
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this atom
+Examples
++let mut atom = Atom::new("He"); +atom.set("foo", Property::Double(22.2)); +atom.set("bar", Property::Bool(false)); + +for (name, property) in atom.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(22.2)); + } else if name == "bar" { + assert_eq!(property, Property::Bool(false)); + } +}
Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for AtomRef<'a>
impl<'a> !Send for AtomRef<'a>
impl<'a> !Sync for AtomRef<'a>
impl<'a> Unpin for AtomRef<'a>
impl<'a> UnwindSafe for AtomRef<'a>
Blanket Implementations
Struct chemfiles::Error [−][src]
Error type for Chemfiles.
++ Fields
status: StatusThe error status code
+message: StringA message describing the error cause
+Implementations
impl Error[src]
impl Error[src]pub fn last_error() -> String[src]
Get the last error message from the C++ library.
+pub fn cleanup()[src]
Clear any error from the C++ library
+Trait Implementations
impl StructuralPartialEq for Error[src]
Auto Trait Implementations
impl RefUnwindSafe for Error
impl Send for Error
impl Sync for Error
impl Unpin for Error
impl UnwindSafe for Error
Blanket Implementations
Struct chemfiles::FormatMetadata [−][src]
pub struct FormatMetadata {Show fields
+ pub name: &'static str,
+ pub extension: Option<&'static str>,
+ pub description: &'static str,
+ pub reference: &'static str,
+ pub read: bool,
+ pub write: bool,
+ pub memory: bool,
+ pub positions: bool,
+ pub velocities: bool,
+ pub unit_cell: bool,
+ pub atoms: bool,
+ pub bonds: bool,
+ pub residues: bool,
+}FormatMetadata contains metadata associated with one format.
+ Fields
name: &'static strName of the format.
+extension: Option<&'static str>Extension associated with the format.
+description: &'static strExtended, user-facing description of the format.
+reference: &'static strURL pointing to the format definition/reference.
+read: boolIs reading files in this format implemented?
+write: boolIs writing files in this format implemented?
+memory: boolDoes this format support in-memory IO?
+positions: boolDoes this format support storing atomic positions?
+velocities: boolDoes this format support storing atomic velocities?
+unit_cell: boolDoes this format support storing unit cell information?
+atoms: boolDoes this format support storing atom names or types?
+bonds: boolDoes this format support storing bonds between atoms?
+residues: boolDoes this format support storing residues?
+Trait Implementations
impl Clone for FormatMetadata[src]
impl Clone for FormatMetadata[src]fn clone(&self) -> FormatMetadata[src]
pub fn clone_from(&mut self, source: &Self)1.0.0[src]
impl PartialEq<FormatMetadata> for FormatMetadata[src]
impl PartialEq<FormatMetadata> for FormatMetadata[src]fn eq(&self, other: &FormatMetadata) -> bool[src]
fn ne(&self, other: &FormatMetadata) -> bool[src]
impl Eq for FormatMetadata[src]
impl StructuralEq for FormatMetadata[src]
impl StructuralPartialEq for FormatMetadata[src]
Auto Trait Implementations
impl RefUnwindSafe for FormatMetadata
impl Send for FormatMetadata
impl Sync for FormatMetadata
impl Unpin for FormatMetadata
impl UnwindSafe for FormatMetadata
Blanket Implementations
Struct chemfiles::Frame [−][src]
pub struct Frame { /* fields omitted */ }A Frame contains data from one simulation step: the current unit
+cell, the topology, the positions, and the velocities of the particles in
+the system. If some information is missing (topology or velocity or unit
+cell), the corresponding data is filled with a default value.
Implementations
impl Frame[src]
impl Frame[src]pub fn new() -> Frame[src]
Create an empty frame. It will be resized by the library as needed.
+Example
++let frame = Frame::new(); + +assert_eq!(frame.size(), 0);
pub fn atom(&self, index: usize) -> AtomRef<'_>[src]
Get a reference to the atom at the given index in this frame.
Panics
+If index is out of bounds.
Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("Zn"), [0.0; 3], None); + +let atom = frame.atom(0); +assert_eq!(atom.name(), "Zn");
pub fn atom_mut(&mut self, index: usize) -> AtomMut<'_>[src]
Get a mutable reference to the atom at the given index in this frame.
Panics
+If index is out of bounds.
Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("Zn"), [0.0; 3], None); + +assert_eq!(frame.atom(0).name(), "Zn"); + +frame.atom_mut(0).set_name("Fe"); +assert_eq!(frame.atom(0).name(), "Fe");
pub fn size(&self) -> usize[src]
Get the current number of atoms in this frame.
+Example
++let mut frame = Frame::new(); +assert_eq!(frame.size(), 0); + +frame.resize(67); +assert_eq!(frame.size(), 67);
pub fn resize(&mut self, natoms: usize)[src]
Resize the positions and the velocities in this frame, to make space for
+natoms atoms. Previous data is conserved, as well as the presence of
+absence of velocities.
Example
++let mut frame = Frame::new(); +frame.resize(67); +assert_eq!(frame.size(), 67);
pub fn add_atom(
&mut self,
atom: &Atom,
position: [f64; 3],
velocity: impl Into<Option<[f64; 3]>>
)[src]
&mut self,
atom: &Atom,
position: [f64; 3],
velocity: impl Into<Option<[f64; 3]>>
)
Add an Atom and the corresponding position and optionally velocity
+data to this frame.
Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("Zn"), [1.0, 1.0, 2.0], None); + +frame.add_velocities(); +frame.add_atom(&Atom::new("Zn"), [-1.0, 1.0, 2.0], [0.2, 0.1, 0.0]);
pub fn remove(&mut self, i: usize)[src]
Remove the atom at index i in this frame.
Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("Zn"), [0.0; 3], None); +frame.add_atom(&Atom::new("Fe"), [0.0; 3], None); +frame.add_atom(&Atom::new("Sn"), [0.0; 3], None); +assert_eq!(frame.size(), 3); + +frame.remove(1); +assert_eq!(frame.size(), 2); +assert_eq!(frame.atom(1).name(), "Sn");
pub fn add_bond(&mut self, i: usize, j: usize)[src]
Add a bond between the atoms at indexes i and j in the frame.
The bond order is set to BondOrder::Unknown.
Example
++let mut frame = Frame::new(); +assert_eq!(frame.topology().bonds_count(), 0); +frame.resize(5); + +frame.add_bond(0, 1); +frame.add_bond(3, 1); +frame.add_bond(2, 4); +assert_eq!(frame.topology().bonds_count(), 3); + +assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown); +assert_eq!(frame.topology().bonds(), vec![[0, 1], [1, 3], [2, 4]]);
pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder)[src]
Add a bond between the atoms at indexes i and j in the frame
+with the given bond order.
Example
++let mut frame = Frame::new(); +assert_eq!(frame.topology().bonds_count(), 0); +frame.resize(2); + +frame.add_bond_with_order(0, 1, BondOrder::Double); +assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Double);
pub fn remove_bond(&mut self, i: usize, j: usize)[src]
Remove any existing bond between the atoms at indexes i and j in
+the frame.
This function does nothing if there is no bond between i and j.
Example
++let mut frame = Frame::new(); +frame.resize(5); + +frame.add_bond(0, 1); +frame.add_bond(3, 1); +frame.add_bond(2, 4); + +let bonds = frame.topology().bonds(); +assert_eq!(bonds, vec![[0, 1], [1, 3], [2, 4]]); + +frame.remove_bond(2, 4); +let bonds = frame.topology().bonds(); +assert_eq!(bonds, vec![[0, 1], [1, 3]]);
pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error>[src]
Add a copy of residue to this frame.
Errors
+This function fails is the residue id is already in this frame’s +topology, or if the residue contain atoms that are already in another +residue.
+Example
++let mut frame = Frame::new(); + +let residue = Residue::new("foo"); +frame.add_residue(&residue).unwrap(); + +let topology = frame.topology(); +assert_eq!(topology.residues_count(), 1); +assert_eq!(topology.residue(0).unwrap().name(), "foo");
pub fn distance(&self, i: usize, j: usize) -> f64[src]
Get the distance between the atoms at indexes i and j in this frame,
+accounting for periodic boundary conditions. The result is expressed in
+Angstroms.
Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("B"), [1.0, 2.0, 3.0], None); + +assert_eq!(frame.distance(0, 1), f64::sqrt(14.0));
pub fn angle(&self, i: usize, j: usize, k: usize) -> f64[src]
Get the angle formed by the atoms at indexes i, j and k in this
+frame, accounting for periodic boundary conditions. The result is
+expressed in radians.
Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None); + +assert_eq!(frame.angle(0, 1, 2), f64::consts::PI / 2.0);
pub fn dihedral(&self, i: usize, j: usize, k: usize, m: usize) -> f64[src]
Get the dihedral angle formed by the atoms at indexes i, j, k and
+m in this frame, accounting for periodic boundary conditions. The
+result is expressed in radians.
Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None); +frame.add_atom(&Atom::new("D"), [0.0, 1.0, 1.0], None); + +assert_eq!(frame.dihedral(0, 1, 2, 3), f64::consts::PI / 2.0);
pub fn out_of_plane(&self, i: usize, j: usize, k: usize, m: usize) -> f64[src]
Get the out of plane distance formed by the atoms at indexes i, j,
+k and m in this frame, accounting for periodic boundary conditions.
+The result is expressed in angstroms.
This is the distance between the atom j and the ikm plane. The j atom +is the center of the improper dihedral angle formed by i, j, k and m.
+Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("B"), [0.0, 0.0, 2.0], None); +frame.add_atom(&Atom::new("C"), [1.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("D"), [0.0, 1.0, 0.0], None); + +assert_eq!(frame.out_of_plane(0, 1, 2, 3), 2.0);
pub fn positions(&self) -> &[[f64; 3]][src]
Get a view into the positions of this frame.
+Example
++let mut frame = Frame::new(); +frame.resize(67); + +let positions = frame.positions(); +assert_eq!(positions.len(), 67); +assert_eq!(positions[0], [0.0, 0.0, 0.0]);
pub fn positions_mut(&mut self) -> &mut [[f64; 3]][src]
Get a mutable view into the positions of this frame.
+Example
++let mut frame = Frame::new(); +frame.resize(67); +{ + let positions = frame.positions_mut(); + assert_eq!(positions[0], [0.0, 0.0, 0.0]); + positions[0] = [1.0, 2.0, 3.0]; +} + +let positions = frame.positions(); +assert_eq!(positions[0], [1.0, 2.0, 3.0]);
pub fn velocities(&self) -> &[[f64; 3]][src]
Get a view into the velocities of this frame.
+Example
++let mut frame = Frame::new(); +frame.resize(67); +frame.add_velocities(); + +let velocities = frame.velocities(); +assert_eq!(velocities.len(), 67); +assert_eq!(velocities[0], [0.0, 0.0, 0.0]);
pub fn velocities_mut(&mut self) -> &mut [[f64; 3]][src]
Get a mutable view into the velocities of this frame.
+Example
++let mut frame = Frame::new(); +frame.resize(67); +frame.add_velocities(); +{ + let velocities = frame.velocities_mut(); + assert_eq!(velocities[0], [0.0, 0.0, 0.0]); + velocities[0] = [1.0, 2.0, 3.0]; +} + +let velocities = frame.velocities(); +assert_eq!(velocities[0], [1.0, 2.0, 3.0]);
pub fn has_velocities(&self) -> bool[src]
Check if this frame contains velocity data.
+Example
++let mut frame = Frame::new(); +assert_eq!(frame.has_velocities(), false); + +frame.add_velocities(); +assert_eq!(frame.has_velocities(), true);
pub fn add_velocities(&mut self)[src]
Add velocity data to this frame. If the frame already have velocities, +this does nothing.
+Example
++let mut frame = Frame::new(); +assert_eq!(frame.has_velocities(), false); + +frame.add_velocities(); +assert_eq!(frame.has_velocities(), true);
pub fn cell(&self) -> UnitCellRef<'_>[src]
Get a reference to the UnitCell from this frame.
Example
++let frame = Frame::new(); + +let cell = frame.cell(); +assert_eq!(cell.shape(), CellShape::Infinite);
pub fn cell_mut(&mut self) -> UnitCellMut<'_>[src]
Get a mutable reference to the UnitCell from this frame.
Example
++let mut frame = Frame::new(); + +assert_eq!(frame.cell().shape(), CellShape::Infinite); + +frame.cell_mut().set_shape(CellShape::Triclinic).unwrap(); +assert_eq!(frame.cell().shape(), CellShape::Triclinic);
pub fn set_cell(&mut self, cell: &UnitCell)[src]
Set the UnitCell of this frame to cell.
Example
++let mut frame = Frame::new(); + +frame.set_cell(&UnitCell::new([10.0, 10.0, 10.0])); + +let cell = frame.cell(); +assert_eq!(cell.shape(), CellShape::Orthorhombic); +assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);
pub fn topology(&self) -> TopologyRef<'_>[src]
Get a reference to the Topology of this frame.
Example
++let mut frame = Frame::new(); +frame.resize(42); + +let topology = frame.topology(); +assert_eq!(topology.size(), 42);
pub fn set_topology(&mut self, topology: &Topology) -> Result<(), Error>[src]
Set the Topology of this frame to topology.
Errors
+This function fails if the topology contains a different number of atoms +than this frame.
+Example
++let mut frame = Frame::new(); +frame.resize(2); + +let mut topology = Topology::new(); +topology.add_atom(&Atom::new("Cl")); +topology.add_atom(&Atom::new("Cl")); +topology.add_bond(0, 1); + +frame.set_topology(&topology).unwrap(); +assert_eq!(frame.atom(0).name(), "Cl");
pub fn step(&self) -> usize[src]
Get this frame step, i.e. the frame number in the trajectory
+Example
++let frame = Frame::new(); +assert_eq!(frame.step(), 0);
pub fn set_step(&mut self, step: usize)[src]
Set this frame step to step.
Example
++let mut frame = Frame::new(); +assert_eq!(frame.step(), 0); + +frame.set_step(10); +assert_eq!(frame.step(), 10);
pub fn guess_bonds(&mut self) -> Result<(), Error>[src]
Guess the bonds, angles and dihedrals in this frame.
The bonds are guessed using a distance-based algorithm, and then angles +and dihedrals are guessed from the bonds.
+Errors
+This function can fail if the covalent radius is unknown for some atoms +in the frame.
+Example
++let mut frame = Frame::new(); + +frame.add_atom(&Atom::new("Cl"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("Cl"), [1.5, 0.0, 0.0], None); +assert_eq!(frame.topology().bonds_count(), 0); + +frame.guess_bonds().unwrap(); +assert_eq!(frame.topology().bonds_count(), 1);
pub fn clear_bonds(&mut self)[src]
Remove all existing bonds, angles, dihedral angles and improper +dihedral angles in the topology of the frame.
+Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("H"), [0.0, 1.0, 0.0], None); + +frame.add_bond(0, 1); +frame.add_bond(1, 2); + +assert_eq!(frame.topology().bonds().len(), 2); +assert_eq!(frame.topology().angles().len(), 1); + +frame.clear_bonds(); +assert!(frame.topology().bonds().is_empty()); +assert!(frame.topology().angles().is_empty());
pub fn set(&mut self, name: &str, property: impl Into<Property>)[src]
Add a new property with the given name to this frame.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
++let mut frame = Frame::new(); +frame.set("a string", "hello"); +frame.set("a double", 4.3); + +assert_eq!(frame.get("a string"), Some(Property::String("hello".into()))); +assert_eq!(frame.get("a double"), Some(Property::Double(4.3)));
pub fn get(&self, name: &str) -> Option<Property>[src]
Get a property with the given name in this frame, if it exist.
Examples
++let mut frame = Frame::new(); +frame.set("foo", Property::Double(22.2)); + +assert_eq!(frame.get("foo"), Some(Property::Double(22.2))); +assert_eq!(frame.get("Bar"), None);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);[src]
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this frame
+Examples
++let mut frame = Frame::new(); +frame.set("foo", Property::Double(22.2)); +frame.set("bar", Property::Bool(false)); + +for (name, property) in frame.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(22.2)); + } else if name == "bar" { + assert_eq!(property, Property::Bool(false)); + } +}
Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Frame
impl !Send for Frame
impl !Sync for Frame
impl Unpin for Frame
impl UnwindSafe for Frame
Blanket Implementations
Struct chemfiles::Match [−][src]
pub struct Match { /* fields omitted */ }A Match is a set of atomic indexes matching a given selection. It can
+mostly be used like a &[usize].
Implementations
impl Match[src]
impl Match[src]pub fn len(&self) -> usize[src]
Get the length of the Match.
+Example
++let atomic_match = Match::new(&[3, 4, 5]); +assert_eq!(atomic_match.len(), 3);
pub fn new(atoms: &[usize]) -> Match[src]
Create a new match containing the atoms in the atoms slice.
Panics
+If the slice contains more than 4 elements, which is the maximal size +of a match.
+Example
++let atomic_match = Match::new(&[3, 4, 5]); +assert_eq!(atomic_match.len(), 3); +assert_eq!(atomic_match[0], 3); +assert_eq!(atomic_match[1], 4); +assert_eq!(atomic_match[2], 5);
pub fn iter(&self) -> Iter<'_, usize>[src]
Iterate over the atomic indexes in the match.
+Example
++let atomic_match = Match::new(&[3, 4, 5]); +let mut iter = atomic_match.iter(); + +assert_eq!(iter.next(), Some(&3)); +assert_eq!(iter.next(), Some(&4)); +assert_eq!(iter.next(), Some(&5)); +assert_eq!(iter.next(), None);
Trait Implementations
impl<'a> IntoIterator for &'a Match[src]
impl<'a> IntoIterator for &'a Match[src]impl Eq for Match[src]
impl StructuralEq for Match[src]
impl StructuralPartialEq for Match[src]
Auto Trait Implementations
impl RefUnwindSafe for Match
impl Send for Match
impl Sync for Match
impl Unpin for Match
impl UnwindSafe for Match
Blanket Implementations
Struct chemfiles::PropertiesIter [−][src]
pub struct PropertiesIter<'a> { /* fields omitted */ }An iterator over the properties in an atom/frame/residue
+Trait Implementations
impl<'a> Iterator for PropertiesIter<'a>[src]
impl<'a> Iterator for PropertiesIter<'a>[src]type Item = (String, Property)
The type of the elements being iterated over.
+fn next(&mut self) -> Option<Self::Item>[src]
fn size_hint(&self) -> (usize, Option<usize>)[src]
fn count(self) -> usize[src]
pub fn last(self) -> Option<Self::Item>1.0.0[src]
pub fn advance_by(&mut self, n: usize) -> Result<(), usize>[src]
pub fn nth(&mut self, n: usize) -> Option<Self::Item>1.0.0[src]
pub fn step_by(self, step: usize) -> StepBy<Self>1.28.0[src]
pub fn chain<U>(self, other: U) -> Chain<Self, <U as IntoIterator>::IntoIter> where
U: IntoIterator<Item = Self::Item>, 1.0.0[src]
U: IntoIterator<Item = Self::Item>,
pub fn zip<U>(self, other: U) -> Zip<Self, <U as IntoIterator>::IntoIter> where
U: IntoIterator, 1.0.0[src]
U: IntoIterator,
pub fn intersperse(self, separator: Self::Item) -> Intersperse<Self> where
Self::Item: Clone, [src]
Self::Item: Clone,
pub fn intersperse_with<G>(self, separator: G) -> IntersperseWith<Self, G> where
G: FnMut() -> Self::Item, [src]
G: FnMut() -> Self::Item,
pub fn map<B, F>(self, f: F) -> Map<Self, F> where
F: FnMut(Self::Item) -> B, 1.0.0[src]
F: FnMut(Self::Item) -> B,
pub fn for_each<F>(self, f: F) where
F: FnMut(Self::Item), 1.21.0[src]
F: FnMut(Self::Item),
pub fn filter<P>(self, predicate: P) -> Filter<Self, P> where
P: FnMut(&Self::Item) -> bool, 1.0.0[src]
P: FnMut(&Self::Item) -> bool,
pub fn filter_map<B, F>(self, f: F) -> FilterMap<Self, F> where
F: FnMut(Self::Item) -> Option<B>, 1.0.0[src]
F: FnMut(Self::Item) -> Option<B>,
pub fn enumerate(self) -> Enumerate<Self>1.0.0[src]
pub fn peekable(self) -> Peekable<Self>1.0.0[src]
pub fn skip_while<P>(self, predicate: P) -> SkipWhile<Self, P> where
P: FnMut(&Self::Item) -> bool, 1.0.0[src]
P: FnMut(&Self::Item) -> bool,
pub fn take_while<P>(self, predicate: P) -> TakeWhile<Self, P> where
P: FnMut(&Self::Item) -> bool, 1.0.0[src]
P: FnMut(&Self::Item) -> bool,
pub fn map_while<B, P>(self, predicate: P) -> MapWhile<Self, P> where
P: FnMut(Self::Item) -> Option<B>, [src]
P: FnMut(Self::Item) -> Option<B>,
pub fn skip(self, n: usize) -> Skip<Self>1.0.0[src]
pub fn take(self, n: usize) -> Take<Self>1.0.0[src]
pub fn scan<St, B, F>(self, initial_state: St, f: F) -> Scan<Self, St, F> where
F: FnMut(&mut St, Self::Item) -> Option<B>, 1.0.0[src]
F: FnMut(&mut St, Self::Item) -> Option<B>,
pub fn flat_map<U, F>(self, f: F) -> FlatMap<Self, U, F> where
F: FnMut(Self::Item) -> U,
U: IntoIterator, 1.0.0[src]
F: FnMut(Self::Item) -> U,
U: IntoIterator,
pub fn flatten(self) -> Flatten<Self> where
Self::Item: IntoIterator, 1.29.0[src]
Self::Item: IntoIterator,
pub fn fuse(self) -> Fuse<Self>1.0.0[src]
pub fn inspect<F>(self, f: F) -> Inspect<Self, F> where
F: FnMut(&Self::Item), 1.0.0[src]
F: FnMut(&Self::Item),
pub fn by_ref(&mut self) -> &mut Self1.0.0[src]
#[must_use = "if you really need to exhaust the iterator, consider `.for_each(drop)` instead"]pub fn collect<B>(self) -> B where
B: FromIterator<Self::Item>, 1.0.0[src]
#[must_use = "if you really need to exhaust the iterator, consider `.for_each(drop)` instead"]
pub fn collect<B>(self) -> B whereB: FromIterator<Self::Item>,
pub fn partition<B, F>(self, f: F) -> (B, B) where
F: FnMut(&Self::Item) -> bool,
B: Default + Extend<Self::Item>, 1.0.0[src]
F: FnMut(&Self::Item) -> bool,
B: Default + Extend<Self::Item>,
pub fn partition_in_place<'a, T, P>(self, predicate: P) -> usize where
Self: DoubleEndedIterator<Item = &'a mut T>,
T: 'a,
P: FnMut(&T) -> bool, [src]
Self: DoubleEndedIterator<Item = &'a mut T>,
T: 'a,
P: FnMut(&T) -> bool,
pub fn is_partitioned<P>(self, predicate: P) -> bool where
P: FnMut(Self::Item) -> bool, [src]
P: FnMut(Self::Item) -> bool,
pub fn try_fold<B, F, R>(&mut self, init: B, f: F) -> R where
F: FnMut(B, Self::Item) -> R,
R: Try<Ok = B>, 1.27.0[src]
F: FnMut(B, Self::Item) -> R,
R: Try<Ok = B>,
pub fn try_for_each<F, R>(&mut self, f: F) -> R where
F: FnMut(Self::Item) -> R,
R: Try<Ok = ()>, 1.27.0[src]
F: FnMut(Self::Item) -> R,
R: Try<Ok = ()>,
pub fn fold<B, F>(self, init: B, f: F) -> B where
F: FnMut(B, Self::Item) -> B, 1.0.0[src]
F: FnMut(B, Self::Item) -> B,
pub fn reduce<F>(self, f: F) -> Option<Self::Item> where
F: FnMut(Self::Item, Self::Item) -> Self::Item, 1.51.0[src]
F: FnMut(Self::Item, Self::Item) -> Self::Item,
pub fn all<F>(&mut self, f: F) -> bool where
F: FnMut(Self::Item) -> bool, 1.0.0[src]
F: FnMut(Self::Item) -> bool,
pub fn any<F>(&mut self, f: F) -> bool where
F: FnMut(Self::Item) -> bool, 1.0.0[src]
F: FnMut(Self::Item) -> bool,
pub fn find<P>(&mut self, predicate: P) -> Option<Self::Item> where
P: FnMut(&Self::Item) -> bool, 1.0.0[src]
P: FnMut(&Self::Item) -> bool,
pub fn find_map<B, F>(&mut self, f: F) -> Option<B> where
F: FnMut(Self::Item) -> Option<B>, 1.30.0[src]
F: FnMut(Self::Item) -> Option<B>,
pub fn try_find<F, R>(
&mut self,
f: F
) -> Result<Option<Self::Item>, <R as Try>::Error> where
F: FnMut(&Self::Item) -> R,
R: Try<Ok = bool>, [src]
&mut self,
f: F
) -> Result<Option<Self::Item>, <R as Try>::Error> where
F: FnMut(&Self::Item) -> R,
R: Try<Ok = bool>,
pub fn position<P>(&mut self, predicate: P) -> Option<usize> where
P: FnMut(Self::Item) -> bool, 1.0.0[src]
P: FnMut(Self::Item) -> bool,
pub fn rposition<P>(&mut self, predicate: P) -> Option<usize> where
Self: ExactSizeIterator + DoubleEndedIterator,
P: FnMut(Self::Item) -> bool, 1.0.0[src]
Self: ExactSizeIterator + DoubleEndedIterator,
P: FnMut(Self::Item) -> bool,
pub fn max(self) -> Option<Self::Item> where
Self::Item: Ord, 1.0.0[src]
Self::Item: Ord,
pub fn min(self) -> Option<Self::Item> where
Self::Item: Ord, 1.0.0[src]
Self::Item: Ord,
pub fn max_by_key<B, F>(self, f: F) -> Option<Self::Item> where
F: FnMut(&Self::Item) -> B,
B: Ord, 1.6.0[src]
F: FnMut(&Self::Item) -> B,
B: Ord,
pub fn max_by<F>(self, compare: F) -> Option<Self::Item> where
F: FnMut(&Self::Item, &Self::Item) -> Ordering, 1.15.0[src]
F: FnMut(&Self::Item, &Self::Item) -> Ordering,
pub fn min_by_key<B, F>(self, f: F) -> Option<Self::Item> where
F: FnMut(&Self::Item) -> B,
B: Ord, 1.6.0[src]
F: FnMut(&Self::Item) -> B,
B: Ord,
pub fn min_by<F>(self, compare: F) -> Option<Self::Item> where
F: FnMut(&Self::Item, &Self::Item) -> Ordering, 1.15.0[src]
F: FnMut(&Self::Item, &Self::Item) -> Ordering,
pub fn rev(self) -> Rev<Self> where
Self: DoubleEndedIterator, 1.0.0[src]
Self: DoubleEndedIterator,
pub fn unzip<A, B, FromA, FromB>(self) -> (FromA, FromB) where
Self: Iterator<Item = (A, B)>,
FromA: Default + Extend<A>,
FromB: Default + Extend<B>, 1.0.0[src]
Self: Iterator<Item = (A, B)>,
FromA: Default + Extend<A>,
FromB: Default + Extend<B>,
pub fn copied<'a, T>(self) -> Copied<Self> where
Self: Iterator<Item = &'a T>,
T: 'a + Copy, 1.36.0[src]
Self: Iterator<Item = &'a T>,
T: 'a + Copy,
pub fn cloned<'a, T>(self) -> Cloned<Self> where
Self: Iterator<Item = &'a T>,
T: 'a + Clone, 1.0.0[src]
Self: Iterator<Item = &'a T>,
T: 'a + Clone,
pub fn cycle(self) -> Cycle<Self> where
Self: Clone, 1.0.0[src]
Self: Clone,
pub fn sum<S>(self) -> S where
S: Sum<Self::Item>, 1.11.0[src]
S: Sum<Self::Item>,
pub fn product<P>(self) -> P where
P: Product<Self::Item>, 1.11.0[src]
P: Product<Self::Item>,
pub fn cmp<I>(self, other: I) -> Ordering where
I: IntoIterator<Item = Self::Item>,
Self::Item: Ord, 1.5.0[src]
I: IntoIterator<Item = Self::Item>,
Self::Item: Ord,
pub fn cmp_by<I, F>(self, other: I, cmp: F) -> Ordering where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,
I: IntoIterator, [src]
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,
I: IntoIterator,
pub fn partial_cmp<I>(self, other: I) -> Option<Ordering> where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>, 1.5.0[src]
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
pub fn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering> where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,
I: IntoIterator, [src]
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,
I: IntoIterator,
pub fn eq<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>, 1.5.0[src]
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>,
pub fn eq_by<I, F>(self, other: I, eq: F) -> bool where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> bool,
I: IntoIterator, [src]
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> bool,
I: IntoIterator,
pub fn ne<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>, 1.5.0[src]
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>,
pub fn lt<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>, 1.5.0[src]
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
pub fn le<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>, 1.5.0[src]
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
pub fn gt<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>, 1.5.0[src]
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
pub fn ge<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>, 1.5.0[src]
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
pub fn is_sorted(self) -> bool where
Self::Item: PartialOrd<Self::Item>, [src]
Self::Item: PartialOrd<Self::Item>,
pub fn is_sorted_by<F>(self, compare: F) -> bool where
F: FnMut(&Self::Item, &Self::Item) -> Option<Ordering>, [src]
F: FnMut(&Self::Item, &Self::Item) -> Option<Ordering>,
pub fn is_sorted_by_key<F, K>(self, f: F) -> bool where
F: FnMut(Self::Item) -> K,
K: PartialOrd<K>, [src]
F: FnMut(Self::Item) -> K,
K: PartialOrd<K>,
Auto Trait Implementations
impl<'a> !RefUnwindSafe for PropertiesIter<'a>
impl<'a> !Send for PropertiesIter<'a>
impl<'a> !Sync for PropertiesIter<'a>
impl<'a> Unpin for PropertiesIter<'a>
impl<'a> !UnwindSafe for PropertiesIter<'a>
Blanket Implementations
Struct chemfiles::Residue [−][src]
pub struct Residue { /* fields omitted */ }A Residue is a group of atoms belonging to the same logical unit. They
+can be small molecules, amino-acids in a protein, monomers in polymers,
+etc.
Implementations
impl Residue[src]
impl Residue[src]pub fn new<'a>(name: impl Into<&'a str>) -> Residue[src]
Create a new residue with the given name
Example
++let residue = Residue::new("ALA"); +assert_eq!(residue.name(), "ALA"); +assert_eq!(residue.id(), None);
pub fn with_id<'a>(name: impl Into<&'a str>, id: i64) -> Residue[src]
Create a new residue with the given name and id as identifier.
Example
++let residue = Residue::with_id("ALA", 67); +assert_eq!(residue.name(), "ALA"); +assert_eq!(residue.id(), Some(67));
pub fn size(&self) -> usize[src]
Get the number of atoms in this residue.
+Example
++let mut residue = Residue::new("water"); +assert_eq!(residue.size(), 0); + +residue.add_atom(0); +residue.add_atom(1); +residue.add_atom(2); +assert_eq!(residue.size(), 3);
pub fn id(&self) -> Option<i64>[src]
Get the identifier of this residue in the initial topology file.
+Example
++let residue = Residue::with_id("", 42); +assert_eq!(residue.id(), Some(42));
pub fn name(&self) -> String[src]
Get the name of this residue.
+Example
++let residue = Residue::new("water"); +assert_eq!(residue.name(), "water");
pub fn add_atom(&mut self, atom: usize)[src]
Add the atom at index atom in this residue.
This will fail if the atom is already in the residue.
+Example
++let mut residue = Residue::new("water"); +assert_eq!(residue.size(), 0); +assert_eq!(residue.contains(56), false); + +residue.add_atom(56); +assert_eq!(residue.size(), 1); +assert_eq!(residue.contains(56), true); + +// Adding the same atom twice is fine +residue.add_atom(56); +assert_eq!(residue.size(), 1);
pub fn contains(&self, atom: usize) -> bool[src]
Check if the atom at index i is in this residue
Example
++let mut residue = Residue::new("water"); +assert_eq!(residue.contains(56), false); + +residue.add_atom(56); +assert_eq!(residue.contains(56), true);
pub fn atoms(&self) -> Vec<usize>[src]
Get the list of atoms of this residue.
+Example
++let mut residue = Residue::new("water"); +assert_eq!(residue.atoms(), vec![]); + +residue.add_atom(56); +assert_eq!(residue.atoms(), vec![56]);
pub fn set(&mut self, name: &str, property: impl Into<Property>)[src]
Add a new property with the given name to this residue.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
++let mut residue = Residue::new("ALA"); +residue.set("a string", "hello"); +residue.set("a double", 3.2); + +assert_eq!(residue.get("a string"), Some(Property::String("hello".into()))); +assert_eq!(residue.get("a double"), Some(Property::Double(3.2)));
pub fn get(&self, name: &str) -> Option<Property>[src]
Get a property with the given name in this frame, if it exist.
Examples
++let mut residue = Residue::new("ALA"); +residue.set("foo", Property::Double(22.2)); + +assert_eq!(residue.get("foo"), Some(Property::Double(22.2))); +assert_eq!(residue.get("Bar"), None);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);[src]
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this frame
+Examples
++let mut residue = Residue::new("ALA"); +residue.set("foo", Property::Double(22.2)); +residue.set("bar", Property::Bool(false)); + +for (name, property) in residue.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(22.2)); + } else if name == "bar" { + assert_eq!(property, Property::Bool(false)); + } +}
Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Residue
impl !Send for Residue
impl !Sync for Residue
impl Unpin for Residue
impl UnwindSafe for Residue
Blanket Implementations
Struct chemfiles::ResidueRef [−][src]
pub struct ResidueRef<'a> { /* fields omitted */ }An analog to a reference to a residue (&Residue)
Methods from Deref<Target = Residue>
pub fn size(&self) -> usize[src]
Get the number of atoms in this residue.
+Example
++let mut residue = Residue::new("water"); +assert_eq!(residue.size(), 0); + +residue.add_atom(0); +residue.add_atom(1); +residue.add_atom(2); +assert_eq!(residue.size(), 3);
pub fn id(&self) -> Option<i64>[src]
Get the identifier of this residue in the initial topology file.
+Example
++let residue = Residue::with_id("", 42); +assert_eq!(residue.id(), Some(42));
pub fn name(&self) -> String[src]
Get the name of this residue.
+Example
++let residue = Residue::new("water"); +assert_eq!(residue.name(), "water");
pub fn contains(&self, atom: usize) -> bool[src]
Check if the atom at index i is in this residue
Example
++let mut residue = Residue::new("water"); +assert_eq!(residue.contains(56), false); + +residue.add_atom(56); +assert_eq!(residue.contains(56), true);
pub fn atoms(&self) -> Vec<usize>[src]
Get the list of atoms of this residue.
+Example
++let mut residue = Residue::new("water"); +assert_eq!(residue.atoms(), vec![]); + +residue.add_atom(56); +assert_eq!(residue.atoms(), vec![56]);
pub fn get(&self, name: &str) -> Option<Property>[src]
Get a property with the given name in this frame, if it exist.
Examples
++let mut residue = Residue::new("ALA"); +residue.set("foo", Property::Double(22.2)); + +assert_eq!(residue.get("foo"), Some(Property::Double(22.2))); +assert_eq!(residue.get("Bar"), None);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);[src]
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this frame
+Examples
++let mut residue = Residue::new("ALA"); +residue.set("foo", Property::Double(22.2)); +residue.set("bar", Property::Bool(false)); + +for (name, property) in residue.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(22.2)); + } else if name == "bar" { + assert_eq!(property, Property::Bool(false)); + } +}
Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for ResidueRef<'a>
impl<'a> !Send for ResidueRef<'a>
impl<'a> !Sync for ResidueRef<'a>
impl<'a> Unpin for ResidueRef<'a>
impl<'a> UnwindSafe for ResidueRef<'a>
Blanket Implementations
Struct chemfiles::Selection [−][src]
pub struct Selection { /* fields omitted */ }A Selection allow to select atoms in a Frame, from a selection
+language. The selection language is built by combining basic operations.
+Each basic operation follows the <selector>[(<variable>)] <operator> <value> structure, where <operator> is a comparison operator in
+== != < <= > >=.
Implementations
impl Selection[src]
impl Selection[src]pub fn new<'a, S: Into<&'a str>>(selection: S) -> Result<Selection, Error>[src]
Create a new selection from the given selection string.
+Errors
+This function fails if the selection string is invalid.
+Example
++let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
pub fn size(&self) -> usize[src]
Get the size of the selection, i.e. the number of atoms we are selecting +together.
+This value is 1 for the ‘atom’ context, 2 for the ‘pair’ and ‘bond’ +context, 3 for the ‘three’ and ‘angles’ context and 4 for the ‘four’ +and ‘dihedral’ context.
+Example
++let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap(); +assert_eq!(selection.size(), 2);
pub fn string(&self) -> String[src]
Get the selection string used to create this selection.
+Example
++let selection = Selection::new("name H").unwrap(); +assert_eq!(selection.string(), "name H");
pub fn evaluate(&mut self, frame: &Frame) -> Vec<Match>[src]
Evaluate a selection for a given frame, and return the corresponding +matches.
+Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None); + +let mut selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap(); +let matches = selection.evaluate(&frame); + +assert_eq!(matches.len(), 2); + +assert_eq!(matches[0].len(), 2); +assert_eq!(matches[0][0], 0); +assert_eq!(matches[0][1], 1); + +assert_eq!(matches[1].len(), 2); +assert_eq!(matches[1][0], 2); +assert_eq!(matches[1][1], 1);
pub fn list(&mut self, frame: &Frame) -> Vec<usize>[src]
Evaluates a selection of size 1 on a given frame. This function
+returns the list of atomic indexes in the frame matching this selection.
Panics
+If the selection size is not 1
+Example
++let mut frame = Frame::new(); +frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None); + +let mut selection = Selection::new("name H").unwrap(); +let matches = selection.list(&frame); + +assert_eq!(matches.len(), 2); +assert_eq!(matches[0], 0); +assert_eq!(matches[1], 2);
Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Selection
impl !Send for Selection
impl !Sync for Selection
impl Unpin for Selection
impl UnwindSafe for Selection
Blanket Implementations
Struct chemfiles::Topology [−][src]
pub struct Topology { /* fields omitted */ }A Topology contains the definition of all the atoms in the system, and
+the liaisons between the atoms (bonds, angles, dihedrals, …). It will
+also contain all the residues information if it is available.
Implementations
impl Topology[src]
impl Topology[src]pub fn new() -> Topology[src]
Create a new empty topology.
+Example
++let topology = Topology::new(); +assert_eq!(topology.size(), 0);
pub fn atom(&self, index: usize) -> AtomRef<'_>[src]
Get a reference of the atom at the given index in this topology.
Panics
+If index is out of bounds.
Example
++let mut topology = Topology::new(); +topology.resize(6); + +let atom = topology.atom(4); +assert_eq!(atom.name(), "");
pub fn atom_mut(&mut self, index: usize) -> AtomMut<'_>[src]
Get a mutable reference to the atom at the given index in this topology.
Panics
+If index is out of bounds.
Example
++let mut topology = Topology::new(); +topology.resize(6); + +assert_eq!(topology.atom(4).name(), ""); + +topology.atom_mut(4).set_name("Fe"); +assert_eq!(topology.atom(4).name(), "Fe");
pub fn size(&self) -> usize[src]
Get the current number of atoms in this topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.size(), 0); + +topology.resize(6); +assert_eq!(topology.size(), 6);
pub fn resize(&mut self, natoms: usize)[src]
Resize this topology to hold natoms atoms, inserting dummy atoms if
+the new size if bigger than the old one.
Example
++let mut topology = Topology::new(); +assert_eq!(topology.size(), 0); + +topology.resize(6); +assert_eq!(topology.size(), 6);
pub fn add_atom(&mut self, atom: &Atom)[src]
Add an Atom at the end of this topology
Example
++let mut topology = Topology::new(); +topology.add_atom(&Atom::new("Mg")); + +let atom = topology.atom(0); +assert_eq!(atom.name(), "Mg");
pub fn remove(&mut self, index: usize)[src]
Remove an Atom from this topology by index. This modify all the
+other atoms indexes.
Panics
+If the index is out of bounds
Example
++let mut topology = Topology::new(); +topology.resize(9); +assert_eq!(topology.size(), 9); + +topology.remove(7); +assert_eq!(topology.size(), 8);
pub fn bonds_count(&self) -> usize[src]
Get the number of bonds in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.bonds_count(), 3);
pub fn angles_count(&self) -> usize[src]
Get the number of angles in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.angles_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.angles_count(), 2);
pub fn dihedrals_count(&self) -> usize[src]
Get the number of dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.dihedrals_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.dihedrals_count(), 1);
pub fn impropers_count(&self) -> usize[src]
Get the number of improper dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.dihedrals_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(0, 2); +topology.add_bond(0, 3); +assert_eq!(topology.impropers_count(), 1);
pub fn bonds(&self) -> Vec<[usize; 2]>[src]
Get the list of bonds in the topology.
+Example
++let mut topology = Topology::new(); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);
pub fn angles(&self) -> Vec<[usize; 3]>[src]
Get the list of angles in the topology.
+Example
++let mut topology = Topology::new(); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);
pub fn dihedrals(&self) -> Vec<[usize; 4]>[src]
Get the list of dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); + +assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);
pub fn impropers(&self) -> Vec<[usize; 4]>[src]
Get the list of improper dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(0, 2); +topology.add_bond(0, 3); + +assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);
pub fn clear_bonds(&mut self)[src]
Remove all existing bonds, angles, dihedral angles and improper +dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(4); +topology.add_bond(0, 1); +topology.add_bond(0, 2); +assert_eq!(topology.bonds_count(), 2); +assert_eq!(topology.angles().len(), 1); + +topology.clear_bonds(); +assert!(topology.bonds().is_empty()); +assert!(topology.angles().is_empty());
pub fn add_bond(&mut self, i: usize, j: usize)[src]
Add a bond between the atoms at indexes i and j in the topology.
The bond order is set to BondOrder::Unknown.
Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(0, 2); +assert_eq!(topology.bonds_count(), 2); + +assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);
pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder)[src]
Add a bond between the atoms at indexes i and j in the topology
+with the given bond order.
Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(2); + +topology.add_bond_with_order(0, 1, BondOrder::Double); +assert_eq!(topology.bond_order(0, 1), BondOrder::Double);
pub fn bond_order(&self, i: usize, j: usize) -> BondOrder[src]
Get the bond order for the bond between the atoms at indexes i and
+j.
Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(2); + +topology.add_bond_with_order(0, 1, BondOrder::Double); +assert_eq!(topology.bond_order(0, 1), BondOrder::Double);
pub fn bond_orders(&self) -> Vec<BondOrder>[src]
Get the bond order for all the bonds in the topology
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(3); + +topology.add_bond_with_order(0, 1, BondOrder::Double); +topology.add_bond_with_order(0, 2, BondOrder::Single); + +assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);
pub fn remove_bond(&mut self, i: usize, j: usize)[src]
Remove any existing bond between the atoms at indexes i and j in
+this topology.
This function does nothing if there is no bond between i and j.
Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(1, 2); +assert_eq!(topology.bonds_count(), 2); + +topology.remove_bond(0, 1); +assert_eq!(topology.bonds_count(), 1); + +// Removing a bond that does not exists is fine +topology.remove_bond(0, 2); +assert_eq!(topology.bonds_count(), 1);
pub fn residue(&self, index: u64) -> Option<ResidueRef<'_>>[src]
Get a reference to the residue at index index from this topology.
The residue index in the topology is not always the same as the residue
+id.
Example
++let mut topology = Topology::new(); +topology.add_residue(&Residue::new("water")).unwrap(); + +let residue = topology.residue(0).unwrap(); +assert_eq!(residue.name(), "water");
pub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef<'_>>[src]
Get a copy of the residue containing the atom at index index in this
+topology, if any.
Example
++let mut topology = Topology::new(); +topology.resize(8); + +let mut residue = Residue::new("water"); +residue.add_atom(0); +residue.add_atom(1); +residue.add_atom(2); +topology.add_residue(&residue).unwrap(); + +let residue = topology.residue_for_atom(0).unwrap(); +assert_eq!(residue.name(), "water"); + +assert!(topology.residue_for_atom(6).is_none());
pub fn residues_count(&self) -> u64[src]
Get the number of residues in this topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.residues_count(), 0); + +topology.add_residue(&Residue::with_id("water", 0)).unwrap(); +topology.add_residue(&Residue::with_id("protein", 1)).unwrap(); +assert_eq!(topology.residues_count(), 2);
pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error>[src]
Add a residue to this topology.
+Errors
+This function fails is the residue id is not already in the topology,
+or if the residue contains atoms that are already in another residue.
Example
++let mut topology = Topology::new(); +topology.add_residue(&Residue::new("water")).unwrap(); + +let residue = topology.residue(0).unwrap(); +assert_eq!(residue.name(), "water");
pub fn are_linked(&self, first: &Residue, second: &Residue) -> bool[src]
Check if the two residues first and second from the topology are
+linked together, i.e. if there is a bond between one atom in the
+first residue and one atom in the second one.
Example
++let mut topology = Topology::new(); + +topology.add_residue(&Residue::with_id("water", 0)).unwrap(); +topology.add_residue(&Residue::with_id("protein", 1)).unwrap(); + +let first = topology.residue(0).unwrap(); +let second = topology.residue(1).unwrap(); +assert_eq!(topology.are_linked(&first, &second), false);
Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Topology
impl !Send for Topology
impl !Sync for Topology
impl Unpin for Topology
impl UnwindSafe for Topology
Blanket Implementations
Struct chemfiles::TopologyRef [−][src]
pub struct TopologyRef<'a> { /* fields omitted */ }An analog to a reference to a topology (&Topology)
Methods from Deref<Target = Topology>
pub fn atom(&self, index: usize) -> AtomRef<'_>[src]
Get a reference of the atom at the given index in this topology.
Panics
+If index is out of bounds.
Example
++let mut topology = Topology::new(); +topology.resize(6); + +let atom = topology.atom(4); +assert_eq!(atom.name(), "");
pub fn size(&self) -> usize[src]
Get the current number of atoms in this topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.size(), 0); + +topology.resize(6); +assert_eq!(topology.size(), 6);
pub fn bonds_count(&self) -> usize[src]
Get the number of bonds in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.bonds_count(), 3);
pub fn angles_count(&self) -> usize[src]
Get the number of angles in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.angles_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.angles_count(), 2);
pub fn dihedrals_count(&self) -> usize[src]
Get the number of dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.dihedrals_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.dihedrals_count(), 1);
pub fn impropers_count(&self) -> usize[src]
Get the number of improper dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.dihedrals_count(), 0); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(0, 2); +topology.add_bond(0, 3); +assert_eq!(topology.impropers_count(), 1);
pub fn bonds(&self) -> Vec<[usize; 2]>[src]
Get the list of bonds in the topology.
+Example
++let mut topology = Topology::new(); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);
pub fn angles(&self) -> Vec<[usize; 3]>[src]
Get the list of angles in the topology.
+Example
++let mut topology = Topology::new(); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); +assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);
pub fn dihedrals(&self) -> Vec<[usize; 4]>[src]
Get the list of dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(2, 1); +topology.add_bond(2, 3); + +assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);
pub fn impropers(&self) -> Vec<[usize; 4]>[src]
Get the list of improper dihedral angles in the topology.
+Example
++let mut topology = Topology::new(); +topology.resize(4); + +topology.add_bond(0, 1); +topology.add_bond(0, 2); +topology.add_bond(0, 3); + +assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);
pub fn bond_order(&self, i: usize, j: usize) -> BondOrder[src]
Get the bond order for the bond between the atoms at indexes i and
+j.
Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(2); + +topology.add_bond_with_order(0, 1, BondOrder::Double); +assert_eq!(topology.bond_order(0, 1), BondOrder::Double);
pub fn bond_orders(&self) -> Vec<BondOrder>[src]
Get the bond order for all the bonds in the topology
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.bonds_count(), 0); +topology.resize(3); + +topology.add_bond_with_order(0, 1, BondOrder::Double); +topology.add_bond_with_order(0, 2, BondOrder::Single); + +assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);
pub fn residue(&self, index: u64) -> Option<ResidueRef<'_>>[src]
Get a reference to the residue at index index from this topology.
The residue index in the topology is not always the same as the residue
+id.
Example
++let mut topology = Topology::new(); +topology.add_residue(&Residue::new("water")).unwrap(); + +let residue = topology.residue(0).unwrap(); +assert_eq!(residue.name(), "water");
pub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef<'_>>[src]
Get a copy of the residue containing the atom at index index in this
+topology, if any.
Example
++let mut topology = Topology::new(); +topology.resize(8); + +let mut residue = Residue::new("water"); +residue.add_atom(0); +residue.add_atom(1); +residue.add_atom(2); +topology.add_residue(&residue).unwrap(); + +let residue = topology.residue_for_atom(0).unwrap(); +assert_eq!(residue.name(), "water"); + +assert!(topology.residue_for_atom(6).is_none());
pub fn residues_count(&self) -> u64[src]
Get the number of residues in this topology.
+Example
++let mut topology = Topology::new(); +assert_eq!(topology.residues_count(), 0); + +topology.add_residue(&Residue::with_id("water", 0)).unwrap(); +topology.add_residue(&Residue::with_id("protein", 1)).unwrap(); +assert_eq!(topology.residues_count(), 2);
pub fn are_linked(&self, first: &Residue, second: &Residue) -> bool[src]
Check if the two residues first and second from the topology are
+linked together, i.e. if there is a bond between one atom in the
+first residue and one atom in the second one.
Example
++let mut topology = Topology::new(); + +topology.add_residue(&Residue::with_id("water", 0)).unwrap(); +topology.add_residue(&Residue::with_id("protein", 1)).unwrap(); + +let first = topology.residue(0).unwrap(); +let second = topology.residue(1).unwrap(); +assert_eq!(topology.are_linked(&first, &second), false);
Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for TopologyRef<'a>
impl<'a> !Send for TopologyRef<'a>
impl<'a> !Sync for TopologyRef<'a>
impl<'a> Unpin for TopologyRef<'a>
impl<'a> UnwindSafe for TopologyRef<'a>
Blanket Implementations
Struct chemfiles::Trajectory [−][src]
pub struct Trajectory { /* fields omitted */ }The Trajectory type is the main entry point when using chemfiles. A
+Trajectory behave a bit like a file, allowing to read and/or write
+Frame.
Implementations
impl Trajectory[src]
impl Trajectory[src]pub fn open<P>(path: P, mode: char) -> Result<Trajectory, Error> where
P: AsRef<Path>, [src]
P: AsRef<Path>,
Open the file at the given path in the given mode.
Valid modes are 'r' for read, 'w' for write and 'a' for append.
Errors
+This function fails if the file is not accessible for the given mode, if +it is incorrectly formatted for the corresponding format, or in case of +I/O errors from the OS.
+Example
++let trajectory = Trajectory::open("water.xyz", 'r').unwrap();
pub fn open_with_format<'a, P, S>(
filename: P,
mode: char,
format: S
) -> Result<Trajectory, Error> where
P: AsRef<Path>,
S: Into<&'a str>, [src]
filename: P,
mode: char,
format: S
) -> Result<Trajectory, Error> where
P: AsRef<Path>,
S: Into<&'a str>,
Open the file at the given path using a specific file format and the
+given mode.
Valid modes are 'r' for read, 'w' for write and 'a' for append.
Specifying a format is needed when the file format does not match the
+extension, or when there is not standard extension for this format. If
+format is an empty string, the format will be guessed from the
+extension.
Errors
+This function fails if the file is not accessible for the given mode, if +it is incorrectly formatted for the corresponding format, or in case of +I/O errors from the OS.
+Example
++let trajectory = Trajectory::open_with_format("water.zeo", 'r', "XYZ").unwrap();
pub fn memory_reader<'a, S>(data: S, format: S) -> Result<Trajectory, Error> where
S: Into<&'a str>, [src]
S: Into<&'a str>,
Read a memory buffer as though it was a formatted file.
+The memory buffer used to store the file is given using the data
+argument. The format parameter is required and should follow the same
+rules as in the main Trajectory constructor.
Errors
+This function fails if the data is incorrectly formatted for the +corresponding format, or if the format do not support in-memory readers.
+Example
++let aromatics = "c1ccccc1\nc1ccco1\nc1ccccn1\n"; +let mut trajectory = Trajectory::memory_reader(aromatics, "SMI").unwrap(); +let mut frame = Frame::new(); +trajectory.read(&mut frame).unwrap(); +assert_eq!(frame.size(), 6);
pub fn memory_writer<'a, S>(format: S) -> Result<Trajectory, Error> where
S: Into<&'a str>, [src]
S: Into<&'a str>,
Write to a memory buffer as though it was a formatted file.
+The format parameter should follow the same rules as in the main
+Trajectory constructor, except that compression specification
+is not supported.
The memory_buffer function can be used to retrieve the data written
+to memory of the Trajectory.
Errors
+This function fails if the format do not support in-memory writers.
+Example
++let trajectory_memory = Trajectory::memory_writer("SMI"); + +// Binary formats typically do not support this feature +assert!(Trajectory::memory_writer("XTC").is_err());
pub fn read(&mut self, frame: &mut Frame) -> Result<(), Error>[src]
Read the next step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of atom +in the next step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format, or in case of I/O errors from the OS.
+Example
++let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); +let mut frame = Frame::new(); + +trajectory.read(&mut frame).unwrap();
pub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error>[src]
Read a specific step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of +atom at this step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format.
+Example
++let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); +let mut frame = Frame::new(); + +trajectory.read_step(10, &mut frame).unwrap();
pub fn write(&mut self, frame: &Frame) -> Result<(), Error>[src]
Write a frame to this trajectory.
Errors
+This function fails if the data is incorrectly formatted for the +corresponding format.
+Example
++let mut trajectory = Trajectory::open("water.pdb", 'w').unwrap(); +let mut frame = Frame::new(); + +trajectory.write(&mut frame).unwrap();
pub fn set_topology(&mut self, topology: &Topology)[src]
Set the topology associated with this trajectory. This topology will
+be used when reading and writing the files, replacing any topology in
+the frames or files.
Example
++let mut topology = Topology::new(); +topology.add_atom(&Atom::new("H")); +topology.add_atom(&Atom::new("O")); +topology.add_atom(&Atom::new("H")); +topology.add_bond(0, 1); +topology.add_bond(1, 2); + +let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); +trajectory.set_topology(&topology);
pub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error> where
P: AsRef<Path>, [src]
P: AsRef<Path>,
Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in format;
+and extracting the topology of this frame.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
++let mut trajectory = Trajectory::open("water.nc", 'r').unwrap(); +trajectory.set_topology_file("topology.pdb").unwrap();
pub fn set_topology_with_format<'a, P, S>(
&mut self,
path: P,
format: S
) -> Result<(), Error> where
P: AsRef<Path>,
S: Into<&'a str>, [src]
&mut self,
path: P,
format: S
) -> Result<(), Error> where
P: AsRef<Path>,
S: Into<&'a str>,
Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in
+format; and extracting the topology of this frame.
If format is an empty string, the format will be guessed from the
+path extension.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
++let mut trajectory = Trajectory::open("water.nc", 'r').unwrap(); +trajectory.set_topology_with_format("topology.mol", "PDB").unwrap();
pub fn set_cell(&mut self, cell: &UnitCell)[src]
Set the unit cell associated with a trajectory. This cell will be
+used when reading and writing the files, replacing any unit cell in the
+frames or files.
Example
++let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); +trajectory.set_cell(&UnitCell::new([10.0, 11.0, 12.5]));
pub fn nsteps(&mut self) -> usize[src]
Get the number of steps (the number of frames) in a trajectory.
+Example
++let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + +println!("This trajectory contains {} steps", trajectory.nsteps());
pub fn memory_buffer(&self) -> Result<&str, Error>[src]
Obtain the memory buffer written to by the trajectory.
+Errors
+This fails if the trajectory was not opened with
+Trajectory::memory_writer.
Example
++let mut trajectory_memory = Trajectory::memory_writer("SMI").unwrap(); + +let mut frame = Frame::new(); +frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None); +frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None); +frame.add_bond_with_order(0, 1, BondOrder::Single); + +trajectory_memory.write(&frame).unwrap(); + +let result = trajectory_memory.memory_buffer(); +assert_eq!(result.unwrap(), "CC\n");
pub fn path(&self) -> String[src]
Get file path for this trajectory.
+Example
++let trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + +assert_eq!(trajectory.path(), "water.xyz");
Trait Implementations
impl Drop for Trajectory[src]
impl Drop for Trajectory[src]Auto Trait Implementations
impl RefUnwindSafe for Trajectory
impl !Send for Trajectory
impl !Sync for Trajectory
impl Unpin for Trajectory
impl UnwindSafe for Trajectory
Blanket Implementations
Struct chemfiles::UnitCell [−][src]
pub struct UnitCell { /* fields omitted */ }An UnitCell represent the box containing the atoms, and its periodicity.
An unit cell is fully represented by three lengths (a, b, c); and three +angles (alpha, beta, gamma). The angles are stored in degrees, and the +lengths in Angstroms.
+A cell also has a matricial representation, by projecting the three base +vector into an orthonormal base. We choose to represent such matrix as an +upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |
+Implementations
impl UnitCell[src]
impl UnitCell[src]pub fn new(lengths: [f64; 3]) -> UnitCell[src]
Create an Orthorhombic UnitCell from the three lengths, in Angstroms.
Example
++let cell = UnitCell::new([30.0, 30.0, 23.0]); + +assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]); +assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); +assert_eq!(cell.shape(), CellShape::Orthorhombic);
pub fn infinite() -> UnitCell[src]
Create an Infinite UnitCell.
Example
++let cell = UnitCell::infinite(); + +assert_eq!(cell.lengths(), [0.0, 0.0, 0.0]); +assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); +assert_eq!(cell.shape(), CellShape::Infinite);
pub fn triclinic(lengths: [f64; 3], angles: [f64; 3]) -> UnitCell[src]
Create an Triclinic UnitCell from the three lengths (in Angstroms)
+and three angles (in degree). alpha is the angle between the vectors
+b and c; beta is the between the vectors a and c and gamma
+is the angle between the vectors a and b.
Example
++let cell = UnitCell::triclinic([10.0, 10.0, 10.0], [98.0, 99.0, 90.0]); + +assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]); +assert_eq!(cell.angles()[0], 98.0); +// Rounding errors might occur due to internal representation +assert!((cell.angles()[1] - 99.0).abs() < 1e-12); +assert_eq!(cell.angles()[2], 90.0); +assert_eq!(cell.shape(), CellShape::Triclinic);
pub fn from_matrix(matrix: [[f64; 3]; 3]) -> UnitCell[src]
Create an UnitCell from a cell matrix. If matrix contains only
+zeros, then an Infinite cell is created. If only the diagonal of the
+matrix is non-zero, then the cell is Orthorhombic. Else a
+Triclinic cell is created. The matrix entries should be in Angstroms.
Panics
+If the matrix has a negative determinant, or more generally is not +representing a unit cell.
+Example
++let cell = UnitCell::from_matrix([ + [1.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0] +]); + +assert_eq!(cell.lengths(), [1.0, 2.0, 3.0]); +assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); +assert_eq!(cell.shape(), CellShape::Orthorhombic);
pub fn lengths(&self) -> [f64; 3][src]
Get the three lengths of the cell, in Angstroms.
+Example
++let cell = UnitCell::new([30.0, 30.0, 23.0]); +assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
pub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error>[src]
Set the three lengths of the cell, in Angstroms.
+Errors
+This function fails if the unit cell is infinite, or if one of the +lengths is negative.
+Example
++let mut cell = UnitCell::new([30.0, 30.0, 23.0]); + +cell.set_lengths([10.0, 30.0, 42.0]).unwrap(); +assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]); + +assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());
pub fn angles(&self) -> [f64; 3][src]
Get the three angles of the cell, in degrees.
+Example
++let cell = UnitCell::new([20.0, 20.0, 20.0]); +assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); + +let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]); +assert_eq!(cell.angles()[0], 100.0); +// Rounding errors might occur due to internal representation +assert!((cell.angles()[1] - 120.0).abs() < 1e-12); +assert_eq!(cell.angles()[2], 90.0);
pub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error>[src]
Set the three angles of the cell, in degrees.
+Errors
+This function fails if the unit cell is not Triclinic.
Example
++let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]); +assert_eq!(cell.angles()[0], 100.0); +// Rounding errors might occur due to internal representation +assert!((cell.angles()[1] - 120.0).abs() < 1e-12); +assert_eq!(cell.angles()[2], 90.0); + +cell.set_angles([90.0, 90.0, 90.0]).unwrap(); +assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
pub fn matrix(&self) -> [[f64; 3]; 3][src]
Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); + +let matrix = cell.matrix(); + +assert_eq!(matrix[0][0], 10.0); +assert_eq!(matrix[1][1], 20.0); +assert_eq!(matrix[2][2], 30.0); + +assert!(matrix[1][2].abs() < 1e-9);
pub fn shape(&self) -> CellShape[src]
Get the shape of the unit cell.
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); +assert_eq!(cell.shape(), CellShape::Orthorhombic);
pub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error>[src]
Set the shape of the unit cell to shape.
Errors
+This can fail if the cell length or angles are incompatible with the +new shape.
+Example
++let mut cell = UnitCell::new([10.0, 20.0, 30.0]); +assert_eq!(cell.shape(), CellShape::Orthorhombic); + +cell.set_shape(CellShape::Triclinic).unwrap(); +assert_eq!(cell.shape(), CellShape::Triclinic);
pub fn volume(&self) -> f64[src]
Get the volume of the unit cell.
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); +assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0);
pub fn wrap(&self, vector: &mut [f64; 3])[src]
Wrap a vector in this unit cell.
Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); + +let mut vector = [12.0, 5.2, -45.3]; +cell.wrap(&mut vector); +assert_eq!(vector, [2.0, 5.2, 14.700000000000003]);
Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for UnitCell
impl !Send for UnitCell
impl !Sync for UnitCell
impl Unpin for UnitCell
impl UnwindSafe for UnitCell
Blanket Implementations
Struct chemfiles::UnitCellMut [−][src]
pub struct UnitCellMut<'a> { /* fields omitted */ }An analog to a mutable reference to an unit cell (&mut UnitCell)
Methods from Deref<Target = UnitCell>
pub fn lengths(&self) -> [f64; 3][src]
Get the three lengths of the cell, in Angstroms.
+Example
++let cell = UnitCell::new([30.0, 30.0, 23.0]); +assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
pub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error>[src]
Set the three lengths of the cell, in Angstroms.
+Errors
+This function fails if the unit cell is infinite, or if one of the +lengths is negative.
+Example
++let mut cell = UnitCell::new([30.0, 30.0, 23.0]); + +cell.set_lengths([10.0, 30.0, 42.0]).unwrap(); +assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]); + +assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());
pub fn angles(&self) -> [f64; 3][src]
Get the three angles of the cell, in degrees.
+Example
++let cell = UnitCell::new([20.0, 20.0, 20.0]); +assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); + +let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]); +assert_eq!(cell.angles()[0], 100.0); +// Rounding errors might occur due to internal representation +assert!((cell.angles()[1] - 120.0).abs() < 1e-12); +assert_eq!(cell.angles()[2], 90.0);
pub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error>[src]
Set the three angles of the cell, in degrees.
+Errors
+This function fails if the unit cell is not Triclinic.
Example
++let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]); +assert_eq!(cell.angles()[0], 100.0); +// Rounding errors might occur due to internal representation +assert!((cell.angles()[1] - 120.0).abs() < 1e-12); +assert_eq!(cell.angles()[2], 90.0); + +cell.set_angles([90.0, 90.0, 90.0]).unwrap(); +assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
pub fn matrix(&self) -> [[f64; 3]; 3][src]
Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); + +let matrix = cell.matrix(); + +assert_eq!(matrix[0][0], 10.0); +assert_eq!(matrix[1][1], 20.0); +assert_eq!(matrix[2][2], 30.0); + +assert!(matrix[1][2].abs() < 1e-9);
pub fn shape(&self) -> CellShape[src]
Get the shape of the unit cell.
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); +assert_eq!(cell.shape(), CellShape::Orthorhombic);
pub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error>[src]
Set the shape of the unit cell to shape.
Errors
+This can fail if the cell length or angles are incompatible with the +new shape.
+Example
++let mut cell = UnitCell::new([10.0, 20.0, 30.0]); +assert_eq!(cell.shape(), CellShape::Orthorhombic); + +cell.set_shape(CellShape::Triclinic).unwrap(); +assert_eq!(cell.shape(), CellShape::Triclinic);
pub fn volume(&self) -> f64[src]
Get the volume of the unit cell.
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); +assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0);
pub fn wrap(&self, vector: &mut [f64; 3])[src]
Wrap a vector in this unit cell.
Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); + +let mut vector = [12.0, 5.2, -45.3]; +cell.wrap(&mut vector); +assert_eq!(vector, [2.0, 5.2, 14.700000000000003]);
Trait Implementations
impl<'a> Deref for UnitCellMut<'a>[src]
impl<'a> Deref for UnitCellMut<'a>[src]Auto Trait Implementations
impl<'a> RefUnwindSafe for UnitCellMut<'a>
impl<'a> !Send for UnitCellMut<'a>
impl<'a> !Sync for UnitCellMut<'a>
impl<'a> Unpin for UnitCellMut<'a>
impl<'a> !UnwindSafe for UnitCellMut<'a>
Blanket Implementations
Struct chemfiles::UnitCellRef [−][src]
pub struct UnitCellRef<'a> { /* fields omitted */ }An analog to a reference to an unit cell (&UnitCell)
Methods from Deref<Target = UnitCell>
pub fn lengths(&self) -> [f64; 3][src]
Get the three lengths of the cell, in Angstroms.
+Example
++let cell = UnitCell::new([30.0, 30.0, 23.0]); +assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
pub fn angles(&self) -> [f64; 3][src]
Get the three angles of the cell, in degrees.
+Example
++let cell = UnitCell::new([20.0, 20.0, 20.0]); +assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); + +let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]); +assert_eq!(cell.angles()[0], 100.0); +// Rounding errors might occur due to internal representation +assert!((cell.angles()[1] - 120.0).abs() < 1e-12); +assert_eq!(cell.angles()[2], 90.0);
pub fn matrix(&self) -> [[f64; 3]; 3][src]
Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); + +let matrix = cell.matrix(); + +assert_eq!(matrix[0][0], 10.0); +assert_eq!(matrix[1][1], 20.0); +assert_eq!(matrix[2][2], 30.0); + +assert!(matrix[1][2].abs() < 1e-9);
pub fn shape(&self) -> CellShape[src]
Get the shape of the unit cell.
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); +assert_eq!(cell.shape(), CellShape::Orthorhombic);
pub fn volume(&self) -> f64[src]
Get the volume of the unit cell.
+Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); +assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0);
pub fn wrap(&self, vector: &mut [f64; 3])[src]
Wrap a vector in this unit cell.
Example
++let cell = UnitCell::new([10.0, 20.0, 30.0]); + +let mut vector = [12.0, 5.2, -45.3]; +cell.wrap(&mut vector); +assert_eq!(vector, [2.0, 5.2, 14.700000000000003]);
Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for UnitCellRef<'a>
impl<'a> !Send for UnitCellRef<'a>
impl<'a> !Sync for UnitCellRef<'a>
impl<'a> Unpin for UnitCellRef<'a>
impl<'a> UnwindSafe for UnitCellRef<'a>
Blanket Implementations
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CellShape","synthetic":false,"types":["chemfiles::cell::CellShape"]},{"text":"impl StructuralEq for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]},{"text":"impl StructuralEq for Match","synthetic":false,"types":["chemfiles::selection::Match"]},{"text":"impl StructuralEq for FormatMetadata","synthetic":false,"types":["chemfiles::misc::FormatMetadata"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.1/implementors/core/marker/trait.StructuralPartialEq.js b/0.10.1/implementors/core/marker/trait.StructuralPartialEq.js new file mode 100644 index 000000000..3a01ca7c6 --- /dev/null +++ b/0.10.1/implementors/core/marker/trait.StructuralPartialEq.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl StructuralPartialEq for Error","synthetic":false,"types":["chemfiles::errors::Error"]},{"text":"impl StructuralPartialEq for Status","synthetic":false,"types":["chemfiles::errors::Status"]},{"text":"impl StructuralPartialEq for CellShape","synthetic":false,"types":["chemfiles::cell::CellShape"]},{"text":"impl StructuralPartialEq for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]},{"text":"impl StructuralPartialEq for Match","synthetic":false,"types":["chemfiles::selection::Match"]},{"text":"impl StructuralPartialEq for Property","synthetic":false,"types":["chemfiles::property::Property"]},{"text":"impl StructuralPartialEq for FormatMetadata","synthetic":false,"types":["chemfiles::misc::FormatMetadata"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.1/implementors/core/marker/trait.Sync.js b/0.10.1/implementors/core/marker/trait.Sync.js new file mode 100644 index 000000000..e7672c774 --- /dev/null +++ b/0.10.1/implementors/core/marker/trait.Sync.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Sync for Error","synthetic":true,"types":["chemfiles::errors::Error"]},{"text":"impl Sync for Status","synthetic":true,"types":["chemfiles::errors::Status"]},{"text":"impl !Sync for Atom","synthetic":true,"types":["chemfiles::atom::Atom"]},{"text":"impl<'a> !Sync for AtomRef<'a>","synthetic":true,"types":["chemfiles::atom::AtomRef"]},{"text":"impl<'a> !Sync for AtomMut<'a>","synthetic":true,"types":["chemfiles::atom::AtomMut"]},{"text":"impl Sync for CellShape","synthetic":true,"types":["chemfiles::cell::CellShape"]},{"text":"impl !Sync for UnitCell","synthetic":true,"types":["chemfiles::cell::UnitCell"]},{"text":"impl<'a> !Sync for UnitCellRef<'a>","synthetic":true,"types":["chemfiles::cell::UnitCellRef"]},{"text":"impl<'a> !Sync for 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No newline at end of file diff --git a/0.10.1/implementors/core/ops/deref/trait.Deref.js b/0.10.1/implementors/core/ops/deref/trait.Deref.js new file mode 100644 index 000000000..752558cba --- /dev/null +++ b/0.10.1/implementors/core/ops/deref/trait.Deref.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl<'a> Deref for AtomRef<'a>","synthetic":false,"types":["chemfiles::atom::AtomRef"]},{"text":"impl<'a> Deref for AtomMut<'a>","synthetic":false,"types":["chemfiles::atom::AtomMut"]},{"text":"impl<'a> Deref for UnitCellRef<'a>","synthetic":false,"types":["chemfiles::cell::UnitCellRef"]},{"text":"impl<'a> Deref for UnitCellMut<'a>","synthetic":false,"types":["chemfiles::cell::UnitCellMut"]},{"text":"impl<'a> Deref for ResidueRef<'a>","synthetic":false,"types":["chemfiles::residue::ResidueRef"]},{"text":"impl<'a> Deref for TopologyRef<'a>","synthetic":false,"types":["chemfiles::topology::TopologyRef"]}]; +if (window.register_implementors) 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+++ b/0.10.1/implementors/core/ops/drop/trait.Drop.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Drop for Atom","synthetic":false,"types":["chemfiles::atom::Atom"]},{"text":"impl Drop for UnitCell","synthetic":false,"types":["chemfiles::cell::UnitCell"]},{"text":"impl Drop for Residue","synthetic":false,"types":["chemfiles::residue::Residue"]},{"text":"impl Drop for Topology","synthetic":false,"types":["chemfiles::topology::Topology"]},{"text":"impl Drop for Frame","synthetic":false,"types":["chemfiles::frame::Frame"]},{"text":"impl Drop for Trajectory","synthetic":false,"types":["chemfiles::trajectory::Trajectory"]},{"text":"impl Drop for Selection","synthetic":false,"types":["chemfiles::selection::Selection"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.1/implementors/core/ops/index/trait.Index.js b/0.10.1/implementors/core/ops/index/trait.Index.js new file mode 100644 index 000000000..3201d6d5b --- /dev/null +++ b/0.10.1/implementors/core/ops/index/trait.Index.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Index<usize> for Match","synthetic":false,"types":["chemfiles::selection::Match"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.1/implementors/std/error/trait.Error.js b/0.10.1/implementors/std/error/trait.Error.js new file mode 100644 index 000000000..b49ff426e --- /dev/null +++ b/0.10.1/implementors/std/error/trait.Error.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Error for Error","synthetic":false,"types":["chemfiles::errors::Error"]}]; +if (window.register_implementors) 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This modify …","Remove the atom at index i in this frame.","Remove any existing bond between the atoms at indexes i …","Remove any existing bond between the atoms at indexes i …","Get a reference to the residue at index index from this …","Get a copy of the residue containing the atom at index …","Does this format support storing residues?","Get the number of residues in this topology.","Resize this topology to hold natoms atoms, inserting …","Resize the positions and the velocities in this frame, to …","Add a new property with the given name to this atom.","Add a new property with the given name to this residue.","Add a new property with the given name to this frame.","Set the three angles of the cell, in degrees.","Set the atom type to atomic_type.","Set the UnitCell of this frame to cell.","Set the unit cell associated with a trajectory. This cell …","Set the atom charge to charge, in number of the electron …","Set the three lengths of the cell, in Angstroms.","Set the atom mass to mass, in atomic mass units.","Set the atom name to name.","Set the shape of the unit cell to shape.","Set this frame step to step.","Set the Topology of this frame to topology.","Set the topology associated with this trajectory. This …","Set the topology associated with this trajectory by …","Set the topology associated with this trajectory by …","Use callback for every chemfiles warning. 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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +use std::ops::{Drop, Deref, DerefMut}; +use std::marker::PhantomData; +use std::ptr; + +use chemfiles_sys::*; +use errors::{check_success, check_not_null}; +use strings; + +use property::{Property, RawProperty, PropertiesIter}; + +/// An `Atom` is a particle in the current `Frame`. It stores the following +/// atomic properties: +/// +/// - atom name; +/// - atom type; +/// - atom mass; +/// - atom charge. +/// +/// The atom name is usually an unique identifier (`H1`, `C_a`) while the +/// atom type will be shared between all particles of the same type: `H`, +/// `Ow`, `CH3`. +pub struct Atom { + handle: *mut CHFL_ATOM, +} + +/// An analog to a reference to an atom (`&Atom`) +pub struct AtomRef<'a> { + inner: Atom, + marker: PhantomData<&'a Atom> +} + +impl<'a> Deref for AtomRef<'a> { + type Target = Atom; + fn deref(&self) -> &Atom { + &self.inner + } +} + +/// An analog to a mutable reference to an atom (`&mut Atom`) +pub struct AtomMut<'a> { + inner: Atom, + marker: PhantomData<&'a mut Atom> +} + +impl<'a> Deref for AtomMut<'a> { + type Target = Atom; + fn deref(&self) -> &Atom { + &self.inner + } +} + +impl<'a> DerefMut for AtomMut<'a> { + fn deref_mut(&mut self) -> &mut Atom { + &mut self.inner + } +} + +impl Clone for Atom { + fn clone(&self) -> Atom { + unsafe { + let new_handle = chfl_atom_copy(self.as_ptr()); + Atom::from_ptr(new_handle) + } + } +} + +impl Atom { + /// Create an owned `Atom` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the + /// pointer. + #[inline] + pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_ATOM) -> Atom { + check_not_null(ptr); + Atom { + handle: ptr + } + } + + /// Create a borrowed `Atom` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the + /// pointer, and the caller is responsible for setting the right lifetime + #[inline] + pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_ATOM) -> AtomRef<'a> { + AtomRef { + inner: Atom::from_ptr(ptr as *mut CHFL_ATOM), + marker: PhantomData, + } + } + + /// Create a mutably borrowed `Atom` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the + /// pointer, and the caller is responsible for setting the right lifetime + #[inline] + pub(crate) unsafe fn ref_mut_from_ptr<'a>(ptr: *mut CHFL_ATOM) -> AtomMut<'a> { + AtomMut { + inner: Atom::from_ptr(ptr), + marker: PhantomData, + } + } + + /// Get the underlying C pointer as a const pointer. + #[inline] + pub(crate) fn as_ptr(&self) -> *const CHFL_ATOM { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer. + #[inline] + pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_ATOM { + self.handle + } + + /// Create an atom with the given `name`, and set the atom type to `name`. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let atom = Atom::new("He"); + /// assert_eq!(atom.name(), "He"); + /// ``` + pub fn new<'a>(name: impl Into<&'a str>) -> Atom { + let buffer = strings::to_c(name.into()); + unsafe { + let handle = chfl_atom(buffer.as_ptr()); + Atom::from_ptr(handle) + } + } + + /// Get the atom mass, in atomic mass units. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let atom = Atom::new("He"); + /// assert_eq!(atom.mass(), 4.002602); + /// ``` + pub fn mass(&self) -> f64 { + let mut mass = 0.0; + unsafe { + check_success(chfl_atom_mass(self.as_ptr(), &mut mass)); + } + return mass; + } + + /// Set the atom mass to `mass`, in atomic mass units. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let mut atom = Atom::new("He"); + /// + /// atom.set_mass(34.9); + /// assert_eq!(atom.mass(), 34.9); + /// ``` + pub fn set_mass(&mut self, mass: f64) { + unsafe { + check_success(chfl_atom_set_mass(self.as_mut_ptr(), mass)); + } + } + + /// Get the atom charge, in number of the electron charge *e*. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let atom = Atom::new("He"); + /// assert_eq!(atom.charge(), 0.0); + /// ``` + pub fn charge(&self) -> f64 { + let mut charge = 0.0; + unsafe { + check_success(chfl_atom_charge(self.as_ptr(), &mut charge)); + } + return charge; + } + + /// Set the atom charge to `charge`, in number of the electron charge *e*. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let mut atom = Atom::new("He"); + /// + /// atom.set_charge(-2.0); + /// assert_eq!(atom.charge(), -2.0); + /// ``` + pub fn set_charge(&mut self, charge: f64) { + unsafe { + check_success(chfl_atom_set_charge(self.as_mut_ptr(), charge)); + } + } + + /// Get the atom name. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let atom = Atom::new("He"); + /// assert_eq!(atom.name(), "He"); + /// ``` + pub fn name(&self) -> String { + let get_name = |ptr, len| unsafe { chfl_atom_name(self.as_ptr(), ptr, len) }; + let name = strings::call_autogrow_buffer(10, get_name).expect("getting name failed"); + return strings::from_c(name.as_ptr()); + } + + /// Get the atom type. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let atom = Atom::new("He"); + /// assert_eq!(atom.atomic_type(), "He"); + /// ``` + pub fn atomic_type(&self) -> String { + let get_type = |ptr, len| unsafe { chfl_atom_type(self.as_ptr(), ptr, len) }; + let buffer = strings::call_autogrow_buffer(10, get_type).expect("getting type failed"); + return strings::from_c(buffer.as_ptr()); + } + + /// Set the atom name to `name`. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let mut atom = Atom::new("He"); + /// + /// atom.set_name("Zn3"); + /// assert_eq!(atom.name(), "Zn3"); + /// ``` + pub fn set_name<'a>(&mut self, name: impl Into<&'a str>) { + let buffer = strings::to_c(name.into()); + unsafe { + check_success(chfl_atom_set_name(self.as_mut_ptr(), buffer.as_ptr())); + } + } + + /// Set the atom type to `atomic_type`. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let mut atom = Atom::new("He"); + /// + /// atom.set_atomic_type("F"); + /// assert_eq!(atom.atomic_type(), "F"); + /// ``` + pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>) { + let buffer = strings::to_c(atomic_type.into()); + unsafe { + check_success(chfl_atom_set_type(self.as_mut_ptr(), buffer.as_ptr())); + } + } + + /// Try to get the full name of the atom from the atomic type. For example, + /// the full name of "He" is "Helium", and so on. If the name can not be + /// found, this function returns the empty string. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// let atom = Atom::new("Zn"); + /// assert_eq!(atom.full_name(), "Zinc"); + /// ``` + pub fn full_name(&self) -> String { + let get_full_name = |ptr, len| unsafe { chfl_atom_full_name(self.as_ptr(), ptr, len) }; + let name = strings::call_autogrow_buffer(10, get_full_name).expect("getting full name failed"); + return strings::from_c(name.as_ptr()); + } + + /// Try to get the Van der Waals radius of the atom from the atomic type. + /// If the radius can not be found, returns 0. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// assert_eq!(Atom::new("He").vdw_radius(), 1.4); + /// assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0); + /// ``` + pub fn vdw_radius(&self) -> f64 { + let mut radius: f64 = 0.0; + unsafe { + check_success(chfl_atom_vdw_radius(self.as_ptr(), &mut radius)); + } + return radius; + } + + /// Try to get the covalent radius of the atom from the atomic type. If the + /// radius can not be found, returns 0. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// assert_eq!(Atom::new("He").covalent_radius(), 0.32); + /// assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0); + /// ``` + pub fn covalent_radius(&self) -> f64 { + let mut radius: f64 = 0.0; + unsafe { + check_success(chfl_atom_covalent_radius(self.as_ptr(), &mut radius)); + } + return radius; + } + + /// Try to get the atomic number of the atom from the atomic type. If the + /// number can not be found, returns 0. + /// + /// # Example + /// ``` + /// # use chemfiles::Atom; + /// assert_eq!(Atom::new("He").atomic_number(), 2); + /// assert_eq!(Atom::new("Xxx").atomic_number(), 0); + /// ``` + pub fn atomic_number(&self) -> u64 { + let mut number = 0; + unsafe { + check_success(chfl_atom_atomic_number(self.as_ptr(), &mut number)); + } + return number; + } + + /// Add a new `property` with the given `name` to this atom. + /// + /// If a property with the same name already exists, this function override + /// the existing property with the new one. + /// + /// # Examples + /// ``` + /// # use chemfiles::{Atom, Property}; + /// let mut atom = Atom::new("He"); + /// atom.set("a bool", true); + /// atom.set("a string", "test"); + /// + /// assert_eq!(atom.get("a bool"), Some(Property::Bool(true))); + /// assert_eq!(atom.get("a string"), Some(Property::String("test".into()))); + /// ``` + pub fn set(&mut self, name: &str, property: impl Into<Property>) { + let buffer = strings::to_c(name); + let property = property.into().as_raw(); + unsafe { + check_success(chfl_atom_set_property( + self.as_mut_ptr(), buffer.as_ptr(), property.as_ptr() + )); + } + } + + + /// Get a property with the given `name` in this atom, if it exist. + /// + /// # Examples + /// ``` + /// # use chemfiles::{Atom, Property}; + /// let mut atom = Atom::new("He"); + /// atom.set("foo", Property::Double(22.2)); + /// + /// assert_eq!(atom.get("foo"), Some(Property::Double(22.2))); + /// assert_eq!(atom.get("Bar"), None); + /// ``` + pub fn get(&self, name: &str) -> Option<Property> { + let buffer = strings::to_c(name); + unsafe { + let handle = chfl_atom_get_property(self.as_ptr(), buffer.as_ptr()); + if handle.is_null() { + None + } else { + let raw = RawProperty::from_ptr(handle); + let property = Property::from_raw(raw); + Some(property) + } + } + } + + /// Get an iterator over all (name, property) pairs for this atom + /// + /// # Examples + /// ``` + /// # use chemfiles::{Atom, Property}; + /// let mut atom = Atom::new("He"); + /// atom.set("foo", Property::Double(22.2)); + /// atom.set("bar", Property::Bool(false)); + /// + /// for (name, property) in atom.properties() { + /// if name == "foo" { + /// assert_eq!(property, Property::Double(22.2)); + /// } else if name == "bar" { + /// assert_eq!(property, Property::Bool(false)); + /// } + /// } + /// ``` + pub fn properties(&self) -> PropertiesIter { + let mut count = 0; + unsafe { + check_success(chfl_atom_properties_count(self.as_ptr(), &mut count)); + } + + #[allow(clippy::cast_possible_truncation)] + let size = count as usize; + let mut c_names = vec![ptr::null_mut(); size]; + unsafe { + check_success(chfl_atom_list_properties(self.as_ptr(), c_names.as_mut_ptr(), count)); + } + + let mut names = Vec::new(); + for ptr in c_names { + names.push(strings::from_c(ptr)); + } + + PropertiesIter { + names: names.into_iter(), + getter: Box::new(move |name| self.get(&*name).expect("failed to get property")) + } + } +} + +impl Drop for Atom { + fn drop(&mut self) { + unsafe { + let _ = chfl_free(self.as_ptr().cast()); + } + } +} + +#[cfg(test)] +mod test { + use super::*; + + #[test] + fn clone() { + let mut atom = Atom::new("He"); + assert_eq!(atom.name(), "He"); + + let copy = atom.clone(); + assert_eq!(copy.name(), "He"); + + atom.set_name("Na"); + assert_eq!(atom.name(), "Na"); + assert_eq!(copy.name(), "He"); + } + + #[test] + fn mass() { + let mut atom = Atom::new("He"); + assert_ulps_eq!(atom.mass(), 4.002602); + atom.set_mass(15.0); + assert_eq!(atom.mass(), 15.0); + } + + #[test] + fn charge() { + let mut atom = Atom::new("He"); + assert_eq!(atom.charge(), 0.0); + atom.set_charge(-1.5); + assert_eq!(atom.charge(), -1.5); + } + + #[test] + fn name() { + let mut atom = Atom::new("He"); + assert_eq!(atom.name(), "He"); + atom.set_name("Zn-12"); + assert_eq!(atom.name(), "Zn-12"); + } + + #[test] + fn atomic_type() { + let mut atom = Atom::new("He"); + assert_eq!(atom.atomic_type(), "He"); + atom.set_atomic_type("Zn"); + assert_eq!(atom.atomic_type(), "Zn"); + } + + #[test] + fn full_name() { + let mut atom = Atom::new("He"); + assert_eq!(atom.full_name(), "Helium"); + + atom.set_atomic_type("Zn"); + assert_eq!(atom.full_name(), "Zinc"); + + let atom = Atom::new("Unknown"); + assert_eq!(atom.full_name(), ""); + } + + #[test] + fn radii() { + let atom = Atom::new("He"); + assert_ulps_eq!(atom.vdw_radius(), 1.4); + assert_ulps_eq!(atom.covalent_radius(), 0.32); + + let atom = Atom::new("Unknown"); + assert_eq!(atom.vdw_radius(), 0.0); + assert_eq!(atom.covalent_radius(), 0.0); + } + + #[test] + fn atomic_number() { + let atom = Atom::new("He"); + assert_eq!(atom.atomic_number(), 2); + + let atom = Atom::new("Unknown"); + assert_eq!(atom.atomic_number(), 0); + } + + #[test] + fn property() { + let mut atom = Atom::new("F"); + + atom.set("foo", -22.0); + assert_eq!(atom.get("foo"), Some(Property::Double(-22.0))); + assert_eq!(atom.get("bar"), None); + + atom.set("bar", Property::String("here".into())); + for (name, property) in atom.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(-22.0)); + } else if name == "bar" { + assert_eq!(property, Property::String("here".into())); + } + } + } +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +use std::ops::{Drop, Deref, DerefMut}; +use std::marker::PhantomData; +use std::ptr; + +use chemfiles_sys::*; +use errors::{check_success, check_not_null, check, Error}; + +/// Available unit cell shapes. +#[derive(Clone, Debug, PartialEq, Eq)] +pub enum CellShape { + /// Orthorhombic cell, with the three angles equals to 90°. + Orthorhombic, + /// Triclinic cell, with any values for the angles. + Triclinic, + /// Infinite cell, to use when there is no cell. + Infinite, +} + +impl From<chfl_cellshape> for CellShape { + fn from(celltype: chfl_cellshape) -> CellShape { + match celltype { + chfl_cellshape::CHFL_CELL_ORTHORHOMBIC => CellShape::Orthorhombic, + chfl_cellshape::CHFL_CELL_TRICLINIC => CellShape::Triclinic, + chfl_cellshape::CHFL_CELL_INFINITE => CellShape::Infinite, + } + } +} + +impl From<CellShape> for chfl_cellshape { + fn from(celltype: CellShape) -> chfl_cellshape { + match celltype { + CellShape::Orthorhombic => chfl_cellshape::CHFL_CELL_ORTHORHOMBIC, + CellShape::Triclinic => chfl_cellshape::CHFL_CELL_TRICLINIC, + CellShape::Infinite => chfl_cellshape::CHFL_CELL_INFINITE, + } + } +} + +/// An `UnitCell` represent the box containing the atoms, and its periodicity. +/// +/// An unit cell is fully represented by three lengths (a, b, c); and three +/// angles (alpha, beta, gamma). The angles are stored in degrees, and the +/// lengths in Angstroms. +/// +/// A cell also has a matricial representation, by projecting the three base +/// vector into an orthonormal base. We choose to represent such matrix as an +/// upper triangular matrix: +/// +/// ```text +/// | a_x b_x c_x | +/// | 0 b_y c_y | +/// | 0 0 c_z | +/// ``` +pub struct UnitCell { + handle: *mut CHFL_CELL, +} + +/// An analog to a reference to an unit cell (`&UnitCell`) +pub struct UnitCellRef<'a> { + inner: UnitCell, + marker: PhantomData<&'a UnitCell> +} + +impl<'a> Deref for UnitCellRef<'a> { + type Target = UnitCell; + fn deref(&self) -> &UnitCell { + &self.inner + } +} + +/// An analog to a mutable reference to an unit cell (`&mut UnitCell`) +pub struct UnitCellMut<'a> { + inner: UnitCell, + marker: PhantomData<&'a mut UnitCell> +} + +impl<'a> Deref for UnitCellMut<'a> { + type Target = UnitCell; + fn deref(&self) -> &UnitCell { + &self.inner + } +} + +impl<'a> DerefMut for UnitCellMut<'a> { + fn deref_mut(&mut self) -> &mut UnitCell { + &mut self.inner + } +} + +impl Clone for UnitCell { + fn clone(&self) -> UnitCell { + unsafe { + let new_handle = chfl_cell_copy(self.as_ptr()); + UnitCell::from_ptr(new_handle) + } + } +} + +impl UnitCell { + /// Create an owned `UnitCell` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the pointer. + #[inline] + pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_CELL) -> UnitCell { + check_not_null(ptr); + UnitCell { + handle: ptr + } + } + + /// Create a borrowed `UnitCell` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the + /// pointer, and the caller is responsible for setting the right lifetime. + #[inline] + pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_CELL) -> UnitCellRef<'a> { + UnitCellRef { + inner: UnitCell::from_ptr(ptr as *mut CHFL_CELL), + marker: PhantomData, + } + } + + /// Create a borrowed `UnitCell` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the + /// pointer, except for it being non-null, and the caller is responsible for + /// setting the right lifetime + #[inline] + pub(crate) unsafe fn ref_mut_from_ptr<'a>(ptr: *mut CHFL_CELL) -> UnitCellMut<'a> { + UnitCellMut { + inner: UnitCell::from_ptr(ptr), + marker: PhantomData, + } + } + + /// Get the underlying C pointer as a const pointer. + #[inline] + pub(crate) fn as_ptr(&self) -> *const CHFL_CELL { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer. + #[inline] + pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_CELL { + self.handle + } + + /// Create an `Orthorhombic` `UnitCell` from the three lengths, in Angstroms. + /// + /// # Example + /// ``` + /// # use chemfiles::{UnitCell, CellShape}; + /// let cell = UnitCell::new([30.0, 30.0, 23.0]); + /// + /// assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]); + /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); + /// assert_eq!(cell.shape(), CellShape::Orthorhombic); + /// ``` + pub fn new(lengths: [f64; 3]) -> UnitCell { + unsafe { + let handle = chfl_cell(lengths.as_ptr(), ptr::null()); + UnitCell::from_ptr(handle) + } + } + + /// Create an `Infinite` `UnitCell`. + /// + /// # Example + /// ``` + /// # use chemfiles::{UnitCell, CellShape}; + /// let cell = UnitCell::infinite(); + /// + /// assert_eq!(cell.lengths(), [0.0, 0.0, 0.0]); + /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); + /// assert_eq!(cell.shape(), CellShape::Infinite); + /// ``` + pub fn infinite() -> UnitCell { + let mut cell = UnitCell::new([0.0, 0.0, 0.0]); + cell.set_shape(CellShape::Infinite).expect("could not set cell shape"); + return cell; + } + + /// Create an `Triclinic` `UnitCell` from the three lengths (in Angstroms) + /// and three angles (in degree). `alpha` is the angle between the vectors + /// `b` and `c`; `beta` is the between the vectors `a` and `c` and `gamma` + /// is the angle between the vectors `a` and `b`. + /// + /// # Example + /// ``` + /// # use chemfiles::{UnitCell, CellShape}; + /// let cell = UnitCell::triclinic([10.0, 10.0, 10.0], [98.0, 99.0, 90.0]); + /// + /// assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]); + /// assert_eq!(cell.angles()[0], 98.0); + /// // Rounding errors might occur due to internal representation + /// assert!((cell.angles()[1] - 99.0).abs() < 1e-12); + /// assert_eq!(cell.angles()[2], 90.0); + /// assert_eq!(cell.shape(), CellShape::Triclinic); + /// ``` + pub fn triclinic(lengths: [f64; 3], angles: [f64; 3]) -> UnitCell { + unsafe { + let handle = chfl_cell(lengths.as_ptr(), angles.as_ptr()); + UnitCell::from_ptr(handle) + } + } + + /// Create an `UnitCell` from a cell matrix. If `matrix` contains only + /// zeros, then an `Infinite` cell is created. If only the diagonal of the + /// matrix is non-zero, then the cell is `Orthorhombic`. Else a + /// `Triclinic` cell is created. The matrix entries should be in Angstroms. + /// + /// # Panics + /// + /// If the matrix has a negative determinant, or more generally is not + /// representing a unit cell. + /// + /// # Example + /// ``` + /// # use chemfiles::{UnitCell, CellShape}; + /// let cell = UnitCell::from_matrix([ + /// [1.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0] + /// ]); + /// + /// assert_eq!(cell.lengths(), [1.0, 2.0, 3.0]); + /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); + /// assert_eq!(cell.shape(), CellShape::Orthorhombic); + /// ``` + pub fn from_matrix(mut matrix: [[f64; 3]; 3]) -> UnitCell { + unsafe { + let handle = chfl_cell_from_matrix(matrix.as_mut_ptr()); + UnitCell::from_ptr(handle) + } + } + + /// Get the three lengths of the cell, in Angstroms. + /// + /// # Example + /// ``` + /// # use chemfiles::UnitCell; + /// let cell = UnitCell::new([30.0, 30.0, 23.0]); + /// assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]); + /// ``` + pub fn lengths(&self) -> [f64; 3] { + let mut lengths = [0.0; 3]; + unsafe { + check_success(chfl_cell_lengths(self.as_ptr(), lengths.as_mut_ptr())); + } + return lengths; + } + + /// Set the three lengths of the cell, in Angstroms. + /// + /// # Errors + /// + /// This function fails if the unit cell is infinite, or if one of the + /// lengths is negative. + /// + /// # Example + /// ``` + /// # use chemfiles::UnitCell; + /// let mut cell = UnitCell::new([30.0, 30.0, 23.0]); + /// + /// cell.set_lengths([10.0, 30.0, 42.0]).unwrap(); + /// assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]); + /// + /// assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err()); + /// ``` + pub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error> { + unsafe { + check(chfl_cell_set_lengths(self.as_mut_ptr(), lengths.as_ptr())) + } + } + + /// Get the three angles of the cell, in degrees. + /// + /// # Example + /// ``` + /// # use chemfiles::UnitCell; + /// let cell = UnitCell::new([20.0, 20.0, 20.0]); + /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); + /// + /// let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]); + /// assert_eq!(cell.angles()[0], 100.0); + /// // Rounding errors might occur due to internal representation + /// assert!((cell.angles()[1] - 120.0).abs() < 1e-12); + /// assert_eq!(cell.angles()[2], 90.0); + /// ``` + pub fn angles(&self) -> [f64; 3] { + let mut angles = [0.0; 3]; + unsafe { + check_success(chfl_cell_angles(self.as_ptr(), angles.as_mut_ptr())); + } + return angles; + } + + /// Set the three angles of the cell, in degrees. + /// + /// # Errors + /// + /// This function fails if the unit cell is not `Triclinic`. + /// + /// # Example + /// ``` + /// # use chemfiles::UnitCell; + /// let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]); + /// assert_eq!(cell.angles()[0], 100.0); + /// // Rounding errors might occur due to internal representation + /// assert!((cell.angles()[1] - 120.0).abs() < 1e-12); + /// assert_eq!(cell.angles()[2], 90.0); + /// + /// cell.set_angles([90.0, 90.0, 90.0]).unwrap(); + /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]); + /// ``` + pub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error> { + unsafe { + check(chfl_cell_set_angles(self.as_mut_ptr(), angles.as_ptr())) + } + } + + /// Get the unit cell matricial representation. + /// + /// The unit cell representation is obtained by aligning the a vector along + /// the *x* axis and putting the b vector in the *xy* plane. This make the + /// matrix an upper triangular matrix: + /// + /// ```text + /// | a_x b_x c_x | + /// | 0 b_y c_y | + /// | 0 0 c_z | + /// ``` + /// + /// # Example + /// ``` + /// # use chemfiles::UnitCell; + /// let cell = UnitCell::new([10.0, 20.0, 30.0]); + /// + /// let matrix = cell.matrix(); + /// + /// assert_eq!(matrix[0][0], 10.0); + /// assert_eq!(matrix[1][1], 20.0); + /// assert_eq!(matrix[2][2], 30.0); + /// + /// assert!(matrix[1][2].abs() < 1e-9); + /// ``` + pub fn matrix(&self) -> [[f64; 3]; 3] { + let mut matrix = [[0.0; 3]; 3]; + unsafe { + check_success(chfl_cell_matrix(self.as_ptr(), matrix.as_mut_ptr())); + } + return matrix; + } + + /// Get the shape of the unit cell. + /// + /// # Example + /// ``` + /// # use chemfiles::{UnitCell, CellShape}; + /// let cell = UnitCell::new([10.0, 20.0, 30.0]); + /// assert_eq!(cell.shape(), CellShape::Orthorhombic); + /// ``` + pub fn shape(&self) -> CellShape { + let mut shape = chfl_cellshape::CHFL_CELL_INFINITE; + unsafe { + check_success(chfl_cell_shape(self.as_ptr(), &mut shape)); + } + return CellShape::from(shape); + } + + /// Set the shape of the unit cell to `shape`. + /// + /// # Errors + /// + /// This can fail if the cell length or angles are incompatible with the + /// new shape. + /// + /// # Example + /// ``` + /// # use chemfiles::{UnitCell, CellShape}; + /// let mut cell = UnitCell::new([10.0, 20.0, 30.0]); + /// assert_eq!(cell.shape(), CellShape::Orthorhombic); + /// + /// cell.set_shape(CellShape::Triclinic).unwrap(); + /// assert_eq!(cell.shape(), CellShape::Triclinic); + /// ``` + pub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error> { + unsafe { + check(chfl_cell_set_shape(self.as_mut_ptr(), shape.into())) + } + } + + /// Get the volume of the unit cell. + /// + /// # Example + /// ``` + /// # use chemfiles::UnitCell; + /// let cell = UnitCell::new([10.0, 20.0, 30.0]); + /// assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0); + /// ``` + pub fn volume(&self) -> f64 { + let mut volume = 0.0; + unsafe { + check_success(chfl_cell_volume(self.as_ptr(), &mut volume)); + } + return volume; + } + + /// Wrap a `vector` in this unit cell. + /// + /// # Example + /// ``` + /// # use chemfiles::UnitCell; + /// let cell = UnitCell::new([10.0, 20.0, 30.0]); + /// + /// let mut vector = [12.0, 5.2, -45.3]; + /// cell.wrap(&mut vector); + /// assert_eq!(vector, [2.0, 5.2, 14.700000000000003]); + /// ``` + pub fn wrap(&self, vector: &mut [f64; 3]) { + unsafe { + check_success(chfl_cell_wrap(self.as_ptr(), vector.as_mut_ptr())) + } + } +} + +impl Drop for UnitCell { + fn drop(&mut self) { + unsafe { + let _ = chfl_free(self.as_ptr().cast()); + } + } +} + + +#[cfg(test)] +mod test { + use super::*; + + #[test] + fn clone() { + let mut cell = UnitCell::new([2.0, 3.0, 4.0]); + assert_eq!(cell.lengths(), [2.0, 3.0, 4.0]); + + let copy = cell.clone(); + assert_eq!(copy.lengths(), [2.0, 3.0, 4.0]); + + cell.set_lengths([10.0, 12.0, 11.0]).unwrap(); + assert_eq!(cell.lengths(), [10.0, 12.0, 11.0]); + assert_eq!(copy.lengths(), [2.0, 3.0, 4.0]); + } + + #[test] + fn lengths() { + let mut cell = UnitCell::new([2.0, 3.0, 4.0]); + assert_eq!(cell.lengths(), [2.0, 3.0, 4.0]); + cell.set_lengths([10.0, 12.0, 11.0]).unwrap(); + assert_eq!(cell.lengths(), [10.0, 12.0, 11.0]); + } + + #[test] + fn angles() { + let mut cell = UnitCell::new([2.0, 3.0, 4.0]); + crate::assert_vector3d_eq(&cell.angles(), &[90.0, 90.0, 90.0], 1e-6); + + cell.set_shape(CellShape::Triclinic).unwrap(); + cell.set_angles([80.0, 89.0, 100.0]).unwrap(); + + crate::assert_vector3d_eq(&cell.angles(), &[80.0, 89.0, 100.0], 1e-6); + + let cell = UnitCell::triclinic([1., 2., 3.], [80., 90., 100.]); + crate::assert_vector3d_eq(&cell.angles(), &[80.0, 90.0, 100.0], 1e-6); + } + + #[test] + fn volume() { + let cell = UnitCell::new([2.0, 3.0, 4.0]); + assert_eq!(cell.volume(), 2.0 * 3.0 * 4.0); + } + + #[test] + fn wrap() { + let cell = UnitCell::new([10.0, 20.0, 30.0]); + let mut vector = [12.0, 5.2, -45.3]; + cell.wrap(&mut vector); + crate::assert_vector3d_eq(&vector, &[2.0, 5.2, 14.7], 1e-6); + } + + #[test] + fn matrix() { + let cell = UnitCell::new([2.0, 3.0, 4.0]); + + let matrix = cell.matrix(); + let result = [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]]; + + for i in 0..3 { + for j in 0..3 { + assert_ulps_eq!(matrix[i][j], result[i][j], epsilon = 1e-12); + } + } + } + + #[test] + fn from_matrix() { + let cell = UnitCell::from_matrix([[10.0, 0.0, 0.0], [0.0, 21.0, 0.0], [0.0, 0.0, 32.0]]); + assert_eq!(cell.shape(), CellShape::Orthorhombic); + assert_eq!(cell.lengths(), [10.0, 21.0, 32.0]); + + let result_matrix = [ + [123.0, 4.08386, 71.7295], + [0.0, 233.964, 133.571], + [0.0, 0.0, 309.901], + ]; + let cell = UnitCell::from_matrix(result_matrix); + + assert_eq!(cell.shape(), CellShape::Triclinic); + for i in 0..3 { + assert_ulps_eq!( + cell.lengths()[i], + [123.0, 234.0, 345.0][i], + epsilon = 1e-3 + ); + assert_ulps_eq!(cell.angles()[i], [67.0, 78.0, 89.0][i], epsilon = 1e-3); + } + + let matrix = cell.matrix(); + for i in 0..3 { + for j in 0..3 { + assert_ulps_eq!(matrix[i][j], result_matrix[i][j], epsilon = 1e-12); + } + } + } + + #[test] + fn shape() { + let cell = UnitCell::new([2.0, 3.0, 4.0]); + assert_eq!(cell.shape(), CellShape::Orthorhombic); + + let cell = UnitCell::infinite(); + assert_eq!(cell.shape(), CellShape::Infinite); + + let cell = UnitCell::triclinic([1.0, 2.0, 3.0], [80.0, 90.0, 100.0]); + assert_eq!(cell.shape(), CellShape::Triclinic); + + let mut cell = UnitCell::new([10.0, 10.0, 10.0]); + assert_eq!(cell.shape(), CellShape::Orthorhombic); + cell.set_shape(CellShape::Triclinic).unwrap(); + assert_eq!(cell.shape(), CellShape::Triclinic); + } +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +extern crate libc; + +use std::error; +use std::fmt; +use std::panic::{self, RefUnwindSafe}; +use std::path::Path; + +use self::libc::c_char; + +use chemfiles_sys::*; +use strings; + +#[derive(Clone, Debug, PartialEq)] +/// Error type for Chemfiles. +pub struct Error { + /// The error status code + pub status: Status, + /// A message describing the error cause + pub message: String, +} + +#[repr(C)] +#[non_exhaustive] +#[derive(Clone, Debug, PartialEq)] +/// Possible causes of error in chemfiles +pub enum Status { + /// No error + Success = chfl_status::CHFL_SUCCESS as isize, + /// Error in memory allocations + MemoryError = chfl_status::CHFL_MEMORY_ERROR as isize, + /// Error while reading or writing a file + FileError = chfl_status::CHFL_FILE_ERROR as isize, + /// Error in file formatting, *i.e.* the file is invalid + FormatError = chfl_status::CHFL_FORMAT_ERROR as isize, + /// Error in selection string syntax + SelectionError = chfl_status::CHFL_SELECTION_ERROR as isize, + /// Error in configuration files syntax + ConfigurationError = chfl_status::CHFL_CONFIGURATION_ERROR as isize, + /// Error for out of bounds indexing + OutOfBounds = chfl_status::CHFL_OUT_OF_BOUNDS as isize, + /// Error related to properties + PropertyError = chfl_status::CHFL_PROPERTY_ERROR as isize, + /// Exception in the C++ chemfiles library + ChemfilesError = chfl_status::CHFL_GENERIC_ERROR as isize, + /// Exception in the C++ standard library + StdCppError = chfl_status::CHFL_CXX_ERROR as isize, + /// The given path is not valid UTF8 + // TODO: rename this to UTF8Error in the next breaking release + UTF8PathError, +} + +impl From<chfl_status> for Error { + fn from(status: chfl_status) -> Error { + let status = match status { + chfl_status::CHFL_SUCCESS => Status::Success, + chfl_status::CHFL_CXX_ERROR => Status::StdCppError, + chfl_status::CHFL_GENERIC_ERROR => Status::ChemfilesError, + chfl_status::CHFL_MEMORY_ERROR => Status::MemoryError, + chfl_status::CHFL_FILE_ERROR => Status::FileError, + chfl_status::CHFL_FORMAT_ERROR => Status::FormatError, + chfl_status::CHFL_SELECTION_ERROR => Status::SelectionError, + chfl_status::CHFL_CONFIGURATION_ERROR => Status::ConfigurationError, + chfl_status::CHFL_OUT_OF_BOUNDS => Status::OutOfBounds, + chfl_status::CHFL_PROPERTY_ERROR => Status::PropertyError, + }; + + let message = Error::last_error(); + Error { + status, + message, + } + } +} + +impl From<std::str::Utf8Error> for Error { + fn from(_: std::str::Utf8Error) -> Self { + Error { + status: Status::UTF8PathError, + message: "failed to convert data to UTF8 string".into(), + } + } +} + +impl Error { + /// Create a new error because the given `path` is invalid UTF-8 data + pub(crate) fn utf8_path_error(path: &Path) -> Error { + Error { + status: Status::UTF8PathError, + message: format!("Could not convert '{}' to UTF8", path.display()), + } + } + + /// Get the last error message from the C++ library. + pub fn last_error() -> String { + unsafe { strings::from_c(chfl_last_error()) } + } + + /// Clear any error from the C++ library + pub fn cleanup() { + unsafe { + check(chfl_clear_errors()).expect("error in chfl_clear_errors. Things went very bad"); + } + } +} + +/// Check return value of a C function, and get the error if needed. +pub(crate) fn check(status: chfl_status) -> Result<(), Error> { + if status == chfl_status::CHFL_SUCCESS { + Ok(()) + } else { + Err(Error::from(status)) + } +} + +/// Check return value of a C function, panic if it failed. +pub(crate) fn check_success(status: chfl_status) { + if status != chfl_status::CHFL_SUCCESS { + panic!("unexpected failure: {}", Error::last_error()); + } +} + +/// Check a pointer for null. +pub(crate) fn check_not_null<T>(ptr: *const T) { + if ptr.is_null() { + panic!("unexpected null pointer: {}", Error::last_error()); + } +} + +pub trait WarningCallback: RefUnwindSafe + Fn(&str) {} +impl<T> WarningCallback for T +where + T: RefUnwindSafe + Fn(&str), +{ +} + +static mut LOGGING_CALLBACK: Option<*mut dyn WarningCallback<Output = ()>> = None; + +extern "C" fn warning_callback(message: *const c_char) { + unsafe { + let callback = &*LOGGING_CALLBACK.expect("No callback provided, this is an internal bug"); + // ignore result. If a panic happened, everything is going badly anyway + let _result = panic::catch_unwind(|| { + callback(&strings::from_c(message)); + }); + } +} + +/// Use `callback` for every chemfiles warning. The callback will be passed +/// the warning message. This will drop any previous warning callback. +pub fn set_warning_callback<F>(callback: F) where F: WarningCallback + 'static { + // box callback to ensure it stays accessible + let callback = Box::into_raw(Box::new(callback)); + unsafe { + if let Some(previous) = LOGGING_CALLBACK { + // set the LOGGING_CALLBACK to the new one + LOGGING_CALLBACK = Some(callback); + // drop the previous callback + let previous = Box::from_raw(previous); + std::mem::drop(previous); + } else { + // set the LOGGING_CALLBACK + LOGGING_CALLBACK = Some(callback); + // Tell C code to use Rust-provided callback + check_success(chfl_set_warning_callback(warning_callback)); + } + } +} + + +impl fmt::Display for Error { + fn fmt(&self, fmt: &mut fmt::Formatter) -> Result<(), fmt::Error> { + write!(fmt, "{}", self.message) + } +} + +impl error::Error for Error { + fn description(&self) -> &str { + match self.status { + Status::Success => "Success", + Status::StdCppError => "Exception from the C++ standard library", + Status::ChemfilesError => "Exception from the chemfiles library", + Status::MemoryError => "Error in memory allocations", + Status::FileError => "Error while reading or writing a file", + Status::FormatError => "Error in file formatting, i.e. the file is invalid", + Status::SelectionError => "Error in selection string syntax", + Status::UTF8PathError => "A string is not valid UTF8", + Status::ConfigurationError => "Error in configuration files", + Status::OutOfBounds => "Out of bounds indexing", + Status::PropertyError => "Error in property", + } + } +} + + +#[cfg(test)] +mod test { + use super::*; + use Trajectory; + + #[test] + fn errors() { + Error::cleanup(); + assert_eq!(Error::last_error(), ""); + assert!(Trajectory::open("nope", 'r').is_err()); + assert_eq!( + Error::last_error(), + "file at \'nope\' does not have an extension, provide a format name to read it" + ); + Error::cleanup(); + assert_eq!(Error::last_error(), ""); + } + + #[test] + fn codes() { + assert_eq!(Error::from(chfl_status::CHFL_SUCCESS).status, Status::Success); + assert_eq!(Error::from(chfl_status::CHFL_CXX_ERROR).status, Status::StdCppError); + assert_eq!(Error::from(chfl_status::CHFL_GENERIC_ERROR).status, Status::ChemfilesError); + assert_eq!(Error::from(chfl_status::CHFL_MEMORY_ERROR).status, Status::MemoryError); + assert_eq!(Error::from(chfl_status::CHFL_FILE_ERROR).status, Status::FileError); + assert_eq!(Error::from(chfl_status::CHFL_FORMAT_ERROR).status, Status::FormatError); + assert_eq!(Error::from(chfl_status::CHFL_SELECTION_ERROR).status, Status::SelectionError); + assert_eq!(Error::from(chfl_status::CHFL_OUT_OF_BOUNDS).status, Status::OutOfBounds); + assert_eq!(Error::from(chfl_status::CHFL_PROPERTY_ERROR).status, Status::PropertyError); + } +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +use std::ops::Drop; +use std::ptr; +use std::slice; + +use chemfiles_sys::*; +use strings; +use errors::{check_not_null, check_success, check, Error}; +use super::{Atom, AtomRef, AtomMut}; +use super::{Topology, TopologyRef, Residue, BondOrder}; +use super::{UnitCell, UnitCellRef, UnitCellMut}; +use property::{Property, RawProperty, PropertiesIter}; + +/// A `Frame` contains data from one simulation step: the current unit +/// cell, the topology, the positions, and the velocities of the particles in +/// the system. If some information is missing (topology or velocity or unit +/// cell), the corresponding data is filled with a default value. +pub struct Frame { + handle: *mut CHFL_FRAME, +} + +impl Clone for Frame { + fn clone(&self) -> Frame { + unsafe { + let new_handle = chfl_frame_copy(self.as_ptr()); + Frame::from_ptr(new_handle) + } + } +} + +impl Frame { + /// Create a `Frame` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the pointer, + /// except for it being non-null. + #[inline] + pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_FRAME) -> Frame { + check_not_null(ptr); + Frame { + handle: ptr + } + } + + /// Get the underlying C pointer as a const pointer. + #[inline] + pub(crate) fn as_ptr(&self) -> *const CHFL_FRAME { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer. + #[inline] + pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_FRAME { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer FROM A SHARED REFERENCE. + /// + /// For uses with functions of the C API using mut pointers for both read + /// and write access. Users should check that this does not lead to multiple + /// mutable borrows + #[inline] + #[allow(non_snake_case)] + pub(crate) fn as_mut_ptr_MANUALLY_CHECKING_BORROW(&self) -> *mut CHFL_FRAME { + self.handle + } + + /// Create an empty frame. It will be resized by the library as needed. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let frame = Frame::new(); + /// + /// assert_eq!(frame.size(), 0); + /// ``` + pub fn new() -> Frame { + unsafe { + Frame::from_ptr(chfl_frame()) + } + } + + /// Get a reference to the atom at the given `index` in this frame. + /// + /// # Panics + /// + /// If `index` is out of bounds. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None); + /// + /// let atom = frame.atom(0); + /// assert_eq!(atom.name(), "Zn"); + /// ``` + pub fn atom(&self, index: usize) -> AtomRef { + unsafe { + let handle = chfl_atom_from_frame( + self.as_mut_ptr_MANUALLY_CHECKING_BORROW(), + index as u64 + ); + Atom::ref_from_ptr(handle) + } + } + + /// Get a mutable reference to the atom at the given `index` in this frame. + /// + /// # Panics + /// + /// If `index` is out of bounds. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None); + /// + /// assert_eq!(frame.atom(0).name(), "Zn"); + /// + /// frame.atom_mut(0).set_name("Fe"); + /// assert_eq!(frame.atom(0).name(), "Fe"); + /// ``` + pub fn atom_mut(&mut self, index: usize) -> AtomMut { + unsafe { + let handle = chfl_atom_from_frame(self.as_mut_ptr(), index as u64); + Atom::ref_mut_from_ptr(handle) + } + } + + /// Get the current number of atoms in this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// assert_eq!(frame.size(), 0); + /// + /// frame.resize(67); + /// assert_eq!(frame.size(), 67); + /// ``` + pub fn size(&self) -> usize { + let mut size = 0; + unsafe { + check_success(chfl_frame_atoms_count(self.as_ptr(), &mut size)); + } + #[allow(clippy::cast_possible_truncation)] + return size as usize; + } + + /// Resize the positions and the velocities in this frame, to make space for + /// `natoms` atoms. Previous data is conserved, as well as the presence of + /// absence of velocities. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// frame.resize(67); + /// assert_eq!(frame.size(), 67); + /// ``` + pub fn resize(&mut self, natoms: usize) { + unsafe { + check_success(chfl_frame_resize(self.as_mut_ptr(), natoms as u64)); + } + } + + /// Add an `Atom` and the corresponding position and optionally velocity + /// data to this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("Zn"), [1.0, 1.0, 2.0], None); + /// + /// frame.add_velocities(); + /// frame.add_atom(&Atom::new("Zn"), [-1.0, 1.0, 2.0], [0.2, 0.1, 0.0]); + /// ``` + pub fn add_atom( + &mut self, + atom: &Atom, + position: [f64; 3], + velocity: impl Into<Option<[f64; 3]>>, + ) + { + let velocity = velocity.into(); + let velocity_ptr = match velocity { + Some(ref data) => data.as_ptr(), + None => ptr::null(), + }; + + unsafe { + check_success(chfl_frame_add_atom( + self.as_mut_ptr(), + atom.as_ptr(), + position.as_ptr(), + velocity_ptr + )); + } + + } + + /// Remove the atom at index `i` in this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None); + /// frame.add_atom(&Atom::new("Fe"), [0.0; 3], None); + /// frame.add_atom(&Atom::new("Sn"), [0.0; 3], None); + /// assert_eq!(frame.size(), 3); + /// + /// frame.remove(1); + /// assert_eq!(frame.size(), 2); + /// assert_eq!(frame.atom(1).name(), "Sn"); + /// ``` + pub fn remove(&mut self, i: usize) { + unsafe { + check_success(chfl_frame_remove(self.as_mut_ptr(), i as u64)); + } + } + + /// Add a bond between the atoms at indexes `i` and `j` in the frame. + /// + /// The bond order is set to `BondOrder::Unknown`. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, BondOrder}; + /// let mut frame = Frame::new(); + /// assert_eq!(frame.topology().bonds_count(), 0); + /// frame.resize(5); + /// + /// frame.add_bond(0, 1); + /// frame.add_bond(3, 1); + /// frame.add_bond(2, 4); + /// assert_eq!(frame.topology().bonds_count(), 3); + /// + /// assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown); + /// assert_eq!(frame.topology().bonds(), vec![[0, 1], [1, 3], [2, 4]]); + /// ``` + pub fn add_bond(&mut self, i: usize, j: usize) { + unsafe { + check_success(chfl_frame_add_bond(self.as_mut_ptr(), i as u64, j as u64)); + } + } + + /// Add a bond between the atoms at indexes `i` and `j` in the frame + /// with the given bond `order`. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, BondOrder}; + /// let mut frame = Frame::new(); + /// assert_eq!(frame.topology().bonds_count(), 0); + /// frame.resize(2); + /// + /// frame.add_bond_with_order(0, 1, BondOrder::Double); + /// assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Double); + /// ``` + pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder) { + unsafe { + check_success(chfl_frame_bond_with_order( + self.as_mut_ptr(), + i as u64, + j as u64, + order.as_raw(), + )); + } + } + + /// Remove any existing bond between the atoms at indexes `i` and `j` in + /// the frame. + /// + /// This function does nothing if there is no bond between `i` and `j`. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// frame.resize(5); + /// + /// frame.add_bond(0, 1); + /// frame.add_bond(3, 1); + /// frame.add_bond(2, 4); + /// + /// let bonds = frame.topology().bonds(); + /// assert_eq!(bonds, vec![[0, 1], [1, 3], [2, 4]]); + /// + /// frame.remove_bond(2, 4); + /// let bonds = frame.topology().bonds(); + /// assert_eq!(bonds, vec![[0, 1], [1, 3]]); + /// ``` + pub fn remove_bond(&mut self, i: usize, j: usize) { + unsafe { + check_success(chfl_frame_remove_bond( + self.as_mut_ptr(), + i as u64, + j as u64, + )); + } + } + + /// Add a copy of `residue` to this frame. + /// + /// # Errors + /// + /// This function fails is the residue id is already in this frame's + /// topology, or if the residue contain atoms that are already in another + /// residue. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Residue}; + /// let mut frame = Frame::new(); + /// + /// let residue = Residue::new("foo"); + /// frame.add_residue(&residue).unwrap(); + /// + /// let topology = frame.topology(); + /// assert_eq!(topology.residues_count(), 1); + /// assert_eq!(topology.residue(0).unwrap().name(), "foo"); + /// ``` + pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error> { + unsafe { + check(chfl_frame_add_residue(self.as_mut_ptr(), residue.as_ptr())) + } + } + + /// Get the distance between the atoms at indexes `i` and `j` in this frame, + /// accounting for periodic boundary conditions. The result is expressed in + /// Angstroms. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("B"), [1.0, 2.0, 3.0], None); + /// + /// assert_eq!(frame.distance(0, 1), f64::sqrt(14.0)); + /// ``` + pub fn distance(&self, i: usize, j: usize) -> f64 { + let mut distance = 0.0; + unsafe { + check_success(chfl_frame_distance( + self.as_ptr(), + i as u64, + j as u64, + &mut distance, + )); + } + return distance; + } + + /// Get the angle formed by the atoms at indexes `i`, `j` and `k` in this + /// frame, accounting for periodic boundary conditions. The result is + /// expressed in radians. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// # use std::f64; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None); + /// + /// assert_eq!(frame.angle(0, 1, 2), f64::consts::PI / 2.0); + /// ``` + pub fn angle(&self, i: usize, j: usize, k: usize) -> f64 { + let mut angle = 0.0; + unsafe { + check_success(chfl_frame_angle( + self.as_ptr(), + i as u64, + j as u64, + k as u64, + &mut angle, + )); + } + return angle; + } + + /// Get the dihedral angle formed by the atoms at indexes `i`, `j`, `k` and + /// `m` in this frame, accounting for periodic boundary conditions. The + /// result is expressed in radians. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// # use std::f64; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None); + /// frame.add_atom(&Atom::new("D"), [0.0, 1.0, 1.0], None); + /// + /// assert_eq!(frame.dihedral(0, 1, 2, 3), f64::consts::PI / 2.0); + /// ``` + pub fn dihedral(&self, i: usize, j: usize, k: usize, m: usize) -> f64 { + let mut dihedral = 0.0; + unsafe { + check_success(chfl_frame_dihedral( + self.as_ptr(), + i as u64, + j as u64, + k as u64, + m as u64, + &mut dihedral, + )); + } + return dihedral; + } + + /// Get the out of plane distance formed by the atoms at indexes `i`, `j`, + /// `k` and `m` in this frame, accounting for periodic boundary conditions. + /// The result is expressed in angstroms. + /// + /// This is the distance between the atom j and the ikm plane. The j atom + /// is the center of the improper dihedral angle formed by i, j, k and m. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 2.0], None); + /// frame.add_atom(&Atom::new("C"), [1.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("D"), [0.0, 1.0, 0.0], None); + /// + /// assert_eq!(frame.out_of_plane(0, 1, 2, 3), 2.0); + /// ``` + pub fn out_of_plane(&self, i: usize, j: usize, k: usize, m: usize) -> f64 { + let mut distance = 0.0; + unsafe { + check_success(chfl_frame_out_of_plane( + self.as_ptr(), + i as u64, + j as u64, + k as u64, + m as u64, + &mut distance, + )); + } + return distance; + } + + /// Get a view into the positions of this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// frame.resize(67); + /// + /// let positions = frame.positions(); + /// assert_eq!(positions.len(), 67); + /// assert_eq!(positions[0], [0.0, 0.0, 0.0]); + /// ``` + pub fn positions(&self) -> &[[f64; 3]] { + let mut ptr = ptr::null_mut(); + let mut natoms = 0; + unsafe { + check_success(chfl_frame_positions( + self.as_mut_ptr_MANUALLY_CHECKING_BORROW(), + &mut ptr, + &mut natoms + )); + } + + #[allow(clippy::cast_possible_truncation)] + let size = natoms as usize; + unsafe { + return slice::from_raw_parts(ptr, size); + } + } + + /// Get a mutable view into the positions of this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// frame.resize(67); + /// { + /// let positions = frame.positions_mut(); + /// assert_eq!(positions[0], [0.0, 0.0, 0.0]); + /// positions[0] = [1.0, 2.0, 3.0]; + /// } + /// + /// let positions = frame.positions(); + /// assert_eq!(positions[0], [1.0, 2.0, 3.0]); + /// ``` + pub fn positions_mut(&mut self) -> &mut [[f64; 3]] { + let mut ptr = ptr::null_mut(); + let mut natoms = 0; + unsafe { + check_success(chfl_frame_positions(self.as_mut_ptr(), &mut ptr, &mut natoms)); + } + #[allow(clippy::cast_possible_truncation)] + let size = natoms as usize; + unsafe { + return slice::from_raw_parts_mut(ptr, size); + } + } + + /// Get a view into the velocities of this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// frame.resize(67); + /// frame.add_velocities(); + /// + /// let velocities = frame.velocities(); + /// assert_eq!(velocities.len(), 67); + /// assert_eq!(velocities[0], [0.0, 0.0, 0.0]); + /// ``` + pub fn velocities(&self) -> &[[f64; 3]] { + let mut ptr = ptr::null_mut(); + let mut natoms = 0; + unsafe { + check_success(chfl_frame_velocities( + self.as_mut_ptr_MANUALLY_CHECKING_BORROW(), + &mut ptr, + &mut natoms + )); + } + #[allow(clippy::cast_possible_truncation)] + let size = natoms as usize; + unsafe { + return slice::from_raw_parts(ptr, size); + } + } + + /// Get a mutable view into the velocities of this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// frame.resize(67); + /// frame.add_velocities(); + /// { + /// let velocities = frame.velocities_mut(); + /// assert_eq!(velocities[0], [0.0, 0.0, 0.0]); + /// velocities[0] = [1.0, 2.0, 3.0]; + /// } + /// + /// let velocities = frame.velocities(); + /// assert_eq!(velocities[0], [1.0, 2.0, 3.0]); + /// ``` + pub fn velocities_mut(&mut self) -> &mut [[f64; 3]] { + let mut ptr = ptr::null_mut(); + let mut natoms = 0; + unsafe { + check_success(chfl_frame_velocities(self.as_mut_ptr(), &mut ptr, &mut natoms)); + } + #[allow(clippy::cast_possible_truncation)] + let size = natoms as usize; + unsafe { + return slice::from_raw_parts_mut(ptr, size); + } + } + + /// Check if this frame contains velocity data. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// assert_eq!(frame.has_velocities(), false); + /// + /// frame.add_velocities(); + /// assert_eq!(frame.has_velocities(), true); + /// ``` + pub fn has_velocities(&self) -> bool { + let mut res = 0; + unsafe { + check_success(chfl_frame_has_velocities(self.as_ptr(), &mut res)); + } + return res != 0; + } + + /// Add velocity data to this frame. If the frame already have velocities, + /// this does nothing. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// assert_eq!(frame.has_velocities(), false); + /// + /// frame.add_velocities(); + /// assert_eq!(frame.has_velocities(), true); + /// ``` + pub fn add_velocities(&mut self) { + unsafe { + check_success(chfl_frame_add_velocities(self.as_mut_ptr())); + } + } + + /// Get a reference to the `UnitCell` from this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, CellShape}; + /// let frame = Frame::new(); + /// + /// let cell = frame.cell(); + /// assert_eq!(cell.shape(), CellShape::Infinite); + /// ``` + pub fn cell(&self) -> UnitCellRef { + unsafe { + let handle = chfl_cell_from_frame(self.as_mut_ptr_MANUALLY_CHECKING_BORROW()); + UnitCell::ref_from_ptr(handle) + } + } + + /// Get a mutable reference to the `UnitCell` from this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, CellShape}; + /// let mut frame = Frame::new(); + /// + /// assert_eq!(frame.cell().shape(), CellShape::Infinite); + /// + /// frame.cell_mut().set_shape(CellShape::Triclinic).unwrap(); + /// assert_eq!(frame.cell().shape(), CellShape::Triclinic); + /// ``` + pub fn cell_mut(&mut self) -> UnitCellMut { + unsafe { + let handle = chfl_cell_from_frame(self.as_mut_ptr()); + UnitCell::ref_mut_from_ptr(handle) + } + } + + /// Set the `UnitCell` of this frame to `cell`. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, UnitCell, CellShape}; + /// let mut frame = Frame::new(); + /// + /// frame.set_cell(&UnitCell::new([10.0, 10.0, 10.0])); + /// + /// let cell = frame.cell(); + /// assert_eq!(cell.shape(), CellShape::Orthorhombic); + /// assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]); + /// ``` + pub fn set_cell(&mut self, cell: &UnitCell) { + unsafe { + check_success(chfl_frame_set_cell(self.as_mut_ptr(), cell.as_ptr())); + } + } + + /// Get a reference to the `Topology` of this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// frame.resize(42); + /// + /// let topology = frame.topology(); + /// assert_eq!(topology.size(), 42); + /// ``` + pub fn topology(&self) -> TopologyRef { + unsafe { + let handle = chfl_topology_from_frame(self.as_ptr()); + Topology::ref_from_ptr(handle) + } + } + + /// Set the `Topology` of this frame to `topology`. + /// + /// # Errors + /// + /// This function fails if the topology contains a different number of atoms + /// than this frame. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Topology, Atom}; + /// let mut frame = Frame::new(); + /// frame.resize(2); + /// + /// let mut topology = Topology::new(); + /// topology.add_atom(&Atom::new("Cl")); + /// topology.add_atom(&Atom::new("Cl")); + /// topology.add_bond(0, 1); + /// + /// frame.set_topology(&topology).unwrap(); + /// assert_eq!(frame.atom(0).name(), "Cl"); + /// ``` + pub fn set_topology(&mut self, topology: &Topology) -> Result<(), Error> { + unsafe { + check(chfl_frame_set_topology(self.as_mut_ptr(), topology.as_ptr())) + } + } + + /// Get this frame step, i.e. the frame number in the trajectory + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let frame = Frame::new(); + /// assert_eq!(frame.step(), 0); + /// ``` + pub fn step(&self) -> usize { + let mut step = 0; + unsafe { + check_success(chfl_frame_step(self.as_ptr(), &mut step)); + } + #[allow(clippy::cast_possible_truncation)] + return step as usize; + } + + /// Set this frame step to `step`. + /// + /// # Example + /// ``` + /// # use chemfiles::Frame; + /// let mut frame = Frame::new(); + /// assert_eq!(frame.step(), 0); + /// + /// frame.set_step(10); + /// assert_eq!(frame.step(), 10); + /// ``` + pub fn set_step(&mut self, step: usize) { + unsafe { + check_success(chfl_frame_set_step(self.as_mut_ptr(), step as u64)); + } + } + + /// Guess the bonds, angles and dihedrals in this `frame`. + /// + /// The bonds are guessed using a distance-based algorithm, and then angles + /// and dihedrals are guessed from the bonds. + /// + /// # Errors + //// + /// This function can fail if the covalent radius is unknown for some atoms + /// in the frame. + /// + /// # Example + /// ``` + /// # use chemfiles::{Frame, Atom}; + /// let mut frame = Frame::new(); + /// + /// frame.add_atom(&Atom::new("Cl"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("Cl"), [1.5, 0.0, 0.0], None); + /// assert_eq!(frame.topology().bonds_count(), 0); + /// + /// frame.guess_bonds().unwrap(); + /// assert_eq!(frame.topology().bonds_count(), 1); + /// ``` + pub fn guess_bonds(&mut self) -> Result<(), Error> { + unsafe { + check(chfl_frame_guess_bonds(self.as_mut_ptr())) + } + } + + /// Remove all existing bonds, angles, dihedral angles and improper + /// dihedral angles in the topology of the frame. + /// + /// # Example + /// ``` + /// # use chemfiles::{Atom, Frame}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("H"), [0.0, 1.0, 0.0], None); + /// + /// frame.add_bond(0, 1); + /// frame.add_bond(1, 2); + /// + /// assert_eq!(frame.topology().bonds().len(), 2); + /// assert_eq!(frame.topology().angles().len(), 1); + /// + /// frame.clear_bonds(); + /// assert!(frame.topology().bonds().is_empty()); + /// assert!(frame.topology().angles().is_empty()); + /// ``` + pub fn clear_bonds(&mut self) { + unsafe { + check_success(chfl_frame_clear_bonds(self.as_mut_ptr())); + } + } + + /// Add a new `property` with the given `name` to this frame. + /// + /// If a property with the same name already exists, this function override + /// the existing property with the new one. + /// + /// # Examples + /// ``` + /// # use chemfiles::{Frame, Property}; + /// let mut frame = Frame::new(); + /// frame.set("a string", "hello"); + /// frame.set("a double", 4.3); + /// + /// assert_eq!(frame.get("a string"), Some(Property::String("hello".into()))); + /// assert_eq!(frame.get("a double"), Some(Property::Double(4.3))); + /// ``` + pub fn set(&mut self, name: &str, property: impl Into<Property>) { + let buffer = strings::to_c(name); + let property = property.into().as_raw(); + unsafe { + check_success(chfl_frame_set_property( + self.as_mut_ptr(), buffer.as_ptr(), property.as_ptr() + )); + } + } + + /// Get a property with the given `name` in this frame, if it exist. + /// + /// # Examples + /// ``` + /// # use chemfiles::{Frame, Property}; + /// let mut frame = Frame::new(); + /// frame.set("foo", Property::Double(22.2)); + /// + /// assert_eq!(frame.get("foo"), Some(Property::Double(22.2))); + /// assert_eq!(frame.get("Bar"), None); + /// ``` + pub fn get(&self, name: &str) -> Option<Property> { + let buffer = strings::to_c(name); + unsafe { + let handle = chfl_frame_get_property(self.as_ptr(), buffer.as_ptr()); + if handle.is_null() { + None + } else { + let raw = RawProperty::from_ptr(handle); + Some(Property::from_raw(raw)) + } + } + } + + /// Get an iterator over all (name, property) pairs for this frame + /// + /// # Examples + /// ``` + /// # use chemfiles::{Frame, Property}; + /// let mut frame = Frame::new(); + /// frame.set("foo", Property::Double(22.2)); + /// frame.set("bar", Property::Bool(false)); + /// + /// for (name, property) in frame.properties() { + /// if name == "foo" { + /// assert_eq!(property, Property::Double(22.2)); + /// } else if name == "bar" { + /// assert_eq!(property, Property::Bool(false)); + /// } + /// } + /// ``` + pub fn properties(&self) -> PropertiesIter { + let mut count = 0; + unsafe { + check_success(chfl_frame_properties_count(self.as_ptr(), &mut count)); + } + + #[allow(clippy::cast_possible_truncation)] + let size = count as usize; + let mut c_names = vec![ptr::null_mut(); size]; + unsafe { + check_success(chfl_frame_list_properties(self.as_ptr(), c_names.as_mut_ptr(), count)); + } + + let mut names = Vec::new(); + for ptr in c_names { + names.push(strings::from_c(ptr)); + } + + PropertiesIter { + names: names.into_iter(), + getter: Box::new(move |name| self.get(&*name).expect("failed to get property")) + } + } +} + +impl Drop for Frame { + fn drop(&mut self) { + unsafe { + let _ = chfl_free(self.as_ptr().cast()); + } + } +} + +#[cfg(test)] +mod test { + use super::*; + use {Atom, Topology, UnitCell}; + + #[test] + fn clone() { + let mut frame = Frame::new(); + assert_eq!(frame.size(), 0); + let copy = frame.clone(); + assert_eq!(copy.size(), 0); + + frame.resize(42); + assert_eq!(frame.size(), 42); + assert_eq!(copy.size(), 0); + } + + #[test] + fn size() { + let mut frame = Frame::new(); + assert_eq!(frame.size(), 0); + + frame.resize(12); + assert_eq!(frame.size(), 12); + } + + #[test] + fn add_atom() { + let mut frame = Frame::new(); + + frame.add_atom(&Atom::new("U"), [1.0, 1.0, 2.0], None); + assert_eq!(frame.size(), 1); + assert_eq!(frame.atom(0).name(), "U"); + + let positions = &[[1.0, 1.0, 2.0]]; + assert_eq!(frame.positions(), positions); + + frame.add_velocities(); + frame.add_atom(&Atom::new("F"), [1.0, 1.0, 2.0], [4.0, 3.0, 2.0]); + assert_eq!(frame.size(), 2); + assert_eq!(frame.atom(0).name(), "U"); + assert_eq!(frame.atom(1).name(), "F"); + + let positions = &[[1.0, 1.0, 2.0], [1.0, 1.0, 2.0]]; + assert_eq!(frame.positions(), positions); + + let velocities = &[[0.0, 0.0, 0.0], [4.0, 3.0, 2.0]]; + assert_eq!(frame.velocities(), velocities); + } + + #[test] + #[should_panic] + fn out_of_bounds_atom() { + let mut frame = Frame::new(); + frame.resize(22); + let _atom = frame.atom(23); + } + + #[test] + fn remove_atom() { + let mut frame = Frame::new(); + frame.add_atom(&Atom::new("U"), [1.0, 1.0, 2.0], None); + frame.add_atom(&Atom::new("F"), [1.0, 1.0, 2.0], None); + + assert_eq!(frame.size(), 2); + assert_eq!(frame.atom(0).name(), "U"); + + frame.remove(0); + assert_eq!(frame.size(), 1); + assert_eq!(frame.atom(0).name(), "F"); + } + + #[test] + #[should_panic] + fn remove_out_of_bounds() { + let mut frame = Frame::new(); + frame.resize(32); + + frame.remove(100); + } + + #[test] + fn positions() { + let mut frame = Frame::new(); + frame.resize(4); + let expected = &[ + [1.0, 2.0, 3.0], + [4.0, 5.0, 6.0], + [7.0, 8.0, 9.0], + [10.0, 11.0, 12.0], + ]; + + frame.positions_mut().clone_from_slice(expected); + assert_eq!(frame.positions(), expected); + } + + #[test] + fn velocities() { + let mut frame = Frame::new(); + frame.resize(4); + assert!(!frame.has_velocities()); + frame.add_velocities(); + assert!(frame.has_velocities()); + + let expected = &[ + [1.0, 2.0, 3.0], + [4.0, 5.0, 6.0], + [7.0, 8.0, 9.0], + [10.0, 11.0, 12.0], + ]; + + frame.velocities_mut().clone_from_slice(expected); + assert_eq!(frame.velocities(), expected); + } + + #[test] + fn cell() { + let mut frame = Frame::new(); + frame.set_cell(&UnitCell::new([3.0, 4.0, 5.0])); + let cell = frame.cell(); + assert_eq!(cell.lengths(), [3.0, 4.0, 5.0]); + } + + #[test] + fn topology() { + let mut frame = Frame::new(); + frame.resize(2); + let mut topology = Topology::new(); + + topology.add_atom(&Atom::new("Zn")); + topology.add_atom(&Atom::new("Ar")); + + assert!(frame.set_topology(&topology).is_ok()); + + let topology = frame.topology(); + + assert_eq!(topology.atom(0).name(), "Zn"); + assert_eq!(topology.atom(1).name(), "Ar"); + + assert_eq!(frame.atom(0).name(), "Zn"); + assert_eq!(frame.atom(1).name(), "Ar"); + } + + #[test] + fn bonds() { + let mut frame = Frame::new(); + frame.resize(12); + assert_eq!(frame.topology().bonds_count(), 0); + + frame.add_bond(0, 1); + frame.add_bond(9, 2); + frame.add_bond_with_order(3, 7, BondOrder::Aromatic); + assert_eq!(frame.topology().bonds_count(), 3); + + assert_eq!(frame.topology().bonds(), vec![[0, 1], [2, 9], [3, 7]]); + let expected = vec![BondOrder::Unknown, BondOrder::Unknown, BondOrder::Aromatic]; + assert_eq!(frame.topology().bond_orders(), expected); + + assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown); + assert_eq!(frame.topology().bond_order(3, 7), BondOrder::Aromatic); + + frame.remove_bond(3, 7); + // Removing unexisting bond is OK if both indexes are in bounds + frame.remove_bond(8, 7); + assert_eq!(frame.topology().bonds_count(), 2); + + frame.clear_bonds(); + assert_eq!(frame.topology().bonds_count(), 0); + } + + #[test] + #[should_panic] + fn out_of_bounds_bonds() { + let mut frame = Frame::new(); + frame.resize(12); + frame.add_bond(300, 7); + } + + #[test] + #[should_panic] + fn out_of_bounds_remove_bond() { + let mut frame = Frame::new(); + frame.resize(12); + frame.remove_bond(300, 7); + } + + #[test] + #[should_panic] + fn out_of_bounds_bonds_with_order() { + let mut frame = Frame::new(); + frame.resize(12); + frame.add_bond_with_order(300, 7, BondOrder::Unknown); + } + + #[test] + fn residues() { + let mut frame = Frame::new(); + assert_eq!(frame.topology().residues_count(), 0); + + let residue = &Residue::new("foobar"); + frame.add_residue(residue).unwrap(); + frame.add_residue(residue).unwrap(); + frame.add_residue(residue).unwrap(); + + assert_eq!(frame.topology().residues_count(), 3); + assert_eq!(frame.topology().residue(0).unwrap().name(), "foobar"); + } + + #[test] + fn step() { + let mut frame = Frame::new(); + assert_eq!(frame.step(), 0); + frame.set_step(42); + assert_eq!(frame.step(), 42); + } + + #[test] + fn property() { + let mut frame = Frame::new(); + frame.set("foo", -22.0); + assert_eq!(frame.get("foo"), Some(Property::Double(-22.0))); + assert_eq!(frame.get("bar"), None); + + frame.set("bar", Property::String("here".into())); + for (name, property) in frame.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(-22.0)); + } else if name == "bar" { + assert_eq!(property, Property::String("here".into())); + } + } + } + + #[test] + fn pbc_geometry() { + use std::f64::consts::PI; + + let mut frame = Frame::new(); + let atom = &Atom::new(""); + + frame.add_atom(atom, [1.0, 0.0, 0.0], None); + frame.add_atom(atom, [0.0, 0.0, 0.0], None); + frame.add_atom(atom, [0.0, 1.0, 0.0], None); + frame.add_atom(atom, [0.0, 1.0, 1.0], None); + frame.add_atom(atom, [0.0, 0.0, 2.0], None); + + assert_eq!(frame.distance(0, 2), f64::sqrt(2.0)); + assert_eq!(frame.angle(0, 1, 2), PI / 2.0); + assert_eq!(frame.dihedral(0, 1, 2, 3), PI / 2.0); + assert_eq!(frame.out_of_plane(1, 4, 0, 2), 2.0); + } +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed + +//! Chemfiles is a multi-language library written in modern C++ for reading and +//! writing from and to molecular trajectory files. These files are created by +//! your favorite theoretical chemistry program, and contains information about +//! atomic or residues names and positions. Some format also have additional +//! information, such as velocities, forces, energy, … +//! +//! This crate expose the C API of chemfiles to Rust, and make all the +//! functionalities accessible. For more information on the C++ library, +//! please see its [documentation][cxx_doc]. Specifically, the following pages +//! are worth reading: +//! +//! - The [overview][overview] of the classes organization; +//! - The list of [supported formats][formats]; +//! - The documentation for the [selection language][selections]; +//! +//! [cxx_doc]: https://chemfiles.org/chemfiles +//! [overview]: https://chemfiles.org/chemfiles/latest/overview.html +//! [formats]: https://chemfiles.org/chemfiles/latest/formats.html +//! [selections]: https://chemfiles.org/chemfiles/latest/selections.html + +#![deny(missing_docs)] +#![warn(trivial_casts, unused_import_braces, variant_size_differences)] +#![warn(unused_results)] +// Configuration for clippy lints +#![warn(clippy::all, clippy::pedantic)] +#![allow(clippy::needless_return, clippy::module_name_repetitions)] +#![allow(clippy::must_use_candidate, clippy::wildcard_imports)] + +// Allow a few more clippy lints in test mode +#![cfg_attr(test, allow(clippy::float_cmp, clippy::unreadable_literal, clippy::shadow_unrelated))] + +// deny(warnings) in doc tests +#![doc(test(attr(deny(warnings))))] +#![doc(test(attr(allow(unused_variables))))] + +#[cfg(test)] +#[macro_use] +extern crate approx; + +extern crate chemfiles_sys; +use chemfiles_sys::{chfl_add_configuration, chfl_version}; + +mod strings; + +mod errors; +pub use errors::{Error, Status}; +pub use errors::set_warning_callback; + +mod atom; +pub use atom::Atom; +pub use atom::AtomRef; +pub use atom::AtomMut; + +mod cell; +pub use cell::UnitCell; +pub use cell::UnitCellRef; +pub use cell::UnitCellMut; +pub use cell::CellShape; + +mod residue; +pub use residue::Residue; +pub use residue::ResidueRef; + +mod topology; +pub use topology::Topology; +pub use topology::TopologyRef; +pub use topology::BondOrder; + +mod frame; +pub use frame::Frame; + +mod trajectory; +pub use trajectory::Trajectory; + +mod selection; +pub use selection::{Match, Selection}; + +mod property; +pub use property::Property; +pub use property::PropertiesIter; + +mod misc; +pub use misc::{FormatMetadata, formats_list, guess_format}; + +/// Get the version of the chemfiles library. +/// +/// # Example +/// ``` +/// let version = chemfiles::version(); +/// assert!(version.starts_with("0.10")); +/// ``` +pub fn version() -> String { + unsafe { strings::from_c(chfl_version()) } +} + +/// Read configuration data from the file at `path`. +/// +/// By default, chemfiles reads configuration from any file named +/// `.chemfiles.toml` in the current directory or any parent directory. This +/// function can be used to add data from another configuration file. Data from +/// the new configuration file will overwrite any existing data. +/// +/// # Errors +/// +/// This function will fail if there is no file at `path`, or if the file is +/// incorrectly formatted. +/// +/// # Example +/// ```no_run +/// chemfiles::add_configuration("local-config.toml").unwrap(); +/// // from now on, the data from "local-config.toml" will be used +/// ``` +pub fn add_configuration<S>(path: S) -> Result<(), Error> +where + S: AsRef<str>, +{ + let buffer = strings::to_c(path.as_ref()); + unsafe { + errors::check(chfl_add_configuration(buffer.as_ptr())) + } +} + +#[cfg(test)] +mod tests { + #[test] + fn version() { + assert!(!crate::version().is_empty()); + assert!(crate::version().starts_with("0.10")); + } +} + +#[cfg(test)] +fn assert_vector3d_eq(lhs: &[f64; 3], rhs: &[f64; 3], eps: f64) { + lhs.iter() + .zip(rhs) + .for_each(|(l, r)| assert_ulps_eq!(l, r, epsilon = eps)); +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2020 Guillaume Fraux -- BSD licensed + +use std::convert::TryInto; +use std::ffi::CStr; + +use chemfiles_sys::{chfl_format_metadata, chfl_formats_list, chfl_free, chfl_guess_format}; +use errors::check_success; + +/// `FormatMetadata` contains metadata associated with one format. +#[allow(clippy::struct_excessive_bools)] +#[derive(Debug, Clone, PartialEq, Eq)] +pub struct FormatMetadata { + /// Name of the format. + pub name: &'static str, + /// Extension associated with the format. + pub extension: Option<&'static str>, + /// Extended, user-facing description of the format. + pub description: &'static str, + /// URL pointing to the format definition/reference. + pub reference: &'static str, + /// Is reading files in this format implemented? + pub read: bool, + /// Is writing files in this format implemented? + pub write: bool, + /// Does this format support in-memory IO? + pub memory: bool, + /// Does this format support storing atomic positions? + pub positions: bool, + /// Does this format support storing atomic velocities? + pub velocities: bool, + /// Does this format support storing unit cell information? + pub unit_cell: bool, + /// Does this format support storing atom names or types? + pub atoms: bool, + /// Does this format support storing bonds between atoms? + pub bonds: bool, + /// Does this format support storing residues? + pub residues: bool, +} + +impl FormatMetadata { + pub(crate) fn from_raw(raw: &chfl_format_metadata) -> Self { + let str_from_ptr = |ptr| unsafe { + CStr::from_ptr(ptr) + .to_str() + .expect("Invalid Rust str from C") + }; + let extension = if raw.extension.is_null() { + None + } else { + Some(str_from_ptr(raw.extension)) + }; + Self { + name: str_from_ptr(raw.name), + extension, + description: str_from_ptr(raw.description), + reference: str_from_ptr(raw.reference), + read: raw.read, + write: raw.write, + memory: raw.memory, + positions: raw.positions, + velocities: raw.velocities, + unit_cell: raw.unit_cell, + atoms: raw.atoms, + bonds: raw.bonds, + residues: raw.residues, + } + } +} + +/// Get the list of formats known by chemfiles, as well as all associated metadata. +/// +/// # Example +/// ``` +/// let formats = chemfiles::formats_list(); +/// println!("chemfiles supports {} formats:", formats.len()); +/// for format in &formats { +/// println!( +/// " {:<15} {}", +/// format.name, +/// format.extension.as_deref().unwrap_or("") +/// ); +/// } +/// ``` +#[must_use] +pub fn formats_list() -> Vec<FormatMetadata> { + let mut formats = std::ptr::null_mut(); + let mut count: u64 = 0; + let formats_slice = unsafe { + check_success(chfl_formats_list(&mut formats, &mut count)); + std::slice::from_raw_parts(formats, count.try_into().expect("failed to convert u64 to usize")) + }; + let formats_vec = formats_slice + .iter() + .map(|fm| FormatMetadata::from_raw(fm)) + .collect(); + unsafe { + let _ = chfl_free(formats as *const _); + } + return formats_vec; +} + +#[allow(clippy::doc_markdown)] +/// Get the format that chemfiles would use to read a file at the given +/// ``path``. +/// +/// The format is mostly guessed from the path extension, chemfiles only tries +/// to read the file to distinguish between CIF and mmCIF files. Opening the +/// file using the returned format string might still fail. For example, it will +/// fail if the file is not actually formatted according to the guessed format; +/// or the format/compression combination is not supported (e.g. `XTC / GZ` will +/// not work since the XTC reader does not support compressed files). +/// +/// The returned format is represented in a way compatible with the various +/// `Trajectory` constructors, i.e. `"<format name> [/ <compression>]"`, where +/// compression is optional. +/// +/// # Examples +/// ``` +/// let format = chemfiles::guess_format("trajectory.xyz.xz"); +/// assert_eq!(format, "XYZ / XZ"); +/// +/// let format = chemfiles::guess_format("trajectory.nc"); +/// assert_eq!(format, "Amber NetCDF"); +/// ``` +pub fn guess_format(path: &str) -> String { + let path = crate::strings::to_c(path); + let mut buffer = vec![0; 128]; + unsafe { + check_success(chfl_guess_format( + path.as_ptr(), buffer.as_mut_ptr(), buffer.len() as u64 + )); + } + return crate::strings::from_c(buffer.as_ptr()); +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +use std::ops::Drop; +use std::vec::IntoIter; + +use chemfiles_sys::*; +use errors::{check, check_not_null, check_success, Error}; +use strings; + +/// A thin wrapper around `CHFL_PROPERTY` +pub(crate) struct RawProperty { + handle: *mut CHFL_PROPERTY, +} + +impl RawProperty { + /// Create a `RawProperty` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the pointer. + pub unsafe fn from_ptr(ptr: *mut CHFL_PROPERTY) -> RawProperty { + check_not_null(ptr); + RawProperty { + handle: ptr + } + } + + /// Get the underlying C pointer as a const pointer. + pub fn as_ptr(&self) -> *const CHFL_PROPERTY { + self.handle + } + + fn double(value: f64) -> RawProperty { + unsafe { + let handle = chfl_property_double(value); + RawProperty::from_ptr(handle) + } + } + + fn bool(value: bool) -> RawProperty { + let value = if value { 1 } else { 0 }; + unsafe { + let handle = chfl_property_bool(value); + RawProperty::from_ptr(handle) + } + } + + fn vector3d(value: [f64; 3]) -> RawProperty { + unsafe { + let handle = chfl_property_vector3d(value.as_ptr()); + RawProperty::from_ptr(handle) + } + } + + fn string(value: &str) -> RawProperty { + let buffer = strings::to_c(value); + unsafe { + let handle = chfl_property_string(buffer.as_ptr()); + RawProperty::from_ptr(handle) + } + } + + fn get_kind(&self) -> chfl_property_kind { + let mut kind = chfl_property_kind::CHFL_PROPERTY_BOOL; + unsafe { + check_success(chfl_property_get_kind(self.as_ptr(), &mut kind)); + } + return kind; + } + + fn get_bool(&self) -> Result<bool, Error> { + let mut value = 0; + unsafe { + check(chfl_property_get_bool(self.as_ptr(), &mut value))?; + } + return Ok(value != 0); + } + + fn get_double(&self) -> Result<f64, Error> { + let mut value = 0.0; + unsafe { + check(chfl_property_get_double(self.as_ptr(), &mut value))?; + } + return Ok(value); + } + + fn get_string(&self) -> Result<String, Error> { + let get_string = |ptr, len| unsafe { chfl_property_get_string(self.as_ptr(), ptr, len) }; + let value = strings::call_autogrow_buffer(64, get_string)?; + return Ok(strings::from_c(value.as_ptr())); + } + + fn get_vector3d(&self) -> Result<[f64; 3], Error> { + let mut value = [0.0; 3]; + unsafe { + check(chfl_property_get_vector3d(self.as_ptr(), value.as_mut_ptr()))?; + } + return Ok(value); + } +} + +impl Drop for RawProperty { + fn drop(&mut self) { + unsafe { + let _ = chfl_free(self.as_ptr().cast()); + } + } +} + +/// A `Property` is a piece of data that can be associated with an `Atom` or a +/// `Frame`. +#[derive(Debug, Clone, PartialEq, PartialOrd)] +pub enum Property { + /// Boolean property + Bool(bool), + /// Floating point property + Double(f64), + /// String property + String(String), + /// 3-dimensional vector property + Vector3D([f64; 3]), +} + +impl From<bool> for Property { + fn from(value: bool) -> Self { + Property::Bool(value) + } +} + +impl From<f64> for Property { + fn from(value: f64) -> Self { + Property::Double(value) + } +} + +impl From<String> for Property { + fn from(value: String) -> Self { + Property::String(value) + } +} + +impl<'a> From<&'a str> for Property { + fn from(value: &'a str) -> Self { + Property::String(value.into()) + } +} + +impl From<[f64; 3]> for Property { + fn from(value: [f64; 3]) -> Self { + Property::Vector3D(value) + } +} + +impl Property { + pub(crate) fn as_raw(&self) -> RawProperty { + match *self { + Property::Bool(value) => RawProperty::bool(value), + Property::Double(value) => RawProperty::double(value), + Property::String(ref value) => RawProperty::string(value), + Property::Vector3D(value) => RawProperty::vector3d(value), + } + } + + #[allow(clippy::needless_pass_by_value)] // raw property + pub(crate) fn from_raw(raw: RawProperty) -> Property { + match raw.get_kind() { + chfl_property_kind::CHFL_PROPERTY_BOOL => { + Property::Bool(raw.get_bool().expect("shoudl be a bool")) + } + chfl_property_kind::CHFL_PROPERTY_DOUBLE => { + Property::Double(raw.get_double().expect("should be a double")) + } + chfl_property_kind::CHFL_PROPERTY_STRING => { + Property::String(raw.get_string().expect("should be a string")) + } + chfl_property_kind::CHFL_PROPERTY_VECTOR3D => { + Property::Vector3D(raw.get_vector3d().expect("should be a vector3d")) + } + } + } +} + +/// An iterator over the properties in an atom/frame/residue +pub struct PropertiesIter<'a> where { + pub(crate) names: IntoIter<String>, + pub(crate) getter: Box<dyn Fn(&str) -> Property + 'a>, +} + +impl<'a> Iterator for PropertiesIter<'a> { + type Item = (String, Property); + fn next(&mut self) -> Option<Self::Item> { + self.names.next().map(|name| { + let property = (self.getter)(&*name); + (name, property) + }) + } + + fn size_hint(&self) -> (usize, Option<usize>) { + self.names.size_hint() + } + + fn count(self) -> usize { + self.names.count() + } +} + +#[cfg(test)] +mod tests { + mod raw { + use super::super::*; + + #[test] + fn bool() { + let property = RawProperty::bool(false); + assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_BOOL); + assert_eq!(property.get_bool(), Ok(false)); + } + + #[test] + fn double() { + let property = RawProperty::double(45.0); + assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_DOUBLE); + assert_eq!(property.get_double(), Ok(45.0)); + } + + #[test] + fn string() { + let property = RawProperty::string("test"); + assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_STRING); + assert_eq!(property.get_string(), Ok("test".into())); + } + + #[test] + fn vector3d() { + let property = RawProperty::vector3d([1.2, 3.4, 5.6]); + assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_VECTOR3D); + assert_eq!(property.get_vector3d(), Ok([1.2, 3.4, 5.6])); + } + } + + mod rust { + use super::super::*; + + #[test] + fn bool() { + let property = Property::Bool(false); + + let raw = property.as_raw(); + assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_BOOL); + assert_eq!(raw.get_bool(), Ok(false)); + + assert_eq!(Property::from_raw(raw), property); + } + + #[test] + fn double() { + let property = Property::Double(45.0); + + let raw = property.as_raw(); + assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_DOUBLE); + assert_eq!(raw.get_double(), Ok(45.0)); + + assert_eq!(Property::from_raw(raw), property); + } + + #[test] + fn string() { + let property = Property::String("test".into()); + + let raw = property.as_raw(); + assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_STRING); + assert_eq!(raw.get_string(), Ok("test".into())); + + assert_eq!(Property::from_raw(raw), property); + + let property = Property::String("long string ".repeat(128)); + let raw = property.as_raw(); + assert_eq!(raw.get_string(), Ok("long string ".repeat(128))); + } + + #[test] + fn vector3d() { + let property = Property::Vector3D([1.2, 3.4, 5.6]); + + let raw = property.as_raw(); + assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_VECTOR3D); + assert_eq!(raw.get_vector3d(), Ok([1.2, 3.4, 5.6])); + + assert_eq!(Property::from_raw(raw), property); + } + } +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +use std::ops::{Drop, Deref}; +use std::marker::PhantomData; +use std::ptr; + +use chemfiles_sys::*; +use errors::{check_not_null, check_success}; +use property::{Property, RawProperty, PropertiesIter}; +use strings; + +/// A `Residue` is a group of atoms belonging to the same logical unit. They +/// can be small molecules, amino-acids in a protein, monomers in polymers, +/// *etc.* +pub struct Residue { + handle: *mut CHFL_RESIDUE, +} + +/// An analog to a reference to a residue (`&Residue`) +pub struct ResidueRef<'a> { + inner: Residue, + marker: PhantomData<&'a Residue> +} + +impl<'a> Deref for ResidueRef<'a> { + type Target = Residue; + fn deref(&self) -> &Residue { + &self.inner + } +} + +impl Clone for Residue { + fn clone(&self) -> Residue { + unsafe { + let new_handle = chfl_residue_copy(self.as_ptr()); + Residue::from_ptr(new_handle) + } + } +} + +impl Residue { + /// Create a `Residue` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the pointer. + #[inline] + pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_RESIDUE) -> Residue { + check_not_null(ptr); + Residue { + handle: ptr + } + } + + /// Create a borrowed `Residue` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the + /// pointer, except for it being non-null, and the caller is responsible + /// for setting the right lifetime + #[inline] + pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_RESIDUE) -> ResidueRef<'a> { + ResidueRef { + inner: Residue::from_ptr(ptr as *mut CHFL_RESIDUE), + marker: PhantomData, + } + } + + /// Get the underlying C pointer as a const pointer. + #[inline] + pub(crate) fn as_ptr(&self) -> *const CHFL_RESIDUE { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer. + #[inline] + pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_RESIDUE { + self.handle + } + + /// Create a new residue with the given `name` + /// + /// # Example + /// ``` + /// # use chemfiles::Residue; + /// let residue = Residue::new("ALA"); + /// assert_eq!(residue.name(), "ALA"); + /// assert_eq!(residue.id(), None); + /// ``` + pub fn new<'a>(name: impl Into<&'a str>) -> Residue { + let buffer = strings::to_c(name.into()); + unsafe { + let handle = chfl_residue(buffer.as_ptr()); + Residue::from_ptr(handle) + } + } + + /// Create a new residue with the given `name` and `id` as identifier. + /// + /// # Example + /// ``` + /// # use chemfiles::Residue; + /// let residue = Residue::with_id("ALA", 67); + /// assert_eq!(residue.name(), "ALA"); + /// assert_eq!(residue.id(), Some(67)); + /// ``` + pub fn with_id<'a>(name: impl Into<&'a str>, id: i64) -> Residue { + let buffer = strings::to_c(name.into()); + unsafe { + let handle = chfl_residue_with_id(buffer.as_ptr(), id); + Residue::from_ptr(handle) + } + } + + /// Get the number of atoms in this residue. + /// + /// # Example + /// ``` + /// # use chemfiles::Residue; + /// let mut residue = Residue::new("water"); + /// assert_eq!(residue.size(), 0); + /// + /// residue.add_atom(0); + /// residue.add_atom(1); + /// residue.add_atom(2); + /// assert_eq!(residue.size(), 3); + /// ``` + pub fn size(&self) -> usize { + let mut size = 0; + unsafe { + check_success(chfl_residue_atoms_count(self.as_ptr(), &mut size)); + } + #[allow(clippy::cast_possible_truncation)] + return size as usize; + } + + /// Get the identifier of this residue in the initial topology file. + /// + /// # Example + /// ``` + /// # use chemfiles::Residue; + /// let residue = Residue::with_id("", 42); + /// assert_eq!(residue.id(), Some(42)); + /// ``` + pub fn id(&self) -> Option<i64> { + let mut resid = 0; + let status = unsafe { + chfl_residue_id(self.as_ptr(), &mut resid) + }; + + if status == chfl_status::CHFL_SUCCESS { + return Some(resid); + } else if status == chfl_status::CHFL_GENERIC_ERROR { + return None; + } + + // call check_success to panic in case of error + check_success(status); + unreachable!(); + } + + /// Get the name of this residue. + /// + /// # Example + /// ``` + /// # use chemfiles::Residue; + /// let residue = Residue::new("water"); + /// assert_eq!(residue.name(), "water"); + /// ``` + pub fn name(&self) -> String { + let get_name = |ptr, len| unsafe { chfl_residue_name(self.as_ptr(), ptr, len) }; + let name = strings::call_autogrow_buffer(64, get_name).expect("getting residue name failed"); + return strings::from_c(name.as_ptr()); + } + + /// Add the atom at index `atom` in this residue. + /// + /// This will fail if the atom is already in the residue. + /// + /// # Example + /// ``` + /// # use chemfiles::Residue; + /// let mut residue = Residue::new("water"); + /// assert_eq!(residue.size(), 0); + /// assert_eq!(residue.contains(56), false); + /// + /// residue.add_atom(56); + /// assert_eq!(residue.size(), 1); + /// assert_eq!(residue.contains(56), true); + /// + /// // Adding the same atom twice is fine + /// residue.add_atom(56); + /// assert_eq!(residue.size(), 1); + /// ``` + pub fn add_atom(&mut self, atom: usize) { + unsafe { + check_success(chfl_residue_add_atom(self.as_mut_ptr(), atom as u64)); + } + } + + /// Check if the atom at index `i` is in this residue + /// + /// # Example + /// ``` + /// # use chemfiles::Residue; + /// let mut residue = Residue::new("water"); + /// assert_eq!(residue.contains(56), false); + /// + /// residue.add_atom(56); + /// assert_eq!(residue.contains(56), true); + /// ``` + pub fn contains(&self, atom: usize) -> bool { + let mut inside = 0; + unsafe { + check_success(chfl_residue_contains(self.as_ptr(), atom as u64, &mut inside)); + } + return inside != 0; + } + + /// Get the list of atoms of this residue. + /// + /// # Example + /// ``` + /// # use chemfiles::Residue; + /// let mut residue = Residue::new("water"); + /// assert_eq!(residue.atoms(), vec![]); + /// + /// residue.add_atom(56); + /// assert_eq!(residue.atoms(), vec![56]); + /// ``` + pub fn atoms(&self) -> Vec<usize> { + let size = self.size(); + let count = size as u64; + let mut indices = vec![u64::max_value(); size]; + unsafe { + check_success(chfl_residue_atoms( + self.as_ptr(), + indices.as_mut_ptr(), + count, + )); + } + #[allow(clippy::cast_possible_truncation)] + return indices.into_iter().map(|idx| idx as usize).collect(); + } + + /// Add a new `property` with the given `name` to this residue. + /// + /// If a property with the same name already exists, this function override + /// the existing property with the new one. + /// + /// # Examples + /// ``` + /// # use chemfiles::{Residue, Property}; + /// let mut residue = Residue::new("ALA"); + /// residue.set("a string", "hello"); + /// residue.set("a double", 3.2); + /// + /// assert_eq!(residue.get("a string"), Some(Property::String("hello".into()))); + /// assert_eq!(residue.get("a double"), Some(Property::Double(3.2))); + /// ``` + pub fn set(&mut self, name: &str, property: impl Into<Property>) { + let buffer = strings::to_c(name); + let property = property.into().as_raw(); + unsafe { + check_success(chfl_residue_set_property( + self.as_mut_ptr(), buffer.as_ptr(), property.as_ptr() + )); + } + } + + /// Get a property with the given `name` in this frame, if it exist. + /// + /// # Examples + /// ``` + /// # use chemfiles::{Residue, Property}; + /// let mut residue = Residue::new("ALA"); + /// residue.set("foo", Property::Double(22.2)); + /// + /// assert_eq!(residue.get("foo"), Some(Property::Double(22.2))); + /// assert_eq!(residue.get("Bar"), None); + /// ``` + pub fn get(&self, name: &str) -> Option<Property> { + let buffer = strings::to_c(name); + unsafe { + let handle = chfl_residue_get_property(self.as_ptr(), buffer.as_ptr()); + if handle.is_null() { + None + } else { + let raw = RawProperty::from_ptr(handle); + Some(Property::from_raw(raw)) + } + } + } + + /// Get an iterator over all (name, property) pairs for this frame + /// + /// # Examples + /// ``` + /// # use chemfiles::{Residue, Property}; + /// let mut residue = Residue::new("ALA"); + /// residue.set("foo", Property::Double(22.2)); + /// residue.set("bar", Property::Bool(false)); + /// + /// for (name, property) in residue.properties() { + /// if name == "foo" { + /// assert_eq!(property, Property::Double(22.2)); + /// } else if name == "bar" { + /// assert_eq!(property, Property::Bool(false)); + /// } + /// } + /// ``` + pub fn properties(&self) -> PropertiesIter { + let mut count = 0; + unsafe { + check_success(chfl_residue_properties_count(self.as_ptr(), &mut count)); + } + + #[allow(clippy::cast_possible_truncation)] + let size = count as usize; + let mut c_names = vec![ptr::null_mut(); size]; + unsafe { + check_success(chfl_residue_list_properties(self.as_ptr(), c_names.as_mut_ptr(), count)); + } + + let mut names = Vec::new(); + for ptr in c_names { + names.push(strings::from_c(ptr)); + } + + PropertiesIter { + names: names.into_iter(), + getter: Box::new(move |name| self.get(&*name).expect("failed to get property")) + } + } +} + +impl Drop for Residue { + fn drop(&mut self) { + unsafe { + let _ = chfl_free(self.as_ptr().cast()); + } + } +} + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + fn clone() { + let mut residue = Residue::new("A"); + assert_eq!(residue.size(), 0); + + let copy = residue.clone(); + assert_eq!(copy.size(), 0); + + residue.add_atom(3); + residue.add_atom(7); + assert_eq!(residue.size(), 2); + assert_eq!(copy.size(), 0); + } + + #[test] + fn name() { + let residue = Residue::new("A"); + assert_eq!(residue.name(), "A"); + } + + #[test] + fn id() { + let residue = Residue::new("A"); + assert_eq!(residue.id(), None); + + let residue = Residue::with_id("A", 42); + assert_eq!(residue.id(), Some(42)); + + let residue = Residue::with_id("A", -3); + assert_eq!(residue.id(), Some(-3)); + } + + #[test] + fn atoms() { + let mut residue = Residue::new("A"); + assert_eq!(residue.size(), 0); + + residue.add_atom(0); + residue.add_atom(3); + residue.add_atom(45); + assert_eq!(residue.size(), 3); + + assert!(residue.contains(3)); + assert!(!residue.contains(5)); + + assert_eq!(residue.atoms(), vec![0, 3, 45]); + } + + #[test] + fn property() { + let mut residue = Residue::new("ALA"); + + residue.set("foo", -22.0); + assert_eq!(residue.get("foo"), Some(Property::Double(-22.0))); + assert_eq!(residue.get("bar"), None); + + residue.set("bar", Property::String("here".into())); + for (name, property) in residue.properties() { + if name == "foo" { + assert_eq!(property, Property::Double(-22.0)); + } else if name == "bar" { + assert_eq!(property, Property::String("here".into())); + } + } + } +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +use std::ops::{Drop, Index}; +use std::iter::IntoIterator; +use std::slice::Iter; + +use chemfiles_sys::*; +use errors::{check, check_not_null, check_success, Error, Status}; +use strings; +use frame::Frame; + +#[derive(Debug, Clone, PartialEq, Eq)] +/// A `Match` is a set of atomic indexes matching a given selection. It can +/// mostly be used like a `&[usize]`. +pub struct Match { + size: usize, + atoms: [usize; 4], +} + +#[allow(clippy::len_without_is_empty)] +impl Match { + /// Get the length of the Match. + /// + /// # Example + /// + /// ``` + /// # use chemfiles::Match; + /// let atomic_match = Match::new(&[3, 4, 5]); + /// assert_eq!(atomic_match.len(), 3); + /// ``` + pub fn len(&self) -> usize { + self.size + } + + /// Create a new match containing the atoms in the `atoms` slice. + /// + /// # Panics + /// + /// If the slice contains more than 4 elements, which is the maximal size + /// of a match. + /// + /// # Example + /// + /// ``` + /// # use chemfiles::Match; + /// let atomic_match = Match::new(&[3, 4, 5]); + /// assert_eq!(atomic_match.len(), 3); + /// assert_eq!(atomic_match[0], 3); + /// assert_eq!(atomic_match[1], 4); + /// assert_eq!(atomic_match[2], 5); + /// ``` + pub fn new(atoms: &[usize]) -> Match { + assert!(atoms.len() <= 4); + let size = atoms.len(); + let mut matches = [usize::max_value(); 4]; + for (i, atom) in atoms.iter().enumerate() { + matches[i] = *atom; + } + Match { + size, + atoms: matches, + } + } + + /// Iterate over the atomic indexes in the match. + /// + /// # Example + /// + /// ``` + /// # use chemfiles::Match; + /// let atomic_match = Match::new(&[3, 4, 5]); + /// let mut iter = atomic_match.iter(); + /// + /// assert_eq!(iter.next(), Some(&3)); + /// assert_eq!(iter.next(), Some(&4)); + /// assert_eq!(iter.next(), Some(&5)); + /// assert_eq!(iter.next(), None); + /// ``` + pub fn iter(&self) -> Iter<usize> { + self.atoms[..self.len()].iter() + } +} + +impl Index<usize> for Match { + type Output = usize; + fn index(&self, i: usize) -> &Self::Output { + assert!(i < self.len()); + &self.atoms[i] + } +} + +impl<'a> IntoIterator for &'a Match { + type Item = &'a usize; + type IntoIter = Iter<'a, usize>; + fn into_iter(self) -> Iter<'a, usize> { + self.atoms[..self.len()].iter() + } +} + +/// A `Selection` allow to select atoms in a `Frame`, from a selection +/// language. The selection language is built by combining basic operations. +/// Each basic operation follows the `<selector>[(<variable>)] <operator> +/// <value>` structure, where `<operator>` is a comparison operator in +/// `== != < <= > >=`. +pub struct Selection { + handle: *mut CHFL_SELECTION, +} + +impl Clone for Selection { + fn clone(&self) -> Selection { + unsafe { + let new_handle = chfl_selection_copy(self.as_ptr()); + Selection::from_ptr(new_handle) + } + } +} + +impl Drop for Selection { + fn drop(&mut self) { + unsafe { + let _ = chfl_free(self.as_ptr().cast()); + } + } +} + +impl Selection { + /// Create a `Selection` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the pointer. + #[inline] + pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_SELECTION) -> Selection { + check_not_null(ptr); + Selection { + handle: ptr + } + } + + /// Get the underlying C pointer as a const pointer. + #[inline] + pub(crate) fn as_ptr(&self) -> *const CHFL_SELECTION { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer. + #[inline] + pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_SELECTION { + self.handle + } + + /// Create a new selection from the given selection string. + /// + /// # Errors + /// + /// This function fails if the selection string is invalid. + /// + /// # Example + /// ``` + /// # use chemfiles::Selection; + /// let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap(); + /// ``` + pub fn new<'a, S: Into<&'a str>>(selection: S) -> Result<Selection, Error> { + let buffer = strings::to_c(selection.into()); + unsafe { + let handle = chfl_selection(buffer.as_ptr()); + if handle.is_null() { + Err(Error { + status: Status::SelectionError, + message: Error::last_error() + }) + } else { + Ok(Selection::from_ptr(handle)) + } + } + } + + /// Get the size of the selection, i.e. the number of atoms we are selecting + /// together. + /// + /// This value is 1 for the 'atom' context, 2 for the 'pair' and 'bond' + /// context, 3 for the 'three' and 'angles' context and 4 for the 'four' + /// and 'dihedral' context. + /// + /// # Example + /// ``` + /// # use chemfiles::Selection; + /// let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap(); + /// assert_eq!(selection.size(), 2); + /// ``` + pub fn size(&self) -> usize { + let mut size = 0; + unsafe { + check_success(chfl_selection_size(self.as_ptr(), &mut size)); + } + #[allow(clippy::cast_possible_truncation)] + return size as usize; + } + + /// Get the selection string used to create this selection. + /// + /// # Example + /// ``` + /// # use chemfiles::Selection; + /// let selection = Selection::new("name H").unwrap(); + /// assert_eq!(selection.string(), "name H"); + /// ``` + pub fn string(&self) -> String { + let get_string = |ptr, len| unsafe { chfl_selection_string(self.as_ptr(), ptr, len) }; + let selection = strings::call_autogrow_buffer(1024, get_string).expect("failed to get selection string"); + return strings::from_c(selection.as_ptr()); + } + + /// Evaluate a selection for a given frame, and return the corresponding + /// matches. + /// + /// # Example + /// ``` + /// # use chemfiles::{Selection, Frame, Atom}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None); + /// + /// let mut selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap(); + /// let matches = selection.evaluate(&frame); + /// + /// assert_eq!(matches.len(), 2); + /// + /// assert_eq!(matches[0].len(), 2); + /// assert_eq!(matches[0][0], 0); + /// assert_eq!(matches[0][1], 1); + /// + /// assert_eq!(matches[1].len(), 2); + /// assert_eq!(matches[1][0], 2); + /// assert_eq!(matches[1][1], 1); + /// ``` + pub fn evaluate(&mut self, frame: &Frame) -> Vec<Match> { + #![allow(clippy::cast_possible_truncation)] + let mut count = 0; + unsafe { + check(chfl_selection_evaluate( + self.as_mut_ptr(), frame.as_ptr(), &mut count + )).expect("failed to evaluate selection"); + } + + let size = count as usize; + let mut chfl_matches = vec![chfl_match { size: 0, atoms: [0; 4] }; size]; + unsafe { + check(chfl_selection_matches( + self.handle, + chfl_matches.as_mut_ptr(), + count + )).expect("failed to extract matches"); + } + + return chfl_matches.into_iter() + .map(|chfl_match| Match { + size: chfl_match.size as usize, + atoms: [ + chfl_match.atoms[0] as usize, + chfl_match.atoms[1] as usize, + chfl_match.atoms[2] as usize, + chfl_match.atoms[3] as usize, + ], + }) + .collect(); + } + + /// Evaluates a selection of size 1 on a given `frame`. This function + /// returns the list of atomic indexes in the frame matching this selection. + /// + /// # Panics + /// + /// If the selection size is not 1 + /// + /// # Example + /// ``` + /// # use chemfiles::{Selection, Frame, Atom}; + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None); + /// + /// let mut selection = Selection::new("name H").unwrap(); + /// let matches = selection.list(&frame); + /// + /// assert_eq!(matches.len(), 2); + /// assert_eq!(matches[0], 0); + /// assert_eq!(matches[1], 2); + /// ``` + pub fn list(&mut self, frame: &Frame) -> Vec<usize> { + if self.size() != 1 { + panic!("can not call `Selection::list` on a multiple selection") + } + return self.evaluate(frame) + .into_iter() + .map(|m| m[0] as usize) + .collect(); + } +} + +#[cfg(test)] +mod tests { + use super::*; + use Frame; + use Topology; + use Atom; + + #[test] + fn clone() { + let selection = Selection::new("name H").unwrap(); + + let copy = selection.clone(); + assert_eq!(selection.size(), 1); + assert_eq!(copy.size(), 1); + } + + fn testing_frame() -> Frame { + let mut topology = Topology::new(); + + topology.add_atom(&Atom::new("H")); + topology.add_atom(&Atom::new("O")); + topology.add_atom(&Atom::new("O")); + topology.add_atom(&Atom::new("H")); + + topology.add_bond(0, 1); + topology.add_bond(1, 2); + topology.add_bond(2, 3); + + let mut frame = Frame::new(); + frame.resize(4); + frame.set_topology(&topology).unwrap(); + return frame; + } + + mod matches { + use super::*; + + #[test] + fn index() { + let m = Match::new(&[1, 2, 3, 4]); + assert_eq!(m[0], 1); + assert_eq!(m[1], 2); + assert_eq!(m[2], 3); + assert_eq!(m[3], 4); + + let m = Match::new(&[1, 2]); + assert_eq!(m[0], 1); + assert_eq!(m[1], 2); + } + + #[test] + fn iter() { + let match_ = Match::new(&[1, 2, 3, 4]); + assert_eq!(match_.iter().copied().collect::<Vec<usize>>(), vec![1, 2, 3, 4]); + + let v = vec![1, 2, 3, 4]; + for (i, &m) in match_.iter().enumerate() { + assert_eq!(v[i], m); + } + } + + #[test] + #[should_panic] + fn out_of_bound() { + let m = Match::new(&[1, 2]); + let _ = m[2]; + } + + #[test] + #[should_panic] + fn too_big() { + let _ = Match::new(&[1, 2, 3, 5, 4]); + } + } + + #[test] + fn size() { + let selection = Selection::new("name H").unwrap(); + assert_eq!(selection.size(), 1); + + let selection = Selection::new("angles: name(#1) H").unwrap(); + assert_eq!(selection.size(), 3); + + let selection = Selection::new("four: name(#1) H").unwrap(); + assert_eq!(selection.size(), 4); + } + + #[test] + fn string() { + let selection = Selection::new("name H").unwrap(); + assert_eq!(selection.string(), "name H"); + + let selection = Selection::new("angles: name(#1) H").unwrap(); + assert_eq!(selection.string(), "angles: name(#1) H"); + } + + #[test] + fn evaluate() { + let frame = testing_frame(); + + let mut selection = Selection::new("name H").unwrap(); + let res = selection.evaluate(&frame); + assert_eq!(res, &[Match::new(&[0]), Match::new(&[3])]); + + let mut selection = Selection::new("angles: all").unwrap(); + let res = selection.evaluate(&frame); + for m in &[Match::new(&[0, 1, 2]), Match::new(&[1, 2, 3])] { + assert!(res.iter().any(|r| r == m)) + } + } + + #[test] + fn list() { + let frame = testing_frame(); + + let mut selection = Selection::new("name H").unwrap(); + let res = selection.list(&frame); + assert_eq!(res, vec![0, 3]); + } + + #[test] + #[should_panic = "can not call `Selection::list` on a multiple selection"] + fn list_on_size_1_selection() { + let frame = testing_frame(); + let mut selection = Selection::new("pairs: name(#1) H").unwrap(); + let _list = selection.list(&frame); + } +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed + +//! String conversions between C and Rust +use std::ffi::{CStr, CString}; + +use chemfiles_sys::chfl_status; +use errors::{check, Error}; + +/// Create a Rust string from a C string. Clones all characters in `buffer`. +pub fn from_c(buffer: *const i8) -> String { + unsafe { + let rust_str = CStr::from_ptr(buffer) + .to_str() + .expect("Invalid Rust string from C"); + return String::from(rust_str); + } +} + +/// Create a C string from a Rust string. +pub fn to_c(string: &str) -> CString { + CString::new(string).expect("Invalid C string from Rust") +} + +/// Check if a string buffer was big enough when passed to a C function +fn buffer_was_big_enough(buffer: &[i8]) -> bool { + let len = buffer.len(); + if len < 2 { + false + } else { + // The C code should always set the last element to 0 + debug_assert_eq!(buffer[len - 1], 0); + buffer[len - 2] == 0 + } +} + +/// Call `callback` C function with a string buffer and it length, using +/// `initial` as the buffer initial size. If the buffer was filled and the +/// result truncated by the C library, grow the buffer and try again until we +/// get all the data. Then return the filled buffer to the caller. +pub fn call_autogrow_buffer<F>(initial: usize, callback: F) -> Result<Vec<i8>, Error> +where + F: Fn(*mut i8, u64) -> chfl_status, +{ + let mut size = initial; + let mut buffer = vec![0; size]; + check(callback(buffer.as_mut_ptr(), buffer.len() as u64))?; + + while !buffer_was_big_enough(&buffer) { + // Grow the buffer and retry + size *= 2; + buffer.resize(size, 0); + check(callback(buffer.as_mut_ptr(), buffer.len() as u64))?; + } + + Ok(buffer) +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +use std::ops::{Drop, Deref}; +use std::marker::PhantomData; + +use chemfiles_sys::*; +use errors::{check, check_not_null, check_success, Error}; +use super::{Atom, AtomRef, AtomMut}; +use super::{Residue, ResidueRef}; + +/// Possible bond order associated with bonds +#[repr(C)] +#[non_exhaustive] +#[derive(Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord)] +pub enum BondOrder { + /// Unknown or unspecified bond order + Unknown = chfl_bond_order::CHFL_BOND_UNKNOWN as isize, + /// Single bond + Single = chfl_bond_order::CHFL_BOND_SINGLE as isize, + /// Double bond + Double = chfl_bond_order::CHFL_BOND_DOUBLE as isize, + /// Triple bond + Triple = chfl_bond_order::CHFL_BOND_TRIPLE as isize, + /// Quadruple bond (present in some metals) + Quadruple = chfl_bond_order::CHFL_BOND_QUADRUPLE as isize, + /// Quintuplet bond (present in some metals) + Quintuplet = chfl_bond_order::CHFL_BOND_QUINTUPLET as isize, + /// Amide bond (required by some file formats) + Amide = chfl_bond_order::CHFL_BOND_AMIDE as isize, + /// Aromatic bond (required by some file formats) + Aromatic = chfl_bond_order::CHFL_BOND_AROMATIC as isize, +} + +impl BondOrder { + pub(crate) fn as_raw(self) -> chfl_bond_order { + match self { + BondOrder::Unknown => chfl_bond_order::CHFL_BOND_UNKNOWN, + BondOrder::Single => chfl_bond_order::CHFL_BOND_SINGLE, + BondOrder::Double => chfl_bond_order::CHFL_BOND_DOUBLE, + BondOrder::Triple => chfl_bond_order::CHFL_BOND_TRIPLE, + BondOrder::Quadruple => chfl_bond_order::CHFL_BOND_QUADRUPLE, + BondOrder::Quintuplet => chfl_bond_order::CHFL_BOND_QUINTUPLET, + BondOrder::Amide => chfl_bond_order::CHFL_BOND_AMIDE, + BondOrder::Aromatic => chfl_bond_order::CHFL_BOND_AROMATIC, + } + } +} + +impl From<chfl_bond_order> for BondOrder { + fn from(order: chfl_bond_order) -> BondOrder { + match order { + chfl_bond_order::CHFL_BOND_UNKNOWN => BondOrder::Unknown, + chfl_bond_order::CHFL_BOND_SINGLE => BondOrder::Single, + chfl_bond_order::CHFL_BOND_DOUBLE => BondOrder::Double, + chfl_bond_order::CHFL_BOND_TRIPLE => BondOrder::Triple, + chfl_bond_order::CHFL_BOND_QUADRUPLE => BondOrder::Quadruple, + chfl_bond_order::CHFL_BOND_QUINTUPLET => BondOrder::Quintuplet, + chfl_bond_order::CHFL_BOND_AMIDE => BondOrder::Amide, + chfl_bond_order::CHFL_BOND_AROMATIC => BondOrder::Aromatic, + } + } +} + +/// A `Topology` contains the definition of all the atoms in the system, and +/// the liaisons between the atoms (bonds, angles, dihedrals, ...). It will +/// also contain all the residues information if it is available. +pub struct Topology { + handle: *mut CHFL_TOPOLOGY, +} + +/// An analog to a reference to a topology (`&Topology`) +pub struct TopologyRef<'a> { + inner: Topology, + marker: PhantomData<&'a Topology> +} + +impl<'a> Deref for TopologyRef<'a> { + type Target = Topology; + fn deref(&self) -> &Topology { + &self.inner + } +} + +impl Clone for Topology { + fn clone(&self) -> Topology { + unsafe { + let new_handle = chfl_topology_copy(self.as_ptr()); + Topology::from_ptr(new_handle) + } + } +} + +impl Topology { + /// Create a `Topology` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the pointer, + /// except for it being non-null. + #[inline] + pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_TOPOLOGY) -> Topology { + check_not_null(ptr); + Topology { + handle: ptr + } + } + + /// Create a borrowed `Topology` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the + /// pointer, except for it being non-null, and the caller is responsible + /// for setting the right lifetime + #[inline] + pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_TOPOLOGY) -> TopologyRef<'a> { + TopologyRef { + inner: Topology::from_ptr(ptr as *mut CHFL_TOPOLOGY), + marker: PhantomData, + } + } + + /// Get the underlying C pointer as a const pointer. + #[inline] + pub(crate) fn as_ptr(&self) -> *const CHFL_TOPOLOGY { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer. + #[inline] + pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_TOPOLOGY { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer FROM A SHARED REFERENCE. + /// + /// For uses with functions of the C API using mut pointers for both read + /// and write access. Users should check that this does not lead to multiple + /// mutable borrows + #[inline] + #[allow(non_snake_case)] + pub(crate) fn as_mut_ptr_MANUALLY_CHECKING_BORROW(&self) -> *mut CHFL_TOPOLOGY { + self.handle + } + + /// Create a new empty topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let topology = Topology::new(); + /// assert_eq!(topology.size(), 0); + /// ``` + pub fn new() -> Topology { + unsafe { + Topology::from_ptr(chfl_topology()) + } + } + + /// Get a reference of the atom at the given `index` in this topology. + /// + /// # Panics + /// + /// If `index` is out of bounds. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// topology.resize(6); + /// + /// let atom = topology.atom(4); + /// assert_eq!(atom.name(), ""); + /// ``` + pub fn atom(&self, index: usize) -> AtomRef { + unsafe { + let handle = chfl_atom_from_topology( + self.as_mut_ptr_MANUALLY_CHECKING_BORROW(), index as u64 + ); + Atom::ref_from_ptr(handle) + } + } + + /// Get a mutable reference to the atom at the given `index` in this topology. + /// + /// # Panics + /// + /// If `index` is out of bounds. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// topology.resize(6); + /// + /// assert_eq!(topology.atom(4).name(), ""); + /// + /// topology.atom_mut(4).set_name("Fe"); + /// assert_eq!(topology.atom(4).name(), "Fe"); + /// ``` + pub fn atom_mut(&mut self, index: usize) -> AtomMut { + unsafe { + let handle = chfl_atom_from_topology( + self.as_mut_ptr(), index as u64 + ); + Atom::ref_mut_from_ptr(handle) + } + } + + /// Get the current number of atoms in this topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.size(), 0); + /// + /// topology.resize(6); + /// assert_eq!(topology.size(), 6); + /// ``` + pub fn size(&self) -> usize { + let mut size = 0; + unsafe { + check_success(chfl_topology_atoms_count(self.as_ptr(), &mut size)); + } + #[allow(clippy::cast_possible_truncation)] + return size as usize; + } + + /// Resize this topology to hold `natoms` atoms, inserting dummy atoms if + /// the new size if bigger than the old one. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.size(), 0); + /// + /// topology.resize(6); + /// assert_eq!(topology.size(), 6); + /// ``` + pub fn resize(&mut self, natoms: usize) { + unsafe { + check_success(chfl_topology_resize(self.as_mut_ptr(), natoms as u64)); + } + } + + /// Add an `Atom` at the end of this topology + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, Atom}; + /// let mut topology = Topology::new(); + /// topology.add_atom(&Atom::new("Mg")); + /// + /// let atom = topology.atom(0); + /// assert_eq!(atom.name(), "Mg"); + /// ``` + pub fn add_atom(&mut self, atom: &Atom) { + unsafe { + check_success(chfl_topology_add_atom(self.as_mut_ptr(), atom.as_ptr())); + } + } + + /// Remove an `Atom` from this topology by `index`. This modify all the + /// other atoms indexes. + /// + /// # Panics + /// + /// If the `index` is out of bounds + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// topology.resize(9); + /// assert_eq!(topology.size(), 9); + /// + /// topology.remove(7); + /// assert_eq!(topology.size(), 8); + /// ``` + pub fn remove(&mut self, index: usize) { + unsafe { + check_success(chfl_topology_remove(self.as_mut_ptr(), index as u64)); + } + } + + /// Get the number of bonds in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.bonds_count(), 0); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(2, 1); + /// topology.add_bond(2, 3); + /// assert_eq!(topology.bonds_count(), 3); + /// ``` + pub fn bonds_count(&self) -> usize { + let mut count = 0; + unsafe { + check_success(chfl_topology_bonds_count(self.as_ptr(), &mut count)); + } + #[allow(clippy::cast_possible_truncation)] + return count as usize; + } + + /// Get the number of angles in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.angles_count(), 0); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(2, 1); + /// topology.add_bond(2, 3); + /// assert_eq!(topology.angles_count(), 2); + /// ``` + pub fn angles_count(&self) -> usize { + let mut count = 0; + unsafe { + check_success(chfl_topology_angles_count(self.as_ptr(), &mut count)); + } + #[allow(clippy::cast_possible_truncation)] + return count as usize; + } + + /// Get the number of dihedral angles in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.dihedrals_count(), 0); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(2, 1); + /// topology.add_bond(2, 3); + /// assert_eq!(topology.dihedrals_count(), 1); + /// ``` + pub fn dihedrals_count(&self) -> usize { + let mut count = 0; + unsafe { + check_success(chfl_topology_dihedrals_count(self.as_ptr(), &mut count)); + } + #[allow(clippy::cast_possible_truncation)] + return count as usize; + } + + /// Get the number of improper dihedral angles in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.dihedrals_count(), 0); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(0, 2); + /// topology.add_bond(0, 3); + /// assert_eq!(topology.impropers_count(), 1); + /// ``` + pub fn impropers_count(&self) -> usize { + let mut count = 0; + unsafe { + check_success(chfl_topology_impropers_count(self.as_ptr(), &mut count)); + } + #[allow(clippy::cast_possible_truncation)] + return count as usize; + } + + /// Get the list of bonds in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(2, 1); + /// topology.add_bond(2, 3); + /// assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]); + /// ``` + pub fn bonds(&self) -> Vec<[usize; 2]> { + let size = self.bonds_count(); + let count = size as u64; + let mut bonds = vec![[u64::max_value(); 2]; size]; + unsafe { + check_success(chfl_topology_bonds(self.as_ptr(), bonds.as_mut_ptr(), count)); + } + #[allow(clippy::cast_possible_truncation)] + return bonds + .into_iter() + .map(|bond| [bond[0] as usize, bond[1] as usize]) + .collect(); + } + + /// Get the list of angles in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(2, 1); + /// topology.add_bond(2, 3); + /// assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]); + /// ``` + pub fn angles(&self) -> Vec<[usize; 3]> { + let size = self.angles_count(); + let count = size as u64; + let mut angles = vec![[u64::max_value(); 3]; size]; + unsafe { + check_success(chfl_topology_angles(self.as_ptr(), angles.as_mut_ptr(), count)); + } + #[allow(clippy::cast_possible_truncation)] + return angles + .into_iter() + .map(|angle| [angle[0] as usize, angle[1] as usize, angle[2] as usize]) + .collect(); + } + + /// Get the list of dihedral angles in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(2, 1); + /// topology.add_bond(2, 3); + /// + /// assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]); + /// ``` + pub fn dihedrals(&self) -> Vec<[usize; 4]> { + let size = self.dihedrals_count(); + let count = size as u64; + let mut dihedrals = vec![[u64::max_value(); 4]; size]; + unsafe { + check_success(chfl_topology_dihedrals( + self.as_ptr(), dihedrals.as_mut_ptr(), count + )); + } + #[allow(clippy::cast_possible_truncation)] + return dihedrals + .into_iter() + .map(|dihedral| { + [ + dihedral[0] as usize, + dihedral[1] as usize, + dihedral[2] as usize, + dihedral[3] as usize, + ] + }) + .collect(); + } + + /// Get the list of improper dihedral angles in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(0, 2); + /// topology.add_bond(0, 3); + /// + /// assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]); + /// ``` + pub fn impropers(&self) -> Vec<[usize; 4]> { + let size = self.impropers_count(); + let count = size as u64; + let mut impropers = vec![[u64::max_value(); 4]; size]; + unsafe { + check_success(chfl_topology_impropers( + self.as_ptr(), impropers.as_mut_ptr(), count + )); + } + #[allow(clippy::cast_possible_truncation)] + return impropers + .into_iter() + .map(|improper| { + [ + improper[0] as usize, + improper[1] as usize, + improper[2] as usize, + improper[3] as usize, + ] + }) + .collect(); + } + + /// Remove all existing bonds, angles, dihedral angles and improper + /// dihedral angles in the topology. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.bonds_count(), 0); + /// topology.resize(4); + /// topology.add_bond(0, 1); + /// topology.add_bond(0, 2); + /// assert_eq!(topology.bonds_count(), 2); + /// assert_eq!(topology.angles().len(), 1); + /// + /// topology.clear_bonds(); + /// assert!(topology.bonds().is_empty()); + /// assert!(topology.angles().is_empty()); + /// ``` + pub fn clear_bonds(&mut self) { + unsafe { + check_success(chfl_topology_clear_bonds(self.as_mut_ptr())); + } + } + + /// Add a bond between the atoms at indexes `i` and `j` in the topology. + /// + /// The bond order is set to `BondOrder::Unknown`. + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, BondOrder}; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.bonds_count(), 0); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(0, 2); + /// assert_eq!(topology.bonds_count(), 2); + /// + /// assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown); + /// ``` + pub fn add_bond(&mut self, i: usize, j: usize) { + unsafe { + check_success(chfl_topology_add_bond(self.as_mut_ptr(), i as u64, j as u64)); + } + } + + /// Add a bond between the atoms at indexes `i` and `j` in the topology + /// with the given bond `order`. + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, BondOrder}; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.bonds_count(), 0); + /// topology.resize(2); + /// + /// topology.add_bond_with_order(0, 1, BondOrder::Double); + /// assert_eq!(topology.bond_order(0, 1), BondOrder::Double); + /// ``` + pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder) { + unsafe { + check_success(chfl_topology_bond_with_order( + self.as_mut_ptr(), i as u64, j as u64, order.as_raw() + )); + } + } + + /// Get the bond order for the bond between the atoms at indexes `i` and + /// `j`. + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, BondOrder}; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.bonds_count(), 0); + /// topology.resize(2); + /// + /// topology.add_bond_with_order(0, 1, BondOrder::Double); + /// assert_eq!(topology.bond_order(0, 1), BondOrder::Double); + /// ``` + pub fn bond_order(&self, i: usize, j: usize) -> BondOrder { + let mut order = chfl_bond_order::CHFL_BOND_UNKNOWN; + unsafe { + check_success(chfl_topology_bond_order( + self.as_ptr(), i as u64, j as u64, &mut order + )); + } + return order.into() + } + + /// Get the bond order for all the bonds in the topology + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, BondOrder}; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.bonds_count(), 0); + /// topology.resize(3); + /// + /// topology.add_bond_with_order(0, 1, BondOrder::Double); + /// topology.add_bond_with_order(0, 2, BondOrder::Single); + /// + /// assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]); + /// ``` + pub fn bond_orders(&self) -> Vec<BondOrder> { + let size = self.bonds_count(); + let count = size as u64; + let mut bonds = vec![BondOrder::Unknown; size]; + unsafe { + check_success(chfl_topology_bond_orders( + self.as_ptr(), + // Casting BondOrder to chfl_bond_order is safe, as they are + // both `repr(C)` enums with the same values. + bonds.as_mut_ptr().cast(), + count + )); + } + return bonds; + } + + /// Remove any existing bond between the atoms at indexes `i` and `j` in + /// this topology. + /// + /// This function does nothing if there is no bond between `i` and `j`. + /// + /// # Example + /// ``` + /// # use chemfiles::Topology; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.bonds_count(), 0); + /// topology.resize(4); + /// + /// topology.add_bond(0, 1); + /// topology.add_bond(1, 2); + /// assert_eq!(topology.bonds_count(), 2); + /// + /// topology.remove_bond(0, 1); + /// assert_eq!(topology.bonds_count(), 1); + /// + /// // Removing a bond that does not exists is fine + /// topology.remove_bond(0, 2); + /// assert_eq!(topology.bonds_count(), 1); + /// ``` + pub fn remove_bond(&mut self, i: usize, j: usize) { + unsafe { + check_success(chfl_topology_remove_bond(self.as_mut_ptr(), i as u64, j as u64)); + } + } + + /// Get a reference to the residue at index `index` from this topology. + /// + /// The residue index in the topology is not always the same as the residue + /// `id`. + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, Residue}; + /// let mut topology = Topology::new(); + /// topology.add_residue(&Residue::new("water")).unwrap(); + /// + /// let residue = topology.residue(0).unwrap(); + /// assert_eq!(residue.name(), "water"); + /// ``` + pub fn residue(&self, index: u64) -> Option<ResidueRef> { + unsafe { + let handle = chfl_residue_from_topology(self.as_ptr(), index as u64); + if handle.is_null() { + None + } else { + Some(Residue::ref_from_ptr(handle)) + } + } + } + + /// Get a copy of the residue containing the atom at index `index` in this + /// topology, if any. + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, Residue}; + /// let mut topology = Topology::new(); + /// topology.resize(8); + /// + /// let mut residue = Residue::new("water"); + /// residue.add_atom(0); + /// residue.add_atom(1); + /// residue.add_atom(2); + /// topology.add_residue(&residue).unwrap(); + /// + /// let residue = topology.residue_for_atom(0).unwrap(); + /// assert_eq!(residue.name(), "water"); + /// + /// assert!(topology.residue_for_atom(6).is_none()); + /// ``` + pub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef> { + let handle = unsafe { + chfl_residue_for_atom(self.as_ptr(), index as u64) + }; + if handle.is_null() { + None + } else { + unsafe { + Some(Residue::ref_from_ptr(handle)) + } + } + } + + /// Get the number of residues in this topology. + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, Residue}; + /// let mut topology = Topology::new(); + /// assert_eq!(topology.residues_count(), 0); + /// + /// topology.add_residue(&Residue::with_id("water", 0)).unwrap(); + /// topology.add_residue(&Residue::with_id("protein", 1)).unwrap(); + /// assert_eq!(topology.residues_count(), 2); + /// ``` + pub fn residues_count(&self) -> u64 { + let mut count = 0; + unsafe { + check_success(chfl_topology_residues_count(self.as_ptr(), &mut count)); + } + return count; + } + + /// Add a residue to this topology. + /// + /// # Errors + /// + /// This function fails is the residue `id` is not already in the topology, + /// or if the residue contains atoms that are already in another residue. + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, Residue}; + /// let mut topology = Topology::new(); + /// topology.add_residue(&Residue::new("water")).unwrap(); + /// + /// let residue = topology.residue(0).unwrap(); + /// assert_eq!(residue.name(), "water"); + /// ``` + pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error> { + unsafe { + check(chfl_topology_add_residue(self.as_mut_ptr(), residue.as_ptr())) + } + } + + /// Check if the two residues `first` and `second` from the `topology` are + /// linked together, *i.e.* if there is a bond between one atom in the + /// first residue and one atom in the second one. + /// + /// # Example + /// ``` + /// # use chemfiles::{Topology, Residue}; + /// let mut topology = Topology::new(); + /// + /// topology.add_residue(&Residue::with_id("water", 0)).unwrap(); + /// topology.add_residue(&Residue::with_id("protein", 1)).unwrap(); + /// + /// let first = topology.residue(0).unwrap(); + /// let second = topology.residue(1).unwrap(); + /// assert_eq!(topology.are_linked(&first, &second), false); + /// ``` + pub fn are_linked(&self, first: &Residue, second: &Residue) -> bool { + let mut linked = 0; + unsafe { + check_success(chfl_topology_residues_linked( + self.as_ptr(), + first.as_ptr(), + second.as_ptr(), + &mut linked + )); + } + return linked != 0; + } +} + +impl Drop for Topology { + fn drop(&mut self) { + unsafe { + let _ = chfl_free(self.as_ptr().cast()); + } + } +} + +#[cfg(test)] +mod test { + use super::*; + use {Atom, Residue}; + + #[test] + fn clone() { + let mut topology = Topology::new(); + assert_eq!(topology.size(), 0); + + let copy = topology.clone(); + assert_eq!(copy.size(), 0); + + topology.resize(10); + assert_eq!(topology.size(), 10); + assert_eq!(copy.size(), 0); + } + + #[test] + fn size() { + let mut topology = Topology::new(); + assert_eq!(topology.size(), 0); + + topology.resize(10); + assert_eq!(topology.size(), 10); + + topology.remove(7); + assert_eq!(topology.size(), 9); + + topology.add_atom(&Atom::new("Hg")); + assert_eq!(topology.size(), 10); + } + + #[test] + fn atoms() { + let mut topology = Topology::new(); + + topology.add_atom(&Atom::new("Hg")); + topology.add_atom(&Atom::new("Mn")); + topology.add_atom(&Atom::new("W")); + topology.add_atom(&Atom::new("Fe")); + + assert_eq!(topology.atom(0).name(), "Hg"); + assert_eq!(topology.atom(3).name(), "Fe"); + } + + #[test] + fn remove() { + let mut topology = Topology::new(); + topology.add_atom(&Atom::new("Hg")); + topology.add_atom(&Atom::new("Mn")); + topology.add_atom(&Atom::new("W")); + topology.add_atom(&Atom::new("Fe")); + + assert_eq!(topology.atom(0).name(), "Hg"); + assert_eq!(topology.atom(2).name(), "W"); + + topology.remove(1); + assert_eq!(topology.atom(0).name(), "Hg"); + assert_eq!(topology.atom(2).name(), "Fe"); + } + + #[test] + #[should_panic] + fn out_of_bounds_remove() { + let mut topology = Topology::new(); + topology.resize(18); + topology.remove(33); + } + + + #[test] + fn bonds() { + let mut topology = Topology::new(); + topology.resize(12); + assert_eq!(topology.bonds_count(), 0); + + topology.add_bond(0, 1); + topology.add_bond(9, 2); + topology.add_bond_with_order(3, 7, BondOrder::Aromatic); + assert_eq!(topology.bonds_count(), 3); + + assert_eq!(topology.bonds(), vec![[0, 1], [2, 9], [3, 7]]); + let expected = vec![BondOrder::Unknown, BondOrder::Unknown, BondOrder::Aromatic]; + assert_eq!(topology.bond_orders(), expected); + + assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown); + assert_eq!(topology.bond_order(3, 7), BondOrder::Aromatic); + + topology.remove_bond(3, 7); + // Removing unexisting bond is OK if both indexes are in bounds + topology.remove_bond(8, 7); + assert_eq!(topology.bonds_count(), 2); + + topology.clear_bonds(); + assert_eq!(topology.bonds_count(), 0); + } + + #[test] + #[should_panic] + fn out_of_bounds_bonds() { + let mut topology = Topology::new(); + topology.resize(12); + topology.add_bond(300, 7); + } + + #[test] + #[should_panic] + fn out_of_bounds_remove_bond() { + let mut topology = Topology::new(); + topology.resize(12); + topology.remove_bond(300, 7); + } + + #[test] + #[should_panic] + fn out_of_bounds_bonds_with_order() { + let mut topology = Topology::new(); + topology.resize(12); + topology.add_bond_with_order(300, 7, BondOrder::Unknown); + } + + #[test] + fn angles() { + let mut topology = Topology::new(); + topology.resize(12); + assert_eq!(topology.angles_count(), 0); + + topology.add_bond(0, 1); + topology.add_bond(1, 2); + topology.add_bond(3, 7); + topology.add_bond(3, 5); + assert_eq!(topology.angles_count(), 2); + + assert_eq!(topology.angles(), vec![[0, 1, 2], [5, 3, 7]]); + + topology.clear_bonds(); + assert_eq!(topology.angles_count(), 0); + } + + #[test] + fn dihedrals() { + let mut topology = Topology::new(); + topology.resize(12); + assert_eq!(topology.dihedrals_count(), 0); + + topology.add_bond(0, 1); + topology.add_bond(1, 2); + topology.add_bond(3, 2); + topology.add_bond(4, 7); + topology.add_bond(4, 5); + topology.add_bond(7, 10); + assert_eq!(topology.dihedrals_count(), 2); + + assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3], [5, 4, 7, 10]]); + + topology.clear_bonds(); + assert_eq!(topology.dihedrals_count(), 0); + } + + #[test] + fn impropers() { + let mut topology = Topology::new(); + topology.resize(12); + assert_eq!(topology.impropers_count(), 0); + + topology.add_bond(0, 1); + topology.add_bond(0, 2); + topology.add_bond(0, 3); + topology.add_bond(4, 7); + topology.add_bond(4, 5); + topology.add_bond(4, 8); + assert_eq!(topology.impropers_count(), 2); + + assert_eq!(topology.impropers(), vec![[1, 0, 2, 3], [5, 4, 7, 8]]); + + topology.clear_bonds(); + assert_eq!(topology.impropers_count(), 0); + } + + #[test] + fn residues() { + let mut topology = Topology::new(); + topology.resize(4); + assert_eq!(topology.residues_count(), 0); + + let mut residue = Residue::new("Foo"); + residue.add_atom(0); + residue.add_atom(2); + + topology.add_residue(&residue).unwrap(); + assert_eq!(topology.residues_count(), 1); + + assert_eq!(topology.residue(0).unwrap().name(), "Foo"); + { + let residue = topology.residue_for_atom(2).unwrap(); + assert_eq!(residue.name(), "Foo"); + } + + let mut residue = Residue::new("Bar"); + residue.add_atom(3); + topology.add_residue(&residue).unwrap(); + assert_eq!(topology.residues_count(), 2); + + let first = topology.residue(0).unwrap(); + let second = topology.residue(0).unwrap(); + assert!(topology.are_linked(&first, &second)); + + // missing residue + assert!(topology.residue_for_atom(1).is_none()); + // out of bounds + assert!(topology.residue_for_atom(67).is_none()); + } +} +
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+// Chemfiles, a modern library for chemistry file reading and writing +// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed +use std::convert::TryInto; +use std::path::Path; +use std::ptr; + +use chemfiles_sys::*; +use errors::{check, check_success, Error, Status}; +use strings; + +use {Frame, Topology, UnitCell}; + +/// The `Trajectory` type is the main entry point when using chemfiles. A +/// `Trajectory` behave a bit like a file, allowing to read and/or write +/// `Frame`. +pub struct Trajectory { + handle: *mut CHFL_TRAJECTORY, +} + +impl Trajectory { + /// Create a `Trajectory` from a C pointer. + /// + /// This function is unsafe because no validity check is made on the pointer. + #[inline] + pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_TRAJECTORY) -> Result<Trajectory, Error> { + if ptr.is_null() { + Err(Error { + status: Status::FileError, + message: Error::last_error() + }) + } else { + Ok(Trajectory { + handle: ptr + }) + } + } + + /// Get the underlying C pointer as a pointer. + #[inline] + pub(crate) fn as_ptr(&self) -> *const CHFL_TRAJECTORY { + self.handle + } + + /// Get the underlying C pointer as a mutable pointer. + #[inline] + pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_TRAJECTORY { + self.handle + } + + /// Open the file at the given `path` in the given `mode`. + /// + /// Valid modes are `'r'` for read, `'w'` for write and `'a'` for append. + /// + /// # Errors + /// + /// This function fails if the file is not accessible for the given mode, if + /// it is incorrectly formatted for the corresponding format, or in case of + /// I/O errors from the OS. + /// + /// # Example + /// ```no_run + /// # use chemfiles::Trajectory; + /// let trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + /// ``` + pub fn open<P>(path: P, mode: char) -> Result<Trajectory, Error> + where + P: AsRef<Path>, + { + let path = path.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(path.as_ref()))?; + + let path = strings::to_c(path); + unsafe { + #[allow(clippy::cast_possible_wrap)] + let handle = chfl_trajectory_open(path.as_ptr(), mode as i8); + Trajectory::from_ptr(handle) + } + } + + /// Open the file at the given `path` using a specific file `format` and the + /// given `mode`. + /// + /// Valid modes are `'r'` for read, `'w'` for write and `'a'` for append. + /// + /// Specifying a format is needed when the file format does not match the + /// extension, or when there is not standard extension for this format. If + /// `format` is an empty string, the format will be guessed from the + /// extension. + /// + /// # Errors + /// + /// This function fails if the file is not accessible for the given mode, if + /// it is incorrectly formatted for the corresponding format, or in case of + /// I/O errors from the OS. + /// + /// # Example + /// ```no_run + /// # use chemfiles::Trajectory; + /// let trajectory = Trajectory::open_with_format("water.zeo", 'r', "XYZ").unwrap(); + /// ``` + pub fn open_with_format<'a, P, S>(filename: P, mode: char, format: S) -> Result<Trajectory, Error> + where + P: AsRef<Path>, + S: Into<&'a str>, + { + let filename = + filename.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(filename.as_ref()))?; + + let filename = strings::to_c(filename); + let format = strings::to_c(format.into()); + unsafe { + #[allow(clippy::cast_possible_wrap)] + let handle = chfl_trajectory_with_format( + filename.as_ptr(), mode as i8, format.as_ptr() + ); + Trajectory::from_ptr(handle) + } + } + + /// Read a memory buffer as though it was a formatted file. + /// + /// The memory buffer used to store the file is given using the `data` + /// argument. The `format` parameter is required and should follow the same + /// rules as in the main `Trajectory` constructor. + /// + /// # Errors + /// + /// This function fails if the data is incorrectly formatted for the + /// corresponding format, or if the format do not support in-memory readers. + /// + /// # Example + /// ``` + /// # use chemfiles::{Trajectory, Frame}; + /// let aromatics = "c1ccccc1\nc1ccco1\nc1ccccn1\n"; + /// let mut trajectory = Trajectory::memory_reader(aromatics, "SMI").unwrap(); + /// let mut frame = Frame::new(); + /// trajectory.read(&mut frame).unwrap(); + /// assert_eq!(frame.size(), 6); + /// ``` + pub fn memory_reader<'a, S>(data: S, format: S) -> Result<Trajectory, Error> + where S: Into<&'a str>, + { + let data = strings::to_c(data.into()); + let format = strings::to_c(format.into()); + unsafe { + let handle = chfl_trajectory_memory_reader( + data.as_ptr(), data.as_bytes().len() as u64, format.as_ptr() + ); + Trajectory::from_ptr(handle) + } + } + + /// Write to a memory buffer as though it was a formatted file. + /// + /// The `format` parameter should follow the same rules as in the main + /// `Trajectory` constructor, except that compression specification + /// is not supported. + /// + /// The `memory_buffer` function can be used to retrieve the data written + /// to memory of the `Trajectory`. + /// + /// # Errors + /// + /// This function fails if the format do not support in-memory writers. + /// + /// # Example + /// ``` + /// # use chemfiles::Trajectory; + /// let trajectory_memory = Trajectory::memory_writer("SMI"); + /// + /// // Binary formats typically do not support this feature + /// assert!(Trajectory::memory_writer("XTC").is_err()); + /// ``` + pub fn memory_writer<'a, S>(format: S) -> Result<Trajectory, Error> + where S: Into<&'a str>, + { + let format = strings::to_c(format.into()); + unsafe { + let handle = chfl_trajectory_memory_writer(format.as_ptr()); + Trajectory::from_ptr(handle) + } + } + + /// Read the next step of this trajectory into a `frame`. + /// + /// If the number of atoms in frame does not correspond to the number of atom + /// in the next step, the frame is resized. + /// + /// # Errors + /// + /// This function fails if the data is incorrectly formatted for the + /// corresponding format, or in case of I/O errors from the OS. + /// + /// # Example + /// ```no_run + /// # use chemfiles::{Trajectory, Frame}; + /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + /// let mut frame = Frame::new(); + /// + /// trajectory.read(&mut frame).unwrap(); + /// ``` + pub fn read(&mut self, frame: &mut Frame) -> Result<(), Error> { + unsafe { + check(chfl_trajectory_read(self.as_mut_ptr(), frame.as_mut_ptr())) + } + } + + /// Read a specific `step` of this trajectory into a `frame`. + /// + /// If the number of atoms in frame does not correspond to the number of + /// atom at this step, the frame is resized. + /// + /// # Errors + /// + /// This function fails if the data is incorrectly formatted for the + /// corresponding format. + /// + /// # Example + /// ```no_run + /// # use chemfiles::{Trajectory, Frame}; + /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + /// let mut frame = Frame::new(); + /// + /// trajectory.read_step(10, &mut frame).unwrap(); + /// ``` + pub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error> { + unsafe { + check(chfl_trajectory_read_step(self.as_mut_ptr(), step as u64, frame.as_mut_ptr())) + } + } + + /// Write a `frame` to this trajectory. + /// + /// # Errors + /// + /// This function fails if the data is incorrectly formatted for the + /// corresponding format. + /// + /// # Example + /// ```no_run + /// # use chemfiles::{Trajectory, Frame}; + /// let mut trajectory = Trajectory::open("water.pdb", 'w').unwrap(); + /// let mut frame = Frame::new(); + /// + /// trajectory.write(&mut frame).unwrap(); + /// ``` + pub fn write(&mut self, frame: &Frame) -> Result<(), Error> { + unsafe { + check(chfl_trajectory_write(self.as_mut_ptr(), frame.as_ptr())) + } + } + + /// Set the `topology` associated with this trajectory. This topology will + /// be used when reading and writing the files, replacing any topology in + /// the frames or files. + /// + /// # Example + /// ```no_run + /// # use chemfiles::{Trajectory, Atom, Topology}; + /// let mut topology = Topology::new(); + /// topology.add_atom(&Atom::new("H")); + /// topology.add_atom(&Atom::new("O")); + /// topology.add_atom(&Atom::new("H")); + /// topology.add_bond(0, 1); + /// topology.add_bond(1, 2); + /// + /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + /// trajectory.set_topology(&topology); + /// ``` + pub fn set_topology(&mut self, topology: &Topology) { + unsafe { + check_success(chfl_trajectory_set_topology(self.as_mut_ptr(), topology.as_ptr())); + } + } + + /// Set the topology associated with this trajectory by reading the first + /// frame of the file at the given `path` using the file format in `format`; + /// and extracting the topology of this frame. + /// + /// # Errors + /// + /// This function fails if the topology file is incorrectly formatted for + /// the corresponding format, or in case of I/O errors from the OS. + /// + /// # Example + /// ```no_run + /// # use chemfiles::Trajectory; + /// let mut trajectory = Trajectory::open("water.nc", 'r').unwrap(); + /// trajectory.set_topology_file("topology.pdb").unwrap(); + /// ``` + pub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error> + where + P: AsRef<Path>, + { + let path = path.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(path.as_ref()))?; + + let path = strings::to_c(path); + unsafe { + check(chfl_trajectory_topology_file(self.as_mut_ptr(), path.as_ptr(), ptr::null())) + } + } + + /// Set the topology associated with this trajectory by reading the first + /// frame of the file at the given `path` using the file format in + /// `format`; and extracting the topology of this frame. + /// + /// If `format` is an empty string, the format will be guessed from the + /// `path` extension. + /// + /// # Errors + /// + /// This function fails if the topology file is incorrectly formatted for + /// the corresponding format, or in case of I/O errors from the OS. + /// + /// # Example + /// ```no_run + /// # use chemfiles::Trajectory; + /// let mut trajectory = Trajectory::open("water.nc", 'r').unwrap(); + /// trajectory.set_topology_with_format("topology.mol", "PDB").unwrap(); + /// ``` + pub fn set_topology_with_format<'a, P, S>(&mut self, path: P, format: S) -> Result<(), Error> + where + P: AsRef<Path>, + S: Into<&'a str>, + { + let path = path.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(path.as_ref()))?; + + let format = strings::to_c(format.into()); + let path = strings::to_c(path); + unsafe { + check(chfl_trajectory_topology_file(self.as_mut_ptr(), path.as_ptr(), format.as_ptr())) + } + } + + /// Set the unit `cell` associated with a trajectory. This cell will be + /// used when reading and writing the files, replacing any unit cell in the + /// frames or files. + /// + /// # Example + /// ```no_run + /// # use chemfiles::{Trajectory, UnitCell}; + /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + /// trajectory.set_cell(&UnitCell::new([10.0, 11.0, 12.5])); + /// ``` + pub fn set_cell(&mut self, cell: &UnitCell) { + unsafe { + check_success(chfl_trajectory_set_cell(self.as_mut_ptr(), cell.as_ptr())); + } + } + + /// Get the number of steps (the number of frames) in a trajectory. + /// + /// # Example + /// ```no_run + /// # use chemfiles::Trajectory; + /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + /// + /// println!("This trajectory contains {} steps", trajectory.nsteps()); + /// ``` + // FIXME should this take &self instead? The file can be modified by this + // function, but the format should reset the state. + pub fn nsteps(&mut self) -> usize { + let mut res = 0; + unsafe { + check(chfl_trajectory_nsteps(self.as_mut_ptr(), &mut res)).expect( + "failed to get the number of steps in this trajectory" + ); + } + #[allow(clippy::cast_possible_truncation)] + return res as usize; + } + + /// Obtain the memory buffer written to by the trajectory. + /// + /// # Errors + /// + /// This fails if the trajectory was not opened with + /// `Trajectory::memory_writer`. + /// + /// # Example + /// ``` + /// # use chemfiles::{Atom, BondOrder, Frame, Trajectory}; + /// let mut trajectory_memory = Trajectory::memory_writer("SMI").unwrap(); + /// + /// let mut frame = Frame::new(); + /// frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None); + /// frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None); + /// frame.add_bond_with_order(0, 1, BondOrder::Single); + /// + /// trajectory_memory.write(&frame).unwrap(); + /// + /// let result = trajectory_memory.memory_buffer(); + /// assert_eq!(result.unwrap(), "CC\n"); + /// ``` + #[allow(clippy::cast_possible_truncation)] + pub fn memory_buffer(&self) -> Result<&str, Error> { + let mut ptr: *const i8 = std::ptr::null(); + let mut count: u64 = 0; + let buffer = unsafe { + check(chfl_trajectory_memory_buffer(self.as_ptr(), &mut ptr, &mut count))?; + std::slice::from_raw_parts( + ptr.cast(), count.try_into().expect("failed to convert u64 to usize") + ) + }; + + let string = std::str::from_utf8(buffer)?; + Ok(string) + } + + /// Get file path for this trajectory. + /// + /// # Example + /// ```no_run + /// # use chemfiles::Trajectory; + /// let trajectory = Trajectory::open("water.xyz", 'r').unwrap(); + /// + /// assert_eq!(trajectory.path(), "water.xyz"); + /// ``` + pub fn path(&self) -> String { + let get_string = |ptr, len| unsafe { chfl_trajectory_path(self.as_ptr(), ptr, len) }; + let path = strings::call_autogrow_buffer(1024, get_string).expect("failed to get path string"); + return strings::from_c(path.as_ptr()); + } +} + +impl Drop for Trajectory { + fn drop(&mut self) { + unsafe { + let _ = chfl_trajectory_close(self.as_ptr()); + } + } +} + +#[cfg(test)] +mod test { + use super::*; + + use std::fs; + use std::path::Path; + use std::io::Read; + + use approx::assert_ulps_eq; + + use {Atom, CellShape, Frame, Topology, UnitCell}; + + #[test] + fn read() { + let root = Path::new(file!()).parent().unwrap().join(".."); + let filename = root.join("data").join("water.xyz"); + let mut file = Trajectory::open(filename.to_str().unwrap(), 'r').unwrap(); + + if cfg!(target_family = "unix") { + assert_eq!(file.path(), "src/../data/water.xyz"); + } else if cfg!(target_family = "windows") { + assert_eq!(file.path(), "src\\..\\data\\water.xyz"); + } else { + panic!("please add test for this OS!"); + } + + assert_eq!(file.nsteps(), 100); + + let mut frame = Frame::new(); + assert!(file.read(&mut frame).is_ok()); + + assert_eq!(frame.size(), 297); + assert_ulps_eq!(frame.positions()[0][0], 0.417219); + assert_ulps_eq!(frame.positions()[0][1], 8.303366); + assert_ulps_eq!(frame.positions()[0][2], 11.737172); + assert_ulps_eq!(frame.positions()[124][0], 5.099554); + assert_ulps_eq!(frame.positions()[124][1], -0.045104); + assert_ulps_eq!(frame.positions()[124][2], 14.153846); + + assert_eq!(frame.atom(0).name(), "O"); + + file.set_cell(&UnitCell::new([30.0, 30.0, 30.0])); + assert!(file.read_step(41, &mut frame).is_ok()); + let cell = frame.cell().clone(); + assert_eq!(cell.lengths(), [30.0, 30.0, 30.0]); + + + assert_ulps_eq!(frame.positions()[0][0], 0.761277); + assert_ulps_eq!(frame.positions()[0][1], 8.106125); + assert_ulps_eq!(frame.positions()[0][2], 10.622949); + assert_ulps_eq!(frame.positions()[124][0], 5.13242); + assert_ulps_eq!(frame.positions()[124][1], 0.079862); + assert_ulps_eq!(frame.positions()[124][2], 14.194161); + + { + let topology = frame.topology(); + assert_eq!(topology.size(), 297); + assert_eq!(topology.bonds_count(), 0); + } + + assert!(frame.guess_bonds().is_ok()); + { + let topology = frame.topology(); + assert_eq!(topology.size(), 297); + assert_eq!(topology.bonds_count(), 180); + assert_eq!(topology.angles_count(), 84); + } + + let mut topology = Topology::new(); + let atom = Atom::new("Cs"); + for _ in 0..297 { + topology.add_atom(&atom); + } + + file.set_topology(&topology); + assert!(file.read_step(10, &mut frame).is_ok()); + assert_eq!(frame.atom(42).name(), "Cs"); + + let filename = root.join("data").join("topology.xyz"); + assert!(file.set_topology_file(filename.to_str().unwrap()).is_ok()); + assert!(file.read(&mut frame).is_ok()); + assert_eq!(frame.atom(100).name(), "Rd"); + + let filename = root.join("data").join("helium.xyz.but.not.really"); + let filename = filename.to_str().unwrap(); + let mut file = Trajectory::open_with_format(filename, 'r', "XYZ").unwrap(); + assert!(file.read(&mut frame).is_ok()); + assert_eq!(frame.size(), 125); + } + + fn write_file(path: &str) { + let mut file = Trajectory::open(path, 'w').unwrap(); + let mut frame = Frame::new(); + frame.resize(4); + + for position in frame.positions_mut() { + *position = [1.0, 2.0, 3.0]; + } + + let mut topology = Topology::new(); + let atom = Atom::new("X"); + for _ in 0..4 { + topology.add_atom(&atom); + } + frame.set_topology(&topology).unwrap(); + assert!(file.write(&frame).is_ok()); + } + + #[test] + fn write() { + let filename = "test-tmp.xyz"; + write_file(filename); + + let expected_content = "4 +Properties=species:S:1:pos:R:3 +X 1 2 3 +X 1 2 3 +X 1 2 3 +X 1 2 3".lines().collect::<Vec<_>>(); + + let mut file = fs::File::open(filename).unwrap(); + let mut content = String::new(); + let _ = file.read_to_string(&mut content).unwrap(); + + assert_eq!(expected_content, content.lines().collect::<Vec<_>>()); + fs::remove_file(filename).unwrap(); + } + + #[test] + fn memory() { + // formats in decreasing order of their memory buffer length to check null termination + for format in &["CSSR", "GRO", "XYZ"] { + let mut frame_write = Frame::new(); + frame_write.add_atom(&Atom::new("H"), [1.5, 3.0, -10.0], None); + frame_write.add_atom(&Atom::new("O"), [2.3, -1.4, 50.0], None); + frame_write.add_atom(&Atom::new("H"), [-1.5, 10.0, 0.0], None); + let cell = UnitCell::new([10.0, 11.0, 12.5]); + + let mut trajectory_write = Trajectory::memory_writer(*format).unwrap(); + trajectory_write.set_cell(&cell); + trajectory_write.write(&frame_write).unwrap(); + + let buffer = trajectory_write.memory_buffer().unwrap(); + let mut trajectory_read = Trajectory::memory_reader(buffer, *format).unwrap(); + let mut frame_read = Frame::new(); + trajectory_read.read(&mut frame_read).unwrap(); + + assert_eq!(trajectory_read.nsteps(), 1); + assert_eq!(frame_read.cell().shape(), CellShape::Orthorhombic); + assert_eq!(frame_read.size(), 3); + assert_eq!(frame_read.atom(1).name(), "O"); + crate::assert_vector3d_eq(&frame_read.positions()[2], &[-1.5, 10.0, 0.0], 1e-4); + } + } +} +
List of all items[−] + +
Structs
- Atom
- AtomMut
- AtomRef
- Error
- FormatMetadata
- Frame
- Match
- PropertiesIter
- Residue
- ResidueRef
- Selection
- Topology
- TopologyRef
- Trajectory
- UnitCell
- UnitCellMut
- UnitCellRef
Enums
Functions
Redirecting to ../../chemfiles/struct.Atom.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/atom/struct.AtomMut.html b/0.10.2/chemfiles/atom/struct.AtomMut.html new file mode 100644 index 000000000..2843d6f36 --- /dev/null +++ b/0.10.2/chemfiles/atom/struct.AtomMut.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.AtomMut.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/atom/struct.AtomRef.html b/0.10.2/chemfiles/atom/struct.AtomRef.html new file mode 100644 index 000000000..fc21ff8b9 --- /dev/null +++ b/0.10.2/chemfiles/atom/struct.AtomRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.AtomRef.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/cell/enum.CellShape.html b/0.10.2/chemfiles/cell/enum.CellShape.html new file mode 100644 index 000000000..9d3d95dbc --- /dev/null +++ b/0.10.2/chemfiles/cell/enum.CellShape.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/enum.CellShape.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/cell/struct.UnitCell.html b/0.10.2/chemfiles/cell/struct.UnitCell.html new file mode 100644 index 000000000..c199c7635 --- /dev/null +++ b/0.10.2/chemfiles/cell/struct.UnitCell.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.UnitCell.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/cell/struct.UnitCellMut.html b/0.10.2/chemfiles/cell/struct.UnitCellMut.html new file mode 100644 index 000000000..a07e76605 --- /dev/null +++ b/0.10.2/chemfiles/cell/struct.UnitCellMut.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.UnitCellMut.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/cell/struct.UnitCellRef.html b/0.10.2/chemfiles/cell/struct.UnitCellRef.html new file mode 100644 index 000000000..7455c76ac --- /dev/null +++ b/0.10.2/chemfiles/cell/struct.UnitCellRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.UnitCellRef.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/enum.BondOrder.html b/0.10.2/chemfiles/enum.BondOrder.html new file mode 100644 index 000000000..29e964670 --- /dev/null +++ b/0.10.2/chemfiles/enum.BondOrder.html @@ -0,0 +1,54 @@ +Enum chemfiles::BondOrder [−][src]
#[repr(C)]
+#[non_exhaustive]
+pub enum BondOrder {
+ Unknown,
+ Single,
+ Double,
+ Triple,
+ Quadruple,
+ Quintuplet,
+ Amide,
+ Aromatic,
+}Expand description
Possible bond order associated with bonds
+Variants (Non-exhaustive)
This enum is marked as non-exhaustive
Non-exhaustive enums could have additional variants added in future. Therefore, when matching against variants of non-exhaustive enums, an extra wildcard arm must be added to account for any future variants.
Unknown or unspecified bond order
+Single bond
+Double bond
+Triple bond
+Quadruple bond (present in some metals)
+Quintuplet bond (present in some metals)
+Amide bond (required by some file formats)
+Aromatic bond (required by some file formats)
+Trait Implementations
This method returns an ordering between self and other values if one exists. Read more
This method tests less than (for self and other) and is used by the < operator. Read more
This method tests less than or equal to (for self and other) and is used by the <=
+operator. Read more
This method tests greater than (for self and other) and is used by the > operator. Read more
Auto Trait Implementations
impl RefUnwindSafe for BondOrder
impl UnwindSafe for BondOrder
Blanket Implementations
Mutably borrows from an owned value. Read more
+Enum chemfiles::CellShape [−][src]
pub enum CellShape {
+ Orthorhombic,
+ Triclinic,
+ Infinite,
+}Expand description
Available unit cell shapes.
+Variants
Orthorhombic cell, with the three angles equals to 90°.
+Triclinic cell, with any values for the angles.
+Infinite cell, to use when there is no cell.
+Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for CellShape
impl UnwindSafe for CellShape
Blanket Implementations
Mutably borrows from an owned value. Read more
+Enum chemfiles::Property [−][src]
Expand description
A Property is a piece of data that can be associated with an Atom or a
+Frame.
Variants
Bool(bool)Boolean property
+Tuple Fields of Bool
0: boolDouble(f64)Floating point property
+Tuple Fields of Double
0: f64String(String)String property
+Tuple Fields of String
0: String3-dimensional vector property
+Trait Implementations
This method returns an ordering between self and other values if one exists. Read more
This method tests less than (for self and other) and is used by the < operator. Read more
This method tests less than or equal to (for self and other) and is used by the <=
+operator. Read more
This method tests greater than (for self and other) and is used by the > operator. Read more
Auto Trait Implementations
impl RefUnwindSafe for Property
impl UnwindSafe for Property
Blanket Implementations
Mutably borrows from an owned value. Read more
+Enum chemfiles::Status [−][src]
#[repr(C)]
+#[non_exhaustive]
+pub enum Status {
+ Success,
+ MemoryError,
+ FileError,
+ FormatError,
+ SelectionError,
+ ConfigurationError,
+ OutOfBounds,
+ PropertyError,
+ ChemfilesError,
+ StdCppError,
+ UTF8PathError,
+}Expand description
Possible causes of error in chemfiles
+Variants (Non-exhaustive)
This enum is marked as non-exhaustive
Non-exhaustive enums could have additional variants added in future. Therefore, when matching against variants of non-exhaustive enums, an extra wildcard arm must be added to account for any future variants.
No error
+Error in memory allocations
+Error while reading or writing a file
+Error in file formatting, i.e. the file is invalid
+Error in selection string syntax
+Error in configuration files syntax
+Error for out of bounds indexing
+Error related to properties
+Exception in the C++ chemfiles library
+Exception in the C++ standard library
+The given path is not valid UTF8
+Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Status
impl UnwindSafe for Status
Blanket Implementations
Mutably borrows from an owned value. Read more
+Redirecting to ../../chemfiles/enum.Status.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/errors/fn.set_warning_callback.html b/0.10.2/chemfiles/errors/fn.set_warning_callback.html new file mode 100644 index 000000000..97bc2a1ba --- /dev/null +++ b/0.10.2/chemfiles/errors/fn.set_warning_callback.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/fn.set_warning_callback.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/errors/struct.Error.html b/0.10.2/chemfiles/errors/struct.Error.html new file mode 100644 index 000000000..34339c749 --- /dev/null +++ b/0.10.2/chemfiles/errors/struct.Error.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Error.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/fn.add_configuration.html b/0.10.2/chemfiles/fn.add_configuration.html new file mode 100644 index 000000000..20795ff00 --- /dev/null +++ b/0.10.2/chemfiles/fn.add_configuration.html @@ -0,0 +1,14 @@ +Function chemfiles::add_configuration [−][src]
pub fn add_configuration<S>(path: S) -> Result<(), Error> where
S: AsRef<str>, Expand description
Read configuration data from the file at path.
By default, chemfiles reads configuration from any file named
+.chemfiles.toml in the current directory or any parent directory. This
+function can be used to add data from another configuration file. Data from
+the new configuration file will overwrite any existing data.
Errors
+This function will fail if there is no file at path, or if the file is
+incorrectly formatted.
Example
+chemfiles::add_configuration("local-config.toml").unwrap();
+// from now on, the data from "local-config.toml" will be usedFunction chemfiles::formats_list [−][src]
pub fn formats_list() -> Vec<FormatMetadata>Expand description
Get the list of formats known by chemfiles, as well as all associated metadata.
+Example
+let formats = chemfiles::formats_list();
+println!("chemfiles supports {} formats:", formats.len());
+for format in &formats {
+ println!(
+ " {:<15} {}",
+ format.name,
+ format.extension.as_deref().unwrap_or("")
+ );
+}Function chemfiles::guess_format [−][src]
pub fn guess_format(path: &str) -> StringExpand description
Get the format that chemfiles would use to read a file at the given
+path.
The format is mostly guessed from the path extension, chemfiles only tries
+to read the file to distinguish between CIF and mmCIF files. Opening the
+file using the returned format string might still fail. For example, it will
+fail if the file is not actually formatted according to the guessed format;
+or the format/compression combination is not supported (e.g. XTC / GZ will
+not work since the XTC reader does not support compressed files).
The returned format is represented in a way compatible with the various
+Trajectory constructors, i.e. "<format name> [/ <compression>]", where
+compression is optional.
Examples
+let format = chemfiles::guess_format("trajectory.xyz.xz");
+assert_eq!(format, "XYZ / XZ");
+
+let format = chemfiles::guess_format("trajectory.nc");
+assert_eq!(format, "Amber NetCDF");Function chemfiles::set_warning_callback [−][src]
pub fn set_warning_callback<F>(callback: F) where
F: WarningCallback + 'static, Expand description
Use callback for every chemfiles warning. The callback will be passed
+the warning message. This will drop any previous warning callback.
Function chemfiles::version [−][src]
pub fn version() -> StringExpand description
Get the version of the chemfiles library.
+Example
+let version = chemfiles::version();
+assert!(version.starts_with("0.10"));Redirecting to ../../chemfiles/struct.Frame.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/index.html b/0.10.2/chemfiles/index.html new file mode 100644 index 000000000..72a761b21 --- /dev/null +++ b/0.10.2/chemfiles/index.html @@ -0,0 +1,63 @@ +Crate chemfiles[−][src]
Expand description
Chemfiles is a multi-language library written in modern C++ for reading and +writing from and to molecular trajectory files. These files are created by +your favorite theoretical chemistry program, and contains information about +atomic or residues names and positions. Some format also have additional +information, such as velocities, forces, energy, …
+This crate expose the C API of chemfiles to Rust, and make all the +functionalities accessible. For more information on the C++ library, +please see its documentation. Specifically, the following pages +are worth reading:
+-
+
- The overview of the classes organization; +
- The list of supported formats; +
- The documentation for the selection language; +
Structs
+An Atom is a particle in the current Frame. It stores the following
+atomic properties:
An analog to a mutable reference to an atom (&mut Atom)
An analog to a reference to an atom (&Atom)
Error type for Chemfiles.
+FormatMetadata contains metadata associated with one format.
A Frame contains data from one simulation step: the current unit
+cell, the topology, the positions, and the velocities of the particles in
+the system. If some information is missing (topology or velocity or unit
+cell), the corresponding data is filled with a default value.
A Match is a set of atomic indexes matching a given selection. It can
+mostly be used like a &[usize].
An iterator over the properties in an atom/frame/residue
+A Residue is a group of atoms belonging to the same logical unit. They
+can be small molecules, amino-acids in a protein, monomers in polymers,
+etc.
An analog to a reference to a residue (&Residue)
A Selection allow to select atoms in a Frame, from a selection
+language. The selection language is built by combining basic operations.
+Each basic operation follows the <selector>[(<variable>)] <operator> <value> structure, where <operator> is a comparison operator in
+== != < <= > >=.
A Topology contains the definition of all the atoms in the system, and
+the liaisons between the atoms (bonds, angles, dihedrals, …). It will
+also contain all the residues information if it is available.
An analog to a reference to a topology (&Topology)
The Trajectory type is the main entry point when using chemfiles. A
+Trajectory behave a bit like a file, allowing to read and/or write
+Frame.
An UnitCell represent the box containing the atoms, and its periodicity.
An analog to a mutable reference to an unit cell (&mut UnitCell)
An analog to a reference to an unit cell (&UnitCell)
Enums
+Possible bond order associated with bonds
+Available unit cell shapes.
+A Property is a piece of data that can be associated with an Atom or a
+Frame.
Possible causes of error in chemfiles
+Functions
+Read configuration data from the file at path.
Get the list of formats known by chemfiles, as well as all associated metadata.
+Get the format that chemfiles would use to read a file at the given
+path.
Use callback for every chemfiles warning. The callback will be passed
+the warning message. This will drop any previous warning callback.
Get the version of the chemfiles library.
+Redirecting to ../../chemfiles/fn.formats_list.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/misc/fn.guess_format.html b/0.10.2/chemfiles/misc/fn.guess_format.html new file mode 100644 index 000000000..681a66ce5 --- /dev/null +++ b/0.10.2/chemfiles/misc/fn.guess_format.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/fn.guess_format.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/misc/struct.FormatMetadata.html b/0.10.2/chemfiles/misc/struct.FormatMetadata.html new file mode 100644 index 000000000..10fda814b --- /dev/null +++ b/0.10.2/chemfiles/misc/struct.FormatMetadata.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.FormatMetadata.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/property/enum.Property.html b/0.10.2/chemfiles/property/enum.Property.html new file mode 100644 index 000000000..87bfc97da --- /dev/null +++ b/0.10.2/chemfiles/property/enum.Property.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/enum.Property.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/property/struct.PropertiesIter.html b/0.10.2/chemfiles/property/struct.PropertiesIter.html new file mode 100644 index 000000000..2faef8a54 --- /dev/null +++ b/0.10.2/chemfiles/property/struct.PropertiesIter.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.PropertiesIter.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/residue/struct.Residue.html b/0.10.2/chemfiles/residue/struct.Residue.html new file mode 100644 index 000000000..e8f25ad8a --- /dev/null +++ b/0.10.2/chemfiles/residue/struct.Residue.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Residue.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/residue/struct.ResidueRef.html b/0.10.2/chemfiles/residue/struct.ResidueRef.html new file mode 100644 index 000000000..9d26d5daa --- /dev/null +++ b/0.10.2/chemfiles/residue/struct.ResidueRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.ResidueRef.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/selection/struct.Match.html b/0.10.2/chemfiles/selection/struct.Match.html new file mode 100644 index 000000000..3c7b0b709 --- /dev/null +++ b/0.10.2/chemfiles/selection/struct.Match.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Match.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/selection/struct.Selection.html b/0.10.2/chemfiles/selection/struct.Selection.html new file mode 100644 index 000000000..8ed2b5d77 --- /dev/null +++ b/0.10.2/chemfiles/selection/struct.Selection.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Selection.html...
+ + + \ No newline at end of file diff --git a/0.10.2/chemfiles/sidebar-items.js b/0.10.2/chemfiles/sidebar-items.js new file mode 100644 index 000000000..dc3572b15 --- /dev/null +++ b/0.10.2/chemfiles/sidebar-items.js @@ -0,0 +1 @@ +initSidebarItems({"enum":[["BondOrder","Possible bond order associated with bonds"],["CellShape","Available unit cell shapes."],["Property","A `Property` is a piece of data that can be associated with an `Atom` or a `Frame`."],["Status","Possible causes of error in chemfiles"]],"fn":[["add_configuration","Read configuration data from the file at `path`."],["formats_list","Get the list of formats known by chemfiles, as well as all associated metadata."],["guess_format","Get the format that chemfiles would use to read a file at the given `path`."],["set_warning_callback","Use `callback` for every chemfiles warning. The callback will be passed the warning message. This will drop any previous warning callback."],["version","Get the version of the chemfiles library."]],"struct":[["Atom","An `Atom` is a particle in the current `Frame`. It stores the following atomic properties:"],["AtomMut","An analog to a mutable reference to an atom (`&mut Atom`)"],["AtomRef","An analog to a reference to an atom (`&Atom`)"],["Error","Error type for Chemfiles."],["FormatMetadata","`FormatMetadata` contains metadata associated with one format."],["Frame","A `Frame` contains data from one simulation step: the current unit cell, the topology, the positions, and the velocities of the particles in the system. If some information is missing (topology or velocity or unit cell), the corresponding data is filled with a default value."],["Match","A `Match` is a set of atomic indexes matching a given selection. It can mostly be used like a `&[usize]`."],["PropertiesIter","An iterator over the properties in an atom/frame/residue"],["Residue","A `Residue` is a group of atoms belonging to the same logical unit. They can be small molecules, amino-acids in a protein, monomers in polymers, etc."],["ResidueRef","An analog to a reference to a residue (`&Residue`)"],["Selection","A `Selection` allow to select atoms in a `Frame`, from a selection language. The selection language is built by combining basic operations. Each basic operation follows the `Struct chemfiles::Atom [−][src]
pub struct Atom { /* fields omitted */ }Expand description
An Atom is a particle in the current Frame. It stores the following
+atomic properties:
-
+
- atom name; +
- atom type; +
- atom mass; +
- atom charge. +
The atom name is usually an unique identifier (H1, C_a) while the
+atom type will be shared between all particles of the same type: H,
+Ow, CH3.
Implementations
Create an atom with the given name, and set the atom type to name.
Example
+let atom = Atom::new("He");
+assert_eq!(atom.name(), "He");Get the atom mass, in atomic mass units.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.mass(), 4.002602);Set the atom mass to mass, in atomic mass units.
Example
+let mut atom = Atom::new("He");
+
+atom.set_mass(34.9);
+assert_eq!(atom.mass(), 34.9);Get the atom charge, in number of the electron charge e.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.charge(), 0.0);Set the atom charge to charge, in number of the electron charge e.
Example
+let mut atom = Atom::new("He");
+
+atom.set_charge(-2.0);
+assert_eq!(atom.charge(), -2.0);Set the atom name to name.
Example
+let mut atom = Atom::new("He");
+
+atom.set_name("Zn3");
+assert_eq!(atom.name(), "Zn3");Set the atom type to atomic_type.
Example
+let mut atom = Atom::new("He");
+
+atom.set_atomic_type("F");
+assert_eq!(atom.atomic_type(), "F");Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
+let atom = Atom::new("Zn");
+assert_eq!(atom.full_name(), "Zinc");Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").atomic_number(), 2);
+assert_eq!(Atom::new("Xxx").atomic_number(), 0);Add a new property with the given name to this atom.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut atom = Atom::new("He");
+atom.set("a bool", true);
+atom.set("a string", "test");
+
+assert_eq!(atom.get("a bool"), Some(Property::Bool(true)));
+assert_eq!(atom.get("a string"), Some(Property::String("test".into())));Get a property with the given name in this atom, if it exist.
Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+
+assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(atom.get("Bar"), None);pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this atom
+Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+atom.set("bar", Property::Bool(false));
+
+for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Atom
impl UnwindSafe for Atom
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::AtomMut [−][src]
pub struct AtomMut<'a> { /* fields omitted */ }Expand description
An analog to a mutable reference to an atom (&mut Atom)
Methods from Deref<Target = Atom>
Get the atom mass, in atomic mass units.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.mass(), 4.002602);Set the atom mass to mass, in atomic mass units.
Example
+let mut atom = Atom::new("He");
+
+atom.set_mass(34.9);
+assert_eq!(atom.mass(), 34.9);Get the atom charge, in number of the electron charge e.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.charge(), 0.0);Set the atom charge to charge, in number of the electron charge e.
Example
+let mut atom = Atom::new("He");
+
+atom.set_charge(-2.0);
+assert_eq!(atom.charge(), -2.0);Set the atom name to name.
Example
+let mut atom = Atom::new("He");
+
+atom.set_name("Zn3");
+assert_eq!(atom.name(), "Zn3");Set the atom type to atomic_type.
Example
+let mut atom = Atom::new("He");
+
+atom.set_atomic_type("F");
+assert_eq!(atom.atomic_type(), "F");Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
+let atom = Atom::new("Zn");
+assert_eq!(atom.full_name(), "Zinc");Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").atomic_number(), 2);
+assert_eq!(Atom::new("Xxx").atomic_number(), 0);Add a new property with the given name to this atom.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut atom = Atom::new("He");
+atom.set("a bool", true);
+atom.set("a string", "test");
+
+assert_eq!(atom.get("a bool"), Some(Property::Bool(true)));
+assert_eq!(atom.get("a string"), Some(Property::String("test".into())));Get a property with the given name in this atom, if it exist.
Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+
+assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(atom.get("Bar"), None);pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this atom
+Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+atom.set("bar", Property::Bool(false));
+
+for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for AtomMut<'a>
impl<'a> !UnwindSafe for AtomMut<'a>
Blanket Implementations
Struct chemfiles::AtomRef [−][src]
pub struct AtomRef<'a> { /* fields omitted */ }Expand description
An analog to a reference to an atom (&Atom)
Methods from Deref<Target = Atom>
Get the atom mass, in atomic mass units.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.mass(), 4.002602);Get the atom charge, in number of the electron charge e.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.charge(), 0.0);Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
+let atom = Atom::new("Zn");
+assert_eq!(atom.full_name(), "Zinc");Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").atomic_number(), 2);
+assert_eq!(Atom::new("Xxx").atomic_number(), 0);Get a property with the given name in this atom, if it exist.
Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+
+assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(atom.get("Bar"), None);pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this atom
+Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+atom.set("bar", Property::Bool(false));
+
+for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for AtomRef<'a>
impl<'a> UnwindSafe for AtomRef<'a>
Blanket Implementations
Struct chemfiles::Error [−][src]
Expand description
Error type for Chemfiles.
+Fields
status: StatusThe error status code
+message: StringA message describing the error cause
+Implementations
Get the last error message from the C++ library.
+Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Error
impl UnwindSafe for Error
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::FormatMetadata [−][src]
pub struct FormatMetadata {Show 13 fields
+ pub name: &'static str,
+ pub extension: Option<&'static str>,
+ pub description: &'static str,
+ pub reference: &'static str,
+ pub read: bool,
+ pub write: bool,
+ pub memory: bool,
+ pub positions: bool,
+ pub velocities: bool,
+ pub unit_cell: bool,
+ pub atoms: bool,
+ pub bonds: bool,
+ pub residues: bool,
+}Expand description
FormatMetadata contains metadata associated with one format.
Fields
name: &'static strName of the format.
+extension: Option<&'static str>Extension associated with the format.
+description: &'static strExtended, user-facing description of the format.
+reference: &'static strURL pointing to the format definition/reference.
+read: boolIs reading files in this format implemented?
+write: boolIs writing files in this format implemented?
+memory: boolDoes this format support in-memory IO?
+positions: boolDoes this format support storing atomic positions?
+velocities: boolDoes this format support storing atomic velocities?
+unit_cell: boolDoes this format support storing unit cell information?
+atoms: boolDoes this format support storing atom names or types?
+bonds: boolDoes this format support storing bonds between atoms?
+residues: boolDoes this format support storing residues?
+Trait Implementations
This method tests for self and other values to be equal, and is used
+by ==. Read more
This method tests for !=.
Auto Trait Implementations
impl RefUnwindSafe for FormatMetadata
impl Send for FormatMetadata
impl Sync for FormatMetadata
impl Unpin for FormatMetadata
impl UnwindSafe for FormatMetadata
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::Frame [−][src]
pub struct Frame { /* fields omitted */ }Expand description
A Frame contains data from one simulation step: the current unit
+cell, the topology, the positions, and the velocities of the particles in
+the system. If some information is missing (topology or velocity or unit
+cell), the corresponding data is filled with a default value.
Implementations
Create an empty frame. It will be resized by the library as needed.
+Example
+let frame = Frame::new();
+
+assert_eq!(frame.size(), 0);Get a mutable reference to the atom at the given index in this frame.
Panics
+If index is out of bounds.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+
+assert_eq!(frame.atom(0).name(), "Zn");
+
+frame.atom_mut(0).set_name("Fe");
+assert_eq!(frame.atom(0).name(), "Fe");Get the current number of atoms in this frame.
+Example
+let mut frame = Frame::new();
+assert_eq!(frame.size(), 0);
+
+frame.resize(67);
+assert_eq!(frame.size(), 67);Resize the positions and the velocities in this frame, to make space for
+natoms atoms. Previous data is conserved, as well as the presence of
+absence of velocities.
Example
+let mut frame = Frame::new();
+frame.resize(67);
+assert_eq!(frame.size(), 67);Add an Atom and the corresponding position and optionally velocity
+data to this frame.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("Zn"), [1.0, 1.0, 2.0], None);
+
+frame.add_velocities();
+frame.add_atom(&Atom::new("Zn"), [-1.0, 1.0, 2.0], [0.2, 0.1, 0.0]);Remove the atom at index i in this frame.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+frame.add_atom(&Atom::new("Fe"), [0.0; 3], None);
+frame.add_atom(&Atom::new("Sn"), [0.0; 3], None);
+assert_eq!(frame.size(), 3);
+
+frame.remove(1);
+assert_eq!(frame.size(), 2);
+assert_eq!(frame.atom(1).name(), "Sn");Add a bond between the atoms at indexes i and j in the frame.
The bond order is set to BondOrder::Unknown.
Example
+let mut frame = Frame::new();
+assert_eq!(frame.topology().bonds_count(), 0);
+frame.resize(5);
+
+frame.add_bond(0, 1);
+frame.add_bond(3, 1);
+frame.add_bond(2, 4);
+assert_eq!(frame.topology().bonds_count(), 3);
+
+assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown);
+assert_eq!(frame.topology().bonds(), vec![[0, 1], [1, 3], [2, 4]]);Add a bond between the atoms at indexes i and j in the frame
+with the given bond order.
Example
+let mut frame = Frame::new();
+assert_eq!(frame.topology().bonds_count(), 0);
+frame.resize(2);
+
+frame.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Double);Remove any existing bond between the atoms at indexes i and j in
+the frame.
This function does nothing if there is no bond between i and j.
Example
+let mut frame = Frame::new();
+frame.resize(5);
+
+frame.add_bond(0, 1);
+frame.add_bond(3, 1);
+frame.add_bond(2, 4);
+
+let bonds = frame.topology().bonds();
+assert_eq!(bonds, vec![[0, 1], [1, 3], [2, 4]]);
+
+frame.remove_bond(2, 4);
+let bonds = frame.topology().bonds();
+assert_eq!(bonds, vec![[0, 1], [1, 3]]);Add a copy of residue to this frame.
Errors
+This function fails is the residue id is already in this frame’s +topology, or if the residue contain atoms that are already in another +residue.
+Example
+let mut frame = Frame::new();
+
+let residue = Residue::new("foo");
+frame.add_residue(&residue).unwrap();
+
+let topology = frame.topology();
+assert_eq!(topology.residues_count(), 1);
+assert_eq!(topology.residue(0).unwrap().name(), "foo");Get the distance between the atoms at indexes i and j in this frame,
+accounting for periodic boundary conditions. The result is expressed in
+Angstroms.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [1.0, 2.0, 3.0], None);
+
+assert_eq!(frame.distance(0, 1), f64::sqrt(14.0));Get the angle formed by the atoms at indexes i, j and k in this
+frame, accounting for periodic boundary conditions. The result is
+expressed in radians.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+
+assert_eq!(frame.angle(0, 1, 2), f64::consts::PI / 2.0);Get the dihedral angle formed by the atoms at indexes i, j, k and
+m in this frame, accounting for periodic boundary conditions. The
+result is expressed in radians.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+frame.add_atom(&Atom::new("D"), [0.0, 1.0, 1.0], None);
+
+assert_eq!(frame.dihedral(0, 1, 2, 3), f64::consts::PI / 2.0);Get the out of plane distance formed by the atoms at indexes i, j,
+k and m in this frame, accounting for periodic boundary conditions.
+The result is expressed in angstroms.
This is the distance between the atom j and the ikm plane. The j atom +is the center of the improper dihedral angle formed by i, j, k and m.
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [0.0, 0.0, 2.0], None);
+frame.add_atom(&Atom::new("C"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("D"), [0.0, 1.0, 0.0], None);
+
+assert_eq!(frame.out_of_plane(0, 1, 2, 3), 2.0);Get a view into the positions of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+
+let positions = frame.positions();
+assert_eq!(positions.len(), 67);
+assert_eq!(positions[0], [0.0, 0.0, 0.0]);Get a mutable view into the positions of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+{
+ let positions = frame.positions_mut();
+ assert_eq!(positions[0], [0.0, 0.0, 0.0]);
+ positions[0] = [1.0, 2.0, 3.0];
+}
+
+let positions = frame.positions();
+assert_eq!(positions[0], [1.0, 2.0, 3.0]);Get a view into the velocities of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+frame.add_velocities();
+
+let velocities = frame.velocities();
+assert_eq!(velocities.len(), 67);
+assert_eq!(velocities[0], [0.0, 0.0, 0.0]);Get a mutable view into the velocities of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+frame.add_velocities();
+{
+ let velocities = frame.velocities_mut();
+ assert_eq!(velocities[0], [0.0, 0.0, 0.0]);
+ velocities[0] = [1.0, 2.0, 3.0];
+}
+
+let velocities = frame.velocities();
+assert_eq!(velocities[0], [1.0, 2.0, 3.0]);Check if this frame contains velocity data.
+Example
+let mut frame = Frame::new();
+assert_eq!(frame.has_velocities(), false);
+
+frame.add_velocities();
+assert_eq!(frame.has_velocities(), true);Add velocity data to this frame. If the frame already have velocities, +this does nothing.
+Example
+let mut frame = Frame::new();
+assert_eq!(frame.has_velocities(), false);
+
+frame.add_velocities();
+assert_eq!(frame.has_velocities(), true);Get a reference to the UnitCell from this frame.
Example
+let frame = Frame::new();
+
+let cell = frame.cell();
+assert_eq!(cell.shape(), CellShape::Infinite);Get a mutable reference to the UnitCell from this frame.
Example
+let mut frame = Frame::new();
+
+assert_eq!(frame.cell().shape(), CellShape::Infinite);
+
+frame.cell_mut().set_shape(CellShape::Triclinic).unwrap();
+assert_eq!(frame.cell().shape(), CellShape::Triclinic);Set the UnitCell of this frame to cell.
Example
+let mut frame = Frame::new();
+
+frame.set_cell(&UnitCell::new([10.0, 10.0, 10.0]));
+
+let cell = frame.cell();
+assert_eq!(cell.shape(), CellShape::Orthorhombic);
+assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);Get a reference to the Topology of this frame.
Example
+let mut frame = Frame::new();
+frame.resize(42);
+
+let topology = frame.topology();
+assert_eq!(topology.size(), 42);Set the Topology of this frame to topology.
Errors
+This function fails if the topology contains a different number of atoms +than this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(2);
+
+let mut topology = Topology::new();
+topology.add_atom(&Atom::new("Cl"));
+topology.add_atom(&Atom::new("Cl"));
+topology.add_bond(0, 1);
+
+frame.set_topology(&topology).unwrap();
+assert_eq!(frame.atom(0).name(), "Cl");Get this frame step, i.e. the frame number in the trajectory
+Example
+let frame = Frame::new();
+assert_eq!(frame.step(), 0);Set this frame step to step.
Example
+let mut frame = Frame::new();
+assert_eq!(frame.step(), 0);
+
+frame.set_step(10);
+assert_eq!(frame.step(), 10);Guess the bonds, angles and dihedrals in this frame.
The bonds are guessed using a distance-based algorithm, and then angles +and dihedrals are guessed from the bonds.
+Errors
+This function can fail if the covalent radius is unknown for some atoms +in the frame.
+Example
+let mut frame = Frame::new();
+
+frame.add_atom(&Atom::new("Cl"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("Cl"), [1.5, 0.0, 0.0], None);
+assert_eq!(frame.topology().bonds_count(), 0);
+
+frame.guess_bonds().unwrap();
+assert_eq!(frame.topology().bonds_count(), 1);Remove all existing bonds, angles, dihedral angles and improper +dihedral angles in the topology of the frame.
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [0.0, 1.0, 0.0], None);
+
+frame.add_bond(0, 1);
+frame.add_bond(1, 2);
+
+assert_eq!(frame.topology().bonds().len(), 2);
+assert_eq!(frame.topology().angles().len(), 1);
+
+frame.clear_bonds();
+assert!(frame.topology().bonds().is_empty());
+assert!(frame.topology().angles().is_empty());Add a new property with the given name to this frame.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut frame = Frame::new();
+frame.set("a string", "hello");
+frame.set("a double", 4.3);
+
+assert_eq!(frame.get("a string"), Some(Property::String("hello".into())));
+assert_eq!(frame.get("a double"), Some(Property::Double(4.3)));Get a property with the given name in this frame, if it exist.
Examples
+let mut frame = Frame::new();
+frame.set("foo", Property::Double(22.2));
+
+assert_eq!(frame.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(frame.get("Bar"), None);pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this frame
+Examples
+let mut frame = Frame::new();
+frame.set("foo", Property::Double(22.2));
+frame.set("bar", Property::Bool(false));
+
+for (name, property) in frame.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Frame
impl UnwindSafe for Frame
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::Match [−][src]
pub struct Match { /* fields omitted */ }Expand description
A Match is a set of atomic indexes matching a given selection. It can
+mostly be used like a &[usize].
Implementations
Get the length of the Match.
+Example
+let atomic_match = Match::new(&[3, 4, 5]);
+assert_eq!(atomic_match.len(), 3);Create a new match containing the atoms in the atoms slice.
Panics
+If the slice contains more than 4 elements, which is the maximal size +of a match.
+Example
+let atomic_match = Match::new(&[3, 4, 5]);
+assert_eq!(atomic_match.len(), 3);
+assert_eq!(atomic_match[0], 3);
+assert_eq!(atomic_match[1], 4);
+assert_eq!(atomic_match[2], 5);Iterate over the atomic indexes in the match.
+Example
+let atomic_match = Match::new(&[3, 4, 5]);
+let mut iter = atomic_match.iter();
+
+assert_eq!(iter.next(), Some(&3));
+assert_eq!(iter.next(), Some(&4));
+assert_eq!(iter.next(), Some(&5));
+assert_eq!(iter.next(), None);Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Match
impl UnwindSafe for Match
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::PropertiesIter [−][src]
pub struct PropertiesIter<'a> { /* fields omitted */ }Expand description
An iterator over the properties in an atom/frame/residue
+Trait Implementations
Advances the iterator and returns the next value. Read more
+Returns the bounds on the remaining length of the iterator. Read more
+Consumes the iterator, counting the number of iterations and returning it. Read more
+Consumes the iterator, returning the last element. Read more
+🔬 This is a nightly-only experimental API. (iter_advance_by)
recently added
+Advances the iterator by n elements. Read more
Returns the nth element of the iterator. Read more
Creates an iterator starting at the same point, but stepping by +the given amount at each iteration. Read more
+1.0.0[src]fn chain<U>(self, other: U) -> Chain<Self, <U as IntoIterator>::IntoIter> where
U: IntoIterator<Item = Self::Item>,
1.0.0[src]
fn chain<U>(self, other: U) -> Chain<Self, <U as IntoIterator>::IntoIter> where
U: IntoIterator<Item = Self::Item>,
Takes two iterators and creates a new iterator over both in sequence. Read more
+1.0.0[src]fn zip<U>(self, other: U) -> Zip<Self, <U as IntoIterator>::IntoIter> where
U: IntoIterator,
1.0.0[src]
fn zip<U>(self, other: U) -> Zip<Self, <U as IntoIterator>::IntoIter> where
U: IntoIterator,
‘Zips up’ two iterators into a single iterator of pairs. Read more
+🔬 This is a nightly-only experimental API. (iter_intersperse)
recently added
+Creates a new iterator which places a copy of separator between adjacent
+items of the original iterator. Read more
fn intersperse_with<G>(self, separator: G) -> IntersperseWith<Self, G> where
G: FnMut() -> Self::Item,
fn intersperse_with<G>(self, separator: G) -> IntersperseWith<Self, G> where
G: FnMut() -> Self::Item,
🔬 This is a nightly-only experimental API. (iter_intersperse)
recently added
+Creates a new iterator which places an item generated by separator
+between adjacent items of the original iterator. Read more
Takes a closure and creates an iterator which calls that closure on each +element. Read more
+Calls a closure on each element of an iterator. Read more
+Creates an iterator which uses a closure to determine if an element +should be yielded. Read more
+Creates an iterator that both filters and maps. Read more
+Creates an iterator which gives the current iteration count as well as +the next value. Read more
+Creates an iterator that yields elements based on a predicate. Read more
+🔬 This is a nightly-only experimental API. (iter_map_while)
recently added
+Creates an iterator that both yields elements based on a predicate and maps. Read more
+Creates an iterator that skips the first n elements. Read more
Creates an iterator that yields the first n elements, or fewer
+if the underlying iterator ends sooner. Read more
Creates an iterator that works like map, but flattens nested structure. Read more
+Creates an iterator that flattens nested structure. Read more
+Does something with each element of an iterator, passing the value on. Read more
+Borrows an iterator, rather than consuming it. Read more
+Transforms an iterator into a collection. Read more
+Consumes an iterator, creating two collections from it. Read more
+fn partition_in_place<'a, T, P>(self, predicate: P) -> usize where
Self: DoubleEndedIterator<Item = &'a mut T>,
T: 'a,
P: FnMut(&T) -> bool,
fn partition_in_place<'a, T, P>(self, predicate: P) -> usize where
Self: DoubleEndedIterator<Item = &'a mut T>,
T: 'a,
P: FnMut(&T) -> bool,
🔬 This is a nightly-only experimental API. (iter_partition_in_place)
new API
+Reorders the elements of this iterator in-place according to the given predicate,
+such that all those that return true precede all those that return false.
+Returns the number of true elements found. Read more
🔬 This is a nightly-only experimental API. (iter_is_partitioned)
new API
+Checks if the elements of this iterator are partitioned according to the given predicate,
+such that all those that return true precede all those that return false. Read more
An iterator method that applies a function as long as it returns +successfully, producing a single, final value. Read more
+An iterator method that applies a fallible function to each item in the +iterator, stopping at the first error and returning that error. Read more
+Folds every element into an accumulator by applying an operation, +returning the final result. Read more
+Reduces the elements to a single one, by repeatedly applying a reducing +operation. Read more
+Tests if every element of the iterator matches a predicate. Read more
+Tests if any element of the iterator matches a predicate. Read more
+Searches for an element of an iterator that satisfies a predicate. Read more
+Applies function to the elements of iterator and returns +the first non-none result. Read more
+🔬 This is a nightly-only experimental API. (try_find)
new API
+Applies function to the elements of iterator and returns +the first true result or the first error. Read more
+Searches for an element in an iterator, returning its index. Read more
+1.0.0[src]fn rposition<P>(&mut self, predicate: P) -> Option<usize> where
Self: ExactSizeIterator + DoubleEndedIterator,
P: FnMut(Self::Item) -> bool,
1.0.0[src]
fn rposition<P>(&mut self, predicate: P) -> Option<usize> where
Self: ExactSizeIterator + DoubleEndedIterator,
P: FnMut(Self::Item) -> bool,
Searches for an element in an iterator from the right, returning its +index. Read more
+Returns the maximum element of an iterator. Read more
+Returns the minimum element of an iterator. Read more
+Returns the element that gives the maximum value from the +specified function. Read more
+Returns the element that gives the maximum value with respect to the +specified comparison function. Read more
+Returns the element that gives the minimum value from the +specified function. Read more
+Returns the element that gives the minimum value with respect to the +specified comparison function. Read more
+Reverses an iterator’s direction. Read more
+Converts an iterator of pairs into a pair of containers. Read more
+Creates an iterator which copies all of its elements. Read more
+Repeats an iterator endlessly. Read more
+Sums the elements of an iterator. Read more
+Iterates over the entire iterator, multiplying all the elements Read more
+Lexicographically compares the elements of this Iterator with those
+of another. Read more
fn cmp_by<I, F>(self, other: I, cmp: F) -> Ordering where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,
I: IntoIterator,
fn cmp_by<I, F>(self, other: I, cmp: F) -> Ordering where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,
I: IntoIterator,
🔬 This is a nightly-only experimental API. (
iter_order_by)Lexicographically compares the elements of this Iterator with those
+of another with respect to the specified comparison function. Read more
1.5.0[src]fn partial_cmp<I>(self, other: I) -> Option<Ordering> where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
1.5.0[src]
fn partial_cmp<I>(self, other: I) -> Option<Ordering> where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
Lexicographically compares the elements of this Iterator with those
+of another. Read more
fn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering> where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,
I: IntoIterator,
fn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering> where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,
I: IntoIterator,
🔬 This is a nightly-only experimental API. (
iter_order_by)Lexicographically compares the elements of this Iterator with those
+of another with respect to the specified comparison function. Read more
1.5.0[src]fn eq<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>,
1.5.0[src]
fn eq<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>,
fn eq_by<I, F>(self, other: I, eq: F) -> bool where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> bool,
I: IntoIterator,
fn eq_by<I, F>(self, other: I, eq: F) -> bool where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> bool,
I: IntoIterator,
🔬 This is a nightly-only experimental API. (
iter_order_by)1.5.0[src]fn ne<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>,
1.5.0[src]
fn ne<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>,
1.5.0[src]fn lt<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
1.5.0[src]
fn lt<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
Determines if the elements of this Iterator are lexicographically
+less than those of another. Read more
1.5.0[src]fn le<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
1.5.0[src]
fn le<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
Determines if the elements of this Iterator are lexicographically
+less or equal to those of another. Read more
1.5.0[src]fn gt<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
1.5.0[src]
fn gt<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
Determines if the elements of this Iterator are lexicographically
+greater than those of another. Read more
1.5.0[src]fn ge<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
1.5.0[src]
fn ge<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
Determines if the elements of this Iterator are lexicographically
+greater than or equal to those of another. Read more
🔬 This is a nightly-only experimental API. (is_sorted)
new API
+Checks if the elements of this iterator are sorted. Read more
+🔬 This is a nightly-only experimental API. (is_sorted)
new API
+Checks if the elements of this iterator are sorted using the given comparator function. Read more
+fn is_sorted_by_key<F, K>(self, f: F) -> bool where
F: FnMut(Self::Item) -> K,
K: PartialOrd<K>,
fn is_sorted_by_key<F, K>(self, f: F) -> bool where
F: FnMut(Self::Item) -> K,
K: PartialOrd<K>,
🔬 This is a nightly-only experimental API. (is_sorted)
new API
+Checks if the elements of this iterator are sorted using the given key extraction +function. Read more
+Auto Trait Implementations
impl<'a> !RefUnwindSafe for PropertiesIter<'a>
impl<'a> !Send for PropertiesIter<'a>
impl<'a> !Sync for PropertiesIter<'a>
impl<'a> Unpin for PropertiesIter<'a>
impl<'a> !UnwindSafe for PropertiesIter<'a>
Blanket Implementations
Struct chemfiles::Residue [−][src]
pub struct Residue { /* fields omitted */ }Expand description
A Residue is a group of atoms belonging to the same logical unit. They
+can be small molecules, amino-acids in a protein, monomers in polymers,
+etc.
Implementations
Create a new residue with the given name
Example
+let residue = Residue::new("ALA");
+assert_eq!(residue.name(), "ALA");
+assert_eq!(residue.id(), None);Create a new residue with the given name and id as identifier.
Example
+let residue = Residue::with_id("ALA", 67);
+assert_eq!(residue.name(), "ALA");
+assert_eq!(residue.id(), Some(67));Get the number of atoms in this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.size(), 0);
+
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+assert_eq!(residue.size(), 3);Get the identifier of this residue in the initial topology file.
+Example
+let residue = Residue::with_id("", 42);
+assert_eq!(residue.id(), Some(42));Get the name of this residue.
+Example
+let residue = Residue::new("water");
+assert_eq!(residue.name(), "water");Add the atom at index atom in this residue.
This will fail if the atom is already in the residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.size(), 0);
+assert_eq!(residue.contains(56), false);
+
+residue.add_atom(56);
+assert_eq!(residue.size(), 1);
+assert_eq!(residue.contains(56), true);
+
+// Adding the same atom twice is fine
+residue.add_atom(56);
+assert_eq!(residue.size(), 1);Check if the atom at index i is in this residue
Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.contains(56), false);
+
+residue.add_atom(56);
+assert_eq!(residue.contains(56), true);Get the list of atoms of this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.atoms(), vec![]);
+
+residue.add_atom(56);
+assert_eq!(residue.atoms(), vec![56]);Add a new property with the given name to this residue.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut residue = Residue::new("ALA");
+residue.set("a string", "hello");
+residue.set("a double", 3.2);
+
+assert_eq!(residue.get("a string"), Some(Property::String("hello".into())));
+assert_eq!(residue.get("a double"), Some(Property::Double(3.2)));Get a property with the given name in this frame, if it exist.
Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+
+assert_eq!(residue.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(residue.get("Bar"), None);pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this frame
+Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+residue.set("bar", Property::Bool(false));
+
+for (name, property) in residue.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Residue
impl UnwindSafe for Residue
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::ResidueRef [−][src]
pub struct ResidueRef<'a> { /* fields omitted */ }Expand description
An analog to a reference to a residue (&Residue)
Methods from Deref<Target = Residue>
Get the number of atoms in this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.size(), 0);
+
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+assert_eq!(residue.size(), 3);Get the identifier of this residue in the initial topology file.
+Example
+let residue = Residue::with_id("", 42);
+assert_eq!(residue.id(), Some(42));Get the name of this residue.
+Example
+let residue = Residue::new("water");
+assert_eq!(residue.name(), "water");Check if the atom at index i is in this residue
Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.contains(56), false);
+
+residue.add_atom(56);
+assert_eq!(residue.contains(56), true);Get the list of atoms of this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.atoms(), vec![]);
+
+residue.add_atom(56);
+assert_eq!(residue.atoms(), vec![56]);Get a property with the given name in this frame, if it exist.
Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+
+assert_eq!(residue.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(residue.get("Bar"), None);pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this frame
+Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+residue.set("bar", Property::Bool(false));
+
+for (name, property) in residue.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for ResidueRef<'a>
impl<'a> !Send for ResidueRef<'a>
impl<'a> !Sync for ResidueRef<'a>
impl<'a> Unpin for ResidueRef<'a>
impl<'a> UnwindSafe for ResidueRef<'a>
Blanket Implementations
Struct chemfiles::Selection [−][src]
pub struct Selection { /* fields omitted */ }Expand description
A Selection allow to select atoms in a Frame, from a selection
+language. The selection language is built by combining basic operations.
+Each basic operation follows the <selector>[(<variable>)] <operator> <value> structure, where <operator> is a comparison operator in
+== != < <= > >=.
Implementations
Get the size of the selection, i.e. the number of atoms we are selecting +together.
+This value is 1 for the ‘atom’ context, 2 for the ‘pair’ and ‘bond’ +context, 3 for the ‘three’ and ‘angles’ context and 4 for the ‘four’ +and ‘dihedral’ context.
+Example
+let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+assert_eq!(selection.size(), 2);Get the selection string used to create this selection.
+Example
+let selection = Selection::new("name H").unwrap();
+assert_eq!(selection.string(), "name H");Evaluate a selection for a given frame, and return the corresponding +matches.
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+
+let mut selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+let matches = selection.evaluate(&frame);
+
+assert_eq!(matches.len(), 2);
+
+assert_eq!(matches[0].len(), 2);
+assert_eq!(matches[0][0], 0);
+assert_eq!(matches[0][1], 1);
+
+assert_eq!(matches[1].len(), 2);
+assert_eq!(matches[1][0], 2);
+assert_eq!(matches[1][1], 1);Evaluates a selection of size 1 on a given frame. This function
+returns the list of atomic indexes in the frame matching this selection.
Panics
+If the selection size is not 1
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+
+let mut selection = Selection::new("name H").unwrap();
+let matches = selection.list(&frame);
+
+assert_eq!(matches.len(), 2);
+assert_eq!(matches[0], 0);
+assert_eq!(matches[1], 2);Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Selection
impl UnwindSafe for Selection
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::Topology [−][src]
pub struct Topology { /* fields omitted */ }Expand description
A Topology contains the definition of all the atoms in the system, and
+the liaisons between the atoms (bonds, angles, dihedrals, …). It will
+also contain all the residues information if it is available.
Implementations
Create a new empty topology.
+Example
+let topology = Topology::new();
+assert_eq!(topology.size(), 0);Get a mutable reference to the atom at the given index in this topology.
Panics
+If index is out of bounds.
Example
+let mut topology = Topology::new();
+topology.resize(6);
+
+assert_eq!(topology.atom(4).name(), "");
+
+topology.atom_mut(4).set_name("Fe");
+assert_eq!(topology.atom(4).name(), "Fe");Get the current number of atoms in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.size(), 0);
+
+topology.resize(6);
+assert_eq!(topology.size(), 6);Resize this topology to hold natoms atoms, inserting dummy atoms if
+the new size if bigger than the old one.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.size(), 0);
+
+topology.resize(6);
+assert_eq!(topology.size(), 6);Add an Atom at the end of this topology
Example
+let mut topology = Topology::new();
+topology.add_atom(&Atom::new("Mg"));
+
+let atom = topology.atom(0);
+assert_eq!(atom.name(), "Mg");Get the number of bonds in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds_count(), 3);Get the number of angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.angles_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles_count(), 2);Get the number of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.dihedrals_count(), 1);Get the number of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+assert_eq!(topology.impropers_count(), 1);Get the list of bonds in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);Get the list of angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);Get the list of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+
+assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);Get the list of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+
+assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);Remove all existing bonds, angles, dihedral angles and improper +dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+assert_eq!(topology.bonds_count(), 2);
+assert_eq!(topology.angles().len(), 1);
+
+topology.clear_bonds();
+assert!(topology.bonds().is_empty());
+assert!(topology.angles().is_empty());Add a bond between the atoms at indexes i and j in the topology.
The bond order is set to BondOrder::Unknown.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+assert_eq!(topology.bonds_count(), 2);
+
+assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);Add a bond between the atoms at indexes i and j in the topology
+with the given bond order.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(2);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(topology.bond_order(0, 1), BondOrder::Double);Get the bond order for the bond between the atoms at indexes i and
+j.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(2);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(topology.bond_order(0, 1), BondOrder::Double);Get the bond order for all the bonds in the topology
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(3);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+topology.add_bond_with_order(0, 2, BondOrder::Single);
+
+assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);Remove any existing bond between the atoms at indexes i and j in
+this topology.
This function does nothing if there is no bond between i and j.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(1, 2);
+assert_eq!(topology.bonds_count(), 2);
+
+topology.remove_bond(0, 1);
+assert_eq!(topology.bonds_count(), 1);
+
+// Removing a bond that does not exists is fine
+topology.remove_bond(0, 2);
+assert_eq!(topology.bonds_count(), 1);Get a reference to the residue at index index from this topology.
The residue index in the topology is not always the same as the residue
+id.
Example
+let mut topology = Topology::new();
+topology.add_residue(&Residue::new("water")).unwrap();
+
+let residue = topology.residue(0).unwrap();
+assert_eq!(residue.name(), "water");Get a copy of the residue containing the atom at index index in this
+topology, if any.
Example
+let mut topology = Topology::new();
+topology.resize(8);
+
+let mut residue = Residue::new("water");
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+topology.add_residue(&residue).unwrap();
+
+let residue = topology.residue_for_atom(0).unwrap();
+assert_eq!(residue.name(), "water");
+
+assert!(topology.residue_for_atom(6).is_none());Get the number of residues in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.residues_count(), 0);
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+assert_eq!(topology.residues_count(), 2);Add a residue to this topology.
+Errors
+This function fails is the residue id is not already in the topology,
+or if the residue contains atoms that are already in another residue.
Example
+let mut topology = Topology::new();
+topology.add_residue(&Residue::new("water")).unwrap();
+
+let residue = topology.residue(0).unwrap();
+assert_eq!(residue.name(), "water");Check if the two residues first and second from the topology are
+linked together, i.e. if there is a bond between one atom in the
+first residue and one atom in the second one.
Example
+let mut topology = Topology::new();
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+
+let first = topology.residue(0).unwrap();
+let second = topology.residue(1).unwrap();
+assert_eq!(topology.are_linked(&first, &second), false);Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Topology
impl UnwindSafe for Topology
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::TopologyRef [−][src]
pub struct TopologyRef<'a> { /* fields omitted */ }Expand description
An analog to a reference to a topology (&Topology)
Methods from Deref<Target = Topology>
Get the current number of atoms in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.size(), 0);
+
+topology.resize(6);
+assert_eq!(topology.size(), 6);Get the number of bonds in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds_count(), 3);Get the number of angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.angles_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles_count(), 2);Get the number of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.dihedrals_count(), 1);Get the number of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+assert_eq!(topology.impropers_count(), 1);Get the list of bonds in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);Get the list of angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);Get the list of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+
+assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);Get the list of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+
+assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);Get the bond order for the bond between the atoms at indexes i and
+j.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(2);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(topology.bond_order(0, 1), BondOrder::Double);Get the bond order for all the bonds in the topology
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(3);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+topology.add_bond_with_order(0, 2, BondOrder::Single);
+
+assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);Get a reference to the residue at index index from this topology.
The residue index in the topology is not always the same as the residue
+id.
Example
+let mut topology = Topology::new();
+topology.add_residue(&Residue::new("water")).unwrap();
+
+let residue = topology.residue(0).unwrap();
+assert_eq!(residue.name(), "water");Get a copy of the residue containing the atom at index index in this
+topology, if any.
Example
+let mut topology = Topology::new();
+topology.resize(8);
+
+let mut residue = Residue::new("water");
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+topology.add_residue(&residue).unwrap();
+
+let residue = topology.residue_for_atom(0).unwrap();
+assert_eq!(residue.name(), "water");
+
+assert!(topology.residue_for_atom(6).is_none());Get the number of residues in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.residues_count(), 0);
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+assert_eq!(topology.residues_count(), 2);Check if the two residues first and second from the topology are
+linked together, i.e. if there is a bond between one atom in the
+first residue and one atom in the second one.
Example
+let mut topology = Topology::new();
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+
+let first = topology.residue(0).unwrap();
+let second = topology.residue(1).unwrap();
+assert_eq!(topology.are_linked(&first, &second), false);Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for TopologyRef<'a>
impl<'a> !Send for TopologyRef<'a>
impl<'a> !Sync for TopologyRef<'a>
impl<'a> Unpin for TopologyRef<'a>
impl<'a> UnwindSafe for TopologyRef<'a>
Blanket Implementations
Struct chemfiles::Trajectory [−][src]
pub struct Trajectory { /* fields omitted */ }Expand description
The Trajectory type is the main entry point when using chemfiles. A
+Trajectory behave a bit like a file, allowing to read and/or write
+Frame.
Implementations
Open the file at the given path in the given mode.
Valid modes are 'r' for read, 'w' for write and 'a' for append.
Errors
+This function fails if the file is not accessible for the given mode, if +it is incorrectly formatted for the corresponding format, or in case of +I/O errors from the OS.
+Example
+let trajectory = Trajectory::open("water.xyz", 'r').unwrap();pub fn open_with_format<'a, P, S>(
filename: P,
mode: char,
format: S
) -> Result<Trajectory, Error> where
P: AsRef<Path>,
S: Into<&'a str>,
pub fn open_with_format<'a, P, S>(
filename: P,
mode: char,
format: S
) -> Result<Trajectory, Error> where
P: AsRef<Path>,
S: Into<&'a str>,
Open the file at the given path using a specific file format and the
+given mode.
Valid modes are 'r' for read, 'w' for write and 'a' for append.
Specifying a format is needed when the file format does not match the
+extension, or when there is not standard extension for this format. If
+format is an empty string, the format will be guessed from the
+extension.
Errors
+This function fails if the file is not accessible for the given mode, if +it is incorrectly formatted for the corresponding format, or in case of +I/O errors from the OS.
+Example
+let trajectory = Trajectory::open_with_format("water.zeo", 'r', "XYZ").unwrap();pub fn memory_reader<'a, S>(data: S, format: S) -> Result<Trajectory, Error> where
S: Into<&'a str>,
pub fn memory_reader<'a, S>(data: S, format: S) -> Result<Trajectory, Error> where
S: Into<&'a str>,
Read a memory buffer as though it was a formatted file.
+The memory buffer used to store the file is given using the data
+argument. The format parameter is required and should follow the same
+rules as in the main Trajectory constructor.
Errors
+This function fails if the data is incorrectly formatted for the +corresponding format, or if the format do not support in-memory readers.
+Example
+let aromatics = "c1ccccc1\nc1ccco1\nc1ccccn1\n";
+let mut trajectory = Trajectory::memory_reader(aromatics, "SMI").unwrap();
+let mut frame = Frame::new();
+trajectory.read(&mut frame).unwrap();
+assert_eq!(frame.size(), 6);Write to a memory buffer as though it was a formatted file.
+The format parameter should follow the same rules as in the main
+Trajectory constructor, except that compression specification
+is not supported.
The memory_buffer function can be used to retrieve the data written
+to memory of the Trajectory.
Errors
+This function fails if the format do not support in-memory writers.
+Example
+let trajectory_memory = Trajectory::memory_writer("SMI");
+
+// Binary formats typically do not support this feature
+assert!(Trajectory::memory_writer("XTC").is_err());Read the next step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of atom +in the next step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+let mut frame = Frame::new();
+
+trajectory.read(&mut frame).unwrap();Read a specific step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of +atom at this step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+let mut frame = Frame::new();
+
+trajectory.read_step(10, &mut frame).unwrap();Set the topology associated with this trajectory. This topology will
+be used when reading and writing the files, replacing any topology in
+the frames or files.
Example
+let mut topology = Topology::new();
+topology.add_atom(&Atom::new("H"));
+topology.add_atom(&Atom::new("O"));
+topology.add_atom(&Atom::new("H"));
+topology.add_bond(0, 1);
+topology.add_bond(1, 2);
+
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+trajectory.set_topology(&topology);Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in format;
+and extracting the topology of this frame.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+trajectory.set_topology_file("topology.pdb").unwrap();Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in
+format; and extracting the topology of this frame.
If format is an empty string, the format will be guessed from the
+path extension.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+trajectory.set_topology_with_format("topology.mol", "PDB").unwrap();Set the unit cell associated with a trajectory. This cell will be
+used when reading and writing the files, replacing any unit cell in the
+frames or files.
Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+trajectory.set_cell(&UnitCell::new([10.0, 11.0, 12.5]));Get the number of steps (the number of frames) in a trajectory.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+
+println!("This trajectory contains {} steps", trajectory.nsteps());Obtain the memory buffer written to by the trajectory.
+Errors
+This fails if the trajectory was not opened with
+Trajectory::memory_writer.
Example
+let mut trajectory_memory = Trajectory::memory_writer("SMI").unwrap();
+
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+frame.add_bond_with_order(0, 1, BondOrder::Single);
+
+trajectory_memory.write(&frame).unwrap();
+
+let result = trajectory_memory.memory_buffer();
+assert_eq!(result.unwrap(), "CC\n");Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Trajectory
impl !Send for Trajectory
impl !Sync for Trajectory
impl Unpin for Trajectory
impl UnwindSafe for Trajectory
Blanket Implementations
Struct chemfiles::UnitCell [−][src]
pub struct UnitCell { /* fields omitted */ }Expand description
An UnitCell represent the box containing the atoms, and its periodicity.
An unit cell is fully represented by three lengths (a, b, c); and three +angles (alpha, beta, gamma). The angles are stored in degrees, and the +lengths in Angstroms.
+A cell also has a matricial representation, by projecting the three base +vector into an orthonormal base. We choose to represent such matrix as an +upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |Implementations
Create an Orthorhombic UnitCell from the three lengths, in Angstroms.
Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);Create an Infinite UnitCell.
Example
+let cell = UnitCell::infinite();
+
+assert_eq!(cell.lengths(), [0.0, 0.0, 0.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+assert_eq!(cell.shape(), CellShape::Infinite);Create an Triclinic UnitCell from the three lengths (in Angstroms)
+and three angles (in degree). alpha is the angle between the vectors
+b and c; beta is the between the vectors a and c and gamma
+is the angle between the vectors a and b.
Example
+let cell = UnitCell::triclinic([10.0, 10.0, 10.0], [98.0, 99.0, 90.0]);
+
+assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);
+assert_eq!(cell.angles()[0], 98.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 99.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);
+assert_eq!(cell.shape(), CellShape::Triclinic);Create an UnitCell from a cell matrix. If matrix contains only
+zeros, then an Infinite cell is created. If only the diagonal of the
+matrix is non-zero, then the cell is Orthorhombic. Else a
+Triclinic cell is created. The matrix entries should be in Angstroms.
Panics
+If the matrix has a negative determinant, or more generally is not +representing a unit cell.
+Example
+let cell = UnitCell::from_matrix([
+ [1.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]
+]);
+
+assert_eq!(cell.lengths(), [1.0, 2.0, 3.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);Get the three lengths of the cell, in Angstroms.
+Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);Set the three lengths of the cell, in Angstroms.
+Errors
+This function fails if the unit cell is infinite, or if one of the +lengths is negative.
+Example
+let mut cell = UnitCell::new([30.0, 30.0, 23.0]);
+
+cell.set_lengths([10.0, 30.0, 42.0]).unwrap();
+assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]);
+
+assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());Get the three angles of the cell, in degrees.
+Example
+let cell = UnitCell::new([20.0, 20.0, 20.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+
+let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);Set the three angles of the cell, in degrees.
+Errors
+This function fails if the unit cell is not Triclinic.
Example
+let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);
+
+cell.set_angles([90.0, 90.0, 90.0]).unwrap();
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+
+let matrix = cell.matrix();
+
+assert_eq!(matrix[0][0], 10.0);
+assert_eq!(matrix[1][1], 20.0);
+assert_eq!(matrix[2][2], 30.0);
+
+assert!(matrix[1][2].abs() < 1e-9);Get the shape of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);Set the shape of the unit cell to shape.
Errors
+This can fail if the cell length or angles are incompatible with the +new shape.
+Example
+let mut cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);
+
+cell.set_shape(CellShape::Triclinic).unwrap();
+assert_eq!(cell.shape(), CellShape::Triclinic);Get the volume of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0);Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for UnitCell
impl UnwindSafe for UnitCell
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::UnitCellMut [−][src]
pub struct UnitCellMut<'a> { /* fields omitted */ }Expand description
An analog to a mutable reference to an unit cell (&mut UnitCell)
Methods from Deref<Target = UnitCell>
Get the three lengths of the cell, in Angstroms.
+Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);Set the three lengths of the cell, in Angstroms.
+Errors
+This function fails if the unit cell is infinite, or if one of the +lengths is negative.
+Example
+let mut cell = UnitCell::new([30.0, 30.0, 23.0]);
+
+cell.set_lengths([10.0, 30.0, 42.0]).unwrap();
+assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]);
+
+assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());Get the three angles of the cell, in degrees.
+Example
+let cell = UnitCell::new([20.0, 20.0, 20.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+
+let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);Set the three angles of the cell, in degrees.
+Errors
+This function fails if the unit cell is not Triclinic.
Example
+let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);
+
+cell.set_angles([90.0, 90.0, 90.0]).unwrap();
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+
+let matrix = cell.matrix();
+
+assert_eq!(matrix[0][0], 10.0);
+assert_eq!(matrix[1][1], 20.0);
+assert_eq!(matrix[2][2], 30.0);
+
+assert!(matrix[1][2].abs() < 1e-9);Get the shape of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);Set the shape of the unit cell to shape.
Errors
+This can fail if the cell length or angles are incompatible with the +new shape.
+Example
+let mut cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);
+
+cell.set_shape(CellShape::Triclinic).unwrap();
+assert_eq!(cell.shape(), CellShape::Triclinic);Get the volume of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0);Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for UnitCellMut<'a>
impl<'a> !Send for UnitCellMut<'a>
impl<'a> !Sync for UnitCellMut<'a>
impl<'a> Unpin for UnitCellMut<'a>
impl<'a> !UnwindSafe for UnitCellMut<'a>
Blanket Implementations
Struct chemfiles::UnitCellRef [−][src]
pub struct UnitCellRef<'a> { /* fields omitted */ }Expand description
An analog to a reference to an unit cell (&UnitCell)
Methods from Deref<Target = UnitCell>
Get the three lengths of the cell, in Angstroms.
+Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);Get the three angles of the cell, in degrees.
+Example
+let cell = UnitCell::new([20.0, 20.0, 20.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+
+let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+
+let matrix = cell.matrix();
+
+assert_eq!(matrix[0][0], 10.0);
+assert_eq!(matrix[1][1], 20.0);
+assert_eq!(matrix[2][2], 30.0);
+
+assert!(matrix[1][2].abs() < 1e-9);Get the shape of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);Get the volume of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0);Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for UnitCellRef<'a>
impl<'a> !Send for UnitCellRef<'a>
impl<'a> !Sync for UnitCellRef<'a>
impl<'a> Unpin for UnitCellRef<'a>
impl<'a> UnwindSafe for UnitCellRef<'a>
Blanket Implementations
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All Rights Reserved. Source is a trademark + of Adobe Systems Incorporated in the United States and/or other countries. + + Licensed under the SIL Open Font License, Version 1.1. + See SourceCodePro-LICENSE.txt. + +* Source Serif 4 (SourceSerif4-Regular.ttf.woff2, SourceSerif4-Bold.ttf.woff2, + SourceSerif4-It.ttf.woff2, SourceSerif4-Regular.ttf.woff, + SourceSerif4-Bold.ttf.woff, SourceSerif4-It.ttf.woff): + + Copyright 2014-2021 Adobe (http://www.adobe.com/), with Reserved Font Name + 'Source'. All Rights Reserved. Source is a trademark of Adobe in the United + States and/or other countries. + + Licensed under the SIL Open Font License, Version 1.1. + See SourceSerif4-LICENSE.md. + +This copyright file is intended to be distributed with rustdoc output. diff --git a/0.10.2/doc/FiraSans-LICENSE.txt b/0.10.2/doc/FiraSans-LICENSE.txt new file mode 100644 index 000000000..ff9afab06 --- /dev/null +++ b/0.10.2/doc/FiraSans-LICENSE.txt @@ -0,0 +1,94 @@ +Digitized data copyright (c) 2012-2015, The Mozilla Foundation and Telefonica S.A. +with Reserved Font Name < Fira >, + +This Font Software is licensed under the SIL Open Font License, Version 1.1. +This license is copied below, and is also available with a FAQ at: +http://scripts.sil.org/OFL + + +----------------------------------------------------------- +SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007 +----------------------------------------------------------- + +PREAMBLE +The goals of the Open Font License (OFL) are to stimulate worldwide +development of collaborative font projects, to support the font creation +efforts of academic and linguistic communities, and to provide a free and +open framework in which fonts may be shared and improved in partnership +with others. + +The OFL allows the licensed fonts to be used, studied, modified and +redistributed freely as long as they are not sold by themselves. The +fonts, including any derivative works, can be bundled, embedded, +redistributed and/or sold with any software provided that any reserved +names are not used by derivative works. The fonts and derivatives, +however, cannot be released under any other type of license. The +requirement for fonts to remain under this license does not apply +to any document created using the fonts or their derivatives. + +DEFINITIONS +"Font Software" refers to the set of files released by the Copyright +Holder(s) under this license and clearly marked as such. This may +include source files, build scripts and documentation. + +"Reserved Font Name" refers to any names specified as such after the +copyright statement(s). + +"Original Version" refers to the collection of Font Software components as +distributed by the Copyright Holder(s). + +"Modified Version" refers to any derivative made by adding to, deleting, +or substituting -- in part or in whole -- any of the components of the +Original Version, by changing formats or by porting the Font Software to a +new environment. + +"Author" refers to any designer, engineer, programmer, technical +writer or other person who contributed to the Font Software. + +PERMISSION & CONDITIONS +Permission is hereby granted, free of charge, to any person obtaining +a copy of the Font Software, to use, study, copy, merge, embed, modify, +redistribute, and sell modified and unmodified copies of the Font +Software, subject to the following conditions: + +1) Neither the Font Software nor any of its individual components, +in Original or Modified Versions, may be sold by itself. + +2) Original or Modified Versions of the Font Software may be bundled, +redistributed and/or sold with any software, provided that each copy +contains the above copyright notice and this license. These can be +included either as stand-alone text files, human-readable headers or +in the appropriate machine-readable metadata fields within text or +binary files as long as those fields can be easily viewed by the user. + +3) No Modified Version of the Font Software may use the Reserved Font +Name(s) unless explicit written permission is granted by the corresponding +Copyright Holder. This restriction only applies to the primary font name as +presented to the users. + +4) The name(s) of the Copyright Holder(s) or the Author(s) of the Font +Software shall not be used to promote, endorse or advertise any +Modified Version, except to acknowledge the contribution(s) of the +Copyright Holder(s) and the Author(s) or with their explicit written +permission. + +5) The Font Software, modified or unmodified, in part or in whole, +must be distributed entirely under this license, and must not be +distributed under any other license. The requirement for fonts to +remain under this license does not apply to any document created +using the Font Software. + +TERMINATION +This license becomes null and void if any of the above conditions are +not met. + +DISCLAIMER +THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT +OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE +COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL +DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM +OTHER DEALINGS IN THE FONT SOFTWARE. diff --git a/0.10.2/doc/FiraSans-Medium.woff b/0.10.2/doc/FiraSans-Medium.woff new file mode 100644 index 000000000..7d742c5fb Binary files /dev/null and b/0.10.2/doc/FiraSans-Medium.woff differ diff --git a/0.10.2/doc/FiraSans-Medium.woff2 b/0.10.2/doc/FiraSans-Medium.woff2 new file mode 100644 index 000000000..7a1e5fc54 Binary files /dev/null and b/0.10.2/doc/FiraSans-Medium.woff2 differ diff --git a/0.10.2/doc/FiraSans-Regular.woff b/0.10.2/doc/FiraSans-Regular.woff new file mode 100644 index 000000000..d8e0363f4 Binary files /dev/null and b/0.10.2/doc/FiraSans-Regular.woff differ diff --git a/0.10.2/doc/FiraSans-Regular.woff2 b/0.10.2/doc/FiraSans-Regular.woff2 new file mode 100644 index 000000000..e766e06cc Binary files /dev/null and b/0.10.2/doc/FiraSans-Regular.woff2 differ diff --git a/0.10.2/doc/LICENSE-APACHE.txt b/0.10.2/doc/LICENSE-APACHE.txt new file mode 100644 index 000000000..16fe87b06 --- /dev/null +++ b/0.10.2/doc/LICENSE-APACHE.txt @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + +TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + +1. 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IN NO EVENT +SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY +CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION +OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR +IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +DEALINGS IN THE SOFTWARE. diff --git a/0.10.2/doc/SourceCodePro-It.ttf.woff b/0.10.2/doc/SourceCodePro-It.ttf.woff new file mode 100644 index 000000000..8d68f2feb Binary files /dev/null and b/0.10.2/doc/SourceCodePro-It.ttf.woff differ diff --git a/0.10.2/doc/SourceCodePro-It.ttf.woff2 b/0.10.2/doc/SourceCodePro-It.ttf.woff2 new file mode 100644 index 000000000..462c34efc Binary files /dev/null and b/0.10.2/doc/SourceCodePro-It.ttf.woff2 differ diff --git a/0.10.2/doc/SourceCodePro-LICENSE.txt b/0.10.2/doc/SourceCodePro-LICENSE.txt new file mode 100644 index 000000000..07542572e --- /dev/null +++ b/0.10.2/doc/SourceCodePro-LICENSE.txt @@ -0,0 +1,93 @@ +Copyright 2010, 2012 Adobe Systems Incorporated (http://www.adobe.com/), with Reserved Font Name 'Source'. All Rights Reserved. Source is a trademark of Adobe Systems Incorporated in the United States and/or other countries. + +This Font Software is licensed under the SIL Open Font License, Version 1.1. + +This license is copied below, and is also available with a FAQ at: http://scripts.sil.org/OFL + + +----------------------------------------------------------- +SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007 +----------------------------------------------------------- + +PREAMBLE +The goals of the Open Font License (OFL) are to stimulate worldwide +development of collaborative font projects, to support the font creation +efforts of academic and linguistic communities, and to provide a free and +open framework in which fonts may be shared and improved in partnership +with others. + +The OFL allows the licensed fonts to be used, studied, modified and +redistributed freely as long as they are not sold by themselves. The +fonts, including any derivative works, can be bundled, embedded, +redistributed and/or sold with any software provided that any reserved +names are not used by derivative works. The fonts and derivatives, +however, cannot be released under any other type of license. The +requirement for fonts to remain under this license does not apply +to any document created using the fonts or their derivatives. + +DEFINITIONS +"Font Software" refers to the set of files released by the Copyright +Holder(s) under this license and clearly marked as such. This may +include source files, build scripts and documentation. + +"Reserved Font Name" refers to any names specified as such after the +copyright statement(s). + +"Original Version" refers to the collection of Font Software components as +distributed by the Copyright Holder(s). + +"Modified Version" refers to any derivative made by adding to, deleting, +or substituting -- in part or in whole -- any of the components of the +Original Version, by changing formats or by porting the Font Software to a +new environment. + +"Author" refers to any designer, engineer, programmer, technical +writer or other person who contributed to the Font Software. + +PERMISSION & CONDITIONS +Permission is hereby granted, free of charge, to any person obtaining +a copy of the Font Software, to use, study, copy, merge, embed, modify, +redistribute, and sell modified and unmodified copies of the Font +Software, subject to the following conditions: + +1) Neither the Font Software nor any of its individual components, +in Original or Modified Versions, may be sold by itself. + +2) Original or Modified Versions of the Font Software may be bundled, +redistributed and/or sold with any software, provided that each copy +contains the above copyright notice and this license. These can be +included either as stand-alone text files, human-readable headers or +in the appropriate machine-readable metadata fields within text or +binary files as long as those fields can be easily viewed by the user. + +3) No Modified Version of the Font Software may use the Reserved Font +Name(s) unless explicit written permission is granted by the corresponding +Copyright Holder. This restriction only applies to the primary font name as +presented to the users. + +4) The name(s) of the Copyright Holder(s) or the Author(s) of the Font +Software shall not be used to promote, endorse or advertise any +Modified Version, except to acknowledge the contribution(s) of the +Copyright Holder(s) and the Author(s) or with their explicit written +permission. + +5) The Font Software, modified or unmodified, in part or in whole, +must be distributed entirely under this license, and must not be +distributed under any other license. The requirement for fonts to +remain under this license does not apply to any document created +using the Font Software. + +TERMINATION +This license becomes null and void if any of the above conditions are +not met. + +DISCLAIMER +THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT +OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE +COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL +DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM +OTHER DEALINGS IN THE FONT SOFTWARE. diff --git a/0.10.2/doc/SourceCodePro-Regular.ttf.woff b/0.10.2/doc/SourceCodePro-Regular.ttf.woff new file mode 100644 index 000000000..7be076e1f Binary files /dev/null and b/0.10.2/doc/SourceCodePro-Regular.ttf.woff differ diff --git a/0.10.2/doc/SourceCodePro-Regular.ttf.woff2 b/0.10.2/doc/SourceCodePro-Regular.ttf.woff2 new file mode 100644 index 000000000..10b558e0b Binary files /dev/null and b/0.10.2/doc/SourceCodePro-Regular.ttf.woff2 differ diff --git a/0.10.2/doc/SourceCodePro-Semibold.ttf.woff b/0.10.2/doc/SourceCodePro-Semibold.ttf.woff new file mode 100644 index 000000000..61bc67b80 Binary files /dev/null and b/0.10.2/doc/SourceCodePro-Semibold.ttf.woff differ diff --git a/0.10.2/doc/SourceCodePro-Semibold.ttf.woff2 b/0.10.2/doc/SourceCodePro-Semibold.ttf.woff2 new file mode 100644 index 000000000..5ec64eef0 Binary files /dev/null and b/0.10.2/doc/SourceCodePro-Semibold.ttf.woff2 differ diff --git a/0.10.2/doc/SourceSerif4-Bold.ttf.woff b/0.10.2/doc/SourceSerif4-Bold.ttf.woff new file mode 100644 index 000000000..8ad41888e Binary files /dev/null and b/0.10.2/doc/SourceSerif4-Bold.ttf.woff differ diff --git a/0.10.2/doc/SourceSerif4-Bold.ttf.woff2 b/0.10.2/doc/SourceSerif4-Bold.ttf.woff2 new file mode 100644 index 000000000..db57d2145 Binary files /dev/null and b/0.10.2/doc/SourceSerif4-Bold.ttf.woff2 differ diff --git a/0.10.2/doc/SourceSerif4-It.ttf.woff b/0.10.2/doc/SourceSerif4-It.ttf.woff new file mode 100644 index 000000000..2a34b5c42 Binary files /dev/null and b/0.10.2/doc/SourceSerif4-It.ttf.woff differ diff --git a/0.10.2/doc/SourceSerif4-It.ttf.woff2 b/0.10.2/doc/SourceSerif4-It.ttf.woff2 new file mode 100644 index 000000000..1cbc021a3 Binary files /dev/null and b/0.10.2/doc/SourceSerif4-It.ttf.woff2 differ diff --git a/0.10.2/doc/SourceSerif4-LICENSE.md b/0.10.2/doc/SourceSerif4-LICENSE.md new file mode 100644 index 000000000..68ea18924 --- /dev/null +++ b/0.10.2/doc/SourceSerif4-LICENSE.md @@ -0,0 +1,93 @@ +Copyright 2014-2021 Adobe (http://www.adobe.com/), with Reserved Font Name 'Source'. All Rights Reserved. Source is a trademark of Adobe in the United States and/or other countries. + +This Font Software is licensed under the SIL Open Font License, Version 1.1. + +This license is copied below, and is also available with a FAQ at: http://scripts.sil.org/OFL + + +----------------------------------------------------------- +SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007 +----------------------------------------------------------- + +PREAMBLE +The goals of the Open Font License (OFL) are to stimulate worldwide +development of collaborative font projects, to support the font creation +efforts of academic and linguistic communities, and to provide a free and +open framework in which fonts may be shared and improved in partnership +with others. + +The OFL allows the licensed fonts to be used, studied, modified and +redistributed freely as long as they are not sold by themselves. The +fonts, including any derivative works, can be bundled, embedded, +redistributed and/or sold with any software provided that any reserved +names are not used by derivative works. The fonts and derivatives, +however, cannot be released under any other type of license. The +requirement for fonts to remain under this license does not apply +to any document created using the fonts or their derivatives. + +DEFINITIONS +"Font Software" refers to the set of files released by the Copyright +Holder(s) under this license and clearly marked as such. This may +include source files, build scripts and documentation. + +"Reserved Font Name" refers to any names specified as such after the +copyright statement(s). + +"Original Version" refers to the collection of Font Software components as +distributed by the Copyright Holder(s). + +"Modified Version" refers to any derivative made by adding to, deleting, +or substituting -- in part or in whole -- any of the components of the +Original Version, by changing formats or by porting the Font Software to a +new environment. + +"Author" refers to any designer, engineer, programmer, technical +writer or other person who contributed to the Font Software. + +PERMISSION & CONDITIONS +Permission is hereby granted, free of charge, to any person obtaining +a copy of the Font Software, to use, study, copy, merge, embed, modify, +redistribute, and sell modified and unmodified copies of the Font +Software, subject to the following conditions: + +1) Neither the Font Software nor any of its individual components, +in Original or Modified Versions, may be sold by itself. + +2) Original or Modified Versions of the Font Software may be bundled, +redistributed and/or sold with any software, provided that each copy +contains the above copyright notice and this license. These can be +included either as stand-alone text files, human-readable headers or +in the appropriate machine-readable metadata fields within text or +binary files as long as those fields can be easily viewed by the user. + +3) No Modified Version of the Font Software may use the Reserved Font +Name(s) unless explicit written permission is granted by the corresponding +Copyright Holder. This restriction only applies to the primary font name as +presented to the users. + +4) The name(s) of the Copyright Holder(s) or the Author(s) of the Font +Software shall not be used to promote, endorse or advertise any +Modified Version, except to acknowledge the contribution(s) of the +Copyright Holder(s) and the Author(s) or with their explicit written +permission. + +5) The Font Software, modified or unmodified, in part or in whole, +must be distributed entirely under this license, and must not be +distributed under any other license. The requirement for fonts to +remain under this license does not apply to any document created +using the Font Software. + +TERMINATION +This license becomes null and void if any of the above conditions are +not met. + +DISCLAIMER +THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT +OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE +COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL +DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM +OTHER DEALINGS IN THE FONT SOFTWARE. diff --git a/0.10.2/doc/SourceSerif4-Regular.ttf.woff b/0.10.2/doc/SourceSerif4-Regular.ttf.woff new file mode 100644 index 000000000..45a5521ab Binary files /dev/null and b/0.10.2/doc/SourceSerif4-Regular.ttf.woff differ diff --git a/0.10.2/doc/SourceSerif4-Regular.ttf.woff2 b/0.10.2/doc/SourceSerif4-Regular.ttf.woff2 new file mode 100644 index 000000000..2db73fe2b Binary files /dev/null and b/0.10.2/doc/SourceSerif4-Regular.ttf.woff2 differ diff --git a/0.10.2/doc/ayu.css b/0.10.2/doc/ayu.css new file mode 100644 index 000000000..3444ac5f1 --- /dev/null +++ b/0.10.2/doc/ayu.css @@ -0,0 +1 @@ + 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file mode 100644 index 000000000..0ddbfd642 --- /dev/null +++ b/0.10.2/doc/chemfiles/all.html @@ -0,0 +1,5 @@ +List of all items[−] + +
Structs
- Atom
- AtomMut
- AtomRef
- Error
- FormatMetadata
- Frame
- Match
- PropertiesIter
- Residue
- ResidueRef
- Selection
- Topology
- TopologyRef
- Trajectory
- UnitCell
- UnitCellMut
- UnitCellRef
Enums
Functions
Redirecting to ../../chemfiles/struct.Atom.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/atom/struct.AtomMut.html b/0.10.2/doc/chemfiles/atom/struct.AtomMut.html new file mode 100644 index 000000000..2843d6f36 --- /dev/null +++ b/0.10.2/doc/chemfiles/atom/struct.AtomMut.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.AtomMut.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/atom/struct.AtomRef.html b/0.10.2/doc/chemfiles/atom/struct.AtomRef.html new file mode 100644 index 000000000..fc21ff8b9 --- /dev/null +++ b/0.10.2/doc/chemfiles/atom/struct.AtomRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.AtomRef.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/cell/enum.CellShape.html b/0.10.2/doc/chemfiles/cell/enum.CellShape.html new file mode 100644 index 000000000..9d3d95dbc --- /dev/null +++ b/0.10.2/doc/chemfiles/cell/enum.CellShape.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/enum.CellShape.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/cell/struct.UnitCell.html b/0.10.2/doc/chemfiles/cell/struct.UnitCell.html new file mode 100644 index 000000000..c199c7635 --- /dev/null +++ b/0.10.2/doc/chemfiles/cell/struct.UnitCell.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.UnitCell.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/cell/struct.UnitCellMut.html b/0.10.2/doc/chemfiles/cell/struct.UnitCellMut.html new file mode 100644 index 000000000..a07e76605 --- /dev/null +++ b/0.10.2/doc/chemfiles/cell/struct.UnitCellMut.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.UnitCellMut.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/cell/struct.UnitCellRef.html b/0.10.2/doc/chemfiles/cell/struct.UnitCellRef.html new file mode 100644 index 000000000..7455c76ac --- /dev/null +++ b/0.10.2/doc/chemfiles/cell/struct.UnitCellRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.UnitCellRef.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/enum.BondOrder.html b/0.10.2/doc/chemfiles/enum.BondOrder.html new file mode 100644 index 000000000..29e964670 --- /dev/null +++ b/0.10.2/doc/chemfiles/enum.BondOrder.html @@ -0,0 +1,54 @@ +Enum chemfiles::BondOrder [−][src]
#[repr(C)]
+#[non_exhaustive]
+pub enum BondOrder {
+ Unknown,
+ Single,
+ Double,
+ Triple,
+ Quadruple,
+ Quintuplet,
+ Amide,
+ Aromatic,
+}Expand description
Possible bond order associated with bonds
+Variants (Non-exhaustive)
This enum is marked as non-exhaustive
Non-exhaustive enums could have additional variants added in future. Therefore, when matching against variants of non-exhaustive enums, an extra wildcard arm must be added to account for any future variants.
Unknown or unspecified bond order
+Single bond
+Double bond
+Triple bond
+Quadruple bond (present in some metals)
+Quintuplet bond (present in some metals)
+Amide bond (required by some file formats)
+Aromatic bond (required by some file formats)
+Trait Implementations
This method returns an ordering between self and other values if one exists. Read more
This method tests less than (for self and other) and is used by the < operator. Read more
This method tests less than or equal to (for self and other) and is used by the <=
+operator. Read more
This method tests greater than (for self and other) and is used by the > operator. Read more
Auto Trait Implementations
impl RefUnwindSafe for BondOrder
impl UnwindSafe for BondOrder
Blanket Implementations
Mutably borrows from an owned value. Read more
+Enum chemfiles::CellShape [−][src]
pub enum CellShape {
+ Orthorhombic,
+ Triclinic,
+ Infinite,
+}Expand description
Available unit cell shapes.
+Variants
Orthorhombic cell, with the three angles equals to 90°.
+Triclinic cell, with any values for the angles.
+Infinite cell, to use when there is no cell.
+Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for CellShape
impl UnwindSafe for CellShape
Blanket Implementations
Mutably borrows from an owned value. Read more
+Enum chemfiles::Property [−][src]
Expand description
A Property is a piece of data that can be associated with an Atom or a
+Frame.
Variants
Bool(bool)Boolean property
+Tuple Fields of Bool
0: boolDouble(f64)Floating point property
+Tuple Fields of Double
0: f64String(String)String property
+Tuple Fields of String
0: String3-dimensional vector property
+Trait Implementations
This method returns an ordering between self and other values if one exists. Read more
This method tests less than (for self and other) and is used by the < operator. Read more
This method tests less than or equal to (for self and other) and is used by the <=
+operator. Read more
This method tests greater than (for self and other) and is used by the > operator. Read more
Auto Trait Implementations
impl RefUnwindSafe for Property
impl UnwindSafe for Property
Blanket Implementations
Mutably borrows from an owned value. Read more
+Enum chemfiles::Status [−][src]
#[repr(C)]
+#[non_exhaustive]
+pub enum Status {
+ Success,
+ MemoryError,
+ FileError,
+ FormatError,
+ SelectionError,
+ ConfigurationError,
+ OutOfBounds,
+ PropertyError,
+ ChemfilesError,
+ StdCppError,
+ UTF8PathError,
+}Expand description
Possible causes of error in chemfiles
+Variants (Non-exhaustive)
This enum is marked as non-exhaustive
Non-exhaustive enums could have additional variants added in future. Therefore, when matching against variants of non-exhaustive enums, an extra wildcard arm must be added to account for any future variants.
No error
+Error in memory allocations
+Error while reading or writing a file
+Error in file formatting, i.e. the file is invalid
+Error in selection string syntax
+Error in configuration files syntax
+Error for out of bounds indexing
+Error related to properties
+Exception in the C++ chemfiles library
+Exception in the C++ standard library
+The given path is not valid UTF8
+Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Status
impl UnwindSafe for Status
Blanket Implementations
Mutably borrows from an owned value. Read more
+Redirecting to ../../chemfiles/enum.Status.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/errors/fn.set_warning_callback.html b/0.10.2/doc/chemfiles/errors/fn.set_warning_callback.html new file mode 100644 index 000000000..97bc2a1ba --- /dev/null +++ b/0.10.2/doc/chemfiles/errors/fn.set_warning_callback.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/fn.set_warning_callback.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/errors/struct.Error.html b/0.10.2/doc/chemfiles/errors/struct.Error.html new file mode 100644 index 000000000..34339c749 --- /dev/null +++ b/0.10.2/doc/chemfiles/errors/struct.Error.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Error.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/fn.add_configuration.html b/0.10.2/doc/chemfiles/fn.add_configuration.html new file mode 100644 index 000000000..20795ff00 --- /dev/null +++ b/0.10.2/doc/chemfiles/fn.add_configuration.html @@ -0,0 +1,14 @@ +Function chemfiles::add_configuration [−][src]
pub fn add_configuration<S>(path: S) -> Result<(), Error> where
S: AsRef<str>, Expand description
Read configuration data from the file at path.
By default, chemfiles reads configuration from any file named
+.chemfiles.toml in the current directory or any parent directory. This
+function can be used to add data from another configuration file. Data from
+the new configuration file will overwrite any existing data.
Errors
+This function will fail if there is no file at path, or if the file is
+incorrectly formatted.
Example
+chemfiles::add_configuration("local-config.toml").unwrap();
+// from now on, the data from "local-config.toml" will be usedFunction chemfiles::formats_list [−][src]
pub fn formats_list() -> Vec<FormatMetadata>Expand description
Get the list of formats known by chemfiles, as well as all associated metadata.
+Example
+let formats = chemfiles::formats_list();
+println!("chemfiles supports {} formats:", formats.len());
+for format in &formats {
+ println!(
+ " {:<15} {}",
+ format.name,
+ format.extension.as_deref().unwrap_or("")
+ );
+}Function chemfiles::guess_format [−][src]
pub fn guess_format(path: &str) -> StringExpand description
Get the format that chemfiles would use to read a file at the given
+path.
The format is mostly guessed from the path extension, chemfiles only tries
+to read the file to distinguish between CIF and mmCIF files. Opening the
+file using the returned format string might still fail. For example, it will
+fail if the file is not actually formatted according to the guessed format;
+or the format/compression combination is not supported (e.g. XTC / GZ will
+not work since the XTC reader does not support compressed files).
The returned format is represented in a way compatible with the various
+Trajectory constructors, i.e. "<format name> [/ <compression>]", where
+compression is optional.
Examples
+let format = chemfiles::guess_format("trajectory.xyz.xz");
+assert_eq!(format, "XYZ / XZ");
+
+let format = chemfiles::guess_format("trajectory.nc");
+assert_eq!(format, "Amber NetCDF");Function chemfiles::set_warning_callback [−][src]
pub fn set_warning_callback<F>(callback: F) where
F: WarningCallback + 'static, Expand description
Use callback for every chemfiles warning. The callback will be passed
+the warning message. This will drop any previous warning callback.
Function chemfiles::version [−][src]
pub fn version() -> StringExpand description
Get the version of the chemfiles library.
+Example
+let version = chemfiles::version();
+assert!(version.starts_with("0.10"));Redirecting to ../../chemfiles/struct.Frame.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/index.html b/0.10.2/doc/chemfiles/index.html new file mode 100644 index 000000000..72a761b21 --- /dev/null +++ b/0.10.2/doc/chemfiles/index.html @@ -0,0 +1,63 @@ +Crate chemfiles[−][src]
Expand description
Chemfiles is a multi-language library written in modern C++ for reading and +writing from and to molecular trajectory files. These files are created by +your favorite theoretical chemistry program, and contains information about +atomic or residues names and positions. Some format also have additional +information, such as velocities, forces, energy, …
+This crate expose the C API of chemfiles to Rust, and make all the +functionalities accessible. For more information on the C++ library, +please see its documentation. Specifically, the following pages +are worth reading:
+-
+
- The overview of the classes organization; +
- The list of supported formats; +
- The documentation for the selection language; +
Structs
+An Atom is a particle in the current Frame. It stores the following
+atomic properties:
An analog to a mutable reference to an atom (&mut Atom)
An analog to a reference to an atom (&Atom)
Error type for Chemfiles.
+FormatMetadata contains metadata associated with one format.
A Frame contains data from one simulation step: the current unit
+cell, the topology, the positions, and the velocities of the particles in
+the system. If some information is missing (topology or velocity or unit
+cell), the corresponding data is filled with a default value.
A Match is a set of atomic indexes matching a given selection. It can
+mostly be used like a &[usize].
An iterator over the properties in an atom/frame/residue
+A Residue is a group of atoms belonging to the same logical unit. They
+can be small molecules, amino-acids in a protein, monomers in polymers,
+etc.
An analog to a reference to a residue (&Residue)
A Selection allow to select atoms in a Frame, from a selection
+language. The selection language is built by combining basic operations.
+Each basic operation follows the <selector>[(<variable>)] <operator> <value> structure, where <operator> is a comparison operator in
+== != < <= > >=.
A Topology contains the definition of all the atoms in the system, and
+the liaisons between the atoms (bonds, angles, dihedrals, …). It will
+also contain all the residues information if it is available.
An analog to a reference to a topology (&Topology)
The Trajectory type is the main entry point when using chemfiles. A
+Trajectory behave a bit like a file, allowing to read and/or write
+Frame.
An UnitCell represent the box containing the atoms, and its periodicity.
An analog to a mutable reference to an unit cell (&mut UnitCell)
An analog to a reference to an unit cell (&UnitCell)
Enums
+Possible bond order associated with bonds
+Available unit cell shapes.
+A Property is a piece of data that can be associated with an Atom or a
+Frame.
Possible causes of error in chemfiles
+Functions
+Read configuration data from the file at path.
Get the list of formats known by chemfiles, as well as all associated metadata.
+Get the format that chemfiles would use to read a file at the given
+path.
Use callback for every chemfiles warning. The callback will be passed
+the warning message. This will drop any previous warning callback.
Get the version of the chemfiles library.
+Redirecting to ../../chemfiles/fn.formats_list.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/misc/fn.guess_format.html b/0.10.2/doc/chemfiles/misc/fn.guess_format.html new file mode 100644 index 000000000..681a66ce5 --- /dev/null +++ b/0.10.2/doc/chemfiles/misc/fn.guess_format.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/fn.guess_format.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/misc/struct.FormatMetadata.html b/0.10.2/doc/chemfiles/misc/struct.FormatMetadata.html new file mode 100644 index 000000000..10fda814b --- /dev/null +++ b/0.10.2/doc/chemfiles/misc/struct.FormatMetadata.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.FormatMetadata.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/property/enum.Property.html b/0.10.2/doc/chemfiles/property/enum.Property.html new file mode 100644 index 000000000..87bfc97da --- /dev/null +++ b/0.10.2/doc/chemfiles/property/enum.Property.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/enum.Property.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/property/struct.PropertiesIter.html b/0.10.2/doc/chemfiles/property/struct.PropertiesIter.html new file mode 100644 index 000000000..2faef8a54 --- /dev/null +++ b/0.10.2/doc/chemfiles/property/struct.PropertiesIter.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.PropertiesIter.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/residue/struct.Residue.html b/0.10.2/doc/chemfiles/residue/struct.Residue.html new file mode 100644 index 000000000..e8f25ad8a --- /dev/null +++ b/0.10.2/doc/chemfiles/residue/struct.Residue.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Residue.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/residue/struct.ResidueRef.html b/0.10.2/doc/chemfiles/residue/struct.ResidueRef.html new file mode 100644 index 000000000..9d26d5daa --- /dev/null +++ b/0.10.2/doc/chemfiles/residue/struct.ResidueRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.ResidueRef.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/selection/struct.Match.html b/0.10.2/doc/chemfiles/selection/struct.Match.html new file mode 100644 index 000000000..3c7b0b709 --- /dev/null +++ b/0.10.2/doc/chemfiles/selection/struct.Match.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Match.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/selection/struct.Selection.html b/0.10.2/doc/chemfiles/selection/struct.Selection.html new file mode 100644 index 000000000..8ed2b5d77 --- /dev/null +++ b/0.10.2/doc/chemfiles/selection/struct.Selection.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Selection.html...
+ + + \ No newline at end of file diff --git a/0.10.2/doc/chemfiles/sidebar-items.js b/0.10.2/doc/chemfiles/sidebar-items.js new file mode 100644 index 000000000..dc3572b15 --- /dev/null +++ b/0.10.2/doc/chemfiles/sidebar-items.js @@ -0,0 +1 @@ +initSidebarItems({"enum":[["BondOrder","Possible bond order associated with bonds"],["CellShape","Available unit cell shapes."],["Property","A `Property` is a piece of data that can be associated with an `Atom` or a `Frame`."],["Status","Possible causes of error in chemfiles"]],"fn":[["add_configuration","Read configuration data from the file at `path`."],["formats_list","Get the list of formats known by chemfiles, as well as all associated metadata."],["guess_format","Get the format that chemfiles would use to read a file at the given `path`."],["set_warning_callback","Use `callback` for every chemfiles warning. The callback will be passed the warning message. This will drop any previous warning callback."],["version","Get the version of the chemfiles library."]],"struct":[["Atom","An `Atom` is a particle in the current `Frame`. It stores the following atomic properties:"],["AtomMut","An analog to a mutable reference to an atom (`&mut Atom`)"],["AtomRef","An analog to a reference to an atom (`&Atom`)"],["Error","Error type for Chemfiles."],["FormatMetadata","`FormatMetadata` contains metadata associated with one format."],["Frame","A `Frame` contains data from one simulation step: the current unit cell, the topology, the positions, and the velocities of the particles in the system. If some information is missing (topology or velocity or unit cell), the corresponding data is filled with a default value."],["Match","A `Match` is a set of atomic indexes matching a given selection. It can mostly be used like a `&[usize]`."],["PropertiesIter","An iterator over the properties in an atom/frame/residue"],["Residue","A `Residue` is a group of atoms belonging to the same logical unit. They can be small molecules, amino-acids in a protein, monomers in polymers, etc."],["ResidueRef","An analog to a reference to a residue (`&Residue`)"],["Selection","A `Selection` allow to select atoms in a `Frame`, from a selection language. The selection language is built by combining basic operations. Each basic operation follows the `Struct chemfiles::Atom [−][src]
pub struct Atom { /* fields omitted */ }Expand description
An Atom is a particle in the current Frame. It stores the following
+atomic properties:
-
+
- atom name; +
- atom type; +
- atom mass; +
- atom charge. +
The atom name is usually an unique identifier (H1, C_a) while the
+atom type will be shared between all particles of the same type: H,
+Ow, CH3.
Implementations
Create an atom with the given name, and set the atom type to name.
Example
+let atom = Atom::new("He");
+assert_eq!(atom.name(), "He");Get the atom mass, in atomic mass units.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.mass(), 4.002602);Set the atom mass to mass, in atomic mass units.
Example
+let mut atom = Atom::new("He");
+
+atom.set_mass(34.9);
+assert_eq!(atom.mass(), 34.9);Get the atom charge, in number of the electron charge e.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.charge(), 0.0);Set the atom charge to charge, in number of the electron charge e.
Example
+let mut atom = Atom::new("He");
+
+atom.set_charge(-2.0);
+assert_eq!(atom.charge(), -2.0);Set the atom name to name.
Example
+let mut atom = Atom::new("He");
+
+atom.set_name("Zn3");
+assert_eq!(atom.name(), "Zn3");Set the atom type to atomic_type.
Example
+let mut atom = Atom::new("He");
+
+atom.set_atomic_type("F");
+assert_eq!(atom.atomic_type(), "F");Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
+let atom = Atom::new("Zn");
+assert_eq!(atom.full_name(), "Zinc");Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").atomic_number(), 2);
+assert_eq!(Atom::new("Xxx").atomic_number(), 0);Add a new property with the given name to this atom.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut atom = Atom::new("He");
+atom.set("a bool", true);
+atom.set("a string", "test");
+
+assert_eq!(atom.get("a bool"), Some(Property::Bool(true)));
+assert_eq!(atom.get("a string"), Some(Property::String("test".into())));Get a property with the given name in this atom, if it exist.
Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+
+assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(atom.get("Bar"), None);pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this atom
+Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+atom.set("bar", Property::Bool(false));
+
+for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Atom
impl UnwindSafe for Atom
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::AtomMut [−][src]
pub struct AtomMut<'a> { /* fields omitted */ }Expand description
An analog to a mutable reference to an atom (&mut Atom)
Methods from Deref<Target = Atom>
Get the atom mass, in atomic mass units.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.mass(), 4.002602);Set the atom mass to mass, in atomic mass units.
Example
+let mut atom = Atom::new("He");
+
+atom.set_mass(34.9);
+assert_eq!(atom.mass(), 34.9);Get the atom charge, in number of the electron charge e.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.charge(), 0.0);Set the atom charge to charge, in number of the electron charge e.
Example
+let mut atom = Atom::new("He");
+
+atom.set_charge(-2.0);
+assert_eq!(atom.charge(), -2.0);Set the atom name to name.
Example
+let mut atom = Atom::new("He");
+
+atom.set_name("Zn3");
+assert_eq!(atom.name(), "Zn3");Set the atom type to atomic_type.
Example
+let mut atom = Atom::new("He");
+
+atom.set_atomic_type("F");
+assert_eq!(atom.atomic_type(), "F");Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
+let atom = Atom::new("Zn");
+assert_eq!(atom.full_name(), "Zinc");Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").atomic_number(), 2);
+assert_eq!(Atom::new("Xxx").atomic_number(), 0);Add a new property with the given name to this atom.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut atom = Atom::new("He");
+atom.set("a bool", true);
+atom.set("a string", "test");
+
+assert_eq!(atom.get("a bool"), Some(Property::Bool(true)));
+assert_eq!(atom.get("a string"), Some(Property::String("test".into())));Get a property with the given name in this atom, if it exist.
Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+
+assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(atom.get("Bar"), None);pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this atom
+Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+atom.set("bar", Property::Bool(false));
+
+for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for AtomMut<'a>
impl<'a> !UnwindSafe for AtomMut<'a>
Blanket Implementations
Struct chemfiles::AtomRef [−][src]
pub struct AtomRef<'a> { /* fields omitted */ }Expand description
An analog to a reference to an atom (&Atom)
Methods from Deref<Target = Atom>
Get the atom mass, in atomic mass units.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.mass(), 4.002602);Get the atom charge, in number of the electron charge e.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.charge(), 0.0);Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
+let atom = Atom::new("Zn");
+assert_eq!(atom.full_name(), "Zinc");Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").atomic_number(), 2);
+assert_eq!(Atom::new("Xxx").atomic_number(), 0);Get a property with the given name in this atom, if it exist.
Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+
+assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(atom.get("Bar"), None);pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this atom
+Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+atom.set("bar", Property::Bool(false));
+
+for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for AtomRef<'a>
impl<'a> UnwindSafe for AtomRef<'a>
Blanket Implementations
Struct chemfiles::Error [−][src]
Expand description
Error type for Chemfiles.
+Fields
status: StatusThe error status code
+message: StringA message describing the error cause
+Implementations
Get the last error message from the C++ library.
+Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Error
impl UnwindSafe for Error
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::FormatMetadata [−][src]
pub struct FormatMetadata {Show 13 fields
+ pub name: &'static str,
+ pub extension: Option<&'static str>,
+ pub description: &'static str,
+ pub reference: &'static str,
+ pub read: bool,
+ pub write: bool,
+ pub memory: bool,
+ pub positions: bool,
+ pub velocities: bool,
+ pub unit_cell: bool,
+ pub atoms: bool,
+ pub bonds: bool,
+ pub residues: bool,
+}Expand description
FormatMetadata contains metadata associated with one format.
Fields
name: &'static strName of the format.
+extension: Option<&'static str>Extension associated with the format.
+description: &'static strExtended, user-facing description of the format.
+reference: &'static strURL pointing to the format definition/reference.
+read: boolIs reading files in this format implemented?
+write: boolIs writing files in this format implemented?
+memory: boolDoes this format support in-memory IO?
+positions: boolDoes this format support storing atomic positions?
+velocities: boolDoes this format support storing atomic velocities?
+unit_cell: boolDoes this format support storing unit cell information?
+atoms: boolDoes this format support storing atom names or types?
+bonds: boolDoes this format support storing bonds between atoms?
+residues: boolDoes this format support storing residues?
+Trait Implementations
This method tests for self and other values to be equal, and is used
+by ==. Read more
This method tests for !=.
Auto Trait Implementations
impl RefUnwindSafe for FormatMetadata
impl Send for FormatMetadata
impl Sync for FormatMetadata
impl Unpin for FormatMetadata
impl UnwindSafe for FormatMetadata
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::Frame [−][src]
pub struct Frame { /* fields omitted */ }Expand description
A Frame contains data from one simulation step: the current unit
+cell, the topology, the positions, and the velocities of the particles in
+the system. If some information is missing (topology or velocity or unit
+cell), the corresponding data is filled with a default value.
Implementations
Create an empty frame. It will be resized by the library as needed.
+Example
+let frame = Frame::new();
+
+assert_eq!(frame.size(), 0);Get a mutable reference to the atom at the given index in this frame.
Panics
+If index is out of bounds.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+
+assert_eq!(frame.atom(0).name(), "Zn");
+
+frame.atom_mut(0).set_name("Fe");
+assert_eq!(frame.atom(0).name(), "Fe");Get the current number of atoms in this frame.
+Example
+let mut frame = Frame::new();
+assert_eq!(frame.size(), 0);
+
+frame.resize(67);
+assert_eq!(frame.size(), 67);Resize the positions and the velocities in this frame, to make space for
+natoms atoms. Previous data is conserved, as well as the presence of
+absence of velocities.
Example
+let mut frame = Frame::new();
+frame.resize(67);
+assert_eq!(frame.size(), 67);Add an Atom and the corresponding position and optionally velocity
+data to this frame.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("Zn"), [1.0, 1.0, 2.0], None);
+
+frame.add_velocities();
+frame.add_atom(&Atom::new("Zn"), [-1.0, 1.0, 2.0], [0.2, 0.1, 0.0]);Remove the atom at index i in this frame.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+frame.add_atom(&Atom::new("Fe"), [0.0; 3], None);
+frame.add_atom(&Atom::new("Sn"), [0.0; 3], None);
+assert_eq!(frame.size(), 3);
+
+frame.remove(1);
+assert_eq!(frame.size(), 2);
+assert_eq!(frame.atom(1).name(), "Sn");Add a bond between the atoms at indexes i and j in the frame.
The bond order is set to BondOrder::Unknown.
Example
+let mut frame = Frame::new();
+assert_eq!(frame.topology().bonds_count(), 0);
+frame.resize(5);
+
+frame.add_bond(0, 1);
+frame.add_bond(3, 1);
+frame.add_bond(2, 4);
+assert_eq!(frame.topology().bonds_count(), 3);
+
+assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown);
+assert_eq!(frame.topology().bonds(), vec![[0, 1], [1, 3], [2, 4]]);Add a bond between the atoms at indexes i and j in the frame
+with the given bond order.
Example
+let mut frame = Frame::new();
+assert_eq!(frame.topology().bonds_count(), 0);
+frame.resize(2);
+
+frame.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Double);Remove any existing bond between the atoms at indexes i and j in
+the frame.
This function does nothing if there is no bond between i and j.
Example
+let mut frame = Frame::new();
+frame.resize(5);
+
+frame.add_bond(0, 1);
+frame.add_bond(3, 1);
+frame.add_bond(2, 4);
+
+let bonds = frame.topology().bonds();
+assert_eq!(bonds, vec![[0, 1], [1, 3], [2, 4]]);
+
+frame.remove_bond(2, 4);
+let bonds = frame.topology().bonds();
+assert_eq!(bonds, vec![[0, 1], [1, 3]]);Add a copy of residue to this frame.
Errors
+This function fails is the residue id is already in this frame’s +topology, or if the residue contain atoms that are already in another +residue.
+Example
+let mut frame = Frame::new();
+
+let residue = Residue::new("foo");
+frame.add_residue(&residue).unwrap();
+
+let topology = frame.topology();
+assert_eq!(topology.residues_count(), 1);
+assert_eq!(topology.residue(0).unwrap().name(), "foo");Get the distance between the atoms at indexes i and j in this frame,
+accounting for periodic boundary conditions. The result is expressed in
+Angstroms.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [1.0, 2.0, 3.0], None);
+
+assert_eq!(frame.distance(0, 1), f64::sqrt(14.0));Get the angle formed by the atoms at indexes i, j and k in this
+frame, accounting for periodic boundary conditions. The result is
+expressed in radians.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+
+assert_eq!(frame.angle(0, 1, 2), f64::consts::PI / 2.0);Get the dihedral angle formed by the atoms at indexes i, j, k and
+m in this frame, accounting for periodic boundary conditions. The
+result is expressed in radians.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+frame.add_atom(&Atom::new("D"), [0.0, 1.0, 1.0], None);
+
+assert_eq!(frame.dihedral(0, 1, 2, 3), f64::consts::PI / 2.0);Get the out of plane distance formed by the atoms at indexes i, j,
+k and m in this frame, accounting for periodic boundary conditions.
+The result is expressed in angstroms.
This is the distance between the atom j and the ikm plane. The j atom +is the center of the improper dihedral angle formed by i, j, k and m.
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [0.0, 0.0, 2.0], None);
+frame.add_atom(&Atom::new("C"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("D"), [0.0, 1.0, 0.0], None);
+
+assert_eq!(frame.out_of_plane(0, 1, 2, 3), 2.0);Get a view into the positions of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+
+let positions = frame.positions();
+assert_eq!(positions.len(), 67);
+assert_eq!(positions[0], [0.0, 0.0, 0.0]);Get a mutable view into the positions of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+{
+ let positions = frame.positions_mut();
+ assert_eq!(positions[0], [0.0, 0.0, 0.0]);
+ positions[0] = [1.0, 2.0, 3.0];
+}
+
+let positions = frame.positions();
+assert_eq!(positions[0], [1.0, 2.0, 3.0]);Get a view into the velocities of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+frame.add_velocities();
+
+let velocities = frame.velocities();
+assert_eq!(velocities.len(), 67);
+assert_eq!(velocities[0], [0.0, 0.0, 0.0]);Get a mutable view into the velocities of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+frame.add_velocities();
+{
+ let velocities = frame.velocities_mut();
+ assert_eq!(velocities[0], [0.0, 0.0, 0.0]);
+ velocities[0] = [1.0, 2.0, 3.0];
+}
+
+let velocities = frame.velocities();
+assert_eq!(velocities[0], [1.0, 2.0, 3.0]);Check if this frame contains velocity data.
+Example
+let mut frame = Frame::new();
+assert_eq!(frame.has_velocities(), false);
+
+frame.add_velocities();
+assert_eq!(frame.has_velocities(), true);Add velocity data to this frame. If the frame already have velocities, +this does nothing.
+Example
+let mut frame = Frame::new();
+assert_eq!(frame.has_velocities(), false);
+
+frame.add_velocities();
+assert_eq!(frame.has_velocities(), true);Get a reference to the UnitCell from this frame.
Example
+let frame = Frame::new();
+
+let cell = frame.cell();
+assert_eq!(cell.shape(), CellShape::Infinite);Get a mutable reference to the UnitCell from this frame.
Example
+let mut frame = Frame::new();
+
+assert_eq!(frame.cell().shape(), CellShape::Infinite);
+
+frame.cell_mut().set_shape(CellShape::Triclinic).unwrap();
+assert_eq!(frame.cell().shape(), CellShape::Triclinic);Set the UnitCell of this frame to cell.
Example
+let mut frame = Frame::new();
+
+frame.set_cell(&UnitCell::new([10.0, 10.0, 10.0]));
+
+let cell = frame.cell();
+assert_eq!(cell.shape(), CellShape::Orthorhombic);
+assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);Get a reference to the Topology of this frame.
Example
+let mut frame = Frame::new();
+frame.resize(42);
+
+let topology = frame.topology();
+assert_eq!(topology.size(), 42);Set the Topology of this frame to topology.
Errors
+This function fails if the topology contains a different number of atoms +than this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(2);
+
+let mut topology = Topology::new();
+topology.add_atom(&Atom::new("Cl"));
+topology.add_atom(&Atom::new("Cl"));
+topology.add_bond(0, 1);
+
+frame.set_topology(&topology).unwrap();
+assert_eq!(frame.atom(0).name(), "Cl");Get this frame step, i.e. the frame number in the trajectory
+Example
+let frame = Frame::new();
+assert_eq!(frame.step(), 0);Set this frame step to step.
Example
+let mut frame = Frame::new();
+assert_eq!(frame.step(), 0);
+
+frame.set_step(10);
+assert_eq!(frame.step(), 10);Guess the bonds, angles and dihedrals in this frame.
The bonds are guessed using a distance-based algorithm, and then angles +and dihedrals are guessed from the bonds.
+Errors
+This function can fail if the covalent radius is unknown for some atoms +in the frame.
+Example
+let mut frame = Frame::new();
+
+frame.add_atom(&Atom::new("Cl"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("Cl"), [1.5, 0.0, 0.0], None);
+assert_eq!(frame.topology().bonds_count(), 0);
+
+frame.guess_bonds().unwrap();
+assert_eq!(frame.topology().bonds_count(), 1);Remove all existing bonds, angles, dihedral angles and improper +dihedral angles in the topology of the frame.
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [0.0, 1.0, 0.0], None);
+
+frame.add_bond(0, 1);
+frame.add_bond(1, 2);
+
+assert_eq!(frame.topology().bonds().len(), 2);
+assert_eq!(frame.topology().angles().len(), 1);
+
+frame.clear_bonds();
+assert!(frame.topology().bonds().is_empty());
+assert!(frame.topology().angles().is_empty());Add a new property with the given name to this frame.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut frame = Frame::new();
+frame.set("a string", "hello");
+frame.set("a double", 4.3);
+
+assert_eq!(frame.get("a string"), Some(Property::String("hello".into())));
+assert_eq!(frame.get("a double"), Some(Property::Double(4.3)));Get a property with the given name in this frame, if it exist.
Examples
+let mut frame = Frame::new();
+frame.set("foo", Property::Double(22.2));
+
+assert_eq!(frame.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(frame.get("Bar"), None);pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this frame
+Examples
+let mut frame = Frame::new();
+frame.set("foo", Property::Double(22.2));
+frame.set("bar", Property::Bool(false));
+
+for (name, property) in frame.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Frame
impl UnwindSafe for Frame
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::Match [−][src]
pub struct Match { /* fields omitted */ }Expand description
A Match is a set of atomic indexes matching a given selection. It can
+mostly be used like a &[usize].
Implementations
Get the length of the Match.
+Example
+let atomic_match = Match::new(&[3, 4, 5]);
+assert_eq!(atomic_match.len(), 3);Create a new match containing the atoms in the atoms slice.
Panics
+If the slice contains more than 4 elements, which is the maximal size +of a match.
+Example
+let atomic_match = Match::new(&[3, 4, 5]);
+assert_eq!(atomic_match.len(), 3);
+assert_eq!(atomic_match[0], 3);
+assert_eq!(atomic_match[1], 4);
+assert_eq!(atomic_match[2], 5);Iterate over the atomic indexes in the match.
+Example
+let atomic_match = Match::new(&[3, 4, 5]);
+let mut iter = atomic_match.iter();
+
+assert_eq!(iter.next(), Some(&3));
+assert_eq!(iter.next(), Some(&4));
+assert_eq!(iter.next(), Some(&5));
+assert_eq!(iter.next(), None);Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Match
impl UnwindSafe for Match
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::PropertiesIter [−][src]
pub struct PropertiesIter<'a> { /* fields omitted */ }Expand description
An iterator over the properties in an atom/frame/residue
+Trait Implementations
Advances the iterator and returns the next value. Read more
+Returns the bounds on the remaining length of the iterator. Read more
+Consumes the iterator, counting the number of iterations and returning it. Read more
+Consumes the iterator, returning the last element. Read more
+🔬 This is a nightly-only experimental API. (iter_advance_by)
recently added
+Advances the iterator by n elements. Read more
Returns the nth element of the iterator. Read more
Creates an iterator starting at the same point, but stepping by +the given amount at each iteration. Read more
+1.0.0[src]fn chain<U>(self, other: U) -> Chain<Self, <U as IntoIterator>::IntoIter> where
U: IntoIterator<Item = Self::Item>,
1.0.0[src]
fn chain<U>(self, other: U) -> Chain<Self, <U as IntoIterator>::IntoIter> where
U: IntoIterator<Item = Self::Item>,
Takes two iterators and creates a new iterator over both in sequence. Read more
+1.0.0[src]fn zip<U>(self, other: U) -> Zip<Self, <U as IntoIterator>::IntoIter> where
U: IntoIterator,
1.0.0[src]
fn zip<U>(self, other: U) -> Zip<Self, <U as IntoIterator>::IntoIter> where
U: IntoIterator,
‘Zips up’ two iterators into a single iterator of pairs. Read more
+🔬 This is a nightly-only experimental API. (iter_intersperse)
recently added
+Creates a new iterator which places a copy of separator between adjacent
+items of the original iterator. Read more
fn intersperse_with<G>(self, separator: G) -> IntersperseWith<Self, G> where
G: FnMut() -> Self::Item,
fn intersperse_with<G>(self, separator: G) -> IntersperseWith<Self, G> where
G: FnMut() -> Self::Item,
🔬 This is a nightly-only experimental API. (iter_intersperse)
recently added
+Creates a new iterator which places an item generated by separator
+between adjacent items of the original iterator. Read more
Takes a closure and creates an iterator which calls that closure on each +element. Read more
+Calls a closure on each element of an iterator. Read more
+Creates an iterator which uses a closure to determine if an element +should be yielded. Read more
+Creates an iterator that both filters and maps. Read more
+Creates an iterator which gives the current iteration count as well as +the next value. Read more
+Creates an iterator that yields elements based on a predicate. Read more
+🔬 This is a nightly-only experimental API. (iter_map_while)
recently added
+Creates an iterator that both yields elements based on a predicate and maps. Read more
+Creates an iterator that skips the first n elements. Read more
Creates an iterator that yields the first n elements, or fewer
+if the underlying iterator ends sooner. Read more
Creates an iterator that works like map, but flattens nested structure. Read more
+Creates an iterator that flattens nested structure. Read more
+Does something with each element of an iterator, passing the value on. Read more
+Borrows an iterator, rather than consuming it. Read more
+Transforms an iterator into a collection. Read more
+Consumes an iterator, creating two collections from it. Read more
+fn partition_in_place<'a, T, P>(self, predicate: P) -> usize where
Self: DoubleEndedIterator<Item = &'a mut T>,
T: 'a,
P: FnMut(&T) -> bool,
fn partition_in_place<'a, T, P>(self, predicate: P) -> usize where
Self: DoubleEndedIterator<Item = &'a mut T>,
T: 'a,
P: FnMut(&T) -> bool,
🔬 This is a nightly-only experimental API. (iter_partition_in_place)
new API
+Reorders the elements of this iterator in-place according to the given predicate,
+such that all those that return true precede all those that return false.
+Returns the number of true elements found. Read more
🔬 This is a nightly-only experimental API. (iter_is_partitioned)
new API
+Checks if the elements of this iterator are partitioned according to the given predicate,
+such that all those that return true precede all those that return false. Read more
An iterator method that applies a function as long as it returns +successfully, producing a single, final value. Read more
+An iterator method that applies a fallible function to each item in the +iterator, stopping at the first error and returning that error. Read more
+Folds every element into an accumulator by applying an operation, +returning the final result. Read more
+Reduces the elements to a single one, by repeatedly applying a reducing +operation. Read more
+Tests if every element of the iterator matches a predicate. Read more
+Tests if any element of the iterator matches a predicate. Read more
+Searches for an element of an iterator that satisfies a predicate. Read more
+Applies function to the elements of iterator and returns +the first non-none result. Read more
+🔬 This is a nightly-only experimental API. (try_find)
new API
+Applies function to the elements of iterator and returns +the first true result or the first error. Read more
+Searches for an element in an iterator, returning its index. Read more
+1.0.0[src]fn rposition<P>(&mut self, predicate: P) -> Option<usize> where
Self: ExactSizeIterator + DoubleEndedIterator,
P: FnMut(Self::Item) -> bool,
1.0.0[src]
fn rposition<P>(&mut self, predicate: P) -> Option<usize> where
Self: ExactSizeIterator + DoubleEndedIterator,
P: FnMut(Self::Item) -> bool,
Searches for an element in an iterator from the right, returning its +index. Read more
+Returns the maximum element of an iterator. Read more
+Returns the minimum element of an iterator. Read more
+Returns the element that gives the maximum value from the +specified function. Read more
+Returns the element that gives the maximum value with respect to the +specified comparison function. Read more
+Returns the element that gives the minimum value from the +specified function. Read more
+Returns the element that gives the minimum value with respect to the +specified comparison function. Read more
+Reverses an iterator’s direction. Read more
+Converts an iterator of pairs into a pair of containers. Read more
+Creates an iterator which copies all of its elements. Read more
+Repeats an iterator endlessly. Read more
+Sums the elements of an iterator. Read more
+Iterates over the entire iterator, multiplying all the elements Read more
+Lexicographically compares the elements of this Iterator with those
+of another. Read more
fn cmp_by<I, F>(self, other: I, cmp: F) -> Ordering where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,
I: IntoIterator,
fn cmp_by<I, F>(self, other: I, cmp: F) -> Ordering where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,
I: IntoIterator,
🔬 This is a nightly-only experimental API. (
iter_order_by)Lexicographically compares the elements of this Iterator with those
+of another with respect to the specified comparison function. Read more
1.5.0[src]fn partial_cmp<I>(self, other: I) -> Option<Ordering> where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
1.5.0[src]
fn partial_cmp<I>(self, other: I) -> Option<Ordering> where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
Lexicographically compares the elements of this Iterator with those
+of another. Read more
fn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering> where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,
I: IntoIterator,
fn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering> where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,
I: IntoIterator,
🔬 This is a nightly-only experimental API. (
iter_order_by)Lexicographically compares the elements of this Iterator with those
+of another with respect to the specified comparison function. Read more
1.5.0[src]fn eq<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>,
1.5.0[src]
fn eq<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>,
fn eq_by<I, F>(self, other: I, eq: F) -> bool where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> bool,
I: IntoIterator,
fn eq_by<I, F>(self, other: I, eq: F) -> bool where
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> bool,
I: IntoIterator,
🔬 This is a nightly-only experimental API. (
iter_order_by)1.5.0[src]fn ne<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>,
1.5.0[src]
fn ne<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>,
1.5.0[src]fn lt<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
1.5.0[src]
fn lt<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
Determines if the elements of this Iterator are lexicographically
+less than those of another. Read more
1.5.0[src]fn le<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
1.5.0[src]
fn le<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
Determines if the elements of this Iterator are lexicographically
+less or equal to those of another. Read more
1.5.0[src]fn gt<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
1.5.0[src]
fn gt<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
Determines if the elements of this Iterator are lexicographically
+greater than those of another. Read more
1.5.0[src]fn ge<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
1.5.0[src]
fn ge<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
Determines if the elements of this Iterator are lexicographically
+greater than or equal to those of another. Read more
🔬 This is a nightly-only experimental API. (is_sorted)
new API
+Checks if the elements of this iterator are sorted. Read more
+🔬 This is a nightly-only experimental API. (is_sorted)
new API
+Checks if the elements of this iterator are sorted using the given comparator function. Read more
+fn is_sorted_by_key<F, K>(self, f: F) -> bool where
F: FnMut(Self::Item) -> K,
K: PartialOrd<K>,
fn is_sorted_by_key<F, K>(self, f: F) -> bool where
F: FnMut(Self::Item) -> K,
K: PartialOrd<K>,
🔬 This is a nightly-only experimental API. (is_sorted)
new API
+Checks if the elements of this iterator are sorted using the given key extraction +function. Read more
+Auto Trait Implementations
impl<'a> !RefUnwindSafe for PropertiesIter<'a>
impl<'a> !Send for PropertiesIter<'a>
impl<'a> !Sync for PropertiesIter<'a>
impl<'a> Unpin for PropertiesIter<'a>
impl<'a> !UnwindSafe for PropertiesIter<'a>
Blanket Implementations
Struct chemfiles::Residue [−][src]
pub struct Residue { /* fields omitted */ }Expand description
A Residue is a group of atoms belonging to the same logical unit. They
+can be small molecules, amino-acids in a protein, monomers in polymers,
+etc.
Implementations
Create a new residue with the given name
Example
+let residue = Residue::new("ALA");
+assert_eq!(residue.name(), "ALA");
+assert_eq!(residue.id(), None);Create a new residue with the given name and id as identifier.
Example
+let residue = Residue::with_id("ALA", 67);
+assert_eq!(residue.name(), "ALA");
+assert_eq!(residue.id(), Some(67));Get the number of atoms in this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.size(), 0);
+
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+assert_eq!(residue.size(), 3);Get the identifier of this residue in the initial topology file.
+Example
+let residue = Residue::with_id("", 42);
+assert_eq!(residue.id(), Some(42));Get the name of this residue.
+Example
+let residue = Residue::new("water");
+assert_eq!(residue.name(), "water");Add the atom at index atom in this residue.
This will fail if the atom is already in the residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.size(), 0);
+assert_eq!(residue.contains(56), false);
+
+residue.add_atom(56);
+assert_eq!(residue.size(), 1);
+assert_eq!(residue.contains(56), true);
+
+// Adding the same atom twice is fine
+residue.add_atom(56);
+assert_eq!(residue.size(), 1);Check if the atom at index i is in this residue
Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.contains(56), false);
+
+residue.add_atom(56);
+assert_eq!(residue.contains(56), true);Get the list of atoms of this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.atoms(), vec![]);
+
+residue.add_atom(56);
+assert_eq!(residue.atoms(), vec![56]);Add a new property with the given name to this residue.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut residue = Residue::new("ALA");
+residue.set("a string", "hello");
+residue.set("a double", 3.2);
+
+assert_eq!(residue.get("a string"), Some(Property::String("hello".into())));
+assert_eq!(residue.get("a double"), Some(Property::Double(3.2)));Get a property with the given name in this frame, if it exist.
Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+
+assert_eq!(residue.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(residue.get("Bar"), None);pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this frame
+Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+residue.set("bar", Property::Bool(false));
+
+for (name, property) in residue.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Residue
impl UnwindSafe for Residue
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::ResidueRef [−][src]
pub struct ResidueRef<'a> { /* fields omitted */ }Expand description
An analog to a reference to a residue (&Residue)
Methods from Deref<Target = Residue>
Get the number of atoms in this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.size(), 0);
+
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+assert_eq!(residue.size(), 3);Get the identifier of this residue in the initial topology file.
+Example
+let residue = Residue::with_id("", 42);
+assert_eq!(residue.id(), Some(42));Get the name of this residue.
+Example
+let residue = Residue::new("water");
+assert_eq!(residue.name(), "water");Check if the atom at index i is in this residue
Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.contains(56), false);
+
+residue.add_atom(56);
+assert_eq!(residue.contains(56), true);Get the list of atoms of this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.atoms(), vec![]);
+
+residue.add_atom(56);
+assert_eq!(residue.atoms(), vec![56]);Get a property with the given name in this frame, if it exist.
Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+
+assert_eq!(residue.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(residue.get("Bar"), None);pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Notable traits for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);Get an iterator over all (name, property) pairs for this frame
+Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+residue.set("bar", Property::Bool(false));
+
+for (name, property) in residue.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for ResidueRef<'a>
impl<'a> !Send for ResidueRef<'a>
impl<'a> !Sync for ResidueRef<'a>
impl<'a> Unpin for ResidueRef<'a>
impl<'a> UnwindSafe for ResidueRef<'a>
Blanket Implementations
Struct chemfiles::Selection [−][src]
pub struct Selection { /* fields omitted */ }Expand description
A Selection allow to select atoms in a Frame, from a selection
+language. The selection language is built by combining basic operations.
+Each basic operation follows the <selector>[(<variable>)] <operator> <value> structure, where <operator> is a comparison operator in
+== != < <= > >=.
Implementations
Get the size of the selection, i.e. the number of atoms we are selecting +together.
+This value is 1 for the ‘atom’ context, 2 for the ‘pair’ and ‘bond’ +context, 3 for the ‘three’ and ‘angles’ context and 4 for the ‘four’ +and ‘dihedral’ context.
+Example
+let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+assert_eq!(selection.size(), 2);Get the selection string used to create this selection.
+Example
+let selection = Selection::new("name H").unwrap();
+assert_eq!(selection.string(), "name H");Evaluate a selection for a given frame, and return the corresponding +matches.
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+
+let mut selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+let matches = selection.evaluate(&frame);
+
+assert_eq!(matches.len(), 2);
+
+assert_eq!(matches[0].len(), 2);
+assert_eq!(matches[0][0], 0);
+assert_eq!(matches[0][1], 1);
+
+assert_eq!(matches[1].len(), 2);
+assert_eq!(matches[1][0], 2);
+assert_eq!(matches[1][1], 1);Evaluates a selection of size 1 on a given frame. This function
+returns the list of atomic indexes in the frame matching this selection.
Panics
+If the selection size is not 1
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+
+let mut selection = Selection::new("name H").unwrap();
+let matches = selection.list(&frame);
+
+assert_eq!(matches.len(), 2);
+assert_eq!(matches[0], 0);
+assert_eq!(matches[1], 2);Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Selection
impl UnwindSafe for Selection
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::Topology [−][src]
pub struct Topology { /* fields omitted */ }Expand description
A Topology contains the definition of all the atoms in the system, and
+the liaisons between the atoms (bonds, angles, dihedrals, …). It will
+also contain all the residues information if it is available.
Implementations
Create a new empty topology.
+Example
+let topology = Topology::new();
+assert_eq!(topology.size(), 0);Get a mutable reference to the atom at the given index in this topology.
Panics
+If index is out of bounds.
Example
+let mut topology = Topology::new();
+topology.resize(6);
+
+assert_eq!(topology.atom(4).name(), "");
+
+topology.atom_mut(4).set_name("Fe");
+assert_eq!(topology.atom(4).name(), "Fe");Get the current number of atoms in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.size(), 0);
+
+topology.resize(6);
+assert_eq!(topology.size(), 6);Resize this topology to hold natoms atoms, inserting dummy atoms if
+the new size if bigger than the old one.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.size(), 0);
+
+topology.resize(6);
+assert_eq!(topology.size(), 6);Add an Atom at the end of this topology
Example
+let mut topology = Topology::new();
+topology.add_atom(&Atom::new("Mg"));
+
+let atom = topology.atom(0);
+assert_eq!(atom.name(), "Mg");Get the number of bonds in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds_count(), 3);Get the number of angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.angles_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles_count(), 2);Get the number of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.dihedrals_count(), 1);Get the number of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+assert_eq!(topology.impropers_count(), 1);Get the list of bonds in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);Get the list of angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);Get the list of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+
+assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);Get the list of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+
+assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);Remove all existing bonds, angles, dihedral angles and improper +dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+assert_eq!(topology.bonds_count(), 2);
+assert_eq!(topology.angles().len(), 1);
+
+topology.clear_bonds();
+assert!(topology.bonds().is_empty());
+assert!(topology.angles().is_empty());Add a bond between the atoms at indexes i and j in the topology.
The bond order is set to BondOrder::Unknown.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+assert_eq!(topology.bonds_count(), 2);
+
+assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);Add a bond between the atoms at indexes i and j in the topology
+with the given bond order.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(2);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(topology.bond_order(0, 1), BondOrder::Double);Get the bond order for the bond between the atoms at indexes i and
+j.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(2);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(topology.bond_order(0, 1), BondOrder::Double);Get the bond order for all the bonds in the topology
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(3);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+topology.add_bond_with_order(0, 2, BondOrder::Single);
+
+assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);Remove any existing bond between the atoms at indexes i and j in
+this topology.
This function does nothing if there is no bond between i and j.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(1, 2);
+assert_eq!(topology.bonds_count(), 2);
+
+topology.remove_bond(0, 1);
+assert_eq!(topology.bonds_count(), 1);
+
+// Removing a bond that does not exists is fine
+topology.remove_bond(0, 2);
+assert_eq!(topology.bonds_count(), 1);Get a reference to the residue at index index from this topology.
The residue index in the topology is not always the same as the residue
+id.
Example
+let mut topology = Topology::new();
+topology.add_residue(&Residue::new("water")).unwrap();
+
+let residue = topology.residue(0).unwrap();
+assert_eq!(residue.name(), "water");Get a copy of the residue containing the atom at index index in this
+topology, if any.
Example
+let mut topology = Topology::new();
+topology.resize(8);
+
+let mut residue = Residue::new("water");
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+topology.add_residue(&residue).unwrap();
+
+let residue = topology.residue_for_atom(0).unwrap();
+assert_eq!(residue.name(), "water");
+
+assert!(topology.residue_for_atom(6).is_none());Get the number of residues in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.residues_count(), 0);
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+assert_eq!(topology.residues_count(), 2);Add a residue to this topology.
+Errors
+This function fails is the residue id is not already in the topology,
+or if the residue contains atoms that are already in another residue.
Example
+let mut topology = Topology::new();
+topology.add_residue(&Residue::new("water")).unwrap();
+
+let residue = topology.residue(0).unwrap();
+assert_eq!(residue.name(), "water");Check if the two residues first and second from the topology are
+linked together, i.e. if there is a bond between one atom in the
+first residue and one atom in the second one.
Example
+let mut topology = Topology::new();
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+
+let first = topology.residue(0).unwrap();
+let second = topology.residue(1).unwrap();
+assert_eq!(topology.are_linked(&first, &second), false);Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Topology
impl UnwindSafe for Topology
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::TopologyRef [−][src]
pub struct TopologyRef<'a> { /* fields omitted */ }Expand description
An analog to a reference to a topology (&Topology)
Methods from Deref<Target = Topology>
Get the current number of atoms in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.size(), 0);
+
+topology.resize(6);
+assert_eq!(topology.size(), 6);Get the number of bonds in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds_count(), 3);Get the number of angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.angles_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles_count(), 2);Get the number of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.dihedrals_count(), 1);Get the number of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+assert_eq!(topology.impropers_count(), 1);Get the list of bonds in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);Get the list of angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);Get the list of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+
+assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);Get the list of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+
+assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);Get the bond order for the bond between the atoms at indexes i and
+j.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(2);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(topology.bond_order(0, 1), BondOrder::Double);Get the bond order for all the bonds in the topology
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(3);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+topology.add_bond_with_order(0, 2, BondOrder::Single);
+
+assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);Get a reference to the residue at index index from this topology.
The residue index in the topology is not always the same as the residue
+id.
Example
+let mut topology = Topology::new();
+topology.add_residue(&Residue::new("water")).unwrap();
+
+let residue = topology.residue(0).unwrap();
+assert_eq!(residue.name(), "water");Get a copy of the residue containing the atom at index index in this
+topology, if any.
Example
+let mut topology = Topology::new();
+topology.resize(8);
+
+let mut residue = Residue::new("water");
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+topology.add_residue(&residue).unwrap();
+
+let residue = topology.residue_for_atom(0).unwrap();
+assert_eq!(residue.name(), "water");
+
+assert!(topology.residue_for_atom(6).is_none());Get the number of residues in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.residues_count(), 0);
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+assert_eq!(topology.residues_count(), 2);Check if the two residues first and second from the topology are
+linked together, i.e. if there is a bond between one atom in the
+first residue and one atom in the second one.
Example
+let mut topology = Topology::new();
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+
+let first = topology.residue(0).unwrap();
+let second = topology.residue(1).unwrap();
+assert_eq!(topology.are_linked(&first, &second), false);Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for TopologyRef<'a>
impl<'a> !Send for TopologyRef<'a>
impl<'a> !Sync for TopologyRef<'a>
impl<'a> Unpin for TopologyRef<'a>
impl<'a> UnwindSafe for TopologyRef<'a>
Blanket Implementations
Struct chemfiles::Trajectory [−][src]
pub struct Trajectory { /* fields omitted */ }Expand description
The Trajectory type is the main entry point when using chemfiles. A
+Trajectory behave a bit like a file, allowing to read and/or write
+Frame.
Implementations
Open the file at the given path in the given mode.
Valid modes are 'r' for read, 'w' for write and 'a' for append.
Errors
+This function fails if the file is not accessible for the given mode, if +it is incorrectly formatted for the corresponding format, or in case of +I/O errors from the OS.
+Example
+let trajectory = Trajectory::open("water.xyz", 'r').unwrap();pub fn open_with_format<'a, P, S>(
filename: P,
mode: char,
format: S
) -> Result<Trajectory, Error> where
P: AsRef<Path>,
S: Into<&'a str>,
pub fn open_with_format<'a, P, S>(
filename: P,
mode: char,
format: S
) -> Result<Trajectory, Error> where
P: AsRef<Path>,
S: Into<&'a str>,
Open the file at the given path using a specific file format and the
+given mode.
Valid modes are 'r' for read, 'w' for write and 'a' for append.
Specifying a format is needed when the file format does not match the
+extension, or when there is not standard extension for this format. If
+format is an empty string, the format will be guessed from the
+extension.
Errors
+This function fails if the file is not accessible for the given mode, if +it is incorrectly formatted for the corresponding format, or in case of +I/O errors from the OS.
+Example
+let trajectory = Trajectory::open_with_format("water.zeo", 'r', "XYZ").unwrap();pub fn memory_reader<'a, S>(data: S, format: S) -> Result<Trajectory, Error> where
S: Into<&'a str>,
pub fn memory_reader<'a, S>(data: S, format: S) -> Result<Trajectory, Error> where
S: Into<&'a str>,
Read a memory buffer as though it was a formatted file.
+The memory buffer used to store the file is given using the data
+argument. The format parameter is required and should follow the same
+rules as in the main Trajectory constructor.
Errors
+This function fails if the data is incorrectly formatted for the +corresponding format, or if the format do not support in-memory readers.
+Example
+let aromatics = "c1ccccc1\nc1ccco1\nc1ccccn1\n";
+let mut trajectory = Trajectory::memory_reader(aromatics, "SMI").unwrap();
+let mut frame = Frame::new();
+trajectory.read(&mut frame).unwrap();
+assert_eq!(frame.size(), 6);Write to a memory buffer as though it was a formatted file.
+The format parameter should follow the same rules as in the main
+Trajectory constructor, except that compression specification
+is not supported.
The memory_buffer function can be used to retrieve the data written
+to memory of the Trajectory.
Errors
+This function fails if the format do not support in-memory writers.
+Example
+let trajectory_memory = Trajectory::memory_writer("SMI");
+
+// Binary formats typically do not support this feature
+assert!(Trajectory::memory_writer("XTC").is_err());Read the next step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of atom +in the next step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+let mut frame = Frame::new();
+
+trajectory.read(&mut frame).unwrap();Read a specific step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of +atom at this step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+let mut frame = Frame::new();
+
+trajectory.read_step(10, &mut frame).unwrap();Set the topology associated with this trajectory. This topology will
+be used when reading and writing the files, replacing any topology in
+the frames or files.
Example
+let mut topology = Topology::new();
+topology.add_atom(&Atom::new("H"));
+topology.add_atom(&Atom::new("O"));
+topology.add_atom(&Atom::new("H"));
+topology.add_bond(0, 1);
+topology.add_bond(1, 2);
+
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+trajectory.set_topology(&topology);Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in format;
+and extracting the topology of this frame.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+trajectory.set_topology_file("topology.pdb").unwrap();Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in
+format; and extracting the topology of this frame.
If format is an empty string, the format will be guessed from the
+path extension.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+trajectory.set_topology_with_format("topology.mol", "PDB").unwrap();Set the unit cell associated with a trajectory. This cell will be
+used when reading and writing the files, replacing any unit cell in the
+frames or files.
Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+trajectory.set_cell(&UnitCell::new([10.0, 11.0, 12.5]));Get the number of steps (the number of frames) in a trajectory.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+
+println!("This trajectory contains {} steps", trajectory.nsteps());Obtain the memory buffer written to by the trajectory.
+Errors
+This fails if the trajectory was not opened with
+Trajectory::memory_writer.
Example
+let mut trajectory_memory = Trajectory::memory_writer("SMI").unwrap();
+
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+frame.add_bond_with_order(0, 1, BondOrder::Single);
+
+trajectory_memory.write(&frame).unwrap();
+
+let result = trajectory_memory.memory_buffer();
+assert_eq!(result.unwrap(), "CC\n");Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Trajectory
impl !Send for Trajectory
impl !Sync for Trajectory
impl Unpin for Trajectory
impl UnwindSafe for Trajectory
Blanket Implementations
Struct chemfiles::UnitCell [−][src]
pub struct UnitCell { /* fields omitted */ }Expand description
An UnitCell represent the box containing the atoms, and its periodicity.
An unit cell is fully represented by three lengths (a, b, c); and three +angles (alpha, beta, gamma). The angles are stored in degrees, and the +lengths in Angstroms.
+A cell also has a matricial representation, by projecting the three base +vector into an orthonormal base. We choose to represent such matrix as an +upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |Implementations
Create an Orthorhombic UnitCell from the three lengths, in Angstroms.
Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);Create an Infinite UnitCell.
Example
+let cell = UnitCell::infinite();
+
+assert_eq!(cell.lengths(), [0.0, 0.0, 0.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+assert_eq!(cell.shape(), CellShape::Infinite);Create an Triclinic UnitCell from the three lengths (in Angstroms)
+and three angles (in degree). alpha is the angle between the vectors
+b and c; beta is the between the vectors a and c and gamma
+is the angle between the vectors a and b.
Example
+let cell = UnitCell::triclinic([10.0, 10.0, 10.0], [98.0, 99.0, 90.0]);
+
+assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);
+assert_eq!(cell.angles()[0], 98.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 99.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);
+assert_eq!(cell.shape(), CellShape::Triclinic);Create an UnitCell from a cell matrix. If matrix contains only
+zeros, then an Infinite cell is created. If only the diagonal of the
+matrix is non-zero, then the cell is Orthorhombic. Else a
+Triclinic cell is created. The matrix entries should be in Angstroms.
Panics
+If the matrix has a negative determinant, or more generally is not +representing a unit cell.
+Example
+let cell = UnitCell::from_matrix([
+ [1.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]
+]);
+
+assert_eq!(cell.lengths(), [1.0, 2.0, 3.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);Get the three lengths of the cell, in Angstroms.
+Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);Set the three lengths of the cell, in Angstroms.
+Errors
+This function fails if the unit cell is infinite, or if one of the +lengths is negative.
+Example
+let mut cell = UnitCell::new([30.0, 30.0, 23.0]);
+
+cell.set_lengths([10.0, 30.0, 42.0]).unwrap();
+assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]);
+
+assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());Get the three angles of the cell, in degrees.
+Example
+let cell = UnitCell::new([20.0, 20.0, 20.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+
+let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);Set the three angles of the cell, in degrees.
+Errors
+This function fails if the unit cell is not Triclinic.
Example
+let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);
+
+cell.set_angles([90.0, 90.0, 90.0]).unwrap();
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+
+let matrix = cell.matrix();
+
+assert_eq!(matrix[0][0], 10.0);
+assert_eq!(matrix[1][1], 20.0);
+assert_eq!(matrix[2][2], 30.0);
+
+assert!(matrix[1][2].abs() < 1e-9);Get the shape of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);Set the shape of the unit cell to shape.
Errors
+This can fail if the cell length or angles are incompatible with the +new shape.
+Example
+let mut cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);
+
+cell.set_shape(CellShape::Triclinic).unwrap();
+assert_eq!(cell.shape(), CellShape::Triclinic);Get the volume of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0);Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for UnitCell
impl UnwindSafe for UnitCell
Blanket Implementations
Mutably borrows from an owned value. Read more
+Struct chemfiles::UnitCellMut [−][src]
pub struct UnitCellMut<'a> { /* fields omitted */ }Expand description
An analog to a mutable reference to an unit cell (&mut UnitCell)
Methods from Deref<Target = UnitCell>
Get the three lengths of the cell, in Angstroms.
+Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);Set the three lengths of the cell, in Angstroms.
+Errors
+This function fails if the unit cell is infinite, or if one of the +lengths is negative.
+Example
+let mut cell = UnitCell::new([30.0, 30.0, 23.0]);
+
+cell.set_lengths([10.0, 30.0, 42.0]).unwrap();
+assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]);
+
+assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());Get the three angles of the cell, in degrees.
+Example
+let cell = UnitCell::new([20.0, 20.0, 20.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+
+let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);Set the three angles of the cell, in degrees.
+Errors
+This function fails if the unit cell is not Triclinic.
Example
+let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);
+
+cell.set_angles([90.0, 90.0, 90.0]).unwrap();
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+
+let matrix = cell.matrix();
+
+assert_eq!(matrix[0][0], 10.0);
+assert_eq!(matrix[1][1], 20.0);
+assert_eq!(matrix[2][2], 30.0);
+
+assert!(matrix[1][2].abs() < 1e-9);Get the shape of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);Set the shape of the unit cell to shape.
Errors
+This can fail if the cell length or angles are incompatible with the +new shape.
+Example
+let mut cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);
+
+cell.set_shape(CellShape::Triclinic).unwrap();
+assert_eq!(cell.shape(), CellShape::Triclinic);Get the volume of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0);Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for UnitCellMut<'a>
impl<'a> !Send for UnitCellMut<'a>
impl<'a> !Sync for UnitCellMut<'a>
impl<'a> Unpin for UnitCellMut<'a>
impl<'a> !UnwindSafe for UnitCellMut<'a>
Blanket Implementations
Struct chemfiles::UnitCellRef [−][src]
pub struct UnitCellRef<'a> { /* fields omitted */ }Expand description
An analog to a reference to an unit cell (&UnitCell)
Methods from Deref<Target = UnitCell>
Get the three lengths of the cell, in Angstroms.
+Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);Get the three angles of the cell, in degrees.
+Example
+let cell = UnitCell::new([20.0, 20.0, 20.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+
+let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+
+let matrix = cell.matrix();
+
+assert_eq!(matrix[0][0], 10.0);
+assert_eq!(matrix[1][1], 20.0);
+assert_eq!(matrix[2][2], 30.0);
+
+assert!(matrix[1][2].abs() < 1e-9);Get the shape of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);Get the volume of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0);Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for UnitCellRef<'a>
impl<'a> !Send for UnitCellRef<'a>
impl<'a> !Sync for UnitCellRef<'a>
impl<'a> Unpin for UnitCellRef<'a>
impl<'a> UnwindSafe for UnitCellRef<'a>
Blanket Implementations
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else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.2/doc/implementors/core/cmp/trait.Eq.js b/0.10.2/doc/implementors/core/cmp/trait.Eq.js new file mode 100644 index 000000000..991ad22a1 --- /dev/null +++ b/0.10.2/doc/implementors/core/cmp/trait.Eq.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Eq for CellShape","synthetic":false,"types":["chemfiles::cell::CellShape"]},{"text":"impl Eq for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]},{"text":"impl Eq for Match","synthetic":false,"types":["chemfiles::selection::Match"]},{"text":"impl Eq for FormatMetadata","synthetic":false,"types":["chemfiles::misc::FormatMetadata"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.2/doc/implementors/core/cmp/trait.Ord.js b/0.10.2/doc/implementors/core/cmp/trait.Ord.js new file mode 100644 index 000000000..0784ba4cb --- /dev/null +++ b/0.10.2/doc/implementors/core/cmp/trait.Ord.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Ord for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.2/doc/implementors/core/cmp/trait.PartialEq.js b/0.10.2/doc/implementors/core/cmp/trait.PartialEq.js new file mode 100644 index 000000000..b88724be9 --- /dev/null +++ b/0.10.2/doc/implementors/core/cmp/trait.PartialEq.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl PartialEq<Error> for Error","synthetic":false,"types":["chemfiles::errors::Error"]},{"text":"impl PartialEq<Status> for Status","synthetic":false,"types":["chemfiles::errors::Status"]},{"text":"impl PartialEq<CellShape> for CellShape","synthetic":false,"types":["chemfiles::cell::CellShape"]},{"text":"impl PartialEq<BondOrder> for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]},{"text":"impl PartialEq<Match> for Match","synthetic":false,"types":["chemfiles::selection::Match"]},{"text":"impl PartialEq<Property> for Property","synthetic":false,"types":["chemfiles::property::Property"]},{"text":"impl PartialEq<FormatMetadata> for FormatMetadata","synthetic":false,"types":["chemfiles::misc::FormatMetadata"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.2/doc/implementors/core/cmp/trait.PartialOrd.js b/0.10.2/doc/implementors/core/cmp/trait.PartialOrd.js new file mode 100644 index 000000000..d0dc2d685 --- /dev/null +++ b/0.10.2/doc/implementors/core/cmp/trait.PartialOrd.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl PartialOrd<BondOrder> for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]},{"text":"impl PartialOrd<Property> for Property","synthetic":false,"types":["chemfiles::property::Property"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.2/doc/implementors/core/convert/trait.From.js b/0.10.2/doc/implementors/core/convert/trait.From.js new file mode 100644 index 000000000..156356c1d --- /dev/null +++ b/0.10.2/doc/implementors/core/convert/trait.From.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl From<chfl_status> for Error","synthetic":false,"types":["chemfiles::errors::Error"]},{"text":"impl From<Utf8Error> for Error","synthetic":false,"types":["chemfiles::errors::Error"]},{"text":"impl From<chfl_cellshape> for CellShape","synthetic":false,"types":["chemfiles::cell::CellShape"]},{"text":"impl From<CellShape> for chfl_cellshape","synthetic":false,"types":["chemfiles_sys::chfl_cellshape"]},{"text":"impl From<chfl_bond_order> for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]},{"text":"impl From<bool> for Property","synthetic":false,"types":["chemfiles::property::Property"]},{"text":"impl From<f64> for Property","synthetic":false,"types":["chemfiles::property::Property"]},{"text":"impl From<String> for Property","synthetic":false,"types":["chemfiles::property::Property"]},{"text":"impl<'a> From<&'a str> for Property","synthetic":false,"types":["chemfiles::property::Property"]},{"text":"impl From<[f64; 3]> for Property","synthetic":false,"types":["chemfiles::property::Property"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.2/doc/implementors/core/fmt/trait.Debug.js b/0.10.2/doc/implementors/core/fmt/trait.Debug.js new file mode 100644 index 000000000..21a553777 --- /dev/null +++ b/0.10.2/doc/implementors/core/fmt/trait.Debug.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Debug for Error","synthetic":false,"types":["chemfiles::errors::Error"]},{"text":"impl Debug for Status","synthetic":false,"types":["chemfiles::errors::Status"]},{"text":"impl Debug for CellShape","synthetic":false,"types":["chemfiles::cell::CellShape"]},{"text":"impl Debug for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]},{"text":"impl Debug for Match","synthetic":false,"types":["chemfiles::selection::Match"]},{"text":"impl Debug for Property","synthetic":false,"types":["chemfiles::property::Property"]},{"text":"impl Debug for FormatMetadata","synthetic":false,"types":["chemfiles::misc::FormatMetadata"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.2/doc/implementors/core/fmt/trait.Display.js b/0.10.2/doc/implementors/core/fmt/trait.Display.js new file mode 100644 index 000000000..cdacd5e88 --- /dev/null +++ b/0.10.2/doc/implementors/core/fmt/trait.Display.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Display for Error","synthetic":false,"types":["chemfiles::errors::Error"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.2/doc/implementors/core/iter/traits/collect/trait.IntoIterator.js b/0.10.2/doc/implementors/core/iter/traits/collect/trait.IntoIterator.js new file mode 100644 index 000000000..f478370c2 --- /dev/null +++ b/0.10.2/doc/implementors/core/iter/traits/collect/trait.IntoIterator.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl<'a> IntoIterator for &'a Match","synthetic":false,"types":["chemfiles::selection::Match"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.2/doc/implementors/core/iter/traits/iterator/trait.Iterator.js b/0.10.2/doc/implementors/core/iter/traits/iterator/trait.Iterator.js new file mode 100644 index 000000000..7bef8fef2 --- /dev/null +++ b/0.10.2/doc/implementors/core/iter/traits/iterator/trait.Iterator.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl<'a> Iterator for PropertiesIter<'a>","synthetic":false,"types":["chemfiles::property::PropertiesIter"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.2/doc/implementors/core/marker/trait.Copy.js b/0.10.2/doc/implementors/core/marker/trait.Copy.js new file mode 100644 index 000000000..292291348 --- /dev/null +++ b/0.10.2/doc/implementors/core/marker/trait.Copy.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Copy for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.2/doc/implementors/core/marker/trait.Freeze.js b/0.10.2/doc/implementors/core/marker/trait.Freeze.js new file mode 100644 index 000000000..7a6ceb43d --- /dev/null +++ b/0.10.2/doc/implementors/core/marker/trait.Freeze.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Freeze for Error","synthetic":true,"types":["chemfiles::errors::Error"]},{"text":"impl Freeze for Status","synthetic":true,"types":["chemfiles::errors::Status"]},{"text":"impl Freeze for Atom","synthetic":true,"types":["chemfiles::atom::Atom"]},{"text":"impl<'a> Freeze for AtomRef<'a>","synthetic":true,"types":["chemfiles::atom::AtomRef"]},{"text":"impl<'a> Freeze for AtomMut<'a>","synthetic":true,"types":["chemfiles::atom::AtomMut"]},{"text":"impl Freeze for CellShape","synthetic":true,"types":["chemfiles::cell::CellShape"]},{"text":"impl Freeze for UnitCell","synthetic":true,"types":["chemfiles::cell::UnitCell"]},{"text":"impl<'a> Freeze for UnitCellRef<'a>","synthetic":true,"types":["chemfiles::cell::UnitCellRef"]},{"text":"impl<'a> Freeze for UnitCellMut<'a>","synthetic":true,"types":["chemfiles::cell::UnitCellMut"]},{"text":"impl Freeze for Residue","synthetic":true,"types":["chemfiles::residue::Residue"]},{"text":"impl<'a> Freeze for ResidueRef<'a>","synthetic":true,"types":["chemfiles::residue::ResidueRef"]},{"text":"impl Freeze for BondOrder","synthetic":true,"types":["chemfiles::topology::BondOrder"]},{"text":"impl Freeze for Topology","synthetic":true,"types":["chemfiles::topology::Topology"]},{"text":"impl<'a> Freeze for TopologyRef<'a>","synthetic":true,"types":["chemfiles::topology::TopologyRef"]},{"text":"impl Freeze for Frame","synthetic":true,"types":["chemfiles::frame::Frame"]},{"text":"impl Freeze for Trajectory","synthetic":true,"types":["chemfiles::trajectory::Trajectory"]},{"text":"impl Freeze for Match","synthetic":true,"types":["chemfiles::selection::Match"]},{"text":"impl Freeze for Selection","synthetic":true,"types":["chemfiles::selection::Selection"]},{"text":"impl Freeze for Property","synthetic":true,"types":["chemfiles::property::Property"]},{"text":"impl<'a> Freeze for PropertiesIter<'a>","synthetic":true,"types":["chemfiles::property::PropertiesIter"]},{"text":"impl Freeze for FormatMetadata","synthetic":true,"types":["chemfiles::misc::FormatMetadata"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.2/doc/implementors/core/marker/trait.Send.js b/0.10.2/doc/implementors/core/marker/trait.Send.js new file mode 100644 index 000000000..7e2b45b5e --- /dev/null +++ b/0.10.2/doc/implementors/core/marker/trait.Send.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Send for Error","synthetic":true,"types":["chemfiles::errors::Error"]},{"text":"impl Send for Status","synthetic":true,"types":["chemfiles::errors::Status"]},{"text":"impl !Send for Atom","synthetic":true,"types":["chemfiles::atom::Atom"]},{"text":"impl<'a> !Send for AtomRef<'a>","synthetic":true,"types":["chemfiles::atom::AtomRef"]},{"text":"impl<'a> !Send for 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--- /dev/null +++ b/0.10.2/doc/implementors/core/marker/trait.StructuralEq.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl StructuralEq for CellShape","synthetic":false,"types":["chemfiles::cell::CellShape"]},{"text":"impl StructuralEq for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]},{"text":"impl StructuralEq for Match","synthetic":false,"types":["chemfiles::selection::Match"]},{"text":"impl StructuralEq for FormatMetadata","synthetic":false,"types":["chemfiles::misc::FormatMetadata"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.2/doc/implementors/core/marker/trait.StructuralPartialEq.js b/0.10.2/doc/implementors/core/marker/trait.StructuralPartialEq.js new file mode 100644 index 000000000..f07883adc --- /dev/null +++ b/0.10.2/doc/implementors/core/marker/trait.StructuralPartialEq.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl StructuralPartialEq for Error","synthetic":false,"types":["chemfiles::errors::Error"]},{"text":"impl StructuralPartialEq for Status","synthetic":false,"types":["chemfiles::errors::Status"]},{"text":"impl StructuralPartialEq for CellShape","synthetic":false,"types":["chemfiles::cell::CellShape"]},{"text":"impl StructuralPartialEq for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]},{"text":"impl StructuralPartialEq for Match","synthetic":false,"types":["chemfiles::selection::Match"]},{"text":"impl StructuralPartialEq for Property","synthetic":false,"types":["chemfiles::property::Property"]},{"text":"impl StructuralPartialEq for FormatMetadata","synthetic":false,"types":["chemfiles::misc::FormatMetadata"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.2/doc/implementors/core/marker/trait.Sync.js b/0.10.2/doc/implementors/core/marker/trait.Sync.js new file mode 100644 index 000000000..505c4c942 --- /dev/null +++ b/0.10.2/doc/implementors/core/marker/trait.Sync.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Sync for Error","synthetic":true,"types":["chemfiles::errors::Error"]},{"text":"impl Sync for Status","synthetic":true,"types":["chemfiles::errors::Status"]},{"text":"impl !Sync for Atom","synthetic":true,"types":["chemfiles::atom::Atom"]},{"text":"impl<'a> !Sync for AtomRef<'a>","synthetic":true,"types":["chemfiles::atom::AtomRef"]},{"text":"impl<'a> !Sync for AtomMut<'a>","synthetic":true,"types":["chemfiles::atom::AtomMut"]},{"text":"impl Sync for CellShape","synthetic":true,"types":["chemfiles::cell::CellShape"]},{"text":"impl !Sync for 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It stores the …","An analog to a mutable reference to an atom (&mut Atom)","An analog to a reference to an atom (&Atom)","Possible bond order associated with bonds","Boolean property","Available unit cell shapes.","Exception in the C++ chemfiles library","Error in configuration files syntax","Double bond","Floating point property","Error type for Chemfiles.","Error while reading or writing a file","Error in file formatting, i.e. the file is invalid","FormatMetadata contains metadata associated with one …","A Frame contains data from one simulation step: the …","Infinite cell, to use when there is no cell.","A Match is a set of atomic indexes matching a given …","Error in memory allocations","Orthorhombic cell, with the three angles equals to 90°.","Error for out of bounds indexing","An iterator over the properties in an atom/frame/residue","A Property is a piece of data that can be associated with …","Error related to properties","Quadruple bond (present in some metals)","Quintuplet bond (present in some metals)","A Residue is a group of atoms belonging to the same …","An analog to a reference to a residue (&Residue)","A Selection allow to select atoms in a Frame, from a …","Error in selection string syntax","Single bond","Possible causes of error in chemfiles","Exception in the C++ standard library","String property","No error","A Topology contains the definition of all the atoms in the …","An analog to a reference to a topology (&Topology)","The Trajectory type is the main entry point when using …","Triclinic cell, with any values for the angles.","Triple bond","The given path is not valid UTF8","An UnitCell represent the box containing the atoms, and …","An analog to a mutable reference to an unit cell (…","An analog to a reference to an unit cell (&UnitCell)","Unknown or unspecified bond order","3-dimensional vector property","Add the atom at index atom in this residue.","Add an Atom at the end of this topology","Add an Atom and the corresponding position and optionally …","Add a bond between the atoms at indexes i and j in the …","Add a bond between the atoms at indexes i and j in the …","Add a bond between the atoms at indexes i and j in the …","Add a bond between the atoms at indexes i and j in the …","Read configuration data from the file at path.","Add a residue to this topology.","Add a copy of residue to this frame.","Add velocity data to this frame. If the frame already have …","Get the angle formed by the atoms at indexes i, j and k in …","Get the three angles of the cell, in degrees.","Get the list of angles in the topology.","Get the number of angles in the topology.","Check if the two residues first and second from the …","Get a reference of the atom at the given index in this …","Get a reference to the atom at the given index in this …","Get a mutable reference to the atom at the given index in …","Get a mutable reference to the atom at the given index in …","Try to get the atomic number of the atom from the atomic …","Get the atom type.","Get the list of atoms of this residue.","Does this format support storing atom names or types?","Get the bond order for the bond between the atoms at …","Get the bond order for all the bonds in the topology","Get the list of bonds in the topology.","Does this format support storing bonds between atoms?","Get the number of bonds in the topology.","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","Get a reference to the UnitCell from this frame.","Get a mutable reference to the UnitCell from this frame.","Get the atom charge, in number of the electron charge e.","Clear any error from the C++ library","Remove all existing bonds, angles, dihedral angles and …","Remove all existing bonds, angles, dihedral angles and …","","","","","","","","","","","","","","","","","","","","","","","","","","","","Check if the atom at index i is in this residue","","Try to get the covalent radius of the atom from the atomic …","","","","","","","","","","Extended, user-facing description of the format.","Get the dihedral angle formed by the atoms at indexes i, j…","Get the list of dihedral angles in the topology.","Get the number of dihedral angles in the topology.","Get the distance between the atoms at indexes i and j in …","","","","","","","","","","","","","","","Evaluate a selection for a given frame, and return the …","Extension associated with the format.","","","","","","","","","Get the list of formats known by chemfiles, as well as all …","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","Create an UnitCell from a cell matrix. If matrix contains …","Try to get the full name of the atom from the atomic type. …","Get a property with the given name in this atom, if it …","Get a property with the given name in this frame, if it …","Get a property with the given name in this frame, if it …","Guess the bonds, angles and dihedrals in this frame.","Get the format that chemfiles would use to read a file at …","Check if this frame contains velocity data.","Get the identifier of this residue in the initial topology …","Get the list of improper dihedral angles in the topology.","Get the number of improper dihedral angles in the topology.","","Create an Infinite UnitCell.","","","","","","","","","","","","","","","","","","","","","","","Iterate over the atomic indexes in the match.","Get the last error message from the C++ library.","Get the length of the Match.","Get the three lengths of the cell, in Angstroms.","Evaluates a selection of size 1 on a given frame. This …","Get the atom mass, in atomic mass units.","Get the unit cell matricial representation.","Does this format support in-memory IO?","Obtain the memory buffer written to by the trajectory.","Read a memory buffer as though it was a formatted file.","Write to a memory buffer as though it was a formatted file.","A message describing the error cause","Get the atom name.","Get the name of this residue.","Name of the format.","","","","","Create an atom with the given name, and set the atom type …","Create an Orthorhombic UnitCell from the three lengths, in …","Create a new residue with the given name","Create a new empty topology.","Create an empty frame. 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This modify …","Remove the atom at index i in this frame.","Remove any existing bond between the atoms at indexes i …","Remove any existing bond between the atoms at indexes i …","Get a reference to the residue at index index from this …","Get a copy of the residue containing the atom at index …","Does this format support storing residues?","Get the number of residues in this topology.","Resize this topology to hold natoms atoms, inserting dummy …","Resize the positions and the velocities in this frame, to …","Add a new property with the given name to this atom.","Add a new property with the given name to this residue.","Add a new property with the given name to this frame.","Set the three angles of the cell, in degrees.","Set the atom type to atomic_type.","Set the UnitCell of this frame to cell.","Set the unit cell associated with a trajectory. This cell …","Set the atom charge to charge, in number of the electron …","Set the three lengths of the cell, in Angstroms.","Set the atom mass to mass, in atomic mass units.","Set the atom name to name.","Set the shape of the unit cell to shape.","Set this frame step to step.","Set the Topology of this frame to topology.","Set the topology associated with this trajectory. This …","Set the topology associated with this trajectory by …","Set the topology associated with this trajectory by …","Use callback for every chemfiles warning. The callback …","Get the shape of the unit cell.","Get the number of atoms in this residue.","Get the current number of atoms in this topology.","Get the current number of atoms in this frame.","Get the size of the selection, i.e. the number of atoms we …","","The error status code","Get this frame step, i.e. the frame number in the …","Get the selection string used to create this selection.","","","","","","","","","","","","","","","Get a reference to the Topology of this frame.","Create an Triclinic UnitCell from the three lengths (in …","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","Does this format support storing unit cell information?","Try to get the Van der Waals radius of the atom from the …","Get a view into the velocities of this frame.","Does this format support storing atomic velocities?","Get a mutable view into the velocities of this frame.","Get the version of the chemfiles library.","Get the volume of the unit cell.","Create a new residue with the given name and id as …","Wrap a vector in this unit cell.","Write a frame to this trajectory.","Is writing files in this format 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+}');
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- The Rust Reference "+" for technical details about the language.
- Rust By "+"Example for expository code examples.
- The Rust Book for "+"introductions to language features and the language itself.
- Docs.rs for documentation of crates released on"+" crates.io.
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"+""+makeTabHeader(0,"In Names",ret_others[1])+makeTabHeader(1,"In Parameters",ret_in_args[1])+makeTabHeader(2,"In Return Types",ret_returned[1])+"
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1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371 +372 +373 +374 +375 +376 +377 +378 +379 +380 +381 +382 +383 +384 +385 +386 +387 +388 +389 +390 +391 +392 +393 +394 +395 +396 +397 +398 +399 +400 +401 +402 +403 +404 +405 +406 +407 +408 +409 +410 +411 +412 +413 +414 +415 +416 +417 +418 +419 +420 +421 +422 +423 +424 +425 +426 +427 +428 +429 +430 +431 +432 +433 +434 +435 +436 +437 +438 +439 +440 +441 +442 +443 +444 +445 +446 +447 +448 +449 +450 +451 +452 +453 +454 +455 +456 +457 +458 +459 +460 +461 +462 +463 +464 +465 +466 +467 +468 +469 +470 +471 +472 +473 +474 +475 +476 +477 +478 +479 +480 +481 +482 +483 +484 +485 +486 +487 +488 +489 +490 +491 +492 +493 +494 +495 +496 +497 +498 +499 +500 +501 +502 +503 +504 +505 +506 +507 +508 +509 +510 +511 +512 +513 +514 +515 +516 +517 +518 +519 +520 +521 +522 +523 +524 +525 +526 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::{Drop, Deref, DerefMut};
+use std::marker::PhantomData;
+use std::ptr;
+
+use chemfiles_sys::*;
+use errors::{check_success, check_not_null};
+use strings;
+
+use property::{Property, RawProperty, PropertiesIter};
+
+/// An `Atom` is a particle in the current `Frame`. It stores the following
+/// atomic properties:
+///
+/// - atom name;
+/// - atom type;
+/// - atom mass;
+/// - atom charge.
+///
+/// The atom name is usually an unique identifier (`H1`, `C_a`) while the
+/// atom type will be shared between all particles of the same type: `H`,
+/// `Ow`, `CH3`.
+pub struct Atom {
+ handle: *mut CHFL_ATOM,
+}
+
+/// An analog to a reference to an atom (`&Atom`)
+pub struct AtomRef<'a> {
+ inner: Atom,
+ marker: PhantomData<&'a Atom>
+}
+
+impl<'a> Deref for AtomRef<'a> {
+ type Target = Atom;
+ fn deref(&self) -> &Atom {
+ &self.inner
+ }
+}
+
+/// An analog to a mutable reference to an atom (`&mut Atom`)
+pub struct AtomMut<'a> {
+ inner: Atom,
+ marker: PhantomData<&'a mut Atom>
+}
+
+impl<'a> Deref for AtomMut<'a> {
+ type Target = Atom;
+ fn deref(&self) -> &Atom {
+ &self.inner
+ }
+}
+
+impl<'a> DerefMut for AtomMut<'a> {
+ fn deref_mut(&mut self) -> &mut Atom {
+ &mut self.inner
+ }
+}
+
+impl Clone for Atom {
+ fn clone(&self) -> Atom {
+ unsafe {
+ let new_handle = chfl_atom_copy(self.as_ptr());
+ Atom::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Atom {
+ /// Create an owned `Atom` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_ATOM) -> Atom {
+ check_not_null(ptr);
+ Atom {
+ handle: ptr
+ }
+ }
+
+ /// Create a borrowed `Atom` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, and the caller is responsible for setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_ATOM) -> AtomRef<'a> {
+ AtomRef {
+ inner: Atom::from_ptr(ptr as *mut CHFL_ATOM),
+ marker: PhantomData,
+ }
+ }
+
+ /// Create a mutably borrowed `Atom` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, and the caller is responsible for setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_mut_from_ptr<'a>(ptr: *mut CHFL_ATOM) -> AtomMut<'a> {
+ AtomMut {
+ inner: Atom::from_ptr(ptr),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_ATOM {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_ATOM {
+ self.handle
+ }
+
+ /// Create an atom with the given `name`, and set the atom type to `name`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.name(), "He");
+ /// ```
+ pub fn new<'a>(name: impl Into<&'a str>) -> Atom {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ let handle = chfl_atom(buffer.as_ptr());
+ Atom::from_ptr(handle)
+ }
+ }
+
+ /// Get the atom mass, in atomic mass units.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.mass(), 4.002602);
+ /// ```
+ pub fn mass(&self) -> f64 {
+ let mut mass = 0.0;
+ unsafe {
+ check_success(chfl_atom_mass(self.as_ptr(), &mut mass));
+ }
+ return mass;
+ }
+
+ /// Set the atom mass to `mass`, in atomic mass units.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_mass(34.9);
+ /// assert_eq!(atom.mass(), 34.9);
+ /// ```
+ pub fn set_mass(&mut self, mass: f64) {
+ unsafe {
+ check_success(chfl_atom_set_mass(self.as_mut_ptr(), mass));
+ }
+ }
+
+ /// Get the atom charge, in number of the electron charge *e*.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.charge(), 0.0);
+ /// ```
+ pub fn charge(&self) -> f64 {
+ let mut charge = 0.0;
+ unsafe {
+ check_success(chfl_atom_charge(self.as_ptr(), &mut charge));
+ }
+ return charge;
+ }
+
+ /// Set the atom charge to `charge`, in number of the electron charge *e*.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_charge(-2.0);
+ /// assert_eq!(atom.charge(), -2.0);
+ /// ```
+ pub fn set_charge(&mut self, charge: f64) {
+ unsafe {
+ check_success(chfl_atom_set_charge(self.as_mut_ptr(), charge));
+ }
+ }
+
+ /// Get the atom name.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.name(), "He");
+ /// ```
+ pub fn name(&self) -> String {
+ let get_name = |ptr, len| unsafe { chfl_atom_name(self.as_ptr(), ptr, len) };
+ let name = strings::call_autogrow_buffer(10, get_name).expect("getting name failed");
+ return strings::from_c(name.as_ptr());
+ }
+
+ /// Get the atom type.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.atomic_type(), "He");
+ /// ```
+ pub fn atomic_type(&self) -> String {
+ let get_type = |ptr, len| unsafe { chfl_atom_type(self.as_ptr(), ptr, len) };
+ let buffer = strings::call_autogrow_buffer(10, get_type).expect("getting type failed");
+ return strings::from_c(buffer.as_ptr());
+ }
+
+ /// Set the atom name to `name`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_name("Zn3");
+ /// assert_eq!(atom.name(), "Zn3");
+ /// ```
+ pub fn set_name<'a>(&mut self, name: impl Into<&'a str>) {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ check_success(chfl_atom_set_name(self.as_mut_ptr(), buffer.as_ptr()));
+ }
+ }
+
+ /// Set the atom type to `atomic_type`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_atomic_type("F");
+ /// assert_eq!(atom.atomic_type(), "F");
+ /// ```
+ pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>) {
+ let buffer = strings::to_c(atomic_type.into());
+ unsafe {
+ check_success(chfl_atom_set_type(self.as_mut_ptr(), buffer.as_ptr()));
+ }
+ }
+
+ /// Try to get the full name of the atom from the atomic type. For example,
+ /// the full name of "He" is "Helium", and so on. If the name can not be
+ /// found, this function returns the empty string.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("Zn");
+ /// assert_eq!(atom.full_name(), "Zinc");
+ /// ```
+ pub fn full_name(&self) -> String {
+ let get_full_name = |ptr, len| unsafe { chfl_atom_full_name(self.as_ptr(), ptr, len) };
+ let name = strings::call_autogrow_buffer(10, get_full_name).expect("getting full name failed");
+ return strings::from_c(name.as_ptr());
+ }
+
+ /// Try to get the Van der Waals radius of the atom from the atomic type.
+ /// If the radius can not be found, returns 0.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+ /// assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);
+ /// ```
+ pub fn vdw_radius(&self) -> f64 {
+ let mut radius: f64 = 0.0;
+ unsafe {
+ check_success(chfl_atom_vdw_radius(self.as_ptr(), &mut radius));
+ }
+ return radius;
+ }
+
+ /// Try to get the covalent radius of the atom from the atomic type. If the
+ /// radius can not be found, returns 0.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+ /// assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);
+ /// ```
+ pub fn covalent_radius(&self) -> f64 {
+ let mut radius: f64 = 0.0;
+ unsafe {
+ check_success(chfl_atom_covalent_radius(self.as_ptr(), &mut radius));
+ }
+ return radius;
+ }
+
+ /// Try to get the atomic number of the atom from the atomic type. If the
+ /// number can not be found, returns 0.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// assert_eq!(Atom::new("He").atomic_number(), 2);
+ /// assert_eq!(Atom::new("Xxx").atomic_number(), 0);
+ /// ```
+ pub fn atomic_number(&self) -> u64 {
+ let mut number = 0;
+ unsafe {
+ check_success(chfl_atom_atomic_number(self.as_ptr(), &mut number));
+ }
+ return number;
+ }
+
+ /// Add a new `property` with the given `name` to this atom.
+ ///
+ /// If a property with the same name already exists, this function override
+ /// the existing property with the new one.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Atom, Property};
+ /// let mut atom = Atom::new("He");
+ /// atom.set("a bool", true);
+ /// atom.set("a string", "test");
+ ///
+ /// assert_eq!(atom.get("a bool"), Some(Property::Bool(true)));
+ /// assert_eq!(atom.get("a string"), Some(Property::String("test".into())));
+ /// ```
+ pub fn set(&mut self, name: &str, property: impl Into<Property>) {
+ let buffer = strings::to_c(name);
+ let property = property.into().as_raw();
+ unsafe {
+ check_success(chfl_atom_set_property(
+ self.as_mut_ptr(), buffer.as_ptr(), property.as_ptr()
+ ));
+ }
+ }
+
+
+ /// Get a property with the given `name` in this atom, if it exist.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Atom, Property};
+ /// let mut atom = Atom::new("He");
+ /// atom.set("foo", Property::Double(22.2));
+ ///
+ /// assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+ /// assert_eq!(atom.get("Bar"), None);
+ /// ```
+ pub fn get(&self, name: &str) -> Option<Property> {
+ let buffer = strings::to_c(name);
+ unsafe {
+ let handle = chfl_atom_get_property(self.as_ptr(), buffer.as_ptr());
+ if handle.is_null() {
+ None
+ } else {
+ let raw = RawProperty::from_ptr(handle);
+ let property = Property::from_raw(raw);
+ Some(property)
+ }
+ }
+ }
+
+ /// Get an iterator over all (name, property) pairs for this atom
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Atom, Property};
+ /// let mut atom = Atom::new("He");
+ /// atom.set("foo", Property::Double(22.2));
+ /// atom.set("bar", Property::Bool(false));
+ ///
+ /// for (name, property) in atom.properties() {
+ /// if name == "foo" {
+ /// assert_eq!(property, Property::Double(22.2));
+ /// } else if name == "bar" {
+ /// assert_eq!(property, Property::Bool(false));
+ /// }
+ /// }
+ /// ```
+ pub fn properties(&self) -> PropertiesIter {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_atom_properties_count(self.as_ptr(), &mut count));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = count as usize;
+ let mut c_names = vec![ptr::null_mut(); size];
+ unsafe {
+ check_success(chfl_atom_list_properties(self.as_ptr(), c_names.as_mut_ptr(), count));
+ }
+
+ let mut names = Vec::new();
+ for ptr in c_names {
+ names.push(strings::from_c(ptr));
+ }
+
+ PropertiesIter {
+ names: names.into_iter(),
+ getter: Box::new(move |name| self.get(&*name).expect("failed to get property"))
+ }
+ }
+}
+
+impl Drop for Atom {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.name(), "He");
+
+ let copy = atom.clone();
+ assert_eq!(copy.name(), "He");
+
+ atom.set_name("Na");
+ assert_eq!(atom.name(), "Na");
+ assert_eq!(copy.name(), "He");
+ }
+
+ #[test]
+ fn mass() {
+ let mut atom = Atom::new("He");
+ assert_ulps_eq!(atom.mass(), 4.002602);
+ atom.set_mass(15.0);
+ assert_eq!(atom.mass(), 15.0);
+ }
+
+ #[test]
+ fn charge() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.charge(), 0.0);
+ atom.set_charge(-1.5);
+ assert_eq!(atom.charge(), -1.5);
+ }
+
+ #[test]
+ fn name() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.name(), "He");
+ atom.set_name("Zn-12");
+ assert_eq!(atom.name(), "Zn-12");
+ }
+
+ #[test]
+ fn atomic_type() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.atomic_type(), "He");
+ atom.set_atomic_type("Zn");
+ assert_eq!(atom.atomic_type(), "Zn");
+ }
+
+ #[test]
+ fn full_name() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.full_name(), "Helium");
+
+ atom.set_atomic_type("Zn");
+ assert_eq!(atom.full_name(), "Zinc");
+
+ let atom = Atom::new("Unknown");
+ assert_eq!(atom.full_name(), "");
+ }
+
+ #[test]
+ fn radii() {
+ let atom = Atom::new("He");
+ assert_ulps_eq!(atom.vdw_radius(), 1.4);
+ assert_ulps_eq!(atom.covalent_radius(), 0.32);
+
+ let atom = Atom::new("Unknown");
+ assert_eq!(atom.vdw_radius(), 0.0);
+ assert_eq!(atom.covalent_radius(), 0.0);
+ }
+
+ #[test]
+ fn atomic_number() {
+ let atom = Atom::new("He");
+ assert_eq!(atom.atomic_number(), 2);
+
+ let atom = Atom::new("Unknown");
+ assert_eq!(atom.atomic_number(), 0);
+ }
+
+ #[test]
+ fn property() {
+ let mut atom = Atom::new("F");
+
+ atom.set("foo", -22.0);
+ assert_eq!(atom.get("foo"), Some(Property::Double(-22.0)));
+ assert_eq!(atom.get("bar"), None);
+
+ atom.set("bar", Property::String("here".into()));
+ for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(-22.0));
+ } else if name == "bar" {
+ assert_eq!(property, Property::String("here".into()));
+ }
+ }
+ }
+}
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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::{Drop, Deref, DerefMut};
+use std::marker::PhantomData;
+use std::ptr;
+
+use chemfiles_sys::*;
+use errors::{check_success, check_not_null, check, Error};
+
+/// Available unit cell shapes.
+#[derive(Clone, Debug, PartialEq, Eq)]
+pub enum CellShape {
+ /// Orthorhombic cell, with the three angles equals to 90°.
+ Orthorhombic,
+ /// Triclinic cell, with any values for the angles.
+ Triclinic,
+ /// Infinite cell, to use when there is no cell.
+ Infinite,
+}
+
+impl From<chfl_cellshape> for CellShape {
+ fn from(celltype: chfl_cellshape) -> CellShape {
+ match celltype {
+ chfl_cellshape::CHFL_CELL_ORTHORHOMBIC => CellShape::Orthorhombic,
+ chfl_cellshape::CHFL_CELL_TRICLINIC => CellShape::Triclinic,
+ chfl_cellshape::CHFL_CELL_INFINITE => CellShape::Infinite,
+ }
+ }
+}
+
+impl From<CellShape> for chfl_cellshape {
+ fn from(celltype: CellShape) -> chfl_cellshape {
+ match celltype {
+ CellShape::Orthorhombic => chfl_cellshape::CHFL_CELL_ORTHORHOMBIC,
+ CellShape::Triclinic => chfl_cellshape::CHFL_CELL_TRICLINIC,
+ CellShape::Infinite => chfl_cellshape::CHFL_CELL_INFINITE,
+ }
+ }
+}
+
+/// An `UnitCell` represent the box containing the atoms, and its periodicity.
+///
+/// An unit cell is fully represented by three lengths (a, b, c); and three
+/// angles (alpha, beta, gamma). The angles are stored in degrees, and the
+/// lengths in Angstroms.
+///
+/// A cell also has a matricial representation, by projecting the three base
+/// vector into an orthonormal base. We choose to represent such matrix as an
+/// upper triangular matrix:
+///
+/// ```text
+/// | a_x b_x c_x |
+/// | 0 b_y c_y |
+/// | 0 0 c_z |
+/// ```
+pub struct UnitCell {
+ handle: *mut CHFL_CELL,
+}
+
+/// An analog to a reference to an unit cell (`&UnitCell`)
+pub struct UnitCellRef<'a> {
+ inner: UnitCell,
+ marker: PhantomData<&'a UnitCell>
+}
+
+impl<'a> Deref for UnitCellRef<'a> {
+ type Target = UnitCell;
+ fn deref(&self) -> &UnitCell {
+ &self.inner
+ }
+}
+
+/// An analog to a mutable reference to an unit cell (`&mut UnitCell`)
+pub struct UnitCellMut<'a> {
+ inner: UnitCell,
+ marker: PhantomData<&'a mut UnitCell>
+}
+
+impl<'a> Deref for UnitCellMut<'a> {
+ type Target = UnitCell;
+ fn deref(&self) -> &UnitCell {
+ &self.inner
+ }
+}
+
+impl<'a> DerefMut for UnitCellMut<'a> {
+ fn deref_mut(&mut self) -> &mut UnitCell {
+ &mut self.inner
+ }
+}
+
+impl Clone for UnitCell {
+ fn clone(&self) -> UnitCell {
+ unsafe {
+ let new_handle = chfl_cell_copy(self.as_ptr());
+ UnitCell::from_ptr(new_handle)
+ }
+ }
+}
+
+impl UnitCell {
+ /// Create an owned `UnitCell` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_CELL) -> UnitCell {
+ check_not_null(ptr);
+ UnitCell {
+ handle: ptr
+ }
+ }
+
+ /// Create a borrowed `UnitCell` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, and the caller is responsible for setting the right lifetime.
+ #[inline]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_CELL) -> UnitCellRef<'a> {
+ UnitCellRef {
+ inner: UnitCell::from_ptr(ptr as *mut CHFL_CELL),
+ marker: PhantomData,
+ }
+ }
+
+ /// Create a borrowed `UnitCell` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, except for it being non-null, and the caller is responsible for
+ /// setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_mut_from_ptr<'a>(ptr: *mut CHFL_CELL) -> UnitCellMut<'a> {
+ UnitCellMut {
+ inner: UnitCell::from_ptr(ptr),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_CELL {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_CELL {
+ self.handle
+ }
+
+ /// Create an `Orthorhombic` `UnitCell` from the three lengths, in Angstroms.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::new([30.0, 30.0, 23.0]);
+ ///
+ /// assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// ```
+ pub fn new(lengths: [f64; 3]) -> UnitCell {
+ unsafe {
+ let handle = chfl_cell(lengths.as_ptr(), ptr::null());
+ UnitCell::from_ptr(handle)
+ }
+ }
+
+ /// Create an `Infinite` `UnitCell`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::infinite();
+ ///
+ /// assert_eq!(cell.lengths(), [0.0, 0.0, 0.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// assert_eq!(cell.shape(), CellShape::Infinite);
+ /// ```
+ pub fn infinite() -> UnitCell {
+ let mut cell = UnitCell::new([0.0, 0.0, 0.0]);
+ cell.set_shape(CellShape::Infinite).expect("could not set cell shape");
+ return cell;
+ }
+
+ /// Create an `Triclinic` `UnitCell` from the three lengths (in Angstroms)
+ /// and three angles (in degree). `alpha` is the angle between the vectors
+ /// `b` and `c`; `beta` is the between the vectors `a` and `c` and `gamma`
+ /// is the angle between the vectors `a` and `b`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::triclinic([10.0, 10.0, 10.0], [98.0, 99.0, 90.0]);
+ ///
+ /// assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);
+ /// assert_eq!(cell.angles()[0], 98.0);
+ /// // Rounding errors might occur due to internal representation
+ /// assert!((cell.angles()[1] - 99.0).abs() < 1e-12);
+ /// assert_eq!(cell.angles()[2], 90.0);
+ /// assert_eq!(cell.shape(), CellShape::Triclinic);
+ /// ```
+ pub fn triclinic(lengths: [f64; 3], angles: [f64; 3]) -> UnitCell {
+ unsafe {
+ let handle = chfl_cell(lengths.as_ptr(), angles.as_ptr());
+ UnitCell::from_ptr(handle)
+ }
+ }
+
+ /// Create an `UnitCell` from a cell matrix. If `matrix` contains only
+ /// zeros, then an `Infinite` cell is created. If only the diagonal of the
+ /// matrix is non-zero, then the cell is `Orthorhombic`. Else a
+ /// `Triclinic` cell is created. The matrix entries should be in Angstroms.
+ ///
+ /// # Panics
+ ///
+ /// If the matrix has a negative determinant, or more generally is not
+ /// representing a unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::from_matrix([
+ /// [1.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]
+ /// ]);
+ ///
+ /// assert_eq!(cell.lengths(), [1.0, 2.0, 3.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// ```
+ pub fn from_matrix(mut matrix: [[f64; 3]; 3]) -> UnitCell {
+ unsafe {
+ let handle = chfl_cell_from_matrix(matrix.as_mut_ptr());
+ UnitCell::from_ptr(handle)
+ }
+ }
+
+ /// Get the three lengths of the cell, in Angstroms.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([30.0, 30.0, 23.0]);
+ /// assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
+ /// ```
+ pub fn lengths(&self) -> [f64; 3] {
+ let mut lengths = [0.0; 3];
+ unsafe {
+ check_success(chfl_cell_lengths(self.as_ptr(), lengths.as_mut_ptr()));
+ }
+ return lengths;
+ }
+
+ /// Set the three lengths of the cell, in Angstroms.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the unit cell is infinite, or if one of the
+ /// lengths is negative.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let mut cell = UnitCell::new([30.0, 30.0, 23.0]);
+ ///
+ /// cell.set_lengths([10.0, 30.0, 42.0]).unwrap();
+ /// assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]);
+ ///
+ /// assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());
+ /// ```
+ pub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error> {
+ unsafe {
+ check(chfl_cell_set_lengths(self.as_mut_ptr(), lengths.as_ptr()))
+ }
+ }
+
+ /// Get the three angles of the cell, in degrees.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([20.0, 20.0, 20.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ ///
+ /// let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+ /// assert_eq!(cell.angles()[0], 100.0);
+ /// // Rounding errors might occur due to internal representation
+ /// assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+ /// assert_eq!(cell.angles()[2], 90.0);
+ /// ```
+ pub fn angles(&self) -> [f64; 3] {
+ let mut angles = [0.0; 3];
+ unsafe {
+ check_success(chfl_cell_angles(self.as_ptr(), angles.as_mut_ptr()));
+ }
+ return angles;
+ }
+
+ /// Set the three angles of the cell, in degrees.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the unit cell is not `Triclinic`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+ /// assert_eq!(cell.angles()[0], 100.0);
+ /// // Rounding errors might occur due to internal representation
+ /// assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+ /// assert_eq!(cell.angles()[2], 90.0);
+ ///
+ /// cell.set_angles([90.0, 90.0, 90.0]).unwrap();
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// ```
+ pub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error> {
+ unsafe {
+ check(chfl_cell_set_angles(self.as_mut_ptr(), angles.as_ptr()))
+ }
+ }
+
+ /// Get the unit cell matricial representation.
+ ///
+ /// The unit cell representation is obtained by aligning the a vector along
+ /// the *x* axis and putting the b vector in the *xy* plane. This make the
+ /// matrix an upper triangular matrix:
+ ///
+ /// ```text
+ /// | a_x b_x c_x |
+ /// | 0 b_y c_y |
+ /// | 0 0 c_z |
+ /// ```
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ ///
+ /// let matrix = cell.matrix();
+ ///
+ /// assert_eq!(matrix[0][0], 10.0);
+ /// assert_eq!(matrix[1][1], 20.0);
+ /// assert_eq!(matrix[2][2], 30.0);
+ ///
+ /// assert!(matrix[1][2].abs() < 1e-9);
+ /// ```
+ pub fn matrix(&self) -> [[f64; 3]; 3] {
+ let mut matrix = [[0.0; 3]; 3];
+ unsafe {
+ check_success(chfl_cell_matrix(self.as_ptr(), matrix.as_mut_ptr()));
+ }
+ return matrix;
+ }
+
+ /// Get the shape of the unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// ```
+ pub fn shape(&self) -> CellShape {
+ let mut shape = chfl_cellshape::CHFL_CELL_INFINITE;
+ unsafe {
+ check_success(chfl_cell_shape(self.as_ptr(), &mut shape));
+ }
+ return CellShape::from(shape);
+ }
+
+ /// Set the shape of the unit cell to `shape`.
+ ///
+ /// # Errors
+ ///
+ /// This can fail if the cell length or angles are incompatible with the
+ /// new shape.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let mut cell = UnitCell::new([10.0, 20.0, 30.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ ///
+ /// cell.set_shape(CellShape::Triclinic).unwrap();
+ /// assert_eq!(cell.shape(), CellShape::Triclinic);
+ /// ```
+ pub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error> {
+ unsafe {
+ check(chfl_cell_set_shape(self.as_mut_ptr(), shape.into()))
+ }
+ }
+
+ /// Get the volume of the unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ /// assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0);
+ /// ```
+ pub fn volume(&self) -> f64 {
+ let mut volume = 0.0;
+ unsafe {
+ check_success(chfl_cell_volume(self.as_ptr(), &mut volume));
+ }
+ return volume;
+ }
+
+ /// Wrap a `vector` in this unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ ///
+ /// let mut vector = [12.0, 5.2, -45.3];
+ /// cell.wrap(&mut vector);
+ /// assert_eq!(vector, [2.0, 5.2, 14.700000000000003]);
+ /// ```
+ pub fn wrap(&self, vector: &mut [f64; 3]) {
+ unsafe {
+ check_success(chfl_cell_wrap(self.as_ptr(), vector.as_mut_ptr()));
+ }
+ }
+}
+
+impl Drop for UnitCell {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.lengths(), [2.0, 3.0, 4.0]);
+
+ let copy = cell.clone();
+ assert_eq!(copy.lengths(), [2.0, 3.0, 4.0]);
+
+ cell.set_lengths([10.0, 12.0, 11.0]).unwrap();
+ assert_eq!(cell.lengths(), [10.0, 12.0, 11.0]);
+ assert_eq!(copy.lengths(), [2.0, 3.0, 4.0]);
+ }
+
+ #[test]
+ fn lengths() {
+ let mut cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.lengths(), [2.0, 3.0, 4.0]);
+ cell.set_lengths([10.0, 12.0, 11.0]).unwrap();
+ assert_eq!(cell.lengths(), [10.0, 12.0, 11.0]);
+ }
+
+ #[test]
+ fn angles() {
+ let mut cell = UnitCell::new([2.0, 3.0, 4.0]);
+ crate::assert_vector3d_eq(&cell.angles(), &[90.0, 90.0, 90.0], 1e-6);
+
+ cell.set_shape(CellShape::Triclinic).unwrap();
+ cell.set_angles([80.0, 89.0, 100.0]).unwrap();
+
+ crate::assert_vector3d_eq(&cell.angles(), &[80.0, 89.0, 100.0], 1e-6);
+
+ let cell = UnitCell::triclinic([1., 2., 3.], [80., 90., 100.]);
+ crate::assert_vector3d_eq(&cell.angles(), &[80.0, 90.0, 100.0], 1e-6);
+ }
+
+ #[test]
+ fn volume() {
+ let cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.volume(), 2.0 * 3.0 * 4.0);
+ }
+
+ #[test]
+ fn wrap() {
+ let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ let mut vector = [12.0, 5.2, -45.3];
+ cell.wrap(&mut vector);
+ crate::assert_vector3d_eq(&vector, &[2.0, 5.2, 14.7], 1e-6);
+ }
+
+ #[test]
+ fn matrix() {
+ let cell = UnitCell::new([2.0, 3.0, 4.0]);
+
+ let matrix = cell.matrix();
+ let result = [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]];
+
+ for i in 0..3 {
+ for j in 0..3 {
+ assert_ulps_eq!(matrix[i][j], result[i][j], epsilon = 1e-12);
+ }
+ }
+ }
+
+ #[test]
+ fn from_matrix() {
+ let cell = UnitCell::from_matrix([[10.0, 0.0, 0.0], [0.0, 21.0, 0.0], [0.0, 0.0, 32.0]]);
+ assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ assert_eq!(cell.lengths(), [10.0, 21.0, 32.0]);
+
+ let result_matrix = [
+ [123.0, 4.08386, 71.7295],
+ [0.0, 233.964, 133.571],
+ [0.0, 0.0, 309.901],
+ ];
+ let cell = UnitCell::from_matrix(result_matrix);
+
+ assert_eq!(cell.shape(), CellShape::Triclinic);
+ for i in 0..3 {
+ assert_ulps_eq!(
+ cell.lengths()[i],
+ [123.0, 234.0, 345.0][i],
+ epsilon = 1e-3
+ );
+ assert_ulps_eq!(cell.angles()[i], [67.0, 78.0, 89.0][i], epsilon = 1e-3);
+ }
+
+ let matrix = cell.matrix();
+ for i in 0..3 {
+ for j in 0..3 {
+ assert_ulps_eq!(matrix[i][j], result_matrix[i][j], epsilon = 1e-12);
+ }
+ }
+ }
+
+ #[test]
+ fn shape() {
+ let cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.shape(), CellShape::Orthorhombic);
+
+ let cell = UnitCell::infinite();
+ assert_eq!(cell.shape(), CellShape::Infinite);
+
+ let cell = UnitCell::triclinic([1.0, 2.0, 3.0], [80.0, 90.0, 100.0]);
+ assert_eq!(cell.shape(), CellShape::Triclinic);
+
+ let mut cell = UnitCell::new([10.0, 10.0, 10.0]);
+ assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ cell.set_shape(CellShape::Triclinic).unwrap();
+ assert_eq!(cell.shape(), CellShape::Triclinic);
+ }
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+extern crate libc;
+
+use std::error;
+use std::fmt;
+use std::panic::{self, RefUnwindSafe};
+use std::path::Path;
+
+use self::libc::c_char;
+
+use chemfiles_sys::*;
+use strings;
+
+#[derive(Clone, Debug, PartialEq)]
+/// Error type for Chemfiles.
+pub struct Error {
+ /// The error status code
+ pub status: Status,
+ /// A message describing the error cause
+ pub message: String,
+}
+
+#[repr(C)]
+#[non_exhaustive]
+#[derive(Clone, Debug, PartialEq)]
+/// Possible causes of error in chemfiles
+pub enum Status {
+ /// No error
+ Success = chfl_status::CHFL_SUCCESS as isize,
+ /// Error in memory allocations
+ MemoryError = chfl_status::CHFL_MEMORY_ERROR as isize,
+ /// Error while reading or writing a file
+ FileError = chfl_status::CHFL_FILE_ERROR as isize,
+ /// Error in file formatting, *i.e.* the file is invalid
+ FormatError = chfl_status::CHFL_FORMAT_ERROR as isize,
+ /// Error in selection string syntax
+ SelectionError = chfl_status::CHFL_SELECTION_ERROR as isize,
+ /// Error in configuration files syntax
+ ConfigurationError = chfl_status::CHFL_CONFIGURATION_ERROR as isize,
+ /// Error for out of bounds indexing
+ OutOfBounds = chfl_status::CHFL_OUT_OF_BOUNDS as isize,
+ /// Error related to properties
+ PropertyError = chfl_status::CHFL_PROPERTY_ERROR as isize,
+ /// Exception in the C++ chemfiles library
+ ChemfilesError = chfl_status::CHFL_GENERIC_ERROR as isize,
+ /// Exception in the C++ standard library
+ StdCppError = chfl_status::CHFL_CXX_ERROR as isize,
+ /// The given path is not valid UTF8
+ // TODO: rename this to UTF8Error in the next breaking release
+ UTF8PathError,
+}
+
+impl From<chfl_status> for Error {
+ fn from(status: chfl_status) -> Error {
+ let status = match status {
+ chfl_status::CHFL_SUCCESS => Status::Success,
+ chfl_status::CHFL_CXX_ERROR => Status::StdCppError,
+ chfl_status::CHFL_GENERIC_ERROR => Status::ChemfilesError,
+ chfl_status::CHFL_MEMORY_ERROR => Status::MemoryError,
+ chfl_status::CHFL_FILE_ERROR => Status::FileError,
+ chfl_status::CHFL_FORMAT_ERROR => Status::FormatError,
+ chfl_status::CHFL_SELECTION_ERROR => Status::SelectionError,
+ chfl_status::CHFL_CONFIGURATION_ERROR => Status::ConfigurationError,
+ chfl_status::CHFL_OUT_OF_BOUNDS => Status::OutOfBounds,
+ chfl_status::CHFL_PROPERTY_ERROR => Status::PropertyError,
+ };
+
+ let message = Error::last_error();
+ Error {
+ status,
+ message,
+ }
+ }
+}
+
+impl From<std::str::Utf8Error> for Error {
+ fn from(_: std::str::Utf8Error) -> Self {
+ Error {
+ status: Status::UTF8PathError,
+ message: "failed to convert data to UTF8 string".into(),
+ }
+ }
+}
+
+impl Error {
+ /// Create a new error because the given `path` is invalid UTF-8 data
+ pub(crate) fn utf8_path_error(path: &Path) -> Error {
+ Error {
+ status: Status::UTF8PathError,
+ message: format!("Could not convert '{}' to UTF8", path.display()),
+ }
+ }
+
+ /// Get the last error message from the C++ library.
+ pub fn last_error() -> String {
+ unsafe { strings::from_c(chfl_last_error()) }
+ }
+
+ /// Clear any error from the C++ library
+ pub fn cleanup() {
+ unsafe {
+ check(chfl_clear_errors()).expect("error in chfl_clear_errors. Things went very bad");
+ }
+ }
+}
+
+/// Check return value of a C function, and get the error if needed.
+pub(crate) fn check(status: chfl_status) -> Result<(), Error> {
+ if status == chfl_status::CHFL_SUCCESS {
+ Ok(())
+ } else {
+ Err(Error::from(status))
+ }
+}
+
+/// Check return value of a C function, panic if it failed.
+pub(crate) fn check_success(status: chfl_status) {
+ if status != chfl_status::CHFL_SUCCESS {
+ panic!("unexpected failure: {}", Error::last_error());
+ }
+}
+
+/// Check a pointer for null.
+pub(crate) fn check_not_null<T>(ptr: *const T) {
+ if ptr.is_null() {
+ panic!("unexpected null pointer: {}", Error::last_error());
+ }
+}
+
+pub trait WarningCallback: RefUnwindSafe + Fn(&str) {}
+impl<T> WarningCallback for T
+where
+ T: RefUnwindSafe + Fn(&str),
+{
+}
+
+static mut LOGGING_CALLBACK: Option<*mut dyn WarningCallback<Output = ()>> = None;
+
+extern "C" fn warning_callback(message: *const c_char) {
+ unsafe {
+ let callback = &*LOGGING_CALLBACK.expect("No callback provided, this is an internal bug");
+ // ignore result. If a panic happened, everything is going badly anyway
+ let _result = panic::catch_unwind(|| {
+ callback(&strings::from_c(message));
+ });
+ }
+}
+
+/// Use `callback` for every chemfiles warning. The callback will be passed
+/// the warning message. This will drop any previous warning callback.
+pub fn set_warning_callback<F>(callback: F) where F: WarningCallback + 'static {
+ // box callback to ensure it stays accessible
+ let callback = Box::into_raw(Box::new(callback));
+ unsafe {
+ if let Some(previous) = LOGGING_CALLBACK {
+ // drop the previous callback
+ let previous = Box::from_raw(previous);
+ std::mem::drop(previous);
+ // set the LOGGING_CALLBACK to the new one
+ LOGGING_CALLBACK = Some(callback);
+ } else {
+ // set the LOGGING_CALLBACK
+ LOGGING_CALLBACK = Some(callback);
+ // Tell C code to use Rust-provided callback
+ check_success(chfl_set_warning_callback(warning_callback));
+ }
+ }
+}
+
+
+impl fmt::Display for Error {
+ fn fmt(&self, fmt: &mut fmt::Formatter) -> Result<(), fmt::Error> {
+ write!(fmt, "{}", self.message)
+ }
+}
+
+impl error::Error for Error {
+ fn description(&self) -> &str {
+ match self.status {
+ Status::Success => "Success",
+ Status::StdCppError => "Exception from the C++ standard library",
+ Status::ChemfilesError => "Exception from the chemfiles library",
+ Status::MemoryError => "Error in memory allocations",
+ Status::FileError => "Error while reading or writing a file",
+ Status::FormatError => "Error in file formatting, i.e. the file is invalid",
+ Status::SelectionError => "Error in selection string syntax",
+ Status::UTF8PathError => "A string is not valid UTF8",
+ Status::ConfigurationError => "Error in configuration files",
+ Status::OutOfBounds => "Out of bounds indexing",
+ Status::PropertyError => "Error in property",
+ }
+ }
+}
+
+
+#[cfg(test)]
+mod test {
+ use super::*;
+ use Trajectory;
+
+ #[test]
+ fn errors() {
+ Error::cleanup();
+ assert_eq!(Error::last_error(), "");
+ assert!(Trajectory::open("nope", 'r').is_err());
+ assert_eq!(
+ Error::last_error(),
+ "file at \'nope\' does not have an extension, provide a format name to read it"
+ );
+ Error::cleanup();
+ assert_eq!(Error::last_error(), "");
+ }
+
+ #[test]
+ fn codes() {
+ assert_eq!(Error::from(chfl_status::CHFL_SUCCESS).status, Status::Success);
+ assert_eq!(Error::from(chfl_status::CHFL_CXX_ERROR).status, Status::StdCppError);
+ assert_eq!(Error::from(chfl_status::CHFL_GENERIC_ERROR).status, Status::ChemfilesError);
+ assert_eq!(Error::from(chfl_status::CHFL_MEMORY_ERROR).status, Status::MemoryError);
+ assert_eq!(Error::from(chfl_status::CHFL_FILE_ERROR).status, Status::FileError);
+ assert_eq!(Error::from(chfl_status::CHFL_FORMAT_ERROR).status, Status::FormatError);
+ assert_eq!(Error::from(chfl_status::CHFL_SELECTION_ERROR).status, Status::SelectionError);
+ assert_eq!(Error::from(chfl_status::CHFL_OUT_OF_BOUNDS).status, Status::OutOfBounds);
+ assert_eq!(Error::from(chfl_status::CHFL_PROPERTY_ERROR).status, Status::PropertyError);
+ }
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 + 100 + 101 + 102 + 103 + 104 + 105 + 106 + 107 + 108 + 109 + 110 + 111 + 112 + 113 + 114 + 115 + 116 + 117 + 118 + 119 + 120 + 121 + 122 + 123 + 124 + 125 + 126 + 127 + 128 + 129 + 130 + 131 + 132 + 133 + 134 + 135 + 136 + 137 + 138 + 139 + 140 + 141 + 142 + 143 + 144 + 145 + 146 + 147 + 148 + 149 + 150 + 151 + 152 + 153 + 154 + 155 + 156 + 157 + 158 + 159 + 160 + 161 + 162 + 163 + 164 + 165 + 166 + 167 + 168 + 169 + 170 + 171 + 172 + 173 + 174 + 175 + 176 + 177 + 178 + 179 + 180 + 181 + 182 + 183 + 184 + 185 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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::Drop;
+use std::ptr;
+use std::slice;
+
+use chemfiles_sys::*;
+use strings;
+use errors::{check_not_null, check_success, check, Error};
+use super::{Atom, AtomRef, AtomMut};
+use super::{Topology, TopologyRef, Residue, BondOrder};
+use super::{UnitCell, UnitCellRef, UnitCellMut};
+use property::{Property, RawProperty, PropertiesIter};
+
+/// A `Frame` contains data from one simulation step: the current unit
+/// cell, the topology, the positions, and the velocities of the particles in
+/// the system. If some information is missing (topology or velocity or unit
+/// cell), the corresponding data is filled with a default value.
+pub struct Frame {
+ handle: *mut CHFL_FRAME,
+}
+
+impl Clone for Frame {
+ fn clone(&self) -> Frame {
+ unsafe {
+ let new_handle = chfl_frame_copy(self.as_ptr());
+ Frame::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Frame {
+ /// Create a `Frame` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer,
+ /// except for it being non-null.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_FRAME) -> Frame {
+ check_not_null(ptr);
+ Frame {
+ handle: ptr
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_FRAME {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_FRAME {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer FROM A SHARED REFERENCE.
+ ///
+ /// For uses with functions of the C API using mut pointers for both read
+ /// and write access. Users should check that this does not lead to multiple
+ /// mutable borrows
+ #[inline]
+ #[allow(non_snake_case)]
+ pub(crate) fn as_mut_ptr_MANUALLY_CHECKING_BORROW(&self) -> *mut CHFL_FRAME {
+ self.handle
+ }
+
+ /// Create an empty frame. It will be resized by the library as needed.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let frame = Frame::new();
+ ///
+ /// assert_eq!(frame.size(), 0);
+ /// ```
+ pub fn new() -> Frame {
+ unsafe {
+ Frame::from_ptr(chfl_frame())
+ }
+ }
+
+ /// Get a reference to the atom at the given `index` in this frame.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+ ///
+ /// let atom = frame.atom(0);
+ /// assert_eq!(atom.name(), "Zn");
+ /// ```
+ pub fn atom(&self, index: usize) -> AtomRef {
+ unsafe {
+ let handle = chfl_atom_from_frame(
+ self.as_mut_ptr_MANUALLY_CHECKING_BORROW(),
+ index as u64
+ );
+ Atom::ref_from_ptr(handle)
+ }
+ }
+
+ /// Get a mutable reference to the atom at the given `index` in this frame.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+ ///
+ /// assert_eq!(frame.atom(0).name(), "Zn");
+ ///
+ /// frame.atom_mut(0).set_name("Fe");
+ /// assert_eq!(frame.atom(0).name(), "Fe");
+ /// ```
+ pub fn atom_mut(&mut self, index: usize) -> AtomMut {
+ unsafe {
+ let handle = chfl_atom_from_frame(self.as_mut_ptr(), index as u64);
+ Atom::ref_mut_from_ptr(handle)
+ }
+ }
+
+ /// Get the current number of atoms in this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.size(), 0);
+ ///
+ /// frame.resize(67);
+ /// assert_eq!(frame.size(), 67);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(chfl_frame_atoms_count(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Resize the positions and the velocities in this frame, to make space for
+ /// `natoms` atoms. Previous data is conserved, as well as the presence of
+ /// absence of velocities.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// assert_eq!(frame.size(), 67);
+ /// ```
+ pub fn resize(&mut self, natoms: usize) {
+ unsafe {
+ check_success(chfl_frame_resize(self.as_mut_ptr(), natoms as u64));
+ }
+ }
+
+ /// Add an `Atom` and the corresponding position and optionally velocity
+ /// data to this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [1.0, 1.0, 2.0], None);
+ ///
+ /// frame.add_velocities();
+ /// frame.add_atom(&Atom::new("Zn"), [-1.0, 1.0, 2.0], [0.2, 0.1, 0.0]);
+ /// ```
+ pub fn add_atom(
+ &mut self,
+ atom: &Atom,
+ position: [f64; 3],
+ velocity: impl Into<Option<[f64; 3]>>,
+ )
+ {
+ let velocity = velocity.into();
+ let velocity_ptr = match velocity {
+ Some(ref data) => data.as_ptr(),
+ None => ptr::null(),
+ };
+
+ unsafe {
+ check_success(chfl_frame_add_atom(
+ self.as_mut_ptr(),
+ atom.as_ptr(),
+ position.as_ptr(),
+ velocity_ptr
+ ));
+ }
+
+ }
+
+ /// Remove the atom at index `i` in this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+ /// frame.add_atom(&Atom::new("Fe"), [0.0; 3], None);
+ /// frame.add_atom(&Atom::new("Sn"), [0.0; 3], None);
+ /// assert_eq!(frame.size(), 3);
+ ///
+ /// frame.remove(1);
+ /// assert_eq!(frame.size(), 2);
+ /// assert_eq!(frame.atom(1).name(), "Sn");
+ /// ```
+ pub fn remove(&mut self, i: usize) {
+ unsafe {
+ check_success(chfl_frame_remove(self.as_mut_ptr(), i as u64));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the frame.
+ ///
+ /// The bond order is set to `BondOrder::Unknown`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, BondOrder};
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.topology().bonds_count(), 0);
+ /// frame.resize(5);
+ ///
+ /// frame.add_bond(0, 1);
+ /// frame.add_bond(3, 1);
+ /// frame.add_bond(2, 4);
+ /// assert_eq!(frame.topology().bonds_count(), 3);
+ ///
+ /// assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown);
+ /// assert_eq!(frame.topology().bonds(), vec![[0, 1], [1, 3], [2, 4]]);
+ /// ```
+ pub fn add_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(chfl_frame_add_bond(self.as_mut_ptr(), i as u64, j as u64));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the frame
+ /// with the given bond `order`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, BondOrder};
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.topology().bonds_count(), 0);
+ /// frame.resize(2);
+ ///
+ /// frame.add_bond_with_order(0, 1, BondOrder::Double);
+ /// assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Double);
+ /// ```
+ pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder) {
+ unsafe {
+ check_success(chfl_frame_bond_with_order(
+ self.as_mut_ptr(),
+ i as u64,
+ j as u64,
+ order.as_raw(),
+ ));
+ }
+ }
+
+ /// Remove any existing bond between the atoms at indexes `i` and `j` in
+ /// the frame.
+ ///
+ /// This function does nothing if there is no bond between `i` and `j`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(5);
+ ///
+ /// frame.add_bond(0, 1);
+ /// frame.add_bond(3, 1);
+ /// frame.add_bond(2, 4);
+ ///
+ /// let bonds = frame.topology().bonds();
+ /// assert_eq!(bonds, vec![[0, 1], [1, 3], [2, 4]]);
+ ///
+ /// frame.remove_bond(2, 4);
+ /// let bonds = frame.topology().bonds();
+ /// assert_eq!(bonds, vec![[0, 1], [1, 3]]);
+ /// ```
+ pub fn remove_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(chfl_frame_remove_bond(
+ self.as_mut_ptr(),
+ i as u64,
+ j as u64,
+ ));
+ }
+ }
+
+ /// Add a copy of `residue` to this frame.
+ ///
+ /// # Errors
+ ///
+ /// This function fails is the residue id is already in this frame's
+ /// topology, or if the residue contain atoms that are already in another
+ /// residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Residue};
+ /// let mut frame = Frame::new();
+ ///
+ /// let residue = Residue::new("foo");
+ /// frame.add_residue(&residue).unwrap();
+ ///
+ /// let topology = frame.topology();
+ /// assert_eq!(topology.residues_count(), 1);
+ /// assert_eq!(topology.residue(0).unwrap().name(), "foo");
+ /// ```
+ pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error> {
+ unsafe {
+ check(chfl_frame_add_residue(self.as_mut_ptr(), residue.as_ptr()))
+ }
+ }
+
+ /// Get the distance between the atoms at indexes `i` and `j` in this frame,
+ /// accounting for periodic boundary conditions. The result is expressed in
+ /// Angstroms.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [1.0, 2.0, 3.0], None);
+ ///
+ /// assert_eq!(frame.distance(0, 1), f64::sqrt(14.0));
+ /// ```
+ pub fn distance(&self, i: usize, j: usize) -> f64 {
+ let mut distance = 0.0;
+ unsafe {
+ check_success(chfl_frame_distance(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ &mut distance,
+ ));
+ }
+ return distance;
+ }
+
+ /// Get the angle formed by the atoms at indexes `i`, `j` and `k` in this
+ /// frame, accounting for periodic boundary conditions. The result is
+ /// expressed in radians.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// # use std::f64;
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+ ///
+ /// assert_eq!(frame.angle(0, 1, 2), f64::consts::PI / 2.0);
+ /// ```
+ pub fn angle(&self, i: usize, j: usize, k: usize) -> f64 {
+ let mut angle = 0.0;
+ unsafe {
+ check_success(chfl_frame_angle(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ k as u64,
+ &mut angle,
+ ));
+ }
+ return angle;
+ }
+
+ /// Get the dihedral angle formed by the atoms at indexes `i`, `j`, `k` and
+ /// `m` in this frame, accounting for periodic boundary conditions. The
+ /// result is expressed in radians.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// # use std::f64;
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("D"), [0.0, 1.0, 1.0], None);
+ ///
+ /// assert_eq!(frame.dihedral(0, 1, 2, 3), f64::consts::PI / 2.0);
+ /// ```
+ pub fn dihedral(&self, i: usize, j: usize, k: usize, m: usize) -> f64 {
+ let mut dihedral = 0.0;
+ unsafe {
+ check_success(chfl_frame_dihedral(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ k as u64,
+ m as u64,
+ &mut dihedral,
+ ));
+ }
+ return dihedral;
+ }
+
+ /// Get the out of plane distance formed by the atoms at indexes `i`, `j`,
+ /// `k` and `m` in this frame, accounting for periodic boundary conditions.
+ /// The result is expressed in angstroms.
+ ///
+ /// This is the distance between the atom j and the ikm plane. The j atom
+ /// is the center of the improper dihedral angle formed by i, j, k and m.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 2.0], None);
+ /// frame.add_atom(&Atom::new("C"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("D"), [0.0, 1.0, 0.0], None);
+ ///
+ /// assert_eq!(frame.out_of_plane(0, 1, 2, 3), 2.0);
+ /// ```
+ pub fn out_of_plane(&self, i: usize, j: usize, k: usize, m: usize) -> f64 {
+ let mut distance = 0.0;
+ unsafe {
+ check_success(chfl_frame_out_of_plane(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ k as u64,
+ m as u64,
+ &mut distance,
+ ));
+ }
+ return distance;
+ }
+
+ /// Get a view into the positions of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ ///
+ /// let positions = frame.positions();
+ /// assert_eq!(positions.len(), 67);
+ /// assert_eq!(positions[0], [0.0, 0.0, 0.0]);
+ /// ```
+ pub fn positions(&self) -> &[[f64; 3]] {
+ let mut ptr = ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(chfl_frame_positions(
+ self.as_mut_ptr_MANUALLY_CHECKING_BORROW(),
+ &mut ptr,
+ &mut natoms
+ ));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return slice::from_raw_parts(ptr, size);
+ }
+ }
+
+ /// Get a mutable view into the positions of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// {
+ /// let positions = frame.positions_mut();
+ /// assert_eq!(positions[0], [0.0, 0.0, 0.0]);
+ /// positions[0] = [1.0, 2.0, 3.0];
+ /// }
+ ///
+ /// let positions = frame.positions();
+ /// assert_eq!(positions[0], [1.0, 2.0, 3.0]);
+ /// ```
+ pub fn positions_mut(&mut self) -> &mut [[f64; 3]] {
+ let mut ptr = ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(chfl_frame_positions(self.as_mut_ptr(), &mut ptr, &mut natoms));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return slice::from_raw_parts_mut(ptr, size);
+ }
+ }
+
+ /// Get a view into the velocities of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// frame.add_velocities();
+ ///
+ /// let velocities = frame.velocities();
+ /// assert_eq!(velocities.len(), 67);
+ /// assert_eq!(velocities[0], [0.0, 0.0, 0.0]);
+ /// ```
+ pub fn velocities(&self) -> &[[f64; 3]] {
+ let mut ptr = ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(chfl_frame_velocities(
+ self.as_mut_ptr_MANUALLY_CHECKING_BORROW(),
+ &mut ptr,
+ &mut natoms
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return slice::from_raw_parts(ptr, size);
+ }
+ }
+
+ /// Get a mutable view into the velocities of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// frame.add_velocities();
+ /// {
+ /// let velocities = frame.velocities_mut();
+ /// assert_eq!(velocities[0], [0.0, 0.0, 0.0]);
+ /// velocities[0] = [1.0, 2.0, 3.0];
+ /// }
+ ///
+ /// let velocities = frame.velocities();
+ /// assert_eq!(velocities[0], [1.0, 2.0, 3.0]);
+ /// ```
+ pub fn velocities_mut(&mut self) -> &mut [[f64; 3]] {
+ let mut ptr = ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(chfl_frame_velocities(self.as_mut_ptr(), &mut ptr, &mut natoms));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return slice::from_raw_parts_mut(ptr, size);
+ }
+ }
+
+ /// Check if this frame contains velocity data.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.has_velocities(), false);
+ ///
+ /// frame.add_velocities();
+ /// assert_eq!(frame.has_velocities(), true);
+ /// ```
+ pub fn has_velocities(&self) -> bool {
+ let mut res = 0;
+ unsafe {
+ check_success(chfl_frame_has_velocities(self.as_ptr(), &mut res));
+ }
+ return res != 0;
+ }
+
+ /// Add velocity data to this frame. If the frame already have velocities,
+ /// this does nothing.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.has_velocities(), false);
+ ///
+ /// frame.add_velocities();
+ /// assert_eq!(frame.has_velocities(), true);
+ /// ```
+ pub fn add_velocities(&mut self) {
+ unsafe {
+ check_success(chfl_frame_add_velocities(self.as_mut_ptr()));
+ }
+ }
+
+ /// Get a reference to the `UnitCell` from this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, CellShape};
+ /// let frame = Frame::new();
+ ///
+ /// let cell = frame.cell();
+ /// assert_eq!(cell.shape(), CellShape::Infinite);
+ /// ```
+ pub fn cell(&self) -> UnitCellRef {
+ unsafe {
+ let handle = chfl_cell_from_frame(self.as_mut_ptr_MANUALLY_CHECKING_BORROW());
+ UnitCell::ref_from_ptr(handle)
+ }
+ }
+
+ /// Get a mutable reference to the `UnitCell` from this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, CellShape};
+ /// let mut frame = Frame::new();
+ ///
+ /// assert_eq!(frame.cell().shape(), CellShape::Infinite);
+ ///
+ /// frame.cell_mut().set_shape(CellShape::Triclinic).unwrap();
+ /// assert_eq!(frame.cell().shape(), CellShape::Triclinic);
+ /// ```
+ pub fn cell_mut(&mut self) -> UnitCellMut {
+ unsafe {
+ let handle = chfl_cell_from_frame(self.as_mut_ptr());
+ UnitCell::ref_mut_from_ptr(handle)
+ }
+ }
+
+ /// Set the `UnitCell` of this frame to `cell`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, UnitCell, CellShape};
+ /// let mut frame = Frame::new();
+ ///
+ /// frame.set_cell(&UnitCell::new([10.0, 10.0, 10.0]));
+ ///
+ /// let cell = frame.cell();
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);
+ /// ```
+ pub fn set_cell(&mut self, cell: &UnitCell) {
+ unsafe {
+ check_success(chfl_frame_set_cell(self.as_mut_ptr(), cell.as_ptr()));
+ }
+ }
+
+ /// Get a reference to the `Topology` of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(42);
+ ///
+ /// let topology = frame.topology();
+ /// assert_eq!(topology.size(), 42);
+ /// ```
+ pub fn topology(&self) -> TopologyRef {
+ unsafe {
+ let handle = chfl_topology_from_frame(self.as_ptr());
+ Topology::ref_from_ptr(handle)
+ }
+ }
+
+ /// Set the `Topology` of this frame to `topology`.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the topology contains a different number of atoms
+ /// than this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Topology, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.resize(2);
+ ///
+ /// let mut topology = Topology::new();
+ /// topology.add_atom(&Atom::new("Cl"));
+ /// topology.add_atom(&Atom::new("Cl"));
+ /// topology.add_bond(0, 1);
+ ///
+ /// frame.set_topology(&topology).unwrap();
+ /// assert_eq!(frame.atom(0).name(), "Cl");
+ /// ```
+ pub fn set_topology(&mut self, topology: &Topology) -> Result<(), Error> {
+ unsafe {
+ check(chfl_frame_set_topology(self.as_mut_ptr(), topology.as_ptr()))
+ }
+ }
+
+ /// Get this frame step, i.e. the frame number in the trajectory
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let frame = Frame::new();
+ /// assert_eq!(frame.step(), 0);
+ /// ```
+ pub fn step(&self) -> usize {
+ let mut step = 0;
+ unsafe {
+ check_success(chfl_frame_step(self.as_ptr(), &mut step));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return step as usize;
+ }
+
+ /// Set this frame step to `step`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.step(), 0);
+ ///
+ /// frame.set_step(10);
+ /// assert_eq!(frame.step(), 10);
+ /// ```
+ pub fn set_step(&mut self, step: usize) {
+ unsafe {
+ check_success(chfl_frame_set_step(self.as_mut_ptr(), step as u64));
+ }
+ }
+
+ /// Guess the bonds, angles and dihedrals in this `frame`.
+ ///
+ /// The bonds are guessed using a distance-based algorithm, and then angles
+ /// and dihedrals are guessed from the bonds.
+ ///
+ /// # Errors
+ ////
+ /// This function can fail if the covalent radius is unknown for some atoms
+ /// in the frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ ///
+ /// frame.add_atom(&Atom::new("Cl"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("Cl"), [1.5, 0.0, 0.0], None);
+ /// assert_eq!(frame.topology().bonds_count(), 0);
+ ///
+ /// frame.guess_bonds().unwrap();
+ /// assert_eq!(frame.topology().bonds_count(), 1);
+ /// ```
+ pub fn guess_bonds(&mut self) -> Result<(), Error> {
+ unsafe {
+ check(chfl_frame_guess_bonds(self.as_mut_ptr()))
+ }
+ }
+
+ /// Remove all existing bonds, angles, dihedral angles and improper
+ /// dihedral angles in the topology of the frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Atom, Frame};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [0.0, 1.0, 0.0], None);
+ ///
+ /// frame.add_bond(0, 1);
+ /// frame.add_bond(1, 2);
+ ///
+ /// assert_eq!(frame.topology().bonds().len(), 2);
+ /// assert_eq!(frame.topology().angles().len(), 1);
+ ///
+ /// frame.clear_bonds();
+ /// assert!(frame.topology().bonds().is_empty());
+ /// assert!(frame.topology().angles().is_empty());
+ /// ```
+ pub fn clear_bonds(&mut self) {
+ unsafe {
+ check_success(chfl_frame_clear_bonds(self.as_mut_ptr()));
+ }
+ }
+
+ /// Add a new `property` with the given `name` to this frame.
+ ///
+ /// If a property with the same name already exists, this function override
+ /// the existing property with the new one.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Frame, Property};
+ /// let mut frame = Frame::new();
+ /// frame.set("a string", "hello");
+ /// frame.set("a double", 4.3);
+ ///
+ /// assert_eq!(frame.get("a string"), Some(Property::String("hello".into())));
+ /// assert_eq!(frame.get("a double"), Some(Property::Double(4.3)));
+ /// ```
+ pub fn set(&mut self, name: &str, property: impl Into<Property>) {
+ let buffer = strings::to_c(name);
+ let property = property.into().as_raw();
+ unsafe {
+ check_success(chfl_frame_set_property(
+ self.as_mut_ptr(), buffer.as_ptr(), property.as_ptr()
+ ));
+ }
+ }
+
+ /// Get a property with the given `name` in this frame, if it exist.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Frame, Property};
+ /// let mut frame = Frame::new();
+ /// frame.set("foo", Property::Double(22.2));
+ ///
+ /// assert_eq!(frame.get("foo"), Some(Property::Double(22.2)));
+ /// assert_eq!(frame.get("Bar"), None);
+ /// ```
+ pub fn get(&self, name: &str) -> Option<Property> {
+ let buffer = strings::to_c(name);
+ unsafe {
+ let handle = chfl_frame_get_property(self.as_ptr(), buffer.as_ptr());
+ if handle.is_null() {
+ None
+ } else {
+ let raw = RawProperty::from_ptr(handle);
+ Some(Property::from_raw(raw))
+ }
+ }
+ }
+
+ /// Get an iterator over all (name, property) pairs for this frame
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Frame, Property};
+ /// let mut frame = Frame::new();
+ /// frame.set("foo", Property::Double(22.2));
+ /// frame.set("bar", Property::Bool(false));
+ ///
+ /// for (name, property) in frame.properties() {
+ /// if name == "foo" {
+ /// assert_eq!(property, Property::Double(22.2));
+ /// } else if name == "bar" {
+ /// assert_eq!(property, Property::Bool(false));
+ /// }
+ /// }
+ /// ```
+ pub fn properties(&self) -> PropertiesIter {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_frame_properties_count(self.as_ptr(), &mut count));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = count as usize;
+ let mut c_names = vec![ptr::null_mut(); size];
+ unsafe {
+ check_success(chfl_frame_list_properties(self.as_ptr(), c_names.as_mut_ptr(), count));
+ }
+
+ let mut names = Vec::new();
+ for ptr in c_names {
+ names.push(strings::from_c(ptr));
+ }
+
+ PropertiesIter {
+ names: names.into_iter(),
+ getter: Box::new(move |name| self.get(&*name).expect("failed to get property"))
+ }
+ }
+}
+
+impl Drop for Frame {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+ use {Atom, Topology, UnitCell};
+
+ #[test]
+ fn clone() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.size(), 0);
+ let copy = frame.clone();
+ assert_eq!(copy.size(), 0);
+
+ frame.resize(42);
+ assert_eq!(frame.size(), 42);
+ assert_eq!(copy.size(), 0);
+ }
+
+ #[test]
+ fn size() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.size(), 0);
+
+ frame.resize(12);
+ assert_eq!(frame.size(), 12);
+ }
+
+ #[test]
+ fn add_atom() {
+ let mut frame = Frame::new();
+
+ frame.add_atom(&Atom::new("U"), [1.0, 1.0, 2.0], None);
+ assert_eq!(frame.size(), 1);
+ assert_eq!(frame.atom(0).name(), "U");
+
+ let positions = &[[1.0, 1.0, 2.0]];
+ assert_eq!(frame.positions(), positions);
+
+ frame.add_velocities();
+ frame.add_atom(&Atom::new("F"), [1.0, 1.0, 2.0], [4.0, 3.0, 2.0]);
+ assert_eq!(frame.size(), 2);
+ assert_eq!(frame.atom(0).name(), "U");
+ assert_eq!(frame.atom(1).name(), "F");
+
+ let positions = &[[1.0, 1.0, 2.0], [1.0, 1.0, 2.0]];
+ assert_eq!(frame.positions(), positions);
+
+ let velocities = &[[0.0, 0.0, 0.0], [4.0, 3.0, 2.0]];
+ assert_eq!(frame.velocities(), velocities);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_atom() {
+ let mut frame = Frame::new();
+ frame.resize(22);
+ let _atom = frame.atom(23);
+ }
+
+ #[test]
+ fn remove_atom() {
+ let mut frame = Frame::new();
+ frame.add_atom(&Atom::new("U"), [1.0, 1.0, 2.0], None);
+ frame.add_atom(&Atom::new("F"), [1.0, 1.0, 2.0], None);
+
+ assert_eq!(frame.size(), 2);
+ assert_eq!(frame.atom(0).name(), "U");
+
+ frame.remove(0);
+ assert_eq!(frame.size(), 1);
+ assert_eq!(frame.atom(0).name(), "F");
+ }
+
+ #[test]
+ #[should_panic]
+ fn remove_out_of_bounds() {
+ let mut frame = Frame::new();
+ frame.resize(32);
+
+ frame.remove(100);
+ }
+
+ #[test]
+ fn positions() {
+ let mut frame = Frame::new();
+ frame.resize(4);
+ let expected = &[
+ [1.0, 2.0, 3.0],
+ [4.0, 5.0, 6.0],
+ [7.0, 8.0, 9.0],
+ [10.0, 11.0, 12.0],
+ ];
+
+ frame.positions_mut().clone_from_slice(expected);
+ assert_eq!(frame.positions(), expected);
+ }
+
+ #[test]
+ fn velocities() {
+ let mut frame = Frame::new();
+ frame.resize(4);
+ assert!(!frame.has_velocities());
+ frame.add_velocities();
+ assert!(frame.has_velocities());
+
+ let expected = &[
+ [1.0, 2.0, 3.0],
+ [4.0, 5.0, 6.0],
+ [7.0, 8.0, 9.0],
+ [10.0, 11.0, 12.0],
+ ];
+
+ frame.velocities_mut().clone_from_slice(expected);
+ assert_eq!(frame.velocities(), expected);
+ }
+
+ #[test]
+ fn cell() {
+ let mut frame = Frame::new();
+ frame.set_cell(&UnitCell::new([3.0, 4.0, 5.0]));
+ let cell = frame.cell();
+ assert_eq!(cell.lengths(), [3.0, 4.0, 5.0]);
+ }
+
+ #[test]
+ fn topology() {
+ let mut frame = Frame::new();
+ frame.resize(2);
+ let mut topology = Topology::new();
+
+ topology.add_atom(&Atom::new("Zn"));
+ topology.add_atom(&Atom::new("Ar"));
+
+ assert!(frame.set_topology(&topology).is_ok());
+
+ let topology = frame.topology();
+
+ assert_eq!(topology.atom(0).name(), "Zn");
+ assert_eq!(topology.atom(1).name(), "Ar");
+
+ assert_eq!(frame.atom(0).name(), "Zn");
+ assert_eq!(frame.atom(1).name(), "Ar");
+ }
+
+ #[test]
+ fn bonds() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ assert_eq!(frame.topology().bonds_count(), 0);
+
+ frame.add_bond(0, 1);
+ frame.add_bond(9, 2);
+ frame.add_bond_with_order(3, 7, BondOrder::Aromatic);
+ assert_eq!(frame.topology().bonds_count(), 3);
+
+ assert_eq!(frame.topology().bonds(), vec![[0, 1], [2, 9], [3, 7]]);
+ let expected = vec![BondOrder::Unknown, BondOrder::Unknown, BondOrder::Aromatic];
+ assert_eq!(frame.topology().bond_orders(), expected);
+
+ assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown);
+ assert_eq!(frame.topology().bond_order(3, 7), BondOrder::Aromatic);
+
+ frame.remove_bond(3, 7);
+ // Removing unexisting bond is OK if both indexes are in bounds
+ frame.remove_bond(8, 7);
+ assert_eq!(frame.topology().bonds_count(), 2);
+
+ frame.clear_bonds();
+ assert_eq!(frame.topology().bonds_count(), 0);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ frame.add_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_remove_bond() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ frame.remove_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds_with_order() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ frame.add_bond_with_order(300, 7, BondOrder::Unknown);
+ }
+
+ #[test]
+ fn residues() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.topology().residues_count(), 0);
+
+ let residue = &Residue::new("foobar");
+ frame.add_residue(residue).unwrap();
+ frame.add_residue(residue).unwrap();
+ frame.add_residue(residue).unwrap();
+
+ assert_eq!(frame.topology().residues_count(), 3);
+ assert_eq!(frame.topology().residue(0).unwrap().name(), "foobar");
+ }
+
+ #[test]
+ fn step() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.step(), 0);
+ frame.set_step(42);
+ assert_eq!(frame.step(), 42);
+ }
+
+ #[test]
+ fn property() {
+ let mut frame = Frame::new();
+ frame.set("foo", -22.0);
+ assert_eq!(frame.get("foo"), Some(Property::Double(-22.0)));
+ assert_eq!(frame.get("bar"), None);
+
+ frame.set("bar", Property::String("here".into()));
+ for (name, property) in frame.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(-22.0));
+ } else if name == "bar" {
+ assert_eq!(property, Property::String("here".into()));
+ }
+ }
+ }
+
+ #[test]
+ fn pbc_geometry() {
+ use std::f64::consts::PI;
+
+ let mut frame = Frame::new();
+ let atom = &Atom::new("");
+
+ frame.add_atom(atom, [1.0, 0.0, 0.0], None);
+ frame.add_atom(atom, [0.0, 0.0, 0.0], None);
+ frame.add_atom(atom, [0.0, 1.0, 0.0], None);
+ frame.add_atom(atom, [0.0, 1.0, 1.0], None);
+ frame.add_atom(atom, [0.0, 0.0, 2.0], None);
+
+ assert_eq!(frame.distance(0, 2), f64::sqrt(2.0));
+ assert_eq!(frame.angle(0, 1, 2), PI / 2.0);
+ assert_eq!(frame.dihedral(0, 1, 2, 3), PI / 2.0);
+ assert_eq!(frame.out_of_plane(1, 4, 0, 2), 2.0);
+ }
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+
+//! Chemfiles is a multi-language library written in modern C++ for reading and
+//! writing from and to molecular trajectory files. These files are created by
+//! your favorite theoretical chemistry program, and contains information about
+//! atomic or residues names and positions. Some format also have additional
+//! information, such as velocities, forces, energy, …
+//!
+//! This crate expose the C API of chemfiles to Rust, and make all the
+//! functionalities accessible. For more information on the C++ library,
+//! please see its [documentation][cxx_doc]. Specifically, the following pages
+//! are worth reading:
+//!
+//! - The [overview][overview] of the classes organization;
+//! - The list of [supported formats][formats];
+//! - The documentation for the [selection language][selections];
+//!
+//! [cxx_doc]: https://chemfiles.org/chemfiles
+//! [overview]: https://chemfiles.org/chemfiles/latest/overview.html
+//! [formats]: https://chemfiles.org/chemfiles/latest/formats.html
+//! [selections]: https://chemfiles.org/chemfiles/latest/selections.html
+
+#![deny(missing_docs)]
+#![warn(trivial_casts, unused_import_braces, variant_size_differences)]
+#![warn(unused_results)]
+// Configuration for clippy lints
+#![warn(clippy::all, clippy::pedantic)]
+#![allow(clippy::needless_return, clippy::module_name_repetitions)]
+#![allow(clippy::must_use_candidate, clippy::wildcard_imports)]
+
+// Allow a few more clippy lints in test mode
+#![cfg_attr(test, allow(clippy::float_cmp, clippy::unreadable_literal, clippy::shadow_unrelated))]
+
+// deny(warnings) in doc tests
+#![doc(test(attr(deny(warnings))))]
+#![doc(test(attr(allow(unused_variables))))]
+
+#[cfg(test)]
+#[macro_use]
+extern crate approx;
+
+extern crate chemfiles_sys;
+use chemfiles_sys::{chfl_add_configuration, chfl_version};
+
+mod strings;
+
+mod errors;
+pub use errors::{Error, Status};
+pub use errors::set_warning_callback;
+
+mod atom;
+pub use atom::Atom;
+pub use atom::AtomRef;
+pub use atom::AtomMut;
+
+mod cell;
+pub use cell::UnitCell;
+pub use cell::UnitCellRef;
+pub use cell::UnitCellMut;
+pub use cell::CellShape;
+
+mod residue;
+pub use residue::Residue;
+pub use residue::ResidueRef;
+
+mod topology;
+pub use topology::Topology;
+pub use topology::TopologyRef;
+pub use topology::BondOrder;
+
+mod frame;
+pub use frame::Frame;
+
+mod trajectory;
+pub use trajectory::Trajectory;
+
+mod selection;
+pub use selection::{Match, Selection};
+
+mod property;
+pub use property::Property;
+pub use property::PropertiesIter;
+
+mod misc;
+pub use misc::{FormatMetadata, formats_list, guess_format};
+
+/// Get the version of the chemfiles library.
+///
+/// # Example
+/// ```
+/// let version = chemfiles::version();
+/// assert!(version.starts_with("0.10"));
+/// ```
+pub fn version() -> String {
+ unsafe { strings::from_c(chfl_version()) }
+}
+
+/// Read configuration data from the file at `path`.
+///
+/// By default, chemfiles reads configuration from any file named
+/// `.chemfiles.toml` in the current directory or any parent directory. This
+/// function can be used to add data from another configuration file. Data from
+/// the new configuration file will overwrite any existing data.
+///
+/// # Errors
+///
+/// This function will fail if there is no file at `path`, or if the file is
+/// incorrectly formatted.
+///
+/// # Example
+/// ```no_run
+/// chemfiles::add_configuration("local-config.toml").unwrap();
+/// // from now on, the data from "local-config.toml" will be used
+/// ```
+pub fn add_configuration<S>(path: S) -> Result<(), Error>
+where
+ S: AsRef<str>,
+{
+ let buffer = strings::to_c(path.as_ref());
+ unsafe {
+ errors::check(chfl_add_configuration(buffer.as_ptr()))
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ #[test]
+ fn version() {
+ assert!(!crate::version().is_empty());
+ assert!(crate::version().starts_with("0.10"));
+ }
+}
+
+#[cfg(test)]
+fn assert_vector3d_eq(lhs: &[f64; 3], rhs: &[f64; 3], eps: f64) {
+ lhs.iter()
+ .zip(rhs)
+ .for_each(|(l, r)| assert_ulps_eq!(l, r, epsilon = eps));
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2020 Guillaume Fraux -- BSD licensed
+
+use std::convert::TryInto;
+use std::ffi::CStr;
+
+use chemfiles_sys::{chfl_format_metadata, chfl_formats_list, chfl_free, chfl_guess_format};
+use errors::check_success;
+
+/// `FormatMetadata` contains metadata associated with one format.
+#[allow(clippy::struct_excessive_bools)]
+#[derive(Debug, Clone, PartialEq, Eq)]
+pub struct FormatMetadata {
+ /// Name of the format.
+ pub name: &'static str,
+ /// Extension associated with the format.
+ pub extension: Option<&'static str>,
+ /// Extended, user-facing description of the format.
+ pub description: &'static str,
+ /// URL pointing to the format definition/reference.
+ pub reference: &'static str,
+ /// Is reading files in this format implemented?
+ pub read: bool,
+ /// Is writing files in this format implemented?
+ pub write: bool,
+ /// Does this format support in-memory IO?
+ pub memory: bool,
+ /// Does this format support storing atomic positions?
+ pub positions: bool,
+ /// Does this format support storing atomic velocities?
+ pub velocities: bool,
+ /// Does this format support storing unit cell information?
+ pub unit_cell: bool,
+ /// Does this format support storing atom names or types?
+ pub atoms: bool,
+ /// Does this format support storing bonds between atoms?
+ pub bonds: bool,
+ /// Does this format support storing residues?
+ pub residues: bool,
+}
+
+impl FormatMetadata {
+ pub(crate) fn from_raw(raw: &chfl_format_metadata) -> Self {
+ let str_from_ptr = |ptr| unsafe {
+ CStr::from_ptr(ptr)
+ .to_str()
+ .expect("Invalid Rust str from C")
+ };
+ let extension = if raw.extension.is_null() {
+ None
+ } else {
+ Some(str_from_ptr(raw.extension))
+ };
+ Self {
+ name: str_from_ptr(raw.name),
+ extension,
+ description: str_from_ptr(raw.description),
+ reference: str_from_ptr(raw.reference),
+ read: raw.read,
+ write: raw.write,
+ memory: raw.memory,
+ positions: raw.positions,
+ velocities: raw.velocities,
+ unit_cell: raw.unit_cell,
+ atoms: raw.atoms,
+ bonds: raw.bonds,
+ residues: raw.residues,
+ }
+ }
+}
+
+/// Get the list of formats known by chemfiles, as well as all associated metadata.
+///
+/// # Example
+/// ```
+/// let formats = chemfiles::formats_list();
+/// println!("chemfiles supports {} formats:", formats.len());
+/// for format in &formats {
+/// println!(
+/// " {:<15} {}",
+/// format.name,
+/// format.extension.as_deref().unwrap_or("")
+/// );
+/// }
+/// ```
+#[must_use]
+pub fn formats_list() -> Vec<FormatMetadata> {
+ let mut formats = std::ptr::null_mut();
+ let mut count: u64 = 0;
+ let formats_slice = unsafe {
+ check_success(chfl_formats_list(&mut formats, &mut count));
+ std::slice::from_raw_parts(formats, count.try_into().expect("failed to convert u64 to usize"))
+ };
+ let formats_vec = formats_slice
+ .iter()
+ .map(|fm| FormatMetadata::from_raw(fm))
+ .collect();
+ unsafe {
+ let _ = chfl_free(formats as *const _);
+ }
+ return formats_vec;
+}
+
+#[allow(clippy::doc_markdown)]
+/// Get the format that chemfiles would use to read a file at the given
+/// ``path``.
+///
+/// The format is mostly guessed from the path extension, chemfiles only tries
+/// to read the file to distinguish between CIF and mmCIF files. Opening the
+/// file using the returned format string might still fail. For example, it will
+/// fail if the file is not actually formatted according to the guessed format;
+/// or the format/compression combination is not supported (e.g. `XTC / GZ` will
+/// not work since the XTC reader does not support compressed files).
+///
+/// The returned format is represented in a way compatible with the various
+/// `Trajectory` constructors, i.e. `"<format name> [/ <compression>]"`, where
+/// compression is optional.
+///
+/// # Examples
+/// ```
+/// let format = chemfiles::guess_format("trajectory.xyz.xz");
+/// assert_eq!(format, "XYZ / XZ");
+///
+/// let format = chemfiles::guess_format("trajectory.nc");
+/// assert_eq!(format, "Amber NetCDF");
+/// ```
+pub fn guess_format(path: &str) -> String {
+ let path = crate::strings::to_c(path);
+ let mut buffer = vec![0; 128];
+ unsafe {
+ check_success(chfl_guess_format(
+ path.as_ptr(), buffer.as_mut_ptr(), buffer.len() as u64
+ ));
+ }
+ return crate::strings::from_c(buffer.as_ptr());
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::Drop;
+use std::vec::IntoIter;
+
+use chemfiles_sys::*;
+use errors::{check, check_not_null, check_success, Error};
+use strings;
+
+/// A thin wrapper around `CHFL_PROPERTY`
+pub(crate) struct RawProperty {
+ handle: *mut CHFL_PROPERTY,
+}
+
+impl RawProperty {
+ /// Create a `RawProperty` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ pub unsafe fn from_ptr(ptr: *mut CHFL_PROPERTY) -> RawProperty {
+ check_not_null(ptr);
+ RawProperty {
+ handle: ptr
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ pub fn as_ptr(&self) -> *const CHFL_PROPERTY {
+ self.handle
+ }
+
+ fn double(value: f64) -> RawProperty {
+ unsafe {
+ let handle = chfl_property_double(value);
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn bool(value: bool) -> RawProperty {
+ let value = if value { 1 } else { 0 };
+ unsafe {
+ let handle = chfl_property_bool(value);
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn vector3d(value: [f64; 3]) -> RawProperty {
+ unsafe {
+ let handle = chfl_property_vector3d(value.as_ptr());
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn string(value: &str) -> RawProperty {
+ let buffer = strings::to_c(value);
+ unsafe {
+ let handle = chfl_property_string(buffer.as_ptr());
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn get_kind(&self) -> chfl_property_kind {
+ let mut kind = chfl_property_kind::CHFL_PROPERTY_BOOL;
+ unsafe {
+ check_success(chfl_property_get_kind(self.as_ptr(), &mut kind));
+ }
+ return kind;
+ }
+
+ fn get_bool(&self) -> Result<bool, Error> {
+ let mut value = 0;
+ unsafe {
+ check(chfl_property_get_bool(self.as_ptr(), &mut value))?;
+ }
+ return Ok(value != 0);
+ }
+
+ fn get_double(&self) -> Result<f64, Error> {
+ let mut value = 0.0;
+ unsafe {
+ check(chfl_property_get_double(self.as_ptr(), &mut value))?;
+ }
+ return Ok(value);
+ }
+
+ fn get_string(&self) -> Result<String, Error> {
+ let get_string = |ptr, len| unsafe { chfl_property_get_string(self.as_ptr(), ptr, len) };
+ let value = strings::call_autogrow_buffer(64, get_string)?;
+ return Ok(strings::from_c(value.as_ptr()));
+ }
+
+ fn get_vector3d(&self) -> Result<[f64; 3], Error> {
+ let mut value = [0.0; 3];
+ unsafe {
+ check(chfl_property_get_vector3d(self.as_ptr(), value.as_mut_ptr()))?;
+ }
+ return Ok(value);
+ }
+}
+
+impl Drop for RawProperty {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+/// A `Property` is a piece of data that can be associated with an `Atom` or a
+/// `Frame`.
+#[derive(Debug, Clone, PartialEq, PartialOrd)]
+pub enum Property {
+ /// Boolean property
+ Bool(bool),
+ /// Floating point property
+ Double(f64),
+ /// String property
+ String(String),
+ /// 3-dimensional vector property
+ Vector3D([f64; 3]),
+}
+
+impl From<bool> for Property {
+ fn from(value: bool) -> Self {
+ Property::Bool(value)
+ }
+}
+
+impl From<f64> for Property {
+ fn from(value: f64) -> Self {
+ Property::Double(value)
+ }
+}
+
+impl From<String> for Property {
+ fn from(value: String) -> Self {
+ Property::String(value)
+ }
+}
+
+impl<'a> From<&'a str> for Property {
+ fn from(value: &'a str) -> Self {
+ Property::String(value.into())
+ }
+}
+
+impl From<[f64; 3]> for Property {
+ fn from(value: [f64; 3]) -> Self {
+ Property::Vector3D(value)
+ }
+}
+
+impl Property {
+ pub(crate) fn as_raw(&self) -> RawProperty {
+ match *self {
+ Property::Bool(value) => RawProperty::bool(value),
+ Property::Double(value) => RawProperty::double(value),
+ Property::String(ref value) => RawProperty::string(value),
+ Property::Vector3D(value) => RawProperty::vector3d(value),
+ }
+ }
+
+ #[allow(clippy::needless_pass_by_value)] // raw property
+ pub(crate) fn from_raw(raw: RawProperty) -> Property {
+ match raw.get_kind() {
+ chfl_property_kind::CHFL_PROPERTY_BOOL => {
+ Property::Bool(raw.get_bool().expect("shoudl be a bool"))
+ }
+ chfl_property_kind::CHFL_PROPERTY_DOUBLE => {
+ Property::Double(raw.get_double().expect("should be a double"))
+ }
+ chfl_property_kind::CHFL_PROPERTY_STRING => {
+ Property::String(raw.get_string().expect("should be a string"))
+ }
+ chfl_property_kind::CHFL_PROPERTY_VECTOR3D => {
+ Property::Vector3D(raw.get_vector3d().expect("should be a vector3d"))
+ }
+ }
+ }
+}
+
+/// An iterator over the properties in an atom/frame/residue
+pub struct PropertiesIter<'a> where {
+ pub(crate) names: IntoIter<String>,
+ pub(crate) getter: Box<dyn Fn(&str) -> Property + 'a>,
+}
+
+impl<'a> Iterator for PropertiesIter<'a> {
+ type Item = (String, Property);
+ fn next(&mut self) -> Option<Self::Item> {
+ self.names.next().map(|name| {
+ let property = (self.getter)(&*name);
+ (name, property)
+ })
+ }
+
+ fn size_hint(&self) -> (usize, Option<usize>) {
+ self.names.size_hint()
+ }
+
+ fn count(self) -> usize {
+ self.names.count()
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ mod raw {
+ use super::super::*;
+
+ #[test]
+ fn bool() {
+ let property = RawProperty::bool(false);
+ assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_BOOL);
+ assert_eq!(property.get_bool(), Ok(false));
+ }
+
+ #[test]
+ fn double() {
+ let property = RawProperty::double(45.0);
+ assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_DOUBLE);
+ assert_eq!(property.get_double(), Ok(45.0));
+ }
+
+ #[test]
+ fn string() {
+ let property = RawProperty::string("test");
+ assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_STRING);
+ assert_eq!(property.get_string(), Ok("test".into()));
+ }
+
+ #[test]
+ fn vector3d() {
+ let property = RawProperty::vector3d([1.2, 3.4, 5.6]);
+ assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_VECTOR3D);
+ assert_eq!(property.get_vector3d(), Ok([1.2, 3.4, 5.6]));
+ }
+ }
+
+ mod rust {
+ use super::super::*;
+
+ #[test]
+ fn bool() {
+ let property = Property::Bool(false);
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_BOOL);
+ assert_eq!(raw.get_bool(), Ok(false));
+
+ assert_eq!(Property::from_raw(raw), property);
+ }
+
+ #[test]
+ fn double() {
+ let property = Property::Double(45.0);
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_DOUBLE);
+ assert_eq!(raw.get_double(), Ok(45.0));
+
+ assert_eq!(Property::from_raw(raw), property);
+ }
+
+ #[test]
+ fn string() {
+ let property = Property::String("test".into());
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_STRING);
+ assert_eq!(raw.get_string(), Ok("test".into()));
+
+ assert_eq!(Property::from_raw(raw), property);
+
+ let property = Property::String("long string ".repeat(128));
+ let raw = property.as_raw();
+ assert_eq!(raw.get_string(), Ok("long string ".repeat(128)));
+ }
+
+ #[test]
+ fn vector3d() {
+ let property = Property::Vector3D([1.2, 3.4, 5.6]);
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_VECTOR3D);
+ assert_eq!(raw.get_vector3d(), Ok([1.2, 3.4, 5.6]));
+
+ assert_eq!(Property::from_raw(raw), property);
+ }
+ }
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371 +372 +373 +374 +375 +376 +377 +378 +379 +380 +381 +382 +383 +384 +385 +386 +387 +388 +389 +390 +391 +392 +393 +394 +395 +396 +397 +398 +399 +400 +401 +402 +403 +404 +405 +406 +407 +408 +409 +410 +411 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::{Drop, Deref};
+use std::marker::PhantomData;
+use std::ptr;
+
+use chemfiles_sys::*;
+use errors::{check_not_null, check_success};
+use property::{Property, RawProperty, PropertiesIter};
+use strings;
+
+/// A `Residue` is a group of atoms belonging to the same logical unit. They
+/// can be small molecules, amino-acids in a protein, monomers in polymers,
+/// *etc.*
+pub struct Residue {
+ handle: *mut CHFL_RESIDUE,
+}
+
+/// An analog to a reference to a residue (`&Residue`)
+pub struct ResidueRef<'a> {
+ inner: Residue,
+ marker: PhantomData<&'a Residue>
+}
+
+impl<'a> Deref for ResidueRef<'a> {
+ type Target = Residue;
+ fn deref(&self) -> &Residue {
+ &self.inner
+ }
+}
+
+impl Clone for Residue {
+ fn clone(&self) -> Residue {
+ unsafe {
+ let new_handle = chfl_residue_copy(self.as_ptr());
+ Residue::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Residue {
+ /// Create a `Residue` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_RESIDUE) -> Residue {
+ check_not_null(ptr);
+ Residue {
+ handle: ptr
+ }
+ }
+
+ /// Create a borrowed `Residue` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, except for it being non-null, and the caller is responsible
+ /// for setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_RESIDUE) -> ResidueRef<'a> {
+ ResidueRef {
+ inner: Residue::from_ptr(ptr as *mut CHFL_RESIDUE),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_RESIDUE {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_RESIDUE {
+ self.handle
+ }
+
+ /// Create a new residue with the given `name`
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::new("ALA");
+ /// assert_eq!(residue.name(), "ALA");
+ /// assert_eq!(residue.id(), None);
+ /// ```
+ pub fn new<'a>(name: impl Into<&'a str>) -> Residue {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ let handle = chfl_residue(buffer.as_ptr());
+ Residue::from_ptr(handle)
+ }
+ }
+
+ /// Create a new residue with the given `name` and `id` as identifier.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::with_id("ALA", 67);
+ /// assert_eq!(residue.name(), "ALA");
+ /// assert_eq!(residue.id(), Some(67));
+ /// ```
+ pub fn with_id<'a>(name: impl Into<&'a str>, id: i64) -> Residue {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ let handle = chfl_residue_with_id(buffer.as_ptr(), id);
+ Residue::from_ptr(handle)
+ }
+ }
+
+ /// Get the number of atoms in this residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.size(), 0);
+ ///
+ /// residue.add_atom(0);
+ /// residue.add_atom(1);
+ /// residue.add_atom(2);
+ /// assert_eq!(residue.size(), 3);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(chfl_residue_atoms_count(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Get the identifier of this residue in the initial topology file.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::with_id("", 42);
+ /// assert_eq!(residue.id(), Some(42));
+ /// ```
+ pub fn id(&self) -> Option<i64> {
+ let mut resid = 0;
+ let status = unsafe {
+ chfl_residue_id(self.as_ptr(), &mut resid)
+ };
+
+ if status == chfl_status::CHFL_SUCCESS {
+ return Some(resid);
+ } else if status == chfl_status::CHFL_GENERIC_ERROR {
+ return None;
+ }
+
+ // call check_success to panic in case of error
+ check_success(status);
+ unreachable!();
+ }
+
+ /// Get the name of this residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::new("water");
+ /// assert_eq!(residue.name(), "water");
+ /// ```
+ pub fn name(&self) -> String {
+ let get_name = |ptr, len| unsafe { chfl_residue_name(self.as_ptr(), ptr, len) };
+ let name = strings::call_autogrow_buffer(64, get_name).expect("getting residue name failed");
+ return strings::from_c(name.as_ptr());
+ }
+
+ /// Add the atom at index `atom` in this residue.
+ ///
+ /// This will fail if the atom is already in the residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.size(), 0);
+ /// assert_eq!(residue.contains(56), false);
+ ///
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.size(), 1);
+ /// assert_eq!(residue.contains(56), true);
+ ///
+ /// // Adding the same atom twice is fine
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.size(), 1);
+ /// ```
+ pub fn add_atom(&mut self, atom: usize) {
+ unsafe {
+ check_success(chfl_residue_add_atom(self.as_mut_ptr(), atom as u64));
+ }
+ }
+
+ /// Check if the atom at index `i` is in this residue
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.contains(56), false);
+ ///
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.contains(56), true);
+ /// ```
+ pub fn contains(&self, atom: usize) -> bool {
+ let mut inside = 0;
+ unsafe {
+ check_success(chfl_residue_contains(self.as_ptr(), atom as u64, &mut inside));
+ }
+ return inside != 0;
+ }
+
+ /// Get the list of atoms of this residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.atoms(), vec![]);
+ ///
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.atoms(), vec![56]);
+ /// ```
+ pub fn atoms(&self) -> Vec<usize> {
+ let size = self.size();
+ let count = size as u64;
+ let mut indices = vec![u64::max_value(); size];
+ unsafe {
+ check_success(chfl_residue_atoms(
+ self.as_ptr(),
+ indices.as_mut_ptr(),
+ count,
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return indices.into_iter().map(|idx| idx as usize).collect();
+ }
+
+ /// Add a new `property` with the given `name` to this residue.
+ ///
+ /// If a property with the same name already exists, this function override
+ /// the existing property with the new one.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Residue, Property};
+ /// let mut residue = Residue::new("ALA");
+ /// residue.set("a string", "hello");
+ /// residue.set("a double", 3.2);
+ ///
+ /// assert_eq!(residue.get("a string"), Some(Property::String("hello".into())));
+ /// assert_eq!(residue.get("a double"), Some(Property::Double(3.2)));
+ /// ```
+ pub fn set(&mut self, name: &str, property: impl Into<Property>) {
+ let buffer = strings::to_c(name);
+ let property = property.into().as_raw();
+ unsafe {
+ check_success(chfl_residue_set_property(
+ self.as_mut_ptr(), buffer.as_ptr(), property.as_ptr()
+ ));
+ }
+ }
+
+ /// Get a property with the given `name` in this frame, if it exist.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Residue, Property};
+ /// let mut residue = Residue::new("ALA");
+ /// residue.set("foo", Property::Double(22.2));
+ ///
+ /// assert_eq!(residue.get("foo"), Some(Property::Double(22.2)));
+ /// assert_eq!(residue.get("Bar"), None);
+ /// ```
+ pub fn get(&self, name: &str) -> Option<Property> {
+ let buffer = strings::to_c(name);
+ unsafe {
+ let handle = chfl_residue_get_property(self.as_ptr(), buffer.as_ptr());
+ if handle.is_null() {
+ None
+ } else {
+ let raw = RawProperty::from_ptr(handle);
+ Some(Property::from_raw(raw))
+ }
+ }
+ }
+
+ /// Get an iterator over all (name, property) pairs for this frame
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Residue, Property};
+ /// let mut residue = Residue::new("ALA");
+ /// residue.set("foo", Property::Double(22.2));
+ /// residue.set("bar", Property::Bool(false));
+ ///
+ /// for (name, property) in residue.properties() {
+ /// if name == "foo" {
+ /// assert_eq!(property, Property::Double(22.2));
+ /// } else if name == "bar" {
+ /// assert_eq!(property, Property::Bool(false));
+ /// }
+ /// }
+ /// ```
+ pub fn properties(&self) -> PropertiesIter {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_residue_properties_count(self.as_ptr(), &mut count));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = count as usize;
+ let mut c_names = vec![ptr::null_mut(); size];
+ unsafe {
+ check_success(chfl_residue_list_properties(self.as_ptr(), c_names.as_mut_ptr(), count));
+ }
+
+ let mut names = Vec::new();
+ for ptr in c_names {
+ names.push(strings::from_c(ptr));
+ }
+
+ PropertiesIter {
+ names: names.into_iter(),
+ getter: Box::new(move |name| self.get(&*name).expect("failed to get property"))
+ }
+ }
+}
+
+impl Drop for Residue {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut residue = Residue::new("A");
+ assert_eq!(residue.size(), 0);
+
+ let copy = residue.clone();
+ assert_eq!(copy.size(), 0);
+
+ residue.add_atom(3);
+ residue.add_atom(7);
+ assert_eq!(residue.size(), 2);
+ assert_eq!(copy.size(), 0);
+ }
+
+ #[test]
+ fn name() {
+ let residue = Residue::new("A");
+ assert_eq!(residue.name(), "A");
+ }
+
+ #[test]
+ fn id() {
+ let residue = Residue::new("A");
+ assert_eq!(residue.id(), None);
+
+ let residue = Residue::with_id("A", 42);
+ assert_eq!(residue.id(), Some(42));
+
+ let residue = Residue::with_id("A", -3);
+ assert_eq!(residue.id(), Some(-3));
+ }
+
+ #[test]
+ fn atoms() {
+ let mut residue = Residue::new("A");
+ assert_eq!(residue.size(), 0);
+
+ residue.add_atom(0);
+ residue.add_atom(3);
+ residue.add_atom(45);
+ assert_eq!(residue.size(), 3);
+
+ assert!(residue.contains(3));
+ assert!(!residue.contains(5));
+
+ assert_eq!(residue.atoms(), vec![0, 3, 45]);
+ }
+
+ #[test]
+ fn property() {
+ let mut residue = Residue::new("ALA");
+
+ residue.set("foo", -22.0);
+ assert_eq!(residue.get("foo"), Some(Property::Double(-22.0)));
+ assert_eq!(residue.get("bar"), None);
+
+ residue.set("bar", Property::String("here".into()));
+ for (name, property) in residue.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(-22.0));
+ } else if name == "bar" {
+ assert_eq!(property, Property::String("here".into()));
+ }
+ }
+ }
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371 +372 +373 +374 +375 +376 +377 +378 +379 +380 +381 +382 +383 +384 +385 +386 +387 +388 +389 +390 +391 +392 +393 +394 +395 +396 +397 +398 +399 +400 +401 +402 +403 +404 +405 +406 +407 +408 +409 +410 +411 +412 +413 +414 +415 +416 +417 +418 +419 +420 +421 +422 +423 +424 +425 +426 +427 +428 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::{Drop, Index};
+use std::iter::IntoIterator;
+use std::slice::Iter;
+
+use chemfiles_sys::*;
+use errors::{check, check_not_null, check_success, Error, Status};
+use strings;
+use frame::Frame;
+
+#[derive(Debug, Clone, PartialEq, Eq)]
+/// A `Match` is a set of atomic indexes matching a given selection. It can
+/// mostly be used like a `&[usize]`.
+pub struct Match {
+ size: usize,
+ atoms: [usize; 4],
+}
+
+#[allow(clippy::len_without_is_empty)]
+impl Match {
+ /// Get the length of the Match.
+ ///
+ /// # Example
+ ///
+ /// ```
+ /// # use chemfiles::Match;
+ /// let atomic_match = Match::new(&[3, 4, 5]);
+ /// assert_eq!(atomic_match.len(), 3);
+ /// ```
+ pub fn len(&self) -> usize {
+ self.size
+ }
+
+ /// Create a new match containing the atoms in the `atoms` slice.
+ ///
+ /// # Panics
+ ///
+ /// If the slice contains more than 4 elements, which is the maximal size
+ /// of a match.
+ ///
+ /// # Example
+ ///
+ /// ```
+ /// # use chemfiles::Match;
+ /// let atomic_match = Match::new(&[3, 4, 5]);
+ /// assert_eq!(atomic_match.len(), 3);
+ /// assert_eq!(atomic_match[0], 3);
+ /// assert_eq!(atomic_match[1], 4);
+ /// assert_eq!(atomic_match[2], 5);
+ /// ```
+ pub fn new(atoms: &[usize]) -> Match {
+ assert!(atoms.len() <= 4);
+ let size = atoms.len();
+ let mut matches = [usize::max_value(); 4];
+ for (i, atom) in atoms.iter().enumerate() {
+ matches[i] = *atom;
+ }
+ Match {
+ size,
+ atoms: matches,
+ }
+ }
+
+ /// Iterate over the atomic indexes in the match.
+ ///
+ /// # Example
+ ///
+ /// ```
+ /// # use chemfiles::Match;
+ /// let atomic_match = Match::new(&[3, 4, 5]);
+ /// let mut iter = atomic_match.iter();
+ ///
+ /// assert_eq!(iter.next(), Some(&3));
+ /// assert_eq!(iter.next(), Some(&4));
+ /// assert_eq!(iter.next(), Some(&5));
+ /// assert_eq!(iter.next(), None);
+ /// ```
+ pub fn iter(&self) -> Iter<usize> {
+ self.atoms[..self.len()].iter()
+ }
+}
+
+impl Index<usize> for Match {
+ type Output = usize;
+ fn index(&self, i: usize) -> &Self::Output {
+ assert!(i < self.len());
+ &self.atoms[i]
+ }
+}
+
+impl<'a> IntoIterator for &'a Match {
+ type Item = &'a usize;
+ type IntoIter = Iter<'a, usize>;
+ fn into_iter(self) -> Iter<'a, usize> {
+ self.atoms[..self.len()].iter()
+ }
+}
+
+/// A `Selection` allow to select atoms in a `Frame`, from a selection
+/// language. The selection language is built by combining basic operations.
+/// Each basic operation follows the `<selector>[(<variable>)] <operator>
+/// <value>` structure, where `<operator>` is a comparison operator in
+/// `== != < <= > >=`.
+pub struct Selection {
+ handle: *mut CHFL_SELECTION,
+}
+
+impl Clone for Selection {
+ fn clone(&self) -> Selection {
+ unsafe {
+ let new_handle = chfl_selection_copy(self.as_ptr());
+ Selection::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Drop for Selection {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+impl Selection {
+ /// Create a `Selection` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_SELECTION) -> Selection {
+ check_not_null(ptr);
+ Selection {
+ handle: ptr
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_SELECTION {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_SELECTION {
+ self.handle
+ }
+
+ /// Create a new selection from the given selection string.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the selection string is invalid.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Selection;
+ /// let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+ /// ```
+ pub fn new<'a, S: Into<&'a str>>(selection: S) -> Result<Selection, Error> {
+ let buffer = strings::to_c(selection.into());
+ unsafe {
+ let handle = chfl_selection(buffer.as_ptr());
+ if handle.is_null() {
+ Err(Error {
+ status: Status::SelectionError,
+ message: Error::last_error()
+ })
+ } else {
+ Ok(Selection::from_ptr(handle))
+ }
+ }
+ }
+
+ /// Get the size of the selection, i.e. the number of atoms we are selecting
+ /// together.
+ ///
+ /// This value is 1 for the 'atom' context, 2 for the 'pair' and 'bond'
+ /// context, 3 for the 'three' and 'angles' context and 4 for the 'four'
+ /// and 'dihedral' context.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Selection;
+ /// let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+ /// assert_eq!(selection.size(), 2);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(chfl_selection_size(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Get the selection string used to create this selection.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Selection;
+ /// let selection = Selection::new("name H").unwrap();
+ /// assert_eq!(selection.string(), "name H");
+ /// ```
+ pub fn string(&self) -> String {
+ let get_string = |ptr, len| unsafe { chfl_selection_string(self.as_ptr(), ptr, len) };
+ let selection = strings::call_autogrow_buffer(1024, get_string).expect("failed to get selection string");
+ return strings::from_c(selection.as_ptr());
+ }
+
+ /// Evaluate a selection for a given frame, and return the corresponding
+ /// matches.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Selection, Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+ ///
+ /// let mut selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+ /// let matches = selection.evaluate(&frame);
+ ///
+ /// assert_eq!(matches.len(), 2);
+ ///
+ /// assert_eq!(matches[0].len(), 2);
+ /// assert_eq!(matches[0][0], 0);
+ /// assert_eq!(matches[0][1], 1);
+ ///
+ /// assert_eq!(matches[1].len(), 2);
+ /// assert_eq!(matches[1][0], 2);
+ /// assert_eq!(matches[1][1], 1);
+ /// ```
+ pub fn evaluate(&mut self, frame: &Frame) -> Vec<Match> {
+ #![allow(clippy::cast_possible_truncation)]
+ let mut count = 0;
+ unsafe {
+ check(chfl_selection_evaluate(
+ self.as_mut_ptr(), frame.as_ptr(), &mut count
+ )).expect("failed to evaluate selection");
+ }
+
+ let size = count as usize;
+ let mut chfl_matches = vec![chfl_match { size: 0, atoms: [0; 4] }; size];
+ unsafe {
+ check(chfl_selection_matches(
+ self.handle,
+ chfl_matches.as_mut_ptr(),
+ count
+ )).expect("failed to extract matches");
+ }
+
+ return chfl_matches.into_iter()
+ .map(|chfl_match| Match {
+ size: chfl_match.size as usize,
+ atoms: [
+ chfl_match.atoms[0] as usize,
+ chfl_match.atoms[1] as usize,
+ chfl_match.atoms[2] as usize,
+ chfl_match.atoms[3] as usize,
+ ],
+ })
+ .collect();
+ }
+
+ /// Evaluates a selection of size 1 on a given `frame`. This function
+ /// returns the list of atomic indexes in the frame matching this selection.
+ ///
+ /// # Panics
+ ///
+ /// If the selection size is not 1
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Selection, Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+ ///
+ /// let mut selection = Selection::new("name H").unwrap();
+ /// let matches = selection.list(&frame);
+ ///
+ /// assert_eq!(matches.len(), 2);
+ /// assert_eq!(matches[0], 0);
+ /// assert_eq!(matches[1], 2);
+ /// ```
+ pub fn list(&mut self, frame: &Frame) -> Vec<usize> {
+ if self.size() != 1 {
+ panic!("can not call `Selection::list` on a multiple selection");
+ }
+ return self.evaluate(frame)
+ .into_iter()
+ .map(|m| m[0] as usize)
+ .collect();
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ use super::*;
+ use Frame;
+ use Topology;
+ use Atom;
+
+ #[test]
+ fn clone() {
+ let selection = Selection::new("name H").unwrap();
+
+ let copy = selection.clone();
+ assert_eq!(selection.size(), 1);
+ assert_eq!(copy.size(), 1);
+ }
+
+ fn testing_frame() -> Frame {
+ let mut topology = Topology::new();
+
+ topology.add_atom(&Atom::new("H"));
+ topology.add_atom(&Atom::new("O"));
+ topology.add_atom(&Atom::new("O"));
+ topology.add_atom(&Atom::new("H"));
+
+ topology.add_bond(0, 1);
+ topology.add_bond(1, 2);
+ topology.add_bond(2, 3);
+
+ let mut frame = Frame::new();
+ frame.resize(4);
+ frame.set_topology(&topology).unwrap();
+ return frame;
+ }
+
+ mod matches {
+ use super::*;
+
+ #[test]
+ fn index() {
+ let m = Match::new(&[1, 2, 3, 4]);
+ assert_eq!(m[0], 1);
+ assert_eq!(m[1], 2);
+ assert_eq!(m[2], 3);
+ assert_eq!(m[3], 4);
+
+ let m = Match::new(&[1, 2]);
+ assert_eq!(m[0], 1);
+ assert_eq!(m[1], 2);
+ }
+
+ #[test]
+ fn iter() {
+ let match_ = Match::new(&[1, 2, 3, 4]);
+ assert_eq!(match_.iter().copied().collect::<Vec<usize>>(), vec![1, 2, 3, 4]);
+
+ let v = vec![1, 2, 3, 4];
+ for (i, &m) in match_.iter().enumerate() {
+ assert_eq!(v[i], m);
+ }
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bound() {
+ let m = Match::new(&[1, 2]);
+ let _ = m[2];
+ }
+
+ #[test]
+ #[should_panic]
+ fn too_big() {
+ let _ = Match::new(&[1, 2, 3, 5, 4]);
+ }
+ }
+
+ #[test]
+ fn size() {
+ let selection = Selection::new("name H").unwrap();
+ assert_eq!(selection.size(), 1);
+
+ let selection = Selection::new("angles: name(#1) H").unwrap();
+ assert_eq!(selection.size(), 3);
+
+ let selection = Selection::new("four: name(#1) H").unwrap();
+ assert_eq!(selection.size(), 4);
+ }
+
+ #[test]
+ fn string() {
+ let selection = Selection::new("name H").unwrap();
+ assert_eq!(selection.string(), "name H");
+
+ let selection = Selection::new("angles: name(#1) H").unwrap();
+ assert_eq!(selection.string(), "angles: name(#1) H");
+ }
+
+ #[test]
+ fn evaluate() {
+ let frame = testing_frame();
+
+ let mut selection = Selection::new("name H").unwrap();
+ let res = selection.evaluate(&frame);
+ assert_eq!(res, &[Match::new(&[0]), Match::new(&[3])]);
+
+ let mut selection = Selection::new("angles: all").unwrap();
+ let res = selection.evaluate(&frame);
+ for m in &[Match::new(&[0, 1, 2]), Match::new(&[1, 2, 3])] {
+ assert!(res.iter().any(|r| r == m));
+ }
+ }
+
+ #[test]
+ fn list() {
+ let frame = testing_frame();
+
+ let mut selection = Selection::new("name H").unwrap();
+ let res = selection.list(&frame);
+ assert_eq!(res, vec![0, 3]);
+ }
+
+ #[test]
+ #[should_panic = "can not call `Selection::list` on a multiple selection"]
+ fn list_on_size_1_selection() {
+ let frame = testing_frame();
+ let mut selection = Selection::new("pairs: name(#1) H").unwrap();
+ let _list = selection.list(&frame);
+ }
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+
+//! String conversions between C and Rust
+use std::ffi::{CStr, CString};
+
+use chemfiles_sys::chfl_status;
+use errors::{check, Error};
+
+/// Create a Rust string from a C string. Clones all characters in `buffer`.
+pub fn from_c(buffer: *const i8) -> String {
+ unsafe {
+ let rust_str = CStr::from_ptr(buffer)
+ .to_str()
+ .expect("Invalid Rust string from C");
+ return String::from(rust_str);
+ }
+}
+
+/// Create a C string from a Rust string.
+pub fn to_c(string: &str) -> CString {
+ CString::new(string).expect("Invalid C string from Rust")
+}
+
+/// Check if a string buffer was big enough when passed to a C function
+fn buffer_was_big_enough(buffer: &[i8]) -> bool {
+ let len = buffer.len();
+ if len < 2 {
+ false
+ } else {
+ // The C code should always set the last element to 0
+ debug_assert_eq!(buffer[len - 1], 0);
+ buffer[len - 2] == 0
+ }
+}
+
+/// Call `callback` C function with a string buffer and it length, using
+/// `initial` as the buffer initial size. If the buffer was filled and the
+/// result truncated by the C library, grow the buffer and try again until we
+/// get all the data. Then return the filled buffer to the caller.
+pub fn call_autogrow_buffer<F>(initial: usize, callback: F) -> Result<Vec<i8>, Error>
+where
+ F: Fn(*mut i8, u64) -> chfl_status,
+{
+ let mut size = initial;
+ let mut buffer = vec![0; size];
+ check(callback(buffer.as_mut_ptr(), buffer.len() as u64))?;
+
+ while !buffer_was_big_enough(&buffer) {
+ // Grow the buffer and retry
+ size *= 2;
+ buffer.resize(size, 0);
+ check(callback(buffer.as_mut_ptr(), buffer.len() as u64))?;
+ }
+
+ Ok(buffer)
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 + 100 + 101 + 102 + 103 + 104 + 105 + 106 + 107 + 108 + 109 + 110 + 111 + 112 + 113 + 114 + 115 + 116 + 117 + 118 + 119 + 120 + 121 + 122 + 123 + 124 + 125 + 126 + 127 + 128 + 129 + 130 + 131 + 132 + 133 + 134 + 135 + 136 + 137 + 138 + 139 + 140 + 141 + 142 + 143 + 144 + 145 + 146 + 147 + 148 + 149 + 150 + 151 + 152 + 153 + 154 + 155 + 156 + 157 + 158 + 159 + 160 + 161 + 162 + 163 + 164 + 165 + 166 + 167 + 168 + 169 + 170 + 171 + 172 + 173 + 174 + 175 + 176 + 177 + 178 + 179 + 180 + 181 + 182 + 183 + 184 + 185 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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::{Drop, Deref};
+use std::marker::PhantomData;
+
+use chemfiles_sys::*;
+use errors::{check, check_not_null, check_success, Error};
+use super::{Atom, AtomRef, AtomMut};
+use super::{Residue, ResidueRef};
+
+/// Possible bond order associated with bonds
+#[repr(C)]
+#[non_exhaustive]
+#[derive(Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord)]
+pub enum BondOrder {
+ /// Unknown or unspecified bond order
+ Unknown = chfl_bond_order::CHFL_BOND_UNKNOWN as isize,
+ /// Single bond
+ Single = chfl_bond_order::CHFL_BOND_SINGLE as isize,
+ /// Double bond
+ Double = chfl_bond_order::CHFL_BOND_DOUBLE as isize,
+ /// Triple bond
+ Triple = chfl_bond_order::CHFL_BOND_TRIPLE as isize,
+ /// Quadruple bond (present in some metals)
+ Quadruple = chfl_bond_order::CHFL_BOND_QUADRUPLE as isize,
+ /// Quintuplet bond (present in some metals)
+ Quintuplet = chfl_bond_order::CHFL_BOND_QUINTUPLET as isize,
+ /// Amide bond (required by some file formats)
+ Amide = chfl_bond_order::CHFL_BOND_AMIDE as isize,
+ /// Aromatic bond (required by some file formats)
+ Aromatic = chfl_bond_order::CHFL_BOND_AROMATIC as isize,
+}
+
+impl BondOrder {
+ pub(crate) fn as_raw(self) -> chfl_bond_order {
+ match self {
+ BondOrder::Unknown => chfl_bond_order::CHFL_BOND_UNKNOWN,
+ BondOrder::Single => chfl_bond_order::CHFL_BOND_SINGLE,
+ BondOrder::Double => chfl_bond_order::CHFL_BOND_DOUBLE,
+ BondOrder::Triple => chfl_bond_order::CHFL_BOND_TRIPLE,
+ BondOrder::Quadruple => chfl_bond_order::CHFL_BOND_QUADRUPLE,
+ BondOrder::Quintuplet => chfl_bond_order::CHFL_BOND_QUINTUPLET,
+ BondOrder::Amide => chfl_bond_order::CHFL_BOND_AMIDE,
+ BondOrder::Aromatic => chfl_bond_order::CHFL_BOND_AROMATIC,
+ }
+ }
+}
+
+impl From<chfl_bond_order> for BondOrder {
+ fn from(order: chfl_bond_order) -> BondOrder {
+ match order {
+ chfl_bond_order::CHFL_BOND_UNKNOWN => BondOrder::Unknown,
+ chfl_bond_order::CHFL_BOND_SINGLE => BondOrder::Single,
+ chfl_bond_order::CHFL_BOND_DOUBLE => BondOrder::Double,
+ chfl_bond_order::CHFL_BOND_TRIPLE => BondOrder::Triple,
+ chfl_bond_order::CHFL_BOND_QUADRUPLE => BondOrder::Quadruple,
+ chfl_bond_order::CHFL_BOND_QUINTUPLET => BondOrder::Quintuplet,
+ chfl_bond_order::CHFL_BOND_AMIDE => BondOrder::Amide,
+ chfl_bond_order::CHFL_BOND_AROMATIC => BondOrder::Aromatic,
+ }
+ }
+}
+
+/// A `Topology` contains the definition of all the atoms in the system, and
+/// the liaisons between the atoms (bonds, angles, dihedrals, ...). It will
+/// also contain all the residues information if it is available.
+pub struct Topology {
+ handle: *mut CHFL_TOPOLOGY,
+}
+
+/// An analog to a reference to a topology (`&Topology`)
+pub struct TopologyRef<'a> {
+ inner: Topology,
+ marker: PhantomData<&'a Topology>
+}
+
+impl<'a> Deref for TopologyRef<'a> {
+ type Target = Topology;
+ fn deref(&self) -> &Topology {
+ &self.inner
+ }
+}
+
+impl Clone for Topology {
+ fn clone(&self) -> Topology {
+ unsafe {
+ let new_handle = chfl_topology_copy(self.as_ptr());
+ Topology::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Topology {
+ /// Create a `Topology` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer,
+ /// except for it being non-null.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_TOPOLOGY) -> Topology {
+ check_not_null(ptr);
+ Topology {
+ handle: ptr
+ }
+ }
+
+ /// Create a borrowed `Topology` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, except for it being non-null, and the caller is responsible
+ /// for setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_TOPOLOGY) -> TopologyRef<'a> {
+ TopologyRef {
+ inner: Topology::from_ptr(ptr as *mut CHFL_TOPOLOGY),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_TOPOLOGY {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_TOPOLOGY {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer FROM A SHARED REFERENCE.
+ ///
+ /// For uses with functions of the C API using mut pointers for both read
+ /// and write access. Users should check that this does not lead to multiple
+ /// mutable borrows
+ #[inline]
+ #[allow(non_snake_case)]
+ pub(crate) fn as_mut_ptr_MANUALLY_CHECKING_BORROW(&self) -> *mut CHFL_TOPOLOGY {
+ self.handle
+ }
+
+ /// Create a new empty topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let topology = Topology::new();
+ /// assert_eq!(topology.size(), 0);
+ /// ```
+ pub fn new() -> Topology {
+ unsafe {
+ Topology::from_ptr(chfl_topology())
+ }
+ }
+
+ /// Get a reference of the atom at the given `index` in this topology.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(6);
+ ///
+ /// let atom = topology.atom(4);
+ /// assert_eq!(atom.name(), "");
+ /// ```
+ pub fn atom(&self, index: usize) -> AtomRef {
+ unsafe {
+ let handle = chfl_atom_from_topology(
+ self.as_mut_ptr_MANUALLY_CHECKING_BORROW(), index as u64
+ );
+ Atom::ref_from_ptr(handle)
+ }
+ }
+
+ /// Get a mutable reference to the atom at the given `index` in this topology.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(6);
+ ///
+ /// assert_eq!(topology.atom(4).name(), "");
+ ///
+ /// topology.atom_mut(4).set_name("Fe");
+ /// assert_eq!(topology.atom(4).name(), "Fe");
+ /// ```
+ pub fn atom_mut(&mut self, index: usize) -> AtomMut {
+ unsafe {
+ let handle = chfl_atom_from_topology(
+ self.as_mut_ptr(), index as u64
+ );
+ Atom::ref_mut_from_ptr(handle)
+ }
+ }
+
+ /// Get the current number of atoms in this topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.size(), 0);
+ ///
+ /// topology.resize(6);
+ /// assert_eq!(topology.size(), 6);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(chfl_topology_atoms_count(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Resize this topology to hold `natoms` atoms, inserting dummy atoms if
+ /// the new size if bigger than the old one.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.size(), 0);
+ ///
+ /// topology.resize(6);
+ /// assert_eq!(topology.size(), 6);
+ /// ```
+ pub fn resize(&mut self, natoms: usize) {
+ unsafe {
+ check_success(chfl_topology_resize(self.as_mut_ptr(), natoms as u64));
+ }
+ }
+
+ /// Add an `Atom` at the end of this topology
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Atom};
+ /// let mut topology = Topology::new();
+ /// topology.add_atom(&Atom::new("Mg"));
+ ///
+ /// let atom = topology.atom(0);
+ /// assert_eq!(atom.name(), "Mg");
+ /// ```
+ pub fn add_atom(&mut self, atom: &Atom) {
+ unsafe {
+ check_success(chfl_topology_add_atom(self.as_mut_ptr(), atom.as_ptr()));
+ }
+ }
+
+ /// Remove an `Atom` from this topology by `index`. This modify all the
+ /// other atoms indexes.
+ ///
+ /// # Panics
+ ///
+ /// If the `index` is out of bounds
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(9);
+ /// assert_eq!(topology.size(), 9);
+ ///
+ /// topology.remove(7);
+ /// assert_eq!(topology.size(), 8);
+ /// ```
+ pub fn remove(&mut self, index: usize) {
+ unsafe {
+ check_success(chfl_topology_remove(self.as_mut_ptr(), index as u64));
+ }
+ }
+
+ /// Get the number of bonds in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.bonds_count(), 3);
+ /// ```
+ pub fn bonds_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_bonds_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the number of angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.angles_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.angles_count(), 2);
+ /// ```
+ pub fn angles_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_angles_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the number of dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.dihedrals_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.dihedrals_count(), 1);
+ /// ```
+ pub fn dihedrals_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_dihedrals_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the number of improper dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.dihedrals_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// topology.add_bond(0, 3);
+ /// assert_eq!(topology.impropers_count(), 1);
+ /// ```
+ pub fn impropers_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_impropers_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the list of bonds in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);
+ /// ```
+ pub fn bonds(&self) -> Vec<[usize; 2]> {
+ let size = self.bonds_count();
+ let count = size as u64;
+ let mut bonds = vec![[u64::max_value(); 2]; size];
+ unsafe {
+ check_success(chfl_topology_bonds(self.as_ptr(), bonds.as_mut_ptr(), count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return bonds
+ .into_iter()
+ .map(|bond| [bond[0] as usize, bond[1] as usize])
+ .collect();
+ }
+
+ /// Get the list of angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);
+ /// ```
+ pub fn angles(&self) -> Vec<[usize; 3]> {
+ let size = self.angles_count();
+ let count = size as u64;
+ let mut angles = vec![[u64::max_value(); 3]; size];
+ unsafe {
+ check_success(chfl_topology_angles(self.as_ptr(), angles.as_mut_ptr(), count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return angles
+ .into_iter()
+ .map(|angle| [angle[0] as usize, angle[1] as usize, angle[2] as usize])
+ .collect();
+ }
+
+ /// Get the list of dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ ///
+ /// assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);
+ /// ```
+ pub fn dihedrals(&self) -> Vec<[usize; 4]> {
+ let size = self.dihedrals_count();
+ let count = size as u64;
+ let mut dihedrals = vec![[u64::max_value(); 4]; size];
+ unsafe {
+ check_success(chfl_topology_dihedrals(
+ self.as_ptr(), dihedrals.as_mut_ptr(), count
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return dihedrals
+ .into_iter()
+ .map(|dihedral| {
+ [
+ dihedral[0] as usize,
+ dihedral[1] as usize,
+ dihedral[2] as usize,
+ dihedral[3] as usize,
+ ]
+ })
+ .collect();
+ }
+
+ /// Get the list of improper dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// topology.add_bond(0, 3);
+ ///
+ /// assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);
+ /// ```
+ pub fn impropers(&self) -> Vec<[usize; 4]> {
+ let size = self.impropers_count();
+ let count = size as u64;
+ let mut impropers = vec![[u64::max_value(); 4]; size];
+ unsafe {
+ check_success(chfl_topology_impropers(
+ self.as_ptr(), impropers.as_mut_ptr(), count
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return impropers
+ .into_iter()
+ .map(|improper| {
+ [
+ improper[0] as usize,
+ improper[1] as usize,
+ improper[2] as usize,
+ improper[3] as usize,
+ ]
+ })
+ .collect();
+ }
+
+ /// Remove all existing bonds, angles, dihedral angles and improper
+ /// dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// assert_eq!(topology.bonds_count(), 2);
+ /// assert_eq!(topology.angles().len(), 1);
+ ///
+ /// topology.clear_bonds();
+ /// assert!(topology.bonds().is_empty());
+ /// assert!(topology.angles().is_empty());
+ /// ```
+ pub fn clear_bonds(&mut self) {
+ unsafe {
+ check_success(chfl_topology_clear_bonds(self.as_mut_ptr()));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the topology.
+ ///
+ /// The bond order is set to `BondOrder::Unknown`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// assert_eq!(topology.bonds_count(), 2);
+ ///
+ /// assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);
+ /// ```
+ pub fn add_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(chfl_topology_add_bond(self.as_mut_ptr(), i as u64, j as u64));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the topology
+ /// with the given bond `order`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(2);
+ ///
+ /// topology.add_bond_with_order(0, 1, BondOrder::Double);
+ /// assert_eq!(topology.bond_order(0, 1), BondOrder::Double);
+ /// ```
+ pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder) {
+ unsafe {
+ check_success(chfl_topology_bond_with_order(
+ self.as_mut_ptr(), i as u64, j as u64, order.as_raw()
+ ));
+ }
+ }
+
+ /// Get the bond order for the bond between the atoms at indexes `i` and
+ /// `j`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(2);
+ ///
+ /// topology.add_bond_with_order(0, 1, BondOrder::Double);
+ /// assert_eq!(topology.bond_order(0, 1), BondOrder::Double);
+ /// ```
+ pub fn bond_order(&self, i: usize, j: usize) -> BondOrder {
+ let mut order = chfl_bond_order::CHFL_BOND_UNKNOWN;
+ unsafe {
+ check_success(chfl_topology_bond_order(
+ self.as_ptr(), i as u64, j as u64, &mut order
+ ));
+ }
+ return order.into()
+ }
+
+ /// Get the bond order for all the bonds in the topology
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(3);
+ ///
+ /// topology.add_bond_with_order(0, 1, BondOrder::Double);
+ /// topology.add_bond_with_order(0, 2, BondOrder::Single);
+ ///
+ /// assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);
+ /// ```
+ pub fn bond_orders(&self) -> Vec<BondOrder> {
+ let size = self.bonds_count();
+ let count = size as u64;
+ let mut bonds = vec![BondOrder::Unknown; size];
+ unsafe {
+ check_success(chfl_topology_bond_orders(
+ self.as_ptr(),
+ // Casting BondOrder to chfl_bond_order is safe, as they are
+ // both `repr(C)` enums with the same values.
+ bonds.as_mut_ptr().cast(),
+ count
+ ));
+ }
+ return bonds;
+ }
+
+ /// Remove any existing bond between the atoms at indexes `i` and `j` in
+ /// this topology.
+ ///
+ /// This function does nothing if there is no bond between `i` and `j`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(1, 2);
+ /// assert_eq!(topology.bonds_count(), 2);
+ ///
+ /// topology.remove_bond(0, 1);
+ /// assert_eq!(topology.bonds_count(), 1);
+ ///
+ /// // Removing a bond that does not exists is fine
+ /// topology.remove_bond(0, 2);
+ /// assert_eq!(topology.bonds_count(), 1);
+ /// ```
+ pub fn remove_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(chfl_topology_remove_bond(self.as_mut_ptr(), i as u64, j as u64));
+ }
+ }
+
+ /// Get a reference to the residue at index `index` from this topology.
+ ///
+ /// The residue index in the topology is not always the same as the residue
+ /// `id`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// topology.add_residue(&Residue::new("water")).unwrap();
+ ///
+ /// let residue = topology.residue(0).unwrap();
+ /// assert_eq!(residue.name(), "water");
+ /// ```
+ pub fn residue(&self, index: u64) -> Option<ResidueRef> {
+ unsafe {
+ let handle = chfl_residue_from_topology(self.as_ptr(), index as u64);
+ if handle.is_null() {
+ None
+ } else {
+ Some(Residue::ref_from_ptr(handle))
+ }
+ }
+ }
+
+ /// Get a copy of the residue containing the atom at index `index` in this
+ /// topology, if any.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// topology.resize(8);
+ ///
+ /// let mut residue = Residue::new("water");
+ /// residue.add_atom(0);
+ /// residue.add_atom(1);
+ /// residue.add_atom(2);
+ /// topology.add_residue(&residue).unwrap();
+ ///
+ /// let residue = topology.residue_for_atom(0).unwrap();
+ /// assert_eq!(residue.name(), "water");
+ ///
+ /// assert!(topology.residue_for_atom(6).is_none());
+ /// ```
+ pub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef> {
+ let handle = unsafe {
+ chfl_residue_for_atom(self.as_ptr(), index as u64)
+ };
+ if handle.is_null() {
+ None
+ } else {
+ unsafe {
+ Some(Residue::ref_from_ptr(handle))
+ }
+ }
+ }
+
+ /// Get the number of residues in this topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.residues_count(), 0);
+ ///
+ /// topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+ /// topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+ /// assert_eq!(topology.residues_count(), 2);
+ /// ```
+ pub fn residues_count(&self) -> u64 {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_residues_count(self.as_ptr(), &mut count));
+ }
+ return count;
+ }
+
+ /// Add a residue to this topology.
+ ///
+ /// # Errors
+ ///
+ /// This function fails is the residue `id` is not already in the topology,
+ /// or if the residue contains atoms that are already in another residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// topology.add_residue(&Residue::new("water")).unwrap();
+ ///
+ /// let residue = topology.residue(0).unwrap();
+ /// assert_eq!(residue.name(), "water");
+ /// ```
+ pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error> {
+ unsafe {
+ check(chfl_topology_add_residue(self.as_mut_ptr(), residue.as_ptr()))
+ }
+ }
+
+ /// Check if the two residues `first` and `second` from the `topology` are
+ /// linked together, *i.e.* if there is a bond between one atom in the
+ /// first residue and one atom in the second one.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ ///
+ /// topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+ /// topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+ ///
+ /// let first = topology.residue(0).unwrap();
+ /// let second = topology.residue(1).unwrap();
+ /// assert_eq!(topology.are_linked(&first, &second), false);
+ /// ```
+ pub fn are_linked(&self, first: &Residue, second: &Residue) -> bool {
+ let mut linked = 0;
+ unsafe {
+ check_success(chfl_topology_residues_linked(
+ self.as_ptr(),
+ first.as_ptr(),
+ second.as_ptr(),
+ &mut linked
+ ));
+ }
+ return linked != 0;
+ }
+}
+
+impl Drop for Topology {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+ use {Atom, Residue};
+
+ #[test]
+ fn clone() {
+ let mut topology = Topology::new();
+ assert_eq!(topology.size(), 0);
+
+ let copy = topology.clone();
+ assert_eq!(copy.size(), 0);
+
+ topology.resize(10);
+ assert_eq!(topology.size(), 10);
+ assert_eq!(copy.size(), 0);
+ }
+
+ #[test]
+ fn size() {
+ let mut topology = Topology::new();
+ assert_eq!(topology.size(), 0);
+
+ topology.resize(10);
+ assert_eq!(topology.size(), 10);
+
+ topology.remove(7);
+ assert_eq!(topology.size(), 9);
+
+ topology.add_atom(&Atom::new("Hg"));
+ assert_eq!(topology.size(), 10);
+ }
+
+ #[test]
+ fn atoms() {
+ let mut topology = Topology::new();
+
+ topology.add_atom(&Atom::new("Hg"));
+ topology.add_atom(&Atom::new("Mn"));
+ topology.add_atom(&Atom::new("W"));
+ topology.add_atom(&Atom::new("Fe"));
+
+ assert_eq!(topology.atom(0).name(), "Hg");
+ assert_eq!(topology.atom(3).name(), "Fe");
+ }
+
+ #[test]
+ fn remove() {
+ let mut topology = Topology::new();
+ topology.add_atom(&Atom::new("Hg"));
+ topology.add_atom(&Atom::new("Mn"));
+ topology.add_atom(&Atom::new("W"));
+ topology.add_atom(&Atom::new("Fe"));
+
+ assert_eq!(topology.atom(0).name(), "Hg");
+ assert_eq!(topology.atom(2).name(), "W");
+
+ topology.remove(1);
+ assert_eq!(topology.atom(0).name(), "Hg");
+ assert_eq!(topology.atom(2).name(), "Fe");
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_remove() {
+ let mut topology = Topology::new();
+ topology.resize(18);
+ topology.remove(33);
+ }
+
+
+ #[test]
+ fn bonds() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.bonds_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(9, 2);
+ topology.add_bond_with_order(3, 7, BondOrder::Aromatic);
+ assert_eq!(topology.bonds_count(), 3);
+
+ assert_eq!(topology.bonds(), vec![[0, 1], [2, 9], [3, 7]]);
+ let expected = vec![BondOrder::Unknown, BondOrder::Unknown, BondOrder::Aromatic];
+ assert_eq!(topology.bond_orders(), expected);
+
+ assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);
+ assert_eq!(topology.bond_order(3, 7), BondOrder::Aromatic);
+
+ topology.remove_bond(3, 7);
+ // Removing unexisting bond is OK if both indexes are in bounds
+ topology.remove_bond(8, 7);
+ assert_eq!(topology.bonds_count(), 2);
+
+ topology.clear_bonds();
+ assert_eq!(topology.bonds_count(), 0);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ topology.add_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_remove_bond() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ topology.remove_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds_with_order() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ topology.add_bond_with_order(300, 7, BondOrder::Unknown);
+ }
+
+ #[test]
+ fn angles() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.angles_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(1, 2);
+ topology.add_bond(3, 7);
+ topology.add_bond(3, 5);
+ assert_eq!(topology.angles_count(), 2);
+
+ assert_eq!(topology.angles(), vec![[0, 1, 2], [5, 3, 7]]);
+
+ topology.clear_bonds();
+ assert_eq!(topology.angles_count(), 0);
+ }
+
+ #[test]
+ fn dihedrals() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.dihedrals_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(1, 2);
+ topology.add_bond(3, 2);
+ topology.add_bond(4, 7);
+ topology.add_bond(4, 5);
+ topology.add_bond(7, 10);
+ assert_eq!(topology.dihedrals_count(), 2);
+
+ assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3], [5, 4, 7, 10]]);
+
+ topology.clear_bonds();
+ assert_eq!(topology.dihedrals_count(), 0);
+ }
+
+ #[test]
+ fn impropers() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.impropers_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(0, 2);
+ topology.add_bond(0, 3);
+ topology.add_bond(4, 7);
+ topology.add_bond(4, 5);
+ topology.add_bond(4, 8);
+ assert_eq!(topology.impropers_count(), 2);
+
+ assert_eq!(topology.impropers(), vec![[1, 0, 2, 3], [5, 4, 7, 8]]);
+
+ topology.clear_bonds();
+ assert_eq!(topology.impropers_count(), 0);
+ }
+
+ #[test]
+ fn residues() {
+ let mut topology = Topology::new();
+ topology.resize(4);
+ assert_eq!(topology.residues_count(), 0);
+
+ let mut residue = Residue::new("Foo");
+ residue.add_atom(0);
+ residue.add_atom(2);
+
+ topology.add_residue(&residue).unwrap();
+ assert_eq!(topology.residues_count(), 1);
+
+ assert_eq!(topology.residue(0).unwrap().name(), "Foo");
+ {
+ let residue = topology.residue_for_atom(2).unwrap();
+ assert_eq!(residue.name(), "Foo");
+ }
+
+ let mut residue = Residue::new("Bar");
+ residue.add_atom(3);
+ topology.add_residue(&residue).unwrap();
+ assert_eq!(topology.residues_count(), 2);
+
+ let first = topology.residue(0).unwrap();
+ let second = topology.residue(0).unwrap();
+ assert!(topology.are_linked(&first, &second));
+
+ // missing residue
+ assert!(topology.residue_for_atom(1).is_none());
+ // out of bounds
+ assert!(topology.residue_for_atom(67).is_none());
+ }
+}
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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::convert::TryInto;
+use std::path::Path;
+use std::ptr;
+
+use chemfiles_sys::*;
+use errors::{check, check_success, Error, Status};
+use strings;
+
+use {Frame, Topology, UnitCell};
+
+/// The `Trajectory` type is the main entry point when using chemfiles. A
+/// `Trajectory` behave a bit like a file, allowing to read and/or write
+/// `Frame`.
+pub struct Trajectory {
+ handle: *mut CHFL_TRAJECTORY,
+}
+
+impl Trajectory {
+ /// Create a `Trajectory` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_TRAJECTORY) -> Result<Trajectory, Error> {
+ if ptr.is_null() {
+ Err(Error {
+ status: Status::FileError,
+ message: Error::last_error()
+ })
+ } else {
+ Ok(Trajectory {
+ handle: ptr
+ })
+ }
+ }
+
+ /// Get the underlying C pointer as a pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_TRAJECTORY {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_TRAJECTORY {
+ self.handle
+ }
+
+ /// Open the file at the given `path` in the given `mode`.
+ ///
+ /// Valid modes are `'r'` for read, `'w'` for write and `'a'` for append.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the file is not accessible for the given mode, if
+ /// it is incorrectly formatted for the corresponding format, or in case of
+ /// I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// ```
+ pub fn open<P>(path: P, mode: char) -> Result<Trajectory, Error>
+ where
+ P: AsRef<Path>,
+ {
+ let path = path.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(path.as_ref()))?;
+
+ let path = strings::to_c(path);
+ unsafe {
+ #[allow(clippy::cast_possible_wrap)]
+ let handle = chfl_trajectory_open(path.as_ptr(), mode as i8);
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Open the file at the given `path` using a specific file `format` and the
+ /// given `mode`.
+ ///
+ /// Valid modes are `'r'` for read, `'w'` for write and `'a'` for append.
+ ///
+ /// Specifying a format is needed when the file format does not match the
+ /// extension, or when there is not standard extension for this format. If
+ /// `format` is an empty string, the format will be guessed from the
+ /// extension.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the file is not accessible for the given mode, if
+ /// it is incorrectly formatted for the corresponding format, or in case of
+ /// I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let trajectory = Trajectory::open_with_format("water.zeo", 'r', "XYZ").unwrap();
+ /// ```
+ pub fn open_with_format<'a, P, S>(filename: P, mode: char, format: S) -> Result<Trajectory, Error>
+ where
+ P: AsRef<Path>,
+ S: Into<&'a str>,
+ {
+ let filename =
+ filename.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(filename.as_ref()))?;
+
+ let filename = strings::to_c(filename);
+ let format = strings::to_c(format.into());
+ unsafe {
+ #[allow(clippy::cast_possible_wrap)]
+ let handle = chfl_trajectory_with_format(
+ filename.as_ptr(), mode as i8, format.as_ptr()
+ );
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Read a memory buffer as though it was a formatted file.
+ ///
+ /// The memory buffer used to store the file is given using the `data`
+ /// argument. The `format` parameter is required and should follow the same
+ /// rules as in the main `Trajectory` constructor.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format, or if the format do not support in-memory readers.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let aromatics = "c1ccccc1\nc1ccco1\nc1ccccn1\n";
+ /// let mut trajectory = Trajectory::memory_reader(aromatics, "SMI").unwrap();
+ /// let mut frame = Frame::new();
+ /// trajectory.read(&mut frame).unwrap();
+ /// assert_eq!(frame.size(), 6);
+ /// ```
+ pub fn memory_reader<'a, S>(data: S, format: S) -> Result<Trajectory, Error>
+ where S: Into<&'a str>,
+ {
+ let data = strings::to_c(data.into());
+ let format = strings::to_c(format.into());
+ unsafe {
+ let handle = chfl_trajectory_memory_reader(
+ data.as_ptr(), data.as_bytes().len() as u64, format.as_ptr()
+ );
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Write to a memory buffer as though it was a formatted file.
+ ///
+ /// The `format` parameter should follow the same rules as in the main
+ /// `Trajectory` constructor, except that compression specification
+ /// is not supported.
+ ///
+ /// The `memory_buffer` function can be used to retrieve the data written
+ /// to memory of the `Trajectory`.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the format do not support in-memory writers.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Trajectory;
+ /// let trajectory_memory = Trajectory::memory_writer("SMI");
+ ///
+ /// // Binary formats typically do not support this feature
+ /// assert!(Trajectory::memory_writer("XTC").is_err());
+ /// ```
+ pub fn memory_writer<'a, S>(format: S) -> Result<Trajectory, Error>
+ where S: Into<&'a str>,
+ {
+ let format = strings::to_c(format.into());
+ unsafe {
+ let handle = chfl_trajectory_memory_writer(format.as_ptr());
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Read the next step of this trajectory into a `frame`.
+ ///
+ /// If the number of atoms in frame does not correspond to the number of atom
+ /// in the next step, the frame is resized.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format, or in case of I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// let mut frame = Frame::new();
+ ///
+ /// trajectory.read(&mut frame).unwrap();
+ /// ```
+ pub fn read(&mut self, frame: &mut Frame) -> Result<(), Error> {
+ unsafe {
+ check(chfl_trajectory_read(self.as_mut_ptr(), frame.as_mut_ptr()))
+ }
+ }
+
+ /// Read a specific `step` of this trajectory into a `frame`.
+ ///
+ /// If the number of atoms in frame does not correspond to the number of
+ /// atom at this step, the frame is resized.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// let mut frame = Frame::new();
+ ///
+ /// trajectory.read_step(10, &mut frame).unwrap();
+ /// ```
+ pub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error> {
+ unsafe {
+ check(chfl_trajectory_read_step(self.as_mut_ptr(), step as u64, frame.as_mut_ptr()))
+ }
+ }
+
+ /// Write a `frame` to this trajectory.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let mut trajectory = Trajectory::open("water.pdb", 'w').unwrap();
+ /// let mut frame = Frame::new();
+ ///
+ /// trajectory.write(&mut frame).unwrap();
+ /// ```
+ pub fn write(&mut self, frame: &Frame) -> Result<(), Error> {
+ unsafe {
+ check(chfl_trajectory_write(self.as_mut_ptr(), frame.as_ptr()))
+ }
+ }
+
+ /// Set the `topology` associated with this trajectory. This topology will
+ /// be used when reading and writing the files, replacing any topology in
+ /// the frames or files.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Atom, Topology};
+ /// let mut topology = Topology::new();
+ /// topology.add_atom(&Atom::new("H"));
+ /// topology.add_atom(&Atom::new("O"));
+ /// topology.add_atom(&Atom::new("H"));
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(1, 2);
+ ///
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// trajectory.set_topology(&topology);
+ /// ```
+ pub fn set_topology(&mut self, topology: &Topology) {
+ unsafe {
+ check_success(chfl_trajectory_set_topology(self.as_mut_ptr(), topology.as_ptr()));
+ }
+ }
+
+ /// Set the topology associated with this trajectory by reading the first
+ /// frame of the file at the given `path` using the file format in `format`;
+ /// and extracting the topology of this frame.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the topology file is incorrectly formatted for
+ /// the corresponding format, or in case of I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+ /// trajectory.set_topology_file("topology.pdb").unwrap();
+ /// ```
+ pub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error>
+ where
+ P: AsRef<Path>,
+ {
+ let path = path.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(path.as_ref()))?;
+
+ let path = strings::to_c(path);
+ unsafe {
+ check(chfl_trajectory_topology_file(self.as_mut_ptr(), path.as_ptr(), ptr::null()))
+ }
+ }
+
+ /// Set the topology associated with this trajectory by reading the first
+ /// frame of the file at the given `path` using the file format in
+ /// `format`; and extracting the topology of this frame.
+ ///
+ /// If `format` is an empty string, the format will be guessed from the
+ /// `path` extension.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the topology file is incorrectly formatted for
+ /// the corresponding format, or in case of I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+ /// trajectory.set_topology_with_format("topology.mol", "PDB").unwrap();
+ /// ```
+ pub fn set_topology_with_format<'a, P, S>(&mut self, path: P, format: S) -> Result<(), Error>
+ where
+ P: AsRef<Path>,
+ S: Into<&'a str>,
+ {
+ let path = path.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(path.as_ref()))?;
+
+ let format = strings::to_c(format.into());
+ let path = strings::to_c(path);
+ unsafe {
+ check(chfl_trajectory_topology_file(self.as_mut_ptr(), path.as_ptr(), format.as_ptr()))
+ }
+ }
+
+ /// Set the unit `cell` associated with a trajectory. This cell will be
+ /// used when reading and writing the files, replacing any unit cell in the
+ /// frames or files.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, UnitCell};
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// trajectory.set_cell(&UnitCell::new([10.0, 11.0, 12.5]));
+ /// ```
+ pub fn set_cell(&mut self, cell: &UnitCell) {
+ unsafe {
+ check_success(chfl_trajectory_set_cell(self.as_mut_ptr(), cell.as_ptr()));
+ }
+ }
+
+ /// Get the number of steps (the number of frames) in a trajectory.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ ///
+ /// println!("This trajectory contains {} steps", trajectory.nsteps());
+ /// ```
+ // FIXME should this take &self instead? The file can be modified by this
+ // function, but the format should reset the state.
+ pub fn nsteps(&mut self) -> usize {
+ let mut res = 0;
+ unsafe {
+ check(chfl_trajectory_nsteps(self.as_mut_ptr(), &mut res)).expect(
+ "failed to get the number of steps in this trajectory"
+ );
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return res as usize;
+ }
+
+ /// Obtain the memory buffer written to by the trajectory.
+ ///
+ /// # Errors
+ ///
+ /// This fails if the trajectory was not opened with
+ /// `Trajectory::memory_writer`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Atom, BondOrder, Frame, Trajectory};
+ /// let mut trajectory_memory = Trajectory::memory_writer("SMI").unwrap();
+ ///
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+ /// frame.add_bond_with_order(0, 1, BondOrder::Single);
+ ///
+ /// trajectory_memory.write(&frame).unwrap();
+ ///
+ /// let result = trajectory_memory.memory_buffer();
+ /// assert_eq!(result.unwrap(), "CC\n");
+ /// ```
+ #[allow(clippy::cast_possible_truncation)]
+ pub fn memory_buffer(&self) -> Result<&str, Error> {
+ let mut ptr: *const i8 = std::ptr::null();
+ let mut count: u64 = 0;
+ let buffer = unsafe {
+ check(chfl_trajectory_memory_buffer(self.as_ptr(), &mut ptr, &mut count))?;
+ std::slice::from_raw_parts(
+ ptr.cast(), count.try_into().expect("failed to convert u64 to usize")
+ )
+ };
+
+ let string = std::str::from_utf8(buffer)?;
+ Ok(string)
+ }
+
+ /// Get file path for this trajectory.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ ///
+ /// assert_eq!(trajectory.path(), "water.xyz");
+ /// ```
+ pub fn path(&self) -> String {
+ let get_string = |ptr, len| unsafe { chfl_trajectory_path(self.as_ptr(), ptr, len) };
+ let path = strings::call_autogrow_buffer(1024, get_string).expect("failed to get path string");
+ return strings::from_c(path.as_ptr());
+ }
+}
+
+impl Drop for Trajectory {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_trajectory_close(self.as_ptr());
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ use std::fs;
+ use std::path::Path;
+ use std::io::Read;
+
+ use approx::assert_ulps_eq;
+
+ use {Atom, CellShape, Frame, Topology, UnitCell};
+
+ #[test]
+ fn read() {
+ let root = Path::new(file!()).parent().unwrap().join("..");
+ let filename = root.join("data").join("water.xyz");
+ let mut file = Trajectory::open(filename.to_str().unwrap(), 'r').unwrap();
+
+ if cfg!(target_family = "unix") {
+ assert_eq!(file.path(), "src/../data/water.xyz");
+ } else if cfg!(target_family = "windows") {
+ assert_eq!(file.path(), "src\\..\\data\\water.xyz");
+ } else {
+ panic!("please add test for this OS!");
+ }
+
+ assert_eq!(file.nsteps(), 100);
+
+ let mut frame = Frame::new();
+ assert!(file.read(&mut frame).is_ok());
+
+ assert_eq!(frame.size(), 297);
+ assert_ulps_eq!(frame.positions()[0][0], 0.417219);
+ assert_ulps_eq!(frame.positions()[0][1], 8.303366);
+ assert_ulps_eq!(frame.positions()[0][2], 11.737172);
+ assert_ulps_eq!(frame.positions()[124][0], 5.099554);
+ assert_ulps_eq!(frame.positions()[124][1], -0.045104);
+ assert_ulps_eq!(frame.positions()[124][2], 14.153846);
+
+ assert_eq!(frame.atom(0).name(), "O");
+
+ file.set_cell(&UnitCell::new([30.0, 30.0, 30.0]));
+ assert!(file.read_step(41, &mut frame).is_ok());
+ let cell = frame.cell().clone();
+ assert_eq!(cell.lengths(), [30.0, 30.0, 30.0]);
+
+
+ assert_ulps_eq!(frame.positions()[0][0], 0.761277);
+ assert_ulps_eq!(frame.positions()[0][1], 8.106125);
+ assert_ulps_eq!(frame.positions()[0][2], 10.622949);
+ assert_ulps_eq!(frame.positions()[124][0], 5.13242);
+ assert_ulps_eq!(frame.positions()[124][1], 0.079862);
+ assert_ulps_eq!(frame.positions()[124][2], 14.194161);
+
+ {
+ let topology = frame.topology();
+ assert_eq!(topology.size(), 297);
+ assert_eq!(topology.bonds_count(), 0);
+ }
+
+ assert!(frame.guess_bonds().is_ok());
+ {
+ let topology = frame.topology();
+ assert_eq!(topology.size(), 297);
+ assert_eq!(topology.bonds_count(), 180);
+ assert_eq!(topology.angles_count(), 84);
+ }
+
+ let mut topology = Topology::new();
+ let atom = Atom::new("Cs");
+ for _ in 0..297 {
+ topology.add_atom(&atom);
+ }
+
+ file.set_topology(&topology);
+ assert!(file.read_step(10, &mut frame).is_ok());
+ assert_eq!(frame.atom(42).name(), "Cs");
+
+ let filename = root.join("data").join("topology.xyz");
+ assert!(file.set_topology_file(filename.to_str().unwrap()).is_ok());
+ assert!(file.read(&mut frame).is_ok());
+ assert_eq!(frame.atom(100).name(), "Rd");
+
+ let filename = root.join("data").join("helium.xyz.but.not.really");
+ let filename = filename.to_str().unwrap();
+ let mut file = Trajectory::open_with_format(filename, 'r', "XYZ").unwrap();
+ assert!(file.read(&mut frame).is_ok());
+ assert_eq!(frame.size(), 125);
+ }
+
+ fn write_file(path: &str) {
+ let mut file = Trajectory::open(path, 'w').unwrap();
+ let mut frame = Frame::new();
+ frame.resize(4);
+
+ for position in frame.positions_mut() {
+ *position = [1.0, 2.0, 3.0];
+ }
+
+ let mut topology = Topology::new();
+ let atom = Atom::new("X");
+ for _ in 0..4 {
+ topology.add_atom(&atom);
+ }
+ frame.set_topology(&topology).unwrap();
+ assert!(file.write(&frame).is_ok());
+ }
+
+ #[test]
+ fn write() {
+ let filename = "test-tmp.xyz";
+ write_file(filename);
+
+ let expected_content = "4
+Properties=species:S:1:pos:R:3
+X 1 2 3
+X 1 2 3
+X 1 2 3
+X 1 2 3".lines().collect::<Vec<_>>();
+
+ let mut file = fs::File::open(filename).unwrap();
+ let mut content = String::new();
+ let _ = file.read_to_string(&mut content).unwrap();
+
+ assert_eq!(expected_content, content.lines().collect::<Vec<_>>());
+ fs::remove_file(filename).unwrap();
+ }
+
+ #[test]
+ fn memory() {
+ // formats in decreasing order of their memory buffer length to check null termination
+ for format in &["CSSR", "GRO", "XYZ"] {
+ let mut frame_write = Frame::new();
+ frame_write.add_atom(&Atom::new("H"), [1.5, 3.0, -10.0], None);
+ frame_write.add_atom(&Atom::new("O"), [2.3, -1.4, 50.0], None);
+ frame_write.add_atom(&Atom::new("H"), [-1.5, 10.0, 0.0], None);
+ let cell = UnitCell::new([10.0, 11.0, 12.5]);
+
+ let mut trajectory_write = Trajectory::memory_writer(*format).unwrap();
+ trajectory_write.set_cell(&cell);
+ trajectory_write.write(&frame_write).unwrap();
+
+ let buffer = trajectory_write.memory_buffer().unwrap();
+ let mut trajectory_read = Trajectory::memory_reader(buffer, *format).unwrap();
+ let mut frame_read = Frame::new();
+ trajectory_read.read(&mut frame_read).unwrap();
+
+ assert_eq!(trajectory_read.nsteps(), 1);
+ assert_eq!(frame_read.cell().shape(), CellShape::Orthorhombic);
+ assert_eq!(frame_read.size(), 3);
+ assert_eq!(frame_read.atom(1).name(), "O");
+ crate::assert_vector3d_eq(&frame_read.positions()[2], &[-1.5, 10.0, 0.0], 1e-4);
+ }
+ }
+}
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All Rights Reserved. Source is a trademark of Adobe Systems Incorporated in the United States and/or other countries. + +This Font Software is licensed under the SIL Open Font License, Version 1.1. + +This license is copied below, and is also available with a FAQ at: http://scripts.sil.org/OFL + + +----------------------------------------------------------- +SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007 +----------------------------------------------------------- + +PREAMBLE +The goals of the Open Font License (OFL) are to stimulate worldwide +development of collaborative font projects, to support the font creation +efforts of academic and linguistic communities, and to provide a free and +open framework in which fonts may be shared and improved in partnership +with others. + +The OFL allows the licensed fonts to be used, studied, modified and +redistributed freely as long as they are not sold by themselves. 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It will be resized by the library …","Create a new selection from the given selection string.","Create a new match containing the atoms in the atoms slice.","","Get the number of steps (the number of frames) in a …","Open the file at the given path in the given mode.","Open the file at the given path using a specific file …","Get the out of plane distance formed by the atoms at …","","","Get file path for this trajectory.","Get a view into the positions of this frame.","Does this format support storing atomic positions?","Get a mutable view into the positions of this frame.","Get an iterator over all (name, property) pairs for this …","Get an iterator over all (name, property) pairs for this …","Get an iterator over all (name, property) pairs for this …","Read the next step of this trajectory into a frame.","Is reading files in this format implemented?","Read a specific step of this trajectory into a frame.","URL pointing to the format definition/reference.","Remove an Atom from this topology by index. This modify …","Remove the atom at index i in this frame.","Remove any existing bond between the atoms at indexes i …","Remove any existing bond between the atoms at indexes i …","Get a reference to the residue at index index from this …","Get a copy of the residue containing the atom at index …","Does this format support storing residues?","Get the number of residues in this topology.","Resize this topology to hold natoms atoms, inserting dummy …","Resize the positions and the velocities in this frame, to …","Add a new property with the given name to this atom.","Add a new property with the given name to this residue.","Add a new property with the given name to this frame.","Set the three angles of the cell, in degrees.","Set the atom type to atomic_type.","Set the UnitCell of this frame to cell.","Set the unit cell associated with a trajectory. This cell …","Set the atom charge to charge, in number of the electron …","Set the three lengths of the cell, in Angstroms.","Set the atom mass to mass, in atomic mass units.","Set the atom name to name.","Set the shape of the unit cell to shape.","Set this frame step to step.","Set the Topology of this frame to topology.","Set the topology associated with this trajectory. This …","Set the topology associated with this trajectory by …","Set the topology associated with this trajectory by …","Use callback for every chemfiles warning. The callback …","Get the shape of the unit cell.","Get the number of atoms in this residue.","Get the current number of atoms in this topology.","Get the current number of atoms in this frame.","Get the size of the selection, i.e. the number of atoms we …","","The error status code","Get this frame step, i.e. the frame number in the …","Get the selection string used to create this selection.","","","","","","","","","","","","","","","Get a reference to the Topology of this frame.","Create an Triclinic UnitCell from the three lengths (in …","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","Does this format support storing unit cell information?","Try to get the Van der Waals radius of the atom from the …","Get a view into the velocities of this frame.","Does this format support storing atomic velocities?","Get a mutable view into the velocities of this frame.","Get the version of the chemfiles library.","Get the volume of the unit cell.","Create a new residue with the given name and id as …","Wrap a vector in this unit cell.","Write a frame to this trajectory.","Is writing files in this format 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+}');
+if (window.initSearch) {window.initSearch(searchIndex)};
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diff --git a/0.10.2/search.js b/0.10.2/search.js
new file mode 100644
index 000000000..91de2a155
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"+""+makeTabHeader(0,"In Names",ret_others[1])+makeTabHeader(1,"In Parameters",ret_in_args[1])+makeTabHeader(2,"In Return Types",ret_returned[1])+"
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1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371 +372 +373 +374 +375 +376 +377 +378 +379 +380 +381 +382 +383 +384 +385 +386 +387 +388 +389 +390 +391 +392 +393 +394 +395 +396 +397 +398 +399 +400 +401 +402 +403 +404 +405 +406 +407 +408 +409 +410 +411 +412 +413 +414 +415 +416 +417 +418 +419 +420 +421 +422 +423 +424 +425 +426 +427 +428 +429 +430 +431 +432 +433 +434 +435 +436 +437 +438 +439 +440 +441 +442 +443 +444 +445 +446 +447 +448 +449 +450 +451 +452 +453 +454 +455 +456 +457 +458 +459 +460 +461 +462 +463 +464 +465 +466 +467 +468 +469 +470 +471 +472 +473 +474 +475 +476 +477 +478 +479 +480 +481 +482 +483 +484 +485 +486 +487 +488 +489 +490 +491 +492 +493 +494 +495 +496 +497 +498 +499 +500 +501 +502 +503 +504 +505 +506 +507 +508 +509 +510 +511 +512 +513 +514 +515 +516 +517 +518 +519 +520 +521 +522 +523 +524 +525 +526 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::{Drop, Deref, DerefMut};
+use std::marker::PhantomData;
+use std::ptr;
+
+use chemfiles_sys::*;
+use errors::{check_success, check_not_null};
+use strings;
+
+use property::{Property, RawProperty, PropertiesIter};
+
+/// An `Atom` is a particle in the current `Frame`. It stores the following
+/// atomic properties:
+///
+/// - atom name;
+/// - atom type;
+/// - atom mass;
+/// - atom charge.
+///
+/// The atom name is usually an unique identifier (`H1`, `C_a`) while the
+/// atom type will be shared between all particles of the same type: `H`,
+/// `Ow`, `CH3`.
+pub struct Atom {
+ handle: *mut CHFL_ATOM,
+}
+
+/// An analog to a reference to an atom (`&Atom`)
+pub struct AtomRef<'a> {
+ inner: Atom,
+ marker: PhantomData<&'a Atom>
+}
+
+impl<'a> Deref for AtomRef<'a> {
+ type Target = Atom;
+ fn deref(&self) -> &Atom {
+ &self.inner
+ }
+}
+
+/// An analog to a mutable reference to an atom (`&mut Atom`)
+pub struct AtomMut<'a> {
+ inner: Atom,
+ marker: PhantomData<&'a mut Atom>
+}
+
+impl<'a> Deref for AtomMut<'a> {
+ type Target = Atom;
+ fn deref(&self) -> &Atom {
+ &self.inner
+ }
+}
+
+impl<'a> DerefMut for AtomMut<'a> {
+ fn deref_mut(&mut self) -> &mut Atom {
+ &mut self.inner
+ }
+}
+
+impl Clone for Atom {
+ fn clone(&self) -> Atom {
+ unsafe {
+ let new_handle = chfl_atom_copy(self.as_ptr());
+ Atom::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Atom {
+ /// Create an owned `Atom` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_ATOM) -> Atom {
+ check_not_null(ptr);
+ Atom {
+ handle: ptr
+ }
+ }
+
+ /// Create a borrowed `Atom` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, and the caller is responsible for setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_ATOM) -> AtomRef<'a> {
+ AtomRef {
+ inner: Atom::from_ptr(ptr as *mut CHFL_ATOM),
+ marker: PhantomData,
+ }
+ }
+
+ /// Create a mutably borrowed `Atom` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, and the caller is responsible for setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_mut_from_ptr<'a>(ptr: *mut CHFL_ATOM) -> AtomMut<'a> {
+ AtomMut {
+ inner: Atom::from_ptr(ptr),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_ATOM {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_ATOM {
+ self.handle
+ }
+
+ /// Create an atom with the given `name`, and set the atom type to `name`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.name(), "He");
+ /// ```
+ pub fn new<'a>(name: impl Into<&'a str>) -> Atom {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ let handle = chfl_atom(buffer.as_ptr());
+ Atom::from_ptr(handle)
+ }
+ }
+
+ /// Get the atom mass, in atomic mass units.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.mass(), 4.002602);
+ /// ```
+ pub fn mass(&self) -> f64 {
+ let mut mass = 0.0;
+ unsafe {
+ check_success(chfl_atom_mass(self.as_ptr(), &mut mass));
+ }
+ return mass;
+ }
+
+ /// Set the atom mass to `mass`, in atomic mass units.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_mass(34.9);
+ /// assert_eq!(atom.mass(), 34.9);
+ /// ```
+ pub fn set_mass(&mut self, mass: f64) {
+ unsafe {
+ check_success(chfl_atom_set_mass(self.as_mut_ptr(), mass));
+ }
+ }
+
+ /// Get the atom charge, in number of the electron charge *e*.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.charge(), 0.0);
+ /// ```
+ pub fn charge(&self) -> f64 {
+ let mut charge = 0.0;
+ unsafe {
+ check_success(chfl_atom_charge(self.as_ptr(), &mut charge));
+ }
+ return charge;
+ }
+
+ /// Set the atom charge to `charge`, in number of the electron charge *e*.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_charge(-2.0);
+ /// assert_eq!(atom.charge(), -2.0);
+ /// ```
+ pub fn set_charge(&mut self, charge: f64) {
+ unsafe {
+ check_success(chfl_atom_set_charge(self.as_mut_ptr(), charge));
+ }
+ }
+
+ /// Get the atom name.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.name(), "He");
+ /// ```
+ pub fn name(&self) -> String {
+ let get_name = |ptr, len| unsafe { chfl_atom_name(self.as_ptr(), ptr, len) };
+ let name = strings::call_autogrow_buffer(10, get_name).expect("getting name failed");
+ return strings::from_c(name.as_ptr());
+ }
+
+ /// Get the atom type.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.atomic_type(), "He");
+ /// ```
+ pub fn atomic_type(&self) -> String {
+ let get_type = |ptr, len| unsafe { chfl_atom_type(self.as_ptr(), ptr, len) };
+ let buffer = strings::call_autogrow_buffer(10, get_type).expect("getting type failed");
+ return strings::from_c(buffer.as_ptr());
+ }
+
+ /// Set the atom name to `name`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_name("Zn3");
+ /// assert_eq!(atom.name(), "Zn3");
+ /// ```
+ pub fn set_name<'a>(&mut self, name: impl Into<&'a str>) {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ check_success(chfl_atom_set_name(self.as_mut_ptr(), buffer.as_ptr()));
+ }
+ }
+
+ /// Set the atom type to `atomic_type`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_atomic_type("F");
+ /// assert_eq!(atom.atomic_type(), "F");
+ /// ```
+ pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>) {
+ let buffer = strings::to_c(atomic_type.into());
+ unsafe {
+ check_success(chfl_atom_set_type(self.as_mut_ptr(), buffer.as_ptr()));
+ }
+ }
+
+ /// Try to get the full name of the atom from the atomic type. For example,
+ /// the full name of "He" is "Helium", and so on. If the name can not be
+ /// found, this function returns the empty string.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("Zn");
+ /// assert_eq!(atom.full_name(), "Zinc");
+ /// ```
+ pub fn full_name(&self) -> String {
+ let get_full_name = |ptr, len| unsafe { chfl_atom_full_name(self.as_ptr(), ptr, len) };
+ let name = strings::call_autogrow_buffer(10, get_full_name).expect("getting full name failed");
+ return strings::from_c(name.as_ptr());
+ }
+
+ /// Try to get the Van der Waals radius of the atom from the atomic type.
+ /// If the radius can not be found, returns 0.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+ /// assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);
+ /// ```
+ pub fn vdw_radius(&self) -> f64 {
+ let mut radius: f64 = 0.0;
+ unsafe {
+ check_success(chfl_atom_vdw_radius(self.as_ptr(), &mut radius));
+ }
+ return radius;
+ }
+
+ /// Try to get the covalent radius of the atom from the atomic type. If the
+ /// radius can not be found, returns 0.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+ /// assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);
+ /// ```
+ pub fn covalent_radius(&self) -> f64 {
+ let mut radius: f64 = 0.0;
+ unsafe {
+ check_success(chfl_atom_covalent_radius(self.as_ptr(), &mut radius));
+ }
+ return radius;
+ }
+
+ /// Try to get the atomic number of the atom from the atomic type. If the
+ /// number can not be found, returns 0.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// assert_eq!(Atom::new("He").atomic_number(), 2);
+ /// assert_eq!(Atom::new("Xxx").atomic_number(), 0);
+ /// ```
+ pub fn atomic_number(&self) -> u64 {
+ let mut number = 0;
+ unsafe {
+ check_success(chfl_atom_atomic_number(self.as_ptr(), &mut number));
+ }
+ return number;
+ }
+
+ /// Add a new `property` with the given `name` to this atom.
+ ///
+ /// If a property with the same name already exists, this function override
+ /// the existing property with the new one.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Atom, Property};
+ /// let mut atom = Atom::new("He");
+ /// atom.set("a bool", true);
+ /// atom.set("a string", "test");
+ ///
+ /// assert_eq!(atom.get("a bool"), Some(Property::Bool(true)));
+ /// assert_eq!(atom.get("a string"), Some(Property::String("test".into())));
+ /// ```
+ pub fn set(&mut self, name: &str, property: impl Into<Property>) {
+ let buffer = strings::to_c(name);
+ let property = property.into().as_raw();
+ unsafe {
+ check_success(chfl_atom_set_property(
+ self.as_mut_ptr(), buffer.as_ptr(), property.as_ptr()
+ ));
+ }
+ }
+
+
+ /// Get a property with the given `name` in this atom, if it exist.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Atom, Property};
+ /// let mut atom = Atom::new("He");
+ /// atom.set("foo", Property::Double(22.2));
+ ///
+ /// assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+ /// assert_eq!(atom.get("Bar"), None);
+ /// ```
+ pub fn get(&self, name: &str) -> Option<Property> {
+ let buffer = strings::to_c(name);
+ unsafe {
+ let handle = chfl_atom_get_property(self.as_ptr(), buffer.as_ptr());
+ if handle.is_null() {
+ None
+ } else {
+ let raw = RawProperty::from_ptr(handle);
+ let property = Property::from_raw(raw);
+ Some(property)
+ }
+ }
+ }
+
+ /// Get an iterator over all (name, property) pairs for this atom
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Atom, Property};
+ /// let mut atom = Atom::new("He");
+ /// atom.set("foo", Property::Double(22.2));
+ /// atom.set("bar", Property::Bool(false));
+ ///
+ /// for (name, property) in atom.properties() {
+ /// if name == "foo" {
+ /// assert_eq!(property, Property::Double(22.2));
+ /// } else if name == "bar" {
+ /// assert_eq!(property, Property::Bool(false));
+ /// }
+ /// }
+ /// ```
+ pub fn properties(&self) -> PropertiesIter {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_atom_properties_count(self.as_ptr(), &mut count));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = count as usize;
+ let mut c_names = vec![ptr::null_mut(); size];
+ unsafe {
+ check_success(chfl_atom_list_properties(self.as_ptr(), c_names.as_mut_ptr(), count));
+ }
+
+ let mut names = Vec::new();
+ for ptr in c_names {
+ names.push(strings::from_c(ptr));
+ }
+
+ PropertiesIter {
+ names: names.into_iter(),
+ getter: Box::new(move |name| self.get(&*name).expect("failed to get property"))
+ }
+ }
+}
+
+impl Drop for Atom {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.name(), "He");
+
+ let copy = atom.clone();
+ assert_eq!(copy.name(), "He");
+
+ atom.set_name("Na");
+ assert_eq!(atom.name(), "Na");
+ assert_eq!(copy.name(), "He");
+ }
+
+ #[test]
+ fn mass() {
+ let mut atom = Atom::new("He");
+ assert_ulps_eq!(atom.mass(), 4.002602);
+ atom.set_mass(15.0);
+ assert_eq!(atom.mass(), 15.0);
+ }
+
+ #[test]
+ fn charge() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.charge(), 0.0);
+ atom.set_charge(-1.5);
+ assert_eq!(atom.charge(), -1.5);
+ }
+
+ #[test]
+ fn name() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.name(), "He");
+ atom.set_name("Zn-12");
+ assert_eq!(atom.name(), "Zn-12");
+ }
+
+ #[test]
+ fn atomic_type() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.atomic_type(), "He");
+ atom.set_atomic_type("Zn");
+ assert_eq!(atom.atomic_type(), "Zn");
+ }
+
+ #[test]
+ fn full_name() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.full_name(), "Helium");
+
+ atom.set_atomic_type("Zn");
+ assert_eq!(atom.full_name(), "Zinc");
+
+ let atom = Atom::new("Unknown");
+ assert_eq!(atom.full_name(), "");
+ }
+
+ #[test]
+ fn radii() {
+ let atom = Atom::new("He");
+ assert_ulps_eq!(atom.vdw_radius(), 1.4);
+ assert_ulps_eq!(atom.covalent_radius(), 0.32);
+
+ let atom = Atom::new("Unknown");
+ assert_eq!(atom.vdw_radius(), 0.0);
+ assert_eq!(atom.covalent_radius(), 0.0);
+ }
+
+ #[test]
+ fn atomic_number() {
+ let atom = Atom::new("He");
+ assert_eq!(atom.atomic_number(), 2);
+
+ let atom = Atom::new("Unknown");
+ assert_eq!(atom.atomic_number(), 0);
+ }
+
+ #[test]
+ fn property() {
+ let mut atom = Atom::new("F");
+
+ atom.set("foo", -22.0);
+ assert_eq!(atom.get("foo"), Some(Property::Double(-22.0)));
+ assert_eq!(atom.get("bar"), None);
+
+ atom.set("bar", Property::String("here".into()));
+ for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(-22.0));
+ } else if name == "bar" {
+ assert_eq!(property, Property::String("here".into()));
+ }
+ }
+ }
+}
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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::{Drop, Deref, DerefMut};
+use std::marker::PhantomData;
+use std::ptr;
+
+use chemfiles_sys::*;
+use errors::{check_success, check_not_null, check, Error};
+
+/// Available unit cell shapes.
+#[derive(Clone, Debug, PartialEq, Eq)]
+pub enum CellShape {
+ /// Orthorhombic cell, with the three angles equals to 90°.
+ Orthorhombic,
+ /// Triclinic cell, with any values for the angles.
+ Triclinic,
+ /// Infinite cell, to use when there is no cell.
+ Infinite,
+}
+
+impl From<chfl_cellshape> for CellShape {
+ fn from(celltype: chfl_cellshape) -> CellShape {
+ match celltype {
+ chfl_cellshape::CHFL_CELL_ORTHORHOMBIC => CellShape::Orthorhombic,
+ chfl_cellshape::CHFL_CELL_TRICLINIC => CellShape::Triclinic,
+ chfl_cellshape::CHFL_CELL_INFINITE => CellShape::Infinite,
+ }
+ }
+}
+
+impl From<CellShape> for chfl_cellshape {
+ fn from(celltype: CellShape) -> chfl_cellshape {
+ match celltype {
+ CellShape::Orthorhombic => chfl_cellshape::CHFL_CELL_ORTHORHOMBIC,
+ CellShape::Triclinic => chfl_cellshape::CHFL_CELL_TRICLINIC,
+ CellShape::Infinite => chfl_cellshape::CHFL_CELL_INFINITE,
+ }
+ }
+}
+
+/// An `UnitCell` represent the box containing the atoms, and its periodicity.
+///
+/// An unit cell is fully represented by three lengths (a, b, c); and three
+/// angles (alpha, beta, gamma). The angles are stored in degrees, and the
+/// lengths in Angstroms.
+///
+/// A cell also has a matricial representation, by projecting the three base
+/// vector into an orthonormal base. We choose to represent such matrix as an
+/// upper triangular matrix:
+///
+/// ```text
+/// | a_x b_x c_x |
+/// | 0 b_y c_y |
+/// | 0 0 c_z |
+/// ```
+pub struct UnitCell {
+ handle: *mut CHFL_CELL,
+}
+
+/// An analog to a reference to an unit cell (`&UnitCell`)
+pub struct UnitCellRef<'a> {
+ inner: UnitCell,
+ marker: PhantomData<&'a UnitCell>
+}
+
+impl<'a> Deref for UnitCellRef<'a> {
+ type Target = UnitCell;
+ fn deref(&self) -> &UnitCell {
+ &self.inner
+ }
+}
+
+/// An analog to a mutable reference to an unit cell (`&mut UnitCell`)
+pub struct UnitCellMut<'a> {
+ inner: UnitCell,
+ marker: PhantomData<&'a mut UnitCell>
+}
+
+impl<'a> Deref for UnitCellMut<'a> {
+ type Target = UnitCell;
+ fn deref(&self) -> &UnitCell {
+ &self.inner
+ }
+}
+
+impl<'a> DerefMut for UnitCellMut<'a> {
+ fn deref_mut(&mut self) -> &mut UnitCell {
+ &mut self.inner
+ }
+}
+
+impl Clone for UnitCell {
+ fn clone(&self) -> UnitCell {
+ unsafe {
+ let new_handle = chfl_cell_copy(self.as_ptr());
+ UnitCell::from_ptr(new_handle)
+ }
+ }
+}
+
+impl UnitCell {
+ /// Create an owned `UnitCell` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_CELL) -> UnitCell {
+ check_not_null(ptr);
+ UnitCell {
+ handle: ptr
+ }
+ }
+
+ /// Create a borrowed `UnitCell` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, and the caller is responsible for setting the right lifetime.
+ #[inline]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_CELL) -> UnitCellRef<'a> {
+ UnitCellRef {
+ inner: UnitCell::from_ptr(ptr as *mut CHFL_CELL),
+ marker: PhantomData,
+ }
+ }
+
+ /// Create a borrowed `UnitCell` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, except for it being non-null, and the caller is responsible for
+ /// setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_mut_from_ptr<'a>(ptr: *mut CHFL_CELL) -> UnitCellMut<'a> {
+ UnitCellMut {
+ inner: UnitCell::from_ptr(ptr),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_CELL {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_CELL {
+ self.handle
+ }
+
+ /// Create an `Orthorhombic` `UnitCell` from the three lengths, in Angstroms.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::new([30.0, 30.0, 23.0]);
+ ///
+ /// assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// ```
+ pub fn new(lengths: [f64; 3]) -> UnitCell {
+ unsafe {
+ let handle = chfl_cell(lengths.as_ptr(), ptr::null());
+ UnitCell::from_ptr(handle)
+ }
+ }
+
+ /// Create an `Infinite` `UnitCell`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::infinite();
+ ///
+ /// assert_eq!(cell.lengths(), [0.0, 0.0, 0.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// assert_eq!(cell.shape(), CellShape::Infinite);
+ /// ```
+ pub fn infinite() -> UnitCell {
+ let mut cell = UnitCell::new([0.0, 0.0, 0.0]);
+ cell.set_shape(CellShape::Infinite).expect("could not set cell shape");
+ return cell;
+ }
+
+ /// Create an `Triclinic` `UnitCell` from the three lengths (in Angstroms)
+ /// and three angles (in degree). `alpha` is the angle between the vectors
+ /// `b` and `c`; `beta` is the between the vectors `a` and `c` and `gamma`
+ /// is the angle between the vectors `a` and `b`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::triclinic([10.0, 10.0, 10.0], [98.0, 99.0, 90.0]);
+ ///
+ /// assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);
+ /// assert_eq!(cell.angles()[0], 98.0);
+ /// // Rounding errors might occur due to internal representation
+ /// assert!((cell.angles()[1] - 99.0).abs() < 1e-12);
+ /// assert_eq!(cell.angles()[2], 90.0);
+ /// assert_eq!(cell.shape(), CellShape::Triclinic);
+ /// ```
+ pub fn triclinic(lengths: [f64; 3], angles: [f64; 3]) -> UnitCell {
+ unsafe {
+ let handle = chfl_cell(lengths.as_ptr(), angles.as_ptr());
+ UnitCell::from_ptr(handle)
+ }
+ }
+
+ /// Create an `UnitCell` from a cell matrix. If `matrix` contains only
+ /// zeros, then an `Infinite` cell is created. If only the diagonal of the
+ /// matrix is non-zero, then the cell is `Orthorhombic`. Else a
+ /// `Triclinic` cell is created. The matrix entries should be in Angstroms.
+ ///
+ /// # Panics
+ ///
+ /// If the matrix has a negative determinant, or more generally is not
+ /// representing a unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::from_matrix([
+ /// [1.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]
+ /// ]);
+ ///
+ /// assert_eq!(cell.lengths(), [1.0, 2.0, 3.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// ```
+ pub fn from_matrix(mut matrix: [[f64; 3]; 3]) -> UnitCell {
+ unsafe {
+ let handle = chfl_cell_from_matrix(matrix.as_mut_ptr());
+ UnitCell::from_ptr(handle)
+ }
+ }
+
+ /// Get the three lengths of the cell, in Angstroms.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([30.0, 30.0, 23.0]);
+ /// assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
+ /// ```
+ pub fn lengths(&self) -> [f64; 3] {
+ let mut lengths = [0.0; 3];
+ unsafe {
+ check_success(chfl_cell_lengths(self.as_ptr(), lengths.as_mut_ptr()));
+ }
+ return lengths;
+ }
+
+ /// Set the three lengths of the cell, in Angstroms.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the unit cell is infinite, or if one of the
+ /// lengths is negative.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let mut cell = UnitCell::new([30.0, 30.0, 23.0]);
+ ///
+ /// cell.set_lengths([10.0, 30.0, 42.0]).unwrap();
+ /// assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]);
+ ///
+ /// assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());
+ /// ```
+ pub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error> {
+ unsafe {
+ check(chfl_cell_set_lengths(self.as_mut_ptr(), lengths.as_ptr()))
+ }
+ }
+
+ /// Get the three angles of the cell, in degrees.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([20.0, 20.0, 20.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ ///
+ /// let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+ /// assert_eq!(cell.angles()[0], 100.0);
+ /// // Rounding errors might occur due to internal representation
+ /// assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+ /// assert_eq!(cell.angles()[2], 90.0);
+ /// ```
+ pub fn angles(&self) -> [f64; 3] {
+ let mut angles = [0.0; 3];
+ unsafe {
+ check_success(chfl_cell_angles(self.as_ptr(), angles.as_mut_ptr()));
+ }
+ return angles;
+ }
+
+ /// Set the three angles of the cell, in degrees.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the unit cell is not `Triclinic`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+ /// assert_eq!(cell.angles()[0], 100.0);
+ /// // Rounding errors might occur due to internal representation
+ /// assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+ /// assert_eq!(cell.angles()[2], 90.0);
+ ///
+ /// cell.set_angles([90.0, 90.0, 90.0]).unwrap();
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// ```
+ pub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error> {
+ unsafe {
+ check(chfl_cell_set_angles(self.as_mut_ptr(), angles.as_ptr()))
+ }
+ }
+
+ /// Get the unit cell matricial representation.
+ ///
+ /// The unit cell representation is obtained by aligning the a vector along
+ /// the *x* axis and putting the b vector in the *xy* plane. This make the
+ /// matrix an upper triangular matrix:
+ ///
+ /// ```text
+ /// | a_x b_x c_x |
+ /// | 0 b_y c_y |
+ /// | 0 0 c_z |
+ /// ```
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ ///
+ /// let matrix = cell.matrix();
+ ///
+ /// assert_eq!(matrix[0][0], 10.0);
+ /// assert_eq!(matrix[1][1], 20.0);
+ /// assert_eq!(matrix[2][2], 30.0);
+ ///
+ /// assert!(matrix[1][2].abs() < 1e-9);
+ /// ```
+ pub fn matrix(&self) -> [[f64; 3]; 3] {
+ let mut matrix = [[0.0; 3]; 3];
+ unsafe {
+ check_success(chfl_cell_matrix(self.as_ptr(), matrix.as_mut_ptr()));
+ }
+ return matrix;
+ }
+
+ /// Get the shape of the unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// ```
+ pub fn shape(&self) -> CellShape {
+ let mut shape = chfl_cellshape::CHFL_CELL_INFINITE;
+ unsafe {
+ check_success(chfl_cell_shape(self.as_ptr(), &mut shape));
+ }
+ return CellShape::from(shape);
+ }
+
+ /// Set the shape of the unit cell to `shape`.
+ ///
+ /// # Errors
+ ///
+ /// This can fail if the cell length or angles are incompatible with the
+ /// new shape.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let mut cell = UnitCell::new([10.0, 20.0, 30.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ ///
+ /// cell.set_shape(CellShape::Triclinic).unwrap();
+ /// assert_eq!(cell.shape(), CellShape::Triclinic);
+ /// ```
+ pub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error> {
+ unsafe {
+ check(chfl_cell_set_shape(self.as_mut_ptr(), shape.into()))
+ }
+ }
+
+ /// Get the volume of the unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ /// assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0);
+ /// ```
+ pub fn volume(&self) -> f64 {
+ let mut volume = 0.0;
+ unsafe {
+ check_success(chfl_cell_volume(self.as_ptr(), &mut volume));
+ }
+ return volume;
+ }
+
+ /// Wrap a `vector` in this unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ ///
+ /// let mut vector = [12.0, 5.2, -45.3];
+ /// cell.wrap(&mut vector);
+ /// assert_eq!(vector, [2.0, 5.2, 14.700000000000003]);
+ /// ```
+ pub fn wrap(&self, vector: &mut [f64; 3]) {
+ unsafe {
+ check_success(chfl_cell_wrap(self.as_ptr(), vector.as_mut_ptr()));
+ }
+ }
+}
+
+impl Drop for UnitCell {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.lengths(), [2.0, 3.0, 4.0]);
+
+ let copy = cell.clone();
+ assert_eq!(copy.lengths(), [2.0, 3.0, 4.0]);
+
+ cell.set_lengths([10.0, 12.0, 11.0]).unwrap();
+ assert_eq!(cell.lengths(), [10.0, 12.0, 11.0]);
+ assert_eq!(copy.lengths(), [2.0, 3.0, 4.0]);
+ }
+
+ #[test]
+ fn lengths() {
+ let mut cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.lengths(), [2.0, 3.0, 4.0]);
+ cell.set_lengths([10.0, 12.0, 11.0]).unwrap();
+ assert_eq!(cell.lengths(), [10.0, 12.0, 11.0]);
+ }
+
+ #[test]
+ fn angles() {
+ let mut cell = UnitCell::new([2.0, 3.0, 4.0]);
+ crate::assert_vector3d_eq(&cell.angles(), &[90.0, 90.0, 90.0], 1e-6);
+
+ cell.set_shape(CellShape::Triclinic).unwrap();
+ cell.set_angles([80.0, 89.0, 100.0]).unwrap();
+
+ crate::assert_vector3d_eq(&cell.angles(), &[80.0, 89.0, 100.0], 1e-6);
+
+ let cell = UnitCell::triclinic([1., 2., 3.], [80., 90., 100.]);
+ crate::assert_vector3d_eq(&cell.angles(), &[80.0, 90.0, 100.0], 1e-6);
+ }
+
+ #[test]
+ fn volume() {
+ let cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.volume(), 2.0 * 3.0 * 4.0);
+ }
+
+ #[test]
+ fn wrap() {
+ let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ let mut vector = [12.0, 5.2, -45.3];
+ cell.wrap(&mut vector);
+ crate::assert_vector3d_eq(&vector, &[2.0, 5.2, 14.7], 1e-6);
+ }
+
+ #[test]
+ fn matrix() {
+ let cell = UnitCell::new([2.0, 3.0, 4.0]);
+
+ let matrix = cell.matrix();
+ let result = [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]];
+
+ for i in 0..3 {
+ for j in 0..3 {
+ assert_ulps_eq!(matrix[i][j], result[i][j], epsilon = 1e-12);
+ }
+ }
+ }
+
+ #[test]
+ fn from_matrix() {
+ let cell = UnitCell::from_matrix([[10.0, 0.0, 0.0], [0.0, 21.0, 0.0], [0.0, 0.0, 32.0]]);
+ assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ assert_eq!(cell.lengths(), [10.0, 21.0, 32.0]);
+
+ let result_matrix = [
+ [123.0, 4.08386, 71.7295],
+ [0.0, 233.964, 133.571],
+ [0.0, 0.0, 309.901],
+ ];
+ let cell = UnitCell::from_matrix(result_matrix);
+
+ assert_eq!(cell.shape(), CellShape::Triclinic);
+ for i in 0..3 {
+ assert_ulps_eq!(
+ cell.lengths()[i],
+ [123.0, 234.0, 345.0][i],
+ epsilon = 1e-3
+ );
+ assert_ulps_eq!(cell.angles()[i], [67.0, 78.0, 89.0][i], epsilon = 1e-3);
+ }
+
+ let matrix = cell.matrix();
+ for i in 0..3 {
+ for j in 0..3 {
+ assert_ulps_eq!(matrix[i][j], result_matrix[i][j], epsilon = 1e-12);
+ }
+ }
+ }
+
+ #[test]
+ fn shape() {
+ let cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.shape(), CellShape::Orthorhombic);
+
+ let cell = UnitCell::infinite();
+ assert_eq!(cell.shape(), CellShape::Infinite);
+
+ let cell = UnitCell::triclinic([1.0, 2.0, 3.0], [80.0, 90.0, 100.0]);
+ assert_eq!(cell.shape(), CellShape::Triclinic);
+
+ let mut cell = UnitCell::new([10.0, 10.0, 10.0]);
+ assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ cell.set_shape(CellShape::Triclinic).unwrap();
+ assert_eq!(cell.shape(), CellShape::Triclinic);
+ }
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+extern crate libc;
+
+use std::error;
+use std::fmt;
+use std::panic::{self, RefUnwindSafe};
+use std::path::Path;
+
+use self::libc::c_char;
+
+use chemfiles_sys::*;
+use strings;
+
+#[derive(Clone, Debug, PartialEq)]
+/// Error type for Chemfiles.
+pub struct Error {
+ /// The error status code
+ pub status: Status,
+ /// A message describing the error cause
+ pub message: String,
+}
+
+#[repr(C)]
+#[non_exhaustive]
+#[derive(Clone, Debug, PartialEq)]
+/// Possible causes of error in chemfiles
+pub enum Status {
+ /// No error
+ Success = chfl_status::CHFL_SUCCESS as isize,
+ /// Error in memory allocations
+ MemoryError = chfl_status::CHFL_MEMORY_ERROR as isize,
+ /// Error while reading or writing a file
+ FileError = chfl_status::CHFL_FILE_ERROR as isize,
+ /// Error in file formatting, *i.e.* the file is invalid
+ FormatError = chfl_status::CHFL_FORMAT_ERROR as isize,
+ /// Error in selection string syntax
+ SelectionError = chfl_status::CHFL_SELECTION_ERROR as isize,
+ /// Error in configuration files syntax
+ ConfigurationError = chfl_status::CHFL_CONFIGURATION_ERROR as isize,
+ /// Error for out of bounds indexing
+ OutOfBounds = chfl_status::CHFL_OUT_OF_BOUNDS as isize,
+ /// Error related to properties
+ PropertyError = chfl_status::CHFL_PROPERTY_ERROR as isize,
+ /// Exception in the C++ chemfiles library
+ ChemfilesError = chfl_status::CHFL_GENERIC_ERROR as isize,
+ /// Exception in the C++ standard library
+ StdCppError = chfl_status::CHFL_CXX_ERROR as isize,
+ /// The given path is not valid UTF8
+ // TODO: rename this to UTF8Error in the next breaking release
+ UTF8PathError,
+}
+
+impl From<chfl_status> for Error {
+ fn from(status: chfl_status) -> Error {
+ let status = match status {
+ chfl_status::CHFL_SUCCESS => Status::Success,
+ chfl_status::CHFL_CXX_ERROR => Status::StdCppError,
+ chfl_status::CHFL_GENERIC_ERROR => Status::ChemfilesError,
+ chfl_status::CHFL_MEMORY_ERROR => Status::MemoryError,
+ chfl_status::CHFL_FILE_ERROR => Status::FileError,
+ chfl_status::CHFL_FORMAT_ERROR => Status::FormatError,
+ chfl_status::CHFL_SELECTION_ERROR => Status::SelectionError,
+ chfl_status::CHFL_CONFIGURATION_ERROR => Status::ConfigurationError,
+ chfl_status::CHFL_OUT_OF_BOUNDS => Status::OutOfBounds,
+ chfl_status::CHFL_PROPERTY_ERROR => Status::PropertyError,
+ };
+
+ let message = Error::last_error();
+ Error {
+ status,
+ message,
+ }
+ }
+}
+
+impl From<std::str::Utf8Error> for Error {
+ fn from(_: std::str::Utf8Error) -> Self {
+ Error {
+ status: Status::UTF8PathError,
+ message: "failed to convert data to UTF8 string".into(),
+ }
+ }
+}
+
+impl Error {
+ /// Create a new error because the given `path` is invalid UTF-8 data
+ pub(crate) fn utf8_path_error(path: &Path) -> Error {
+ Error {
+ status: Status::UTF8PathError,
+ message: format!("Could not convert '{}' to UTF8", path.display()),
+ }
+ }
+
+ /// Get the last error message from the C++ library.
+ pub fn last_error() -> String {
+ unsafe { strings::from_c(chfl_last_error()) }
+ }
+
+ /// Clear any error from the C++ library
+ pub fn cleanup() {
+ unsafe {
+ check(chfl_clear_errors()).expect("error in chfl_clear_errors. Things went very bad");
+ }
+ }
+}
+
+/// Check return value of a C function, and get the error if needed.
+pub(crate) fn check(status: chfl_status) -> Result<(), Error> {
+ if status == chfl_status::CHFL_SUCCESS {
+ Ok(())
+ } else {
+ Err(Error::from(status))
+ }
+}
+
+/// Check return value of a C function, panic if it failed.
+pub(crate) fn check_success(status: chfl_status) {
+ if status != chfl_status::CHFL_SUCCESS {
+ panic!("unexpected failure: {}", Error::last_error());
+ }
+}
+
+/// Check a pointer for null.
+pub(crate) fn check_not_null<T>(ptr: *const T) {
+ if ptr.is_null() {
+ panic!("unexpected null pointer: {}", Error::last_error());
+ }
+}
+
+pub trait WarningCallback: RefUnwindSafe + Fn(&str) {}
+impl<T> WarningCallback for T
+where
+ T: RefUnwindSafe + Fn(&str),
+{
+}
+
+static mut LOGGING_CALLBACK: Option<*mut dyn WarningCallback<Output = ()>> = None;
+
+extern "C" fn warning_callback(message: *const c_char) {
+ unsafe {
+ let callback = &*LOGGING_CALLBACK.expect("No callback provided, this is an internal bug");
+ // ignore result. If a panic happened, everything is going badly anyway
+ let _result = panic::catch_unwind(|| {
+ callback(&strings::from_c(message));
+ });
+ }
+}
+
+/// Use `callback` for every chemfiles warning. The callback will be passed
+/// the warning message. This will drop any previous warning callback.
+pub fn set_warning_callback<F>(callback: F) where F: WarningCallback + 'static {
+ // box callback to ensure it stays accessible
+ let callback = Box::into_raw(Box::new(callback));
+ unsafe {
+ if let Some(previous) = LOGGING_CALLBACK {
+ // drop the previous callback
+ let previous = Box::from_raw(previous);
+ std::mem::drop(previous);
+ // set the LOGGING_CALLBACK to the new one
+ LOGGING_CALLBACK = Some(callback);
+ } else {
+ // set the LOGGING_CALLBACK
+ LOGGING_CALLBACK = Some(callback);
+ // Tell C code to use Rust-provided callback
+ check_success(chfl_set_warning_callback(warning_callback));
+ }
+ }
+}
+
+
+impl fmt::Display for Error {
+ fn fmt(&self, fmt: &mut fmt::Formatter) -> Result<(), fmt::Error> {
+ write!(fmt, "{}", self.message)
+ }
+}
+
+impl error::Error for Error {
+ fn description(&self) -> &str {
+ match self.status {
+ Status::Success => "Success",
+ Status::StdCppError => "Exception from the C++ standard library",
+ Status::ChemfilesError => "Exception from the chemfiles library",
+ Status::MemoryError => "Error in memory allocations",
+ Status::FileError => "Error while reading or writing a file",
+ Status::FormatError => "Error in file formatting, i.e. the file is invalid",
+ Status::SelectionError => "Error in selection string syntax",
+ Status::UTF8PathError => "A string is not valid UTF8",
+ Status::ConfigurationError => "Error in configuration files",
+ Status::OutOfBounds => "Out of bounds indexing",
+ Status::PropertyError => "Error in property",
+ }
+ }
+}
+
+
+#[cfg(test)]
+mod test {
+ use super::*;
+ use Trajectory;
+
+ #[test]
+ fn errors() {
+ Error::cleanup();
+ assert_eq!(Error::last_error(), "");
+ assert!(Trajectory::open("nope", 'r').is_err());
+ assert_eq!(
+ Error::last_error(),
+ "file at \'nope\' does not have an extension, provide a format name to read it"
+ );
+ Error::cleanup();
+ assert_eq!(Error::last_error(), "");
+ }
+
+ #[test]
+ fn codes() {
+ assert_eq!(Error::from(chfl_status::CHFL_SUCCESS).status, Status::Success);
+ assert_eq!(Error::from(chfl_status::CHFL_CXX_ERROR).status, Status::StdCppError);
+ assert_eq!(Error::from(chfl_status::CHFL_GENERIC_ERROR).status, Status::ChemfilesError);
+ assert_eq!(Error::from(chfl_status::CHFL_MEMORY_ERROR).status, Status::MemoryError);
+ assert_eq!(Error::from(chfl_status::CHFL_FILE_ERROR).status, Status::FileError);
+ assert_eq!(Error::from(chfl_status::CHFL_FORMAT_ERROR).status, Status::FormatError);
+ assert_eq!(Error::from(chfl_status::CHFL_SELECTION_ERROR).status, Status::SelectionError);
+ assert_eq!(Error::from(chfl_status::CHFL_OUT_OF_BOUNDS).status, Status::OutOfBounds);
+ assert_eq!(Error::from(chfl_status::CHFL_PROPERTY_ERROR).status, Status::PropertyError);
+ }
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 + 100 + 101 + 102 + 103 + 104 + 105 + 106 + 107 + 108 + 109 + 110 + 111 + 112 + 113 + 114 + 115 + 116 + 117 + 118 + 119 + 120 + 121 + 122 + 123 + 124 + 125 + 126 + 127 + 128 + 129 + 130 + 131 + 132 + 133 + 134 + 135 + 136 + 137 + 138 + 139 + 140 + 141 + 142 + 143 + 144 + 145 + 146 + 147 + 148 + 149 + 150 + 151 + 152 + 153 + 154 + 155 + 156 + 157 + 158 + 159 + 160 + 161 + 162 + 163 + 164 + 165 + 166 + 167 + 168 + 169 + 170 + 171 + 172 + 173 + 174 + 175 + 176 + 177 + 178 + 179 + 180 + 181 + 182 + 183 + 184 + 185 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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::Drop;
+use std::ptr;
+use std::slice;
+
+use chemfiles_sys::*;
+use strings;
+use errors::{check_not_null, check_success, check, Error};
+use super::{Atom, AtomRef, AtomMut};
+use super::{Topology, TopologyRef, Residue, BondOrder};
+use super::{UnitCell, UnitCellRef, UnitCellMut};
+use property::{Property, RawProperty, PropertiesIter};
+
+/// A `Frame` contains data from one simulation step: the current unit
+/// cell, the topology, the positions, and the velocities of the particles in
+/// the system. If some information is missing (topology or velocity or unit
+/// cell), the corresponding data is filled with a default value.
+pub struct Frame {
+ handle: *mut CHFL_FRAME,
+}
+
+impl Clone for Frame {
+ fn clone(&self) -> Frame {
+ unsafe {
+ let new_handle = chfl_frame_copy(self.as_ptr());
+ Frame::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Frame {
+ /// Create a `Frame` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer,
+ /// except for it being non-null.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_FRAME) -> Frame {
+ check_not_null(ptr);
+ Frame {
+ handle: ptr
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_FRAME {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_FRAME {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer FROM A SHARED REFERENCE.
+ ///
+ /// For uses with functions of the C API using mut pointers for both read
+ /// and write access. Users should check that this does not lead to multiple
+ /// mutable borrows
+ #[inline]
+ #[allow(non_snake_case)]
+ pub(crate) fn as_mut_ptr_MANUALLY_CHECKING_BORROW(&self) -> *mut CHFL_FRAME {
+ self.handle
+ }
+
+ /// Create an empty frame. It will be resized by the library as needed.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let frame = Frame::new();
+ ///
+ /// assert_eq!(frame.size(), 0);
+ /// ```
+ pub fn new() -> Frame {
+ unsafe {
+ Frame::from_ptr(chfl_frame())
+ }
+ }
+
+ /// Get a reference to the atom at the given `index` in this frame.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+ ///
+ /// let atom = frame.atom(0);
+ /// assert_eq!(atom.name(), "Zn");
+ /// ```
+ pub fn atom(&self, index: usize) -> AtomRef {
+ unsafe {
+ let handle = chfl_atom_from_frame(
+ self.as_mut_ptr_MANUALLY_CHECKING_BORROW(),
+ index as u64
+ );
+ Atom::ref_from_ptr(handle)
+ }
+ }
+
+ /// Get a mutable reference to the atom at the given `index` in this frame.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+ ///
+ /// assert_eq!(frame.atom(0).name(), "Zn");
+ ///
+ /// frame.atom_mut(0).set_name("Fe");
+ /// assert_eq!(frame.atom(0).name(), "Fe");
+ /// ```
+ pub fn atom_mut(&mut self, index: usize) -> AtomMut {
+ unsafe {
+ let handle = chfl_atom_from_frame(self.as_mut_ptr(), index as u64);
+ Atom::ref_mut_from_ptr(handle)
+ }
+ }
+
+ /// Get the current number of atoms in this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.size(), 0);
+ ///
+ /// frame.resize(67);
+ /// assert_eq!(frame.size(), 67);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(chfl_frame_atoms_count(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Resize the positions and the velocities in this frame, to make space for
+ /// `natoms` atoms. Previous data is conserved, as well as the presence of
+ /// absence of velocities.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// assert_eq!(frame.size(), 67);
+ /// ```
+ pub fn resize(&mut self, natoms: usize) {
+ unsafe {
+ check_success(chfl_frame_resize(self.as_mut_ptr(), natoms as u64));
+ }
+ }
+
+ /// Add an `Atom` and the corresponding position and optionally velocity
+ /// data to this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [1.0, 1.0, 2.0], None);
+ ///
+ /// frame.add_velocities();
+ /// frame.add_atom(&Atom::new("Zn"), [-1.0, 1.0, 2.0], [0.2, 0.1, 0.0]);
+ /// ```
+ pub fn add_atom(
+ &mut self,
+ atom: &Atom,
+ position: [f64; 3],
+ velocity: impl Into<Option<[f64; 3]>>,
+ )
+ {
+ let velocity = velocity.into();
+ let velocity_ptr = match velocity {
+ Some(ref data) => data.as_ptr(),
+ None => ptr::null(),
+ };
+
+ unsafe {
+ check_success(chfl_frame_add_atom(
+ self.as_mut_ptr(),
+ atom.as_ptr(),
+ position.as_ptr(),
+ velocity_ptr
+ ));
+ }
+
+ }
+
+ /// Remove the atom at index `i` in this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+ /// frame.add_atom(&Atom::new("Fe"), [0.0; 3], None);
+ /// frame.add_atom(&Atom::new("Sn"), [0.0; 3], None);
+ /// assert_eq!(frame.size(), 3);
+ ///
+ /// frame.remove(1);
+ /// assert_eq!(frame.size(), 2);
+ /// assert_eq!(frame.atom(1).name(), "Sn");
+ /// ```
+ pub fn remove(&mut self, i: usize) {
+ unsafe {
+ check_success(chfl_frame_remove(self.as_mut_ptr(), i as u64));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the frame.
+ ///
+ /// The bond order is set to `BondOrder::Unknown`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, BondOrder};
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.topology().bonds_count(), 0);
+ /// frame.resize(5);
+ ///
+ /// frame.add_bond(0, 1);
+ /// frame.add_bond(3, 1);
+ /// frame.add_bond(2, 4);
+ /// assert_eq!(frame.topology().bonds_count(), 3);
+ ///
+ /// assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown);
+ /// assert_eq!(frame.topology().bonds(), vec![[0, 1], [1, 3], [2, 4]]);
+ /// ```
+ pub fn add_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(chfl_frame_add_bond(self.as_mut_ptr(), i as u64, j as u64));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the frame
+ /// with the given bond `order`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, BondOrder};
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.topology().bonds_count(), 0);
+ /// frame.resize(2);
+ ///
+ /// frame.add_bond_with_order(0, 1, BondOrder::Double);
+ /// assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Double);
+ /// ```
+ pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder) {
+ unsafe {
+ check_success(chfl_frame_bond_with_order(
+ self.as_mut_ptr(),
+ i as u64,
+ j as u64,
+ order.as_raw(),
+ ));
+ }
+ }
+
+ /// Remove any existing bond between the atoms at indexes `i` and `j` in
+ /// the frame.
+ ///
+ /// This function does nothing if there is no bond between `i` and `j`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(5);
+ ///
+ /// frame.add_bond(0, 1);
+ /// frame.add_bond(3, 1);
+ /// frame.add_bond(2, 4);
+ ///
+ /// let bonds = frame.topology().bonds();
+ /// assert_eq!(bonds, vec![[0, 1], [1, 3], [2, 4]]);
+ ///
+ /// frame.remove_bond(2, 4);
+ /// let bonds = frame.topology().bonds();
+ /// assert_eq!(bonds, vec![[0, 1], [1, 3]]);
+ /// ```
+ pub fn remove_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(chfl_frame_remove_bond(
+ self.as_mut_ptr(),
+ i as u64,
+ j as u64,
+ ));
+ }
+ }
+
+ /// Add a copy of `residue` to this frame.
+ ///
+ /// # Errors
+ ///
+ /// This function fails is the residue id is already in this frame's
+ /// topology, or if the residue contain atoms that are already in another
+ /// residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Residue};
+ /// let mut frame = Frame::new();
+ ///
+ /// let residue = Residue::new("foo");
+ /// frame.add_residue(&residue).unwrap();
+ ///
+ /// let topology = frame.topology();
+ /// assert_eq!(topology.residues_count(), 1);
+ /// assert_eq!(topology.residue(0).unwrap().name(), "foo");
+ /// ```
+ pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error> {
+ unsafe {
+ check(chfl_frame_add_residue(self.as_mut_ptr(), residue.as_ptr()))
+ }
+ }
+
+ /// Get the distance between the atoms at indexes `i` and `j` in this frame,
+ /// accounting for periodic boundary conditions. The result is expressed in
+ /// Angstroms.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [1.0, 2.0, 3.0], None);
+ ///
+ /// assert_eq!(frame.distance(0, 1), f64::sqrt(14.0));
+ /// ```
+ pub fn distance(&self, i: usize, j: usize) -> f64 {
+ let mut distance = 0.0;
+ unsafe {
+ check_success(chfl_frame_distance(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ &mut distance,
+ ));
+ }
+ return distance;
+ }
+
+ /// Get the angle formed by the atoms at indexes `i`, `j` and `k` in this
+ /// frame, accounting for periodic boundary conditions. The result is
+ /// expressed in radians.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// # use std::f64;
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+ ///
+ /// assert_eq!(frame.angle(0, 1, 2), f64::consts::PI / 2.0);
+ /// ```
+ pub fn angle(&self, i: usize, j: usize, k: usize) -> f64 {
+ let mut angle = 0.0;
+ unsafe {
+ check_success(chfl_frame_angle(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ k as u64,
+ &mut angle,
+ ));
+ }
+ return angle;
+ }
+
+ /// Get the dihedral angle formed by the atoms at indexes `i`, `j`, `k` and
+ /// `m` in this frame, accounting for periodic boundary conditions. The
+ /// result is expressed in radians.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// # use std::f64;
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("D"), [0.0, 1.0, 1.0], None);
+ ///
+ /// assert_eq!(frame.dihedral(0, 1, 2, 3), f64::consts::PI / 2.0);
+ /// ```
+ pub fn dihedral(&self, i: usize, j: usize, k: usize, m: usize) -> f64 {
+ let mut dihedral = 0.0;
+ unsafe {
+ check_success(chfl_frame_dihedral(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ k as u64,
+ m as u64,
+ &mut dihedral,
+ ));
+ }
+ return dihedral;
+ }
+
+ /// Get the out of plane distance formed by the atoms at indexes `i`, `j`,
+ /// `k` and `m` in this frame, accounting for periodic boundary conditions.
+ /// The result is expressed in angstroms.
+ ///
+ /// This is the distance between the atom j and the ikm plane. The j atom
+ /// is the center of the improper dihedral angle formed by i, j, k and m.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 2.0], None);
+ /// frame.add_atom(&Atom::new("C"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("D"), [0.0, 1.0, 0.0], None);
+ ///
+ /// assert_eq!(frame.out_of_plane(0, 1, 2, 3), 2.0);
+ /// ```
+ pub fn out_of_plane(&self, i: usize, j: usize, k: usize, m: usize) -> f64 {
+ let mut distance = 0.0;
+ unsafe {
+ check_success(chfl_frame_out_of_plane(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ k as u64,
+ m as u64,
+ &mut distance,
+ ));
+ }
+ return distance;
+ }
+
+ /// Get a view into the positions of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ ///
+ /// let positions = frame.positions();
+ /// assert_eq!(positions.len(), 67);
+ /// assert_eq!(positions[0], [0.0, 0.0, 0.0]);
+ /// ```
+ pub fn positions(&self) -> &[[f64; 3]] {
+ let mut ptr = ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(chfl_frame_positions(
+ self.as_mut_ptr_MANUALLY_CHECKING_BORROW(),
+ &mut ptr,
+ &mut natoms
+ ));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return slice::from_raw_parts(ptr, size);
+ }
+ }
+
+ /// Get a mutable view into the positions of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// {
+ /// let positions = frame.positions_mut();
+ /// assert_eq!(positions[0], [0.0, 0.0, 0.0]);
+ /// positions[0] = [1.0, 2.0, 3.0];
+ /// }
+ ///
+ /// let positions = frame.positions();
+ /// assert_eq!(positions[0], [1.0, 2.0, 3.0]);
+ /// ```
+ pub fn positions_mut(&mut self) -> &mut [[f64; 3]] {
+ let mut ptr = ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(chfl_frame_positions(self.as_mut_ptr(), &mut ptr, &mut natoms));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return slice::from_raw_parts_mut(ptr, size);
+ }
+ }
+
+ /// Get a view into the velocities of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// frame.add_velocities();
+ ///
+ /// let velocities = frame.velocities();
+ /// assert_eq!(velocities.len(), 67);
+ /// assert_eq!(velocities[0], [0.0, 0.0, 0.0]);
+ /// ```
+ pub fn velocities(&self) -> &[[f64; 3]] {
+ let mut ptr = ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(chfl_frame_velocities(
+ self.as_mut_ptr_MANUALLY_CHECKING_BORROW(),
+ &mut ptr,
+ &mut natoms
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return slice::from_raw_parts(ptr, size);
+ }
+ }
+
+ /// Get a mutable view into the velocities of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// frame.add_velocities();
+ /// {
+ /// let velocities = frame.velocities_mut();
+ /// assert_eq!(velocities[0], [0.0, 0.0, 0.0]);
+ /// velocities[0] = [1.0, 2.0, 3.0];
+ /// }
+ ///
+ /// let velocities = frame.velocities();
+ /// assert_eq!(velocities[0], [1.0, 2.0, 3.0]);
+ /// ```
+ pub fn velocities_mut(&mut self) -> &mut [[f64; 3]] {
+ let mut ptr = ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(chfl_frame_velocities(self.as_mut_ptr(), &mut ptr, &mut natoms));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return slice::from_raw_parts_mut(ptr, size);
+ }
+ }
+
+ /// Check if this frame contains velocity data.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.has_velocities(), false);
+ ///
+ /// frame.add_velocities();
+ /// assert_eq!(frame.has_velocities(), true);
+ /// ```
+ pub fn has_velocities(&self) -> bool {
+ let mut res = 0;
+ unsafe {
+ check_success(chfl_frame_has_velocities(self.as_ptr(), &mut res));
+ }
+ return res != 0;
+ }
+
+ /// Add velocity data to this frame. If the frame already have velocities,
+ /// this does nothing.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.has_velocities(), false);
+ ///
+ /// frame.add_velocities();
+ /// assert_eq!(frame.has_velocities(), true);
+ /// ```
+ pub fn add_velocities(&mut self) {
+ unsafe {
+ check_success(chfl_frame_add_velocities(self.as_mut_ptr()));
+ }
+ }
+
+ /// Get a reference to the `UnitCell` from this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, CellShape};
+ /// let frame = Frame::new();
+ ///
+ /// let cell = frame.cell();
+ /// assert_eq!(cell.shape(), CellShape::Infinite);
+ /// ```
+ pub fn cell(&self) -> UnitCellRef {
+ unsafe {
+ let handle = chfl_cell_from_frame(self.as_mut_ptr_MANUALLY_CHECKING_BORROW());
+ UnitCell::ref_from_ptr(handle)
+ }
+ }
+
+ /// Get a mutable reference to the `UnitCell` from this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, CellShape};
+ /// let mut frame = Frame::new();
+ ///
+ /// assert_eq!(frame.cell().shape(), CellShape::Infinite);
+ ///
+ /// frame.cell_mut().set_shape(CellShape::Triclinic).unwrap();
+ /// assert_eq!(frame.cell().shape(), CellShape::Triclinic);
+ /// ```
+ pub fn cell_mut(&mut self) -> UnitCellMut {
+ unsafe {
+ let handle = chfl_cell_from_frame(self.as_mut_ptr());
+ UnitCell::ref_mut_from_ptr(handle)
+ }
+ }
+
+ /// Set the `UnitCell` of this frame to `cell`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, UnitCell, CellShape};
+ /// let mut frame = Frame::new();
+ ///
+ /// frame.set_cell(&UnitCell::new([10.0, 10.0, 10.0]));
+ ///
+ /// let cell = frame.cell();
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);
+ /// ```
+ pub fn set_cell(&mut self, cell: &UnitCell) {
+ unsafe {
+ check_success(chfl_frame_set_cell(self.as_mut_ptr(), cell.as_ptr()));
+ }
+ }
+
+ /// Get a reference to the `Topology` of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(42);
+ ///
+ /// let topology = frame.topology();
+ /// assert_eq!(topology.size(), 42);
+ /// ```
+ pub fn topology(&self) -> TopologyRef {
+ unsafe {
+ let handle = chfl_topology_from_frame(self.as_ptr());
+ Topology::ref_from_ptr(handle)
+ }
+ }
+
+ /// Set the `Topology` of this frame to `topology`.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the topology contains a different number of atoms
+ /// than this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Topology, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.resize(2);
+ ///
+ /// let mut topology = Topology::new();
+ /// topology.add_atom(&Atom::new("Cl"));
+ /// topology.add_atom(&Atom::new("Cl"));
+ /// topology.add_bond(0, 1);
+ ///
+ /// frame.set_topology(&topology).unwrap();
+ /// assert_eq!(frame.atom(0).name(), "Cl");
+ /// ```
+ pub fn set_topology(&mut self, topology: &Topology) -> Result<(), Error> {
+ unsafe {
+ check(chfl_frame_set_topology(self.as_mut_ptr(), topology.as_ptr()))
+ }
+ }
+
+ /// Get this frame step, i.e. the frame number in the trajectory
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let frame = Frame::new();
+ /// assert_eq!(frame.step(), 0);
+ /// ```
+ pub fn step(&self) -> usize {
+ let mut step = 0;
+ unsafe {
+ check_success(chfl_frame_step(self.as_ptr(), &mut step));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return step as usize;
+ }
+
+ /// Set this frame step to `step`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.step(), 0);
+ ///
+ /// frame.set_step(10);
+ /// assert_eq!(frame.step(), 10);
+ /// ```
+ pub fn set_step(&mut self, step: usize) {
+ unsafe {
+ check_success(chfl_frame_set_step(self.as_mut_ptr(), step as u64));
+ }
+ }
+
+ /// Guess the bonds, angles and dihedrals in this `frame`.
+ ///
+ /// The bonds are guessed using a distance-based algorithm, and then angles
+ /// and dihedrals are guessed from the bonds.
+ ///
+ /// # Errors
+ ////
+ /// This function can fail if the covalent radius is unknown for some atoms
+ /// in the frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ ///
+ /// frame.add_atom(&Atom::new("Cl"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("Cl"), [1.5, 0.0, 0.0], None);
+ /// assert_eq!(frame.topology().bonds_count(), 0);
+ ///
+ /// frame.guess_bonds().unwrap();
+ /// assert_eq!(frame.topology().bonds_count(), 1);
+ /// ```
+ pub fn guess_bonds(&mut self) -> Result<(), Error> {
+ unsafe {
+ check(chfl_frame_guess_bonds(self.as_mut_ptr()))
+ }
+ }
+
+ /// Remove all existing bonds, angles, dihedral angles and improper
+ /// dihedral angles in the topology of the frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Atom, Frame};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [0.0, 1.0, 0.0], None);
+ ///
+ /// frame.add_bond(0, 1);
+ /// frame.add_bond(1, 2);
+ ///
+ /// assert_eq!(frame.topology().bonds().len(), 2);
+ /// assert_eq!(frame.topology().angles().len(), 1);
+ ///
+ /// frame.clear_bonds();
+ /// assert!(frame.topology().bonds().is_empty());
+ /// assert!(frame.topology().angles().is_empty());
+ /// ```
+ pub fn clear_bonds(&mut self) {
+ unsafe {
+ check_success(chfl_frame_clear_bonds(self.as_mut_ptr()));
+ }
+ }
+
+ /// Add a new `property` with the given `name` to this frame.
+ ///
+ /// If a property with the same name already exists, this function override
+ /// the existing property with the new one.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Frame, Property};
+ /// let mut frame = Frame::new();
+ /// frame.set("a string", "hello");
+ /// frame.set("a double", 4.3);
+ ///
+ /// assert_eq!(frame.get("a string"), Some(Property::String("hello".into())));
+ /// assert_eq!(frame.get("a double"), Some(Property::Double(4.3)));
+ /// ```
+ pub fn set(&mut self, name: &str, property: impl Into<Property>) {
+ let buffer = strings::to_c(name);
+ let property = property.into().as_raw();
+ unsafe {
+ check_success(chfl_frame_set_property(
+ self.as_mut_ptr(), buffer.as_ptr(), property.as_ptr()
+ ));
+ }
+ }
+
+ /// Get a property with the given `name` in this frame, if it exist.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Frame, Property};
+ /// let mut frame = Frame::new();
+ /// frame.set("foo", Property::Double(22.2));
+ ///
+ /// assert_eq!(frame.get("foo"), Some(Property::Double(22.2)));
+ /// assert_eq!(frame.get("Bar"), None);
+ /// ```
+ pub fn get(&self, name: &str) -> Option<Property> {
+ let buffer = strings::to_c(name);
+ unsafe {
+ let handle = chfl_frame_get_property(self.as_ptr(), buffer.as_ptr());
+ if handle.is_null() {
+ None
+ } else {
+ let raw = RawProperty::from_ptr(handle);
+ Some(Property::from_raw(raw))
+ }
+ }
+ }
+
+ /// Get an iterator over all (name, property) pairs for this frame
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Frame, Property};
+ /// let mut frame = Frame::new();
+ /// frame.set("foo", Property::Double(22.2));
+ /// frame.set("bar", Property::Bool(false));
+ ///
+ /// for (name, property) in frame.properties() {
+ /// if name == "foo" {
+ /// assert_eq!(property, Property::Double(22.2));
+ /// } else if name == "bar" {
+ /// assert_eq!(property, Property::Bool(false));
+ /// }
+ /// }
+ /// ```
+ pub fn properties(&self) -> PropertiesIter {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_frame_properties_count(self.as_ptr(), &mut count));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = count as usize;
+ let mut c_names = vec![ptr::null_mut(); size];
+ unsafe {
+ check_success(chfl_frame_list_properties(self.as_ptr(), c_names.as_mut_ptr(), count));
+ }
+
+ let mut names = Vec::new();
+ for ptr in c_names {
+ names.push(strings::from_c(ptr));
+ }
+
+ PropertiesIter {
+ names: names.into_iter(),
+ getter: Box::new(move |name| self.get(&*name).expect("failed to get property"))
+ }
+ }
+}
+
+impl Drop for Frame {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+ use {Atom, Topology, UnitCell};
+
+ #[test]
+ fn clone() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.size(), 0);
+ let copy = frame.clone();
+ assert_eq!(copy.size(), 0);
+
+ frame.resize(42);
+ assert_eq!(frame.size(), 42);
+ assert_eq!(copy.size(), 0);
+ }
+
+ #[test]
+ fn size() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.size(), 0);
+
+ frame.resize(12);
+ assert_eq!(frame.size(), 12);
+ }
+
+ #[test]
+ fn add_atom() {
+ let mut frame = Frame::new();
+
+ frame.add_atom(&Atom::new("U"), [1.0, 1.0, 2.0], None);
+ assert_eq!(frame.size(), 1);
+ assert_eq!(frame.atom(0).name(), "U");
+
+ let positions = &[[1.0, 1.0, 2.0]];
+ assert_eq!(frame.positions(), positions);
+
+ frame.add_velocities();
+ frame.add_atom(&Atom::new("F"), [1.0, 1.0, 2.0], [4.0, 3.0, 2.0]);
+ assert_eq!(frame.size(), 2);
+ assert_eq!(frame.atom(0).name(), "U");
+ assert_eq!(frame.atom(1).name(), "F");
+
+ let positions = &[[1.0, 1.0, 2.0], [1.0, 1.0, 2.0]];
+ assert_eq!(frame.positions(), positions);
+
+ let velocities = &[[0.0, 0.0, 0.0], [4.0, 3.0, 2.0]];
+ assert_eq!(frame.velocities(), velocities);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_atom() {
+ let mut frame = Frame::new();
+ frame.resize(22);
+ let _atom = frame.atom(23);
+ }
+
+ #[test]
+ fn remove_atom() {
+ let mut frame = Frame::new();
+ frame.add_atom(&Atom::new("U"), [1.0, 1.0, 2.0], None);
+ frame.add_atom(&Atom::new("F"), [1.0, 1.0, 2.0], None);
+
+ assert_eq!(frame.size(), 2);
+ assert_eq!(frame.atom(0).name(), "U");
+
+ frame.remove(0);
+ assert_eq!(frame.size(), 1);
+ assert_eq!(frame.atom(0).name(), "F");
+ }
+
+ #[test]
+ #[should_panic]
+ fn remove_out_of_bounds() {
+ let mut frame = Frame::new();
+ frame.resize(32);
+
+ frame.remove(100);
+ }
+
+ #[test]
+ fn positions() {
+ let mut frame = Frame::new();
+ frame.resize(4);
+ let expected = &[
+ [1.0, 2.0, 3.0],
+ [4.0, 5.0, 6.0],
+ [7.0, 8.0, 9.0],
+ [10.0, 11.0, 12.0],
+ ];
+
+ frame.positions_mut().clone_from_slice(expected);
+ assert_eq!(frame.positions(), expected);
+ }
+
+ #[test]
+ fn velocities() {
+ let mut frame = Frame::new();
+ frame.resize(4);
+ assert!(!frame.has_velocities());
+ frame.add_velocities();
+ assert!(frame.has_velocities());
+
+ let expected = &[
+ [1.0, 2.0, 3.0],
+ [4.0, 5.0, 6.0],
+ [7.0, 8.0, 9.0],
+ [10.0, 11.0, 12.0],
+ ];
+
+ frame.velocities_mut().clone_from_slice(expected);
+ assert_eq!(frame.velocities(), expected);
+ }
+
+ #[test]
+ fn cell() {
+ let mut frame = Frame::new();
+ frame.set_cell(&UnitCell::new([3.0, 4.0, 5.0]));
+ let cell = frame.cell();
+ assert_eq!(cell.lengths(), [3.0, 4.0, 5.0]);
+ }
+
+ #[test]
+ fn topology() {
+ let mut frame = Frame::new();
+ frame.resize(2);
+ let mut topology = Topology::new();
+
+ topology.add_atom(&Atom::new("Zn"));
+ topology.add_atom(&Atom::new("Ar"));
+
+ assert!(frame.set_topology(&topology).is_ok());
+
+ let topology = frame.topology();
+
+ assert_eq!(topology.atom(0).name(), "Zn");
+ assert_eq!(topology.atom(1).name(), "Ar");
+
+ assert_eq!(frame.atom(0).name(), "Zn");
+ assert_eq!(frame.atom(1).name(), "Ar");
+ }
+
+ #[test]
+ fn bonds() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ assert_eq!(frame.topology().bonds_count(), 0);
+
+ frame.add_bond(0, 1);
+ frame.add_bond(9, 2);
+ frame.add_bond_with_order(3, 7, BondOrder::Aromatic);
+ assert_eq!(frame.topology().bonds_count(), 3);
+
+ assert_eq!(frame.topology().bonds(), vec![[0, 1], [2, 9], [3, 7]]);
+ let expected = vec![BondOrder::Unknown, BondOrder::Unknown, BondOrder::Aromatic];
+ assert_eq!(frame.topology().bond_orders(), expected);
+
+ assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown);
+ assert_eq!(frame.topology().bond_order(3, 7), BondOrder::Aromatic);
+
+ frame.remove_bond(3, 7);
+ // Removing unexisting bond is OK if both indexes are in bounds
+ frame.remove_bond(8, 7);
+ assert_eq!(frame.topology().bonds_count(), 2);
+
+ frame.clear_bonds();
+ assert_eq!(frame.topology().bonds_count(), 0);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ frame.add_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_remove_bond() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ frame.remove_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds_with_order() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ frame.add_bond_with_order(300, 7, BondOrder::Unknown);
+ }
+
+ #[test]
+ fn residues() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.topology().residues_count(), 0);
+
+ let residue = &Residue::new("foobar");
+ frame.add_residue(residue).unwrap();
+ frame.add_residue(residue).unwrap();
+ frame.add_residue(residue).unwrap();
+
+ assert_eq!(frame.topology().residues_count(), 3);
+ assert_eq!(frame.topology().residue(0).unwrap().name(), "foobar");
+ }
+
+ #[test]
+ fn step() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.step(), 0);
+ frame.set_step(42);
+ assert_eq!(frame.step(), 42);
+ }
+
+ #[test]
+ fn property() {
+ let mut frame = Frame::new();
+ frame.set("foo", -22.0);
+ assert_eq!(frame.get("foo"), Some(Property::Double(-22.0)));
+ assert_eq!(frame.get("bar"), None);
+
+ frame.set("bar", Property::String("here".into()));
+ for (name, property) in frame.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(-22.0));
+ } else if name == "bar" {
+ assert_eq!(property, Property::String("here".into()));
+ }
+ }
+ }
+
+ #[test]
+ fn pbc_geometry() {
+ use std::f64::consts::PI;
+
+ let mut frame = Frame::new();
+ let atom = &Atom::new("");
+
+ frame.add_atom(atom, [1.0, 0.0, 0.0], None);
+ frame.add_atom(atom, [0.0, 0.0, 0.0], None);
+ frame.add_atom(atom, [0.0, 1.0, 0.0], None);
+ frame.add_atom(atom, [0.0, 1.0, 1.0], None);
+ frame.add_atom(atom, [0.0, 0.0, 2.0], None);
+
+ assert_eq!(frame.distance(0, 2), f64::sqrt(2.0));
+ assert_eq!(frame.angle(0, 1, 2), PI / 2.0);
+ assert_eq!(frame.dihedral(0, 1, 2, 3), PI / 2.0);
+ assert_eq!(frame.out_of_plane(1, 4, 0, 2), 2.0);
+ }
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+
+//! Chemfiles is a multi-language library written in modern C++ for reading and
+//! writing from and to molecular trajectory files. These files are created by
+//! your favorite theoretical chemistry program, and contains information about
+//! atomic or residues names and positions. Some format also have additional
+//! information, such as velocities, forces, energy, …
+//!
+//! This crate expose the C API of chemfiles to Rust, and make all the
+//! functionalities accessible. For more information on the C++ library,
+//! please see its [documentation][cxx_doc]. Specifically, the following pages
+//! are worth reading:
+//!
+//! - The [overview][overview] of the classes organization;
+//! - The list of [supported formats][formats];
+//! - The documentation for the [selection language][selections];
+//!
+//! [cxx_doc]: https://chemfiles.org/chemfiles
+//! [overview]: https://chemfiles.org/chemfiles/latest/overview.html
+//! [formats]: https://chemfiles.org/chemfiles/latest/formats.html
+//! [selections]: https://chemfiles.org/chemfiles/latest/selections.html
+
+#![deny(missing_docs)]
+#![warn(trivial_casts, unused_import_braces, variant_size_differences)]
+#![warn(unused_results)]
+// Configuration for clippy lints
+#![warn(clippy::all, clippy::pedantic)]
+#![allow(clippy::needless_return, clippy::module_name_repetitions)]
+#![allow(clippy::must_use_candidate, clippy::wildcard_imports)]
+
+// Allow a few more clippy lints in test mode
+#![cfg_attr(test, allow(clippy::float_cmp, clippy::unreadable_literal, clippy::shadow_unrelated))]
+
+// deny(warnings) in doc tests
+#![doc(test(attr(deny(warnings))))]
+#![doc(test(attr(allow(unused_variables))))]
+
+#[cfg(test)]
+#[macro_use]
+extern crate approx;
+
+extern crate chemfiles_sys;
+use chemfiles_sys::{chfl_add_configuration, chfl_version};
+
+mod strings;
+
+mod errors;
+pub use errors::{Error, Status};
+pub use errors::set_warning_callback;
+
+mod atom;
+pub use atom::Atom;
+pub use atom::AtomRef;
+pub use atom::AtomMut;
+
+mod cell;
+pub use cell::UnitCell;
+pub use cell::UnitCellRef;
+pub use cell::UnitCellMut;
+pub use cell::CellShape;
+
+mod residue;
+pub use residue::Residue;
+pub use residue::ResidueRef;
+
+mod topology;
+pub use topology::Topology;
+pub use topology::TopologyRef;
+pub use topology::BondOrder;
+
+mod frame;
+pub use frame::Frame;
+
+mod trajectory;
+pub use trajectory::Trajectory;
+
+mod selection;
+pub use selection::{Match, Selection};
+
+mod property;
+pub use property::Property;
+pub use property::PropertiesIter;
+
+mod misc;
+pub use misc::{FormatMetadata, formats_list, guess_format};
+
+/// Get the version of the chemfiles library.
+///
+/// # Example
+/// ```
+/// let version = chemfiles::version();
+/// assert!(version.starts_with("0.10"));
+/// ```
+pub fn version() -> String {
+ unsafe { strings::from_c(chfl_version()) }
+}
+
+/// Read configuration data from the file at `path`.
+///
+/// By default, chemfiles reads configuration from any file named
+/// `.chemfiles.toml` in the current directory or any parent directory. This
+/// function can be used to add data from another configuration file. Data from
+/// the new configuration file will overwrite any existing data.
+///
+/// # Errors
+///
+/// This function will fail if there is no file at `path`, or if the file is
+/// incorrectly formatted.
+///
+/// # Example
+/// ```no_run
+/// chemfiles::add_configuration("local-config.toml").unwrap();
+/// // from now on, the data from "local-config.toml" will be used
+/// ```
+pub fn add_configuration<S>(path: S) -> Result<(), Error>
+where
+ S: AsRef<str>,
+{
+ let buffer = strings::to_c(path.as_ref());
+ unsafe {
+ errors::check(chfl_add_configuration(buffer.as_ptr()))
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ #[test]
+ fn version() {
+ assert!(!crate::version().is_empty());
+ assert!(crate::version().starts_with("0.10"));
+ }
+}
+
+#[cfg(test)]
+fn assert_vector3d_eq(lhs: &[f64; 3], rhs: &[f64; 3], eps: f64) {
+ lhs.iter()
+ .zip(rhs)
+ .for_each(|(l, r)| assert_ulps_eq!(l, r, epsilon = eps));
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2020 Guillaume Fraux -- BSD licensed
+
+use std::convert::TryInto;
+use std::ffi::CStr;
+
+use chemfiles_sys::{chfl_format_metadata, chfl_formats_list, chfl_free, chfl_guess_format};
+use errors::check_success;
+
+/// `FormatMetadata` contains metadata associated with one format.
+#[allow(clippy::struct_excessive_bools)]
+#[derive(Debug, Clone, PartialEq, Eq)]
+pub struct FormatMetadata {
+ /// Name of the format.
+ pub name: &'static str,
+ /// Extension associated with the format.
+ pub extension: Option<&'static str>,
+ /// Extended, user-facing description of the format.
+ pub description: &'static str,
+ /// URL pointing to the format definition/reference.
+ pub reference: &'static str,
+ /// Is reading files in this format implemented?
+ pub read: bool,
+ /// Is writing files in this format implemented?
+ pub write: bool,
+ /// Does this format support in-memory IO?
+ pub memory: bool,
+ /// Does this format support storing atomic positions?
+ pub positions: bool,
+ /// Does this format support storing atomic velocities?
+ pub velocities: bool,
+ /// Does this format support storing unit cell information?
+ pub unit_cell: bool,
+ /// Does this format support storing atom names or types?
+ pub atoms: bool,
+ /// Does this format support storing bonds between atoms?
+ pub bonds: bool,
+ /// Does this format support storing residues?
+ pub residues: bool,
+}
+
+impl FormatMetadata {
+ pub(crate) fn from_raw(raw: &chfl_format_metadata) -> Self {
+ let str_from_ptr = |ptr| unsafe {
+ CStr::from_ptr(ptr)
+ .to_str()
+ .expect("Invalid Rust str from C")
+ };
+ let extension = if raw.extension.is_null() {
+ None
+ } else {
+ Some(str_from_ptr(raw.extension))
+ };
+ Self {
+ name: str_from_ptr(raw.name),
+ extension,
+ description: str_from_ptr(raw.description),
+ reference: str_from_ptr(raw.reference),
+ read: raw.read,
+ write: raw.write,
+ memory: raw.memory,
+ positions: raw.positions,
+ velocities: raw.velocities,
+ unit_cell: raw.unit_cell,
+ atoms: raw.atoms,
+ bonds: raw.bonds,
+ residues: raw.residues,
+ }
+ }
+}
+
+/// Get the list of formats known by chemfiles, as well as all associated metadata.
+///
+/// # Example
+/// ```
+/// let formats = chemfiles::formats_list();
+/// println!("chemfiles supports {} formats:", formats.len());
+/// for format in &formats {
+/// println!(
+/// " {:<15} {}",
+/// format.name,
+/// format.extension.as_deref().unwrap_or("")
+/// );
+/// }
+/// ```
+#[must_use]
+pub fn formats_list() -> Vec<FormatMetadata> {
+ let mut formats = std::ptr::null_mut();
+ let mut count: u64 = 0;
+ let formats_slice = unsafe {
+ check_success(chfl_formats_list(&mut formats, &mut count));
+ std::slice::from_raw_parts(formats, count.try_into().expect("failed to convert u64 to usize"))
+ };
+ let formats_vec = formats_slice
+ .iter()
+ .map(|fm| FormatMetadata::from_raw(fm))
+ .collect();
+ unsafe {
+ let _ = chfl_free(formats as *const _);
+ }
+ return formats_vec;
+}
+
+#[allow(clippy::doc_markdown)]
+/// Get the format that chemfiles would use to read a file at the given
+/// ``path``.
+///
+/// The format is mostly guessed from the path extension, chemfiles only tries
+/// to read the file to distinguish between CIF and mmCIF files. Opening the
+/// file using the returned format string might still fail. For example, it will
+/// fail if the file is not actually formatted according to the guessed format;
+/// or the format/compression combination is not supported (e.g. `XTC / GZ` will
+/// not work since the XTC reader does not support compressed files).
+///
+/// The returned format is represented in a way compatible with the various
+/// `Trajectory` constructors, i.e. `"<format name> [/ <compression>]"`, where
+/// compression is optional.
+///
+/// # Examples
+/// ```
+/// let format = chemfiles::guess_format("trajectory.xyz.xz");
+/// assert_eq!(format, "XYZ / XZ");
+///
+/// let format = chemfiles::guess_format("trajectory.nc");
+/// assert_eq!(format, "Amber NetCDF");
+/// ```
+pub fn guess_format(path: &str) -> String {
+ let path = crate::strings::to_c(path);
+ let mut buffer = vec![0; 128];
+ unsafe {
+ check_success(chfl_guess_format(
+ path.as_ptr(), buffer.as_mut_ptr(), buffer.len() as u64
+ ));
+ }
+ return crate::strings::from_c(buffer.as_ptr());
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::Drop;
+use std::vec::IntoIter;
+
+use chemfiles_sys::*;
+use errors::{check, check_not_null, check_success, Error};
+use strings;
+
+/// A thin wrapper around `CHFL_PROPERTY`
+pub(crate) struct RawProperty {
+ handle: *mut CHFL_PROPERTY,
+}
+
+impl RawProperty {
+ /// Create a `RawProperty` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ pub unsafe fn from_ptr(ptr: *mut CHFL_PROPERTY) -> RawProperty {
+ check_not_null(ptr);
+ RawProperty {
+ handle: ptr
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ pub fn as_ptr(&self) -> *const CHFL_PROPERTY {
+ self.handle
+ }
+
+ fn double(value: f64) -> RawProperty {
+ unsafe {
+ let handle = chfl_property_double(value);
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn bool(value: bool) -> RawProperty {
+ let value = if value { 1 } else { 0 };
+ unsafe {
+ let handle = chfl_property_bool(value);
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn vector3d(value: [f64; 3]) -> RawProperty {
+ unsafe {
+ let handle = chfl_property_vector3d(value.as_ptr());
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn string(value: &str) -> RawProperty {
+ let buffer = strings::to_c(value);
+ unsafe {
+ let handle = chfl_property_string(buffer.as_ptr());
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn get_kind(&self) -> chfl_property_kind {
+ let mut kind = chfl_property_kind::CHFL_PROPERTY_BOOL;
+ unsafe {
+ check_success(chfl_property_get_kind(self.as_ptr(), &mut kind));
+ }
+ return kind;
+ }
+
+ fn get_bool(&self) -> Result<bool, Error> {
+ let mut value = 0;
+ unsafe {
+ check(chfl_property_get_bool(self.as_ptr(), &mut value))?;
+ }
+ return Ok(value != 0);
+ }
+
+ fn get_double(&self) -> Result<f64, Error> {
+ let mut value = 0.0;
+ unsafe {
+ check(chfl_property_get_double(self.as_ptr(), &mut value))?;
+ }
+ return Ok(value);
+ }
+
+ fn get_string(&self) -> Result<String, Error> {
+ let get_string = |ptr, len| unsafe { chfl_property_get_string(self.as_ptr(), ptr, len) };
+ let value = strings::call_autogrow_buffer(64, get_string)?;
+ return Ok(strings::from_c(value.as_ptr()));
+ }
+
+ fn get_vector3d(&self) -> Result<[f64; 3], Error> {
+ let mut value = [0.0; 3];
+ unsafe {
+ check(chfl_property_get_vector3d(self.as_ptr(), value.as_mut_ptr()))?;
+ }
+ return Ok(value);
+ }
+}
+
+impl Drop for RawProperty {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+/// A `Property` is a piece of data that can be associated with an `Atom` or a
+/// `Frame`.
+#[derive(Debug, Clone, PartialEq, PartialOrd)]
+pub enum Property {
+ /// Boolean property
+ Bool(bool),
+ /// Floating point property
+ Double(f64),
+ /// String property
+ String(String),
+ /// 3-dimensional vector property
+ Vector3D([f64; 3]),
+}
+
+impl From<bool> for Property {
+ fn from(value: bool) -> Self {
+ Property::Bool(value)
+ }
+}
+
+impl From<f64> for Property {
+ fn from(value: f64) -> Self {
+ Property::Double(value)
+ }
+}
+
+impl From<String> for Property {
+ fn from(value: String) -> Self {
+ Property::String(value)
+ }
+}
+
+impl<'a> From<&'a str> for Property {
+ fn from(value: &'a str) -> Self {
+ Property::String(value.into())
+ }
+}
+
+impl From<[f64; 3]> for Property {
+ fn from(value: [f64; 3]) -> Self {
+ Property::Vector3D(value)
+ }
+}
+
+impl Property {
+ pub(crate) fn as_raw(&self) -> RawProperty {
+ match *self {
+ Property::Bool(value) => RawProperty::bool(value),
+ Property::Double(value) => RawProperty::double(value),
+ Property::String(ref value) => RawProperty::string(value),
+ Property::Vector3D(value) => RawProperty::vector3d(value),
+ }
+ }
+
+ #[allow(clippy::needless_pass_by_value)] // raw property
+ pub(crate) fn from_raw(raw: RawProperty) -> Property {
+ match raw.get_kind() {
+ chfl_property_kind::CHFL_PROPERTY_BOOL => {
+ Property::Bool(raw.get_bool().expect("shoudl be a bool"))
+ }
+ chfl_property_kind::CHFL_PROPERTY_DOUBLE => {
+ Property::Double(raw.get_double().expect("should be a double"))
+ }
+ chfl_property_kind::CHFL_PROPERTY_STRING => {
+ Property::String(raw.get_string().expect("should be a string"))
+ }
+ chfl_property_kind::CHFL_PROPERTY_VECTOR3D => {
+ Property::Vector3D(raw.get_vector3d().expect("should be a vector3d"))
+ }
+ }
+ }
+}
+
+/// An iterator over the properties in an atom/frame/residue
+pub struct PropertiesIter<'a> where {
+ pub(crate) names: IntoIter<String>,
+ pub(crate) getter: Box<dyn Fn(&str) -> Property + 'a>,
+}
+
+impl<'a> Iterator for PropertiesIter<'a> {
+ type Item = (String, Property);
+ fn next(&mut self) -> Option<Self::Item> {
+ self.names.next().map(|name| {
+ let property = (self.getter)(&*name);
+ (name, property)
+ })
+ }
+
+ fn size_hint(&self) -> (usize, Option<usize>) {
+ self.names.size_hint()
+ }
+
+ fn count(self) -> usize {
+ self.names.count()
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ mod raw {
+ use super::super::*;
+
+ #[test]
+ fn bool() {
+ let property = RawProperty::bool(false);
+ assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_BOOL);
+ assert_eq!(property.get_bool(), Ok(false));
+ }
+
+ #[test]
+ fn double() {
+ let property = RawProperty::double(45.0);
+ assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_DOUBLE);
+ assert_eq!(property.get_double(), Ok(45.0));
+ }
+
+ #[test]
+ fn string() {
+ let property = RawProperty::string("test");
+ assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_STRING);
+ assert_eq!(property.get_string(), Ok("test".into()));
+ }
+
+ #[test]
+ fn vector3d() {
+ let property = RawProperty::vector3d([1.2, 3.4, 5.6]);
+ assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_VECTOR3D);
+ assert_eq!(property.get_vector3d(), Ok([1.2, 3.4, 5.6]));
+ }
+ }
+
+ mod rust {
+ use super::super::*;
+
+ #[test]
+ fn bool() {
+ let property = Property::Bool(false);
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_BOOL);
+ assert_eq!(raw.get_bool(), Ok(false));
+
+ assert_eq!(Property::from_raw(raw), property);
+ }
+
+ #[test]
+ fn double() {
+ let property = Property::Double(45.0);
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_DOUBLE);
+ assert_eq!(raw.get_double(), Ok(45.0));
+
+ assert_eq!(Property::from_raw(raw), property);
+ }
+
+ #[test]
+ fn string() {
+ let property = Property::String("test".into());
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_STRING);
+ assert_eq!(raw.get_string(), Ok("test".into()));
+
+ assert_eq!(Property::from_raw(raw), property);
+
+ let property = Property::String("long string ".repeat(128));
+ let raw = property.as_raw();
+ assert_eq!(raw.get_string(), Ok("long string ".repeat(128)));
+ }
+
+ #[test]
+ fn vector3d() {
+ let property = Property::Vector3D([1.2, 3.4, 5.6]);
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_VECTOR3D);
+ assert_eq!(raw.get_vector3d(), Ok([1.2, 3.4, 5.6]));
+
+ assert_eq!(Property::from_raw(raw), property);
+ }
+ }
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371 +372 +373 +374 +375 +376 +377 +378 +379 +380 +381 +382 +383 +384 +385 +386 +387 +388 +389 +390 +391 +392 +393 +394 +395 +396 +397 +398 +399 +400 +401 +402 +403 +404 +405 +406 +407 +408 +409 +410 +411 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::{Drop, Deref};
+use std::marker::PhantomData;
+use std::ptr;
+
+use chemfiles_sys::*;
+use errors::{check_not_null, check_success};
+use property::{Property, RawProperty, PropertiesIter};
+use strings;
+
+/// A `Residue` is a group of atoms belonging to the same logical unit. They
+/// can be small molecules, amino-acids in a protein, monomers in polymers,
+/// *etc.*
+pub struct Residue {
+ handle: *mut CHFL_RESIDUE,
+}
+
+/// An analog to a reference to a residue (`&Residue`)
+pub struct ResidueRef<'a> {
+ inner: Residue,
+ marker: PhantomData<&'a Residue>
+}
+
+impl<'a> Deref for ResidueRef<'a> {
+ type Target = Residue;
+ fn deref(&self) -> &Residue {
+ &self.inner
+ }
+}
+
+impl Clone for Residue {
+ fn clone(&self) -> Residue {
+ unsafe {
+ let new_handle = chfl_residue_copy(self.as_ptr());
+ Residue::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Residue {
+ /// Create a `Residue` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_RESIDUE) -> Residue {
+ check_not_null(ptr);
+ Residue {
+ handle: ptr
+ }
+ }
+
+ /// Create a borrowed `Residue` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, except for it being non-null, and the caller is responsible
+ /// for setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_RESIDUE) -> ResidueRef<'a> {
+ ResidueRef {
+ inner: Residue::from_ptr(ptr as *mut CHFL_RESIDUE),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_RESIDUE {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_RESIDUE {
+ self.handle
+ }
+
+ /// Create a new residue with the given `name`
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::new("ALA");
+ /// assert_eq!(residue.name(), "ALA");
+ /// assert_eq!(residue.id(), None);
+ /// ```
+ pub fn new<'a>(name: impl Into<&'a str>) -> Residue {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ let handle = chfl_residue(buffer.as_ptr());
+ Residue::from_ptr(handle)
+ }
+ }
+
+ /// Create a new residue with the given `name` and `id` as identifier.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::with_id("ALA", 67);
+ /// assert_eq!(residue.name(), "ALA");
+ /// assert_eq!(residue.id(), Some(67));
+ /// ```
+ pub fn with_id<'a>(name: impl Into<&'a str>, id: i64) -> Residue {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ let handle = chfl_residue_with_id(buffer.as_ptr(), id);
+ Residue::from_ptr(handle)
+ }
+ }
+
+ /// Get the number of atoms in this residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.size(), 0);
+ ///
+ /// residue.add_atom(0);
+ /// residue.add_atom(1);
+ /// residue.add_atom(2);
+ /// assert_eq!(residue.size(), 3);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(chfl_residue_atoms_count(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Get the identifier of this residue in the initial topology file.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::with_id("", 42);
+ /// assert_eq!(residue.id(), Some(42));
+ /// ```
+ pub fn id(&self) -> Option<i64> {
+ let mut resid = 0;
+ let status = unsafe {
+ chfl_residue_id(self.as_ptr(), &mut resid)
+ };
+
+ if status == chfl_status::CHFL_SUCCESS {
+ return Some(resid);
+ } else if status == chfl_status::CHFL_GENERIC_ERROR {
+ return None;
+ }
+
+ // call check_success to panic in case of error
+ check_success(status);
+ unreachable!();
+ }
+
+ /// Get the name of this residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::new("water");
+ /// assert_eq!(residue.name(), "water");
+ /// ```
+ pub fn name(&self) -> String {
+ let get_name = |ptr, len| unsafe { chfl_residue_name(self.as_ptr(), ptr, len) };
+ let name = strings::call_autogrow_buffer(64, get_name).expect("getting residue name failed");
+ return strings::from_c(name.as_ptr());
+ }
+
+ /// Add the atom at index `atom` in this residue.
+ ///
+ /// This will fail if the atom is already in the residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.size(), 0);
+ /// assert_eq!(residue.contains(56), false);
+ ///
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.size(), 1);
+ /// assert_eq!(residue.contains(56), true);
+ ///
+ /// // Adding the same atom twice is fine
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.size(), 1);
+ /// ```
+ pub fn add_atom(&mut self, atom: usize) {
+ unsafe {
+ check_success(chfl_residue_add_atom(self.as_mut_ptr(), atom as u64));
+ }
+ }
+
+ /// Check if the atom at index `i` is in this residue
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.contains(56), false);
+ ///
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.contains(56), true);
+ /// ```
+ pub fn contains(&self, atom: usize) -> bool {
+ let mut inside = 0;
+ unsafe {
+ check_success(chfl_residue_contains(self.as_ptr(), atom as u64, &mut inside));
+ }
+ return inside != 0;
+ }
+
+ /// Get the list of atoms of this residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.atoms(), vec![]);
+ ///
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.atoms(), vec![56]);
+ /// ```
+ pub fn atoms(&self) -> Vec<usize> {
+ let size = self.size();
+ let count = size as u64;
+ let mut indices = vec![u64::max_value(); size];
+ unsafe {
+ check_success(chfl_residue_atoms(
+ self.as_ptr(),
+ indices.as_mut_ptr(),
+ count,
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return indices.into_iter().map(|idx| idx as usize).collect();
+ }
+
+ /// Add a new `property` with the given `name` to this residue.
+ ///
+ /// If a property with the same name already exists, this function override
+ /// the existing property with the new one.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Residue, Property};
+ /// let mut residue = Residue::new("ALA");
+ /// residue.set("a string", "hello");
+ /// residue.set("a double", 3.2);
+ ///
+ /// assert_eq!(residue.get("a string"), Some(Property::String("hello".into())));
+ /// assert_eq!(residue.get("a double"), Some(Property::Double(3.2)));
+ /// ```
+ pub fn set(&mut self, name: &str, property: impl Into<Property>) {
+ let buffer = strings::to_c(name);
+ let property = property.into().as_raw();
+ unsafe {
+ check_success(chfl_residue_set_property(
+ self.as_mut_ptr(), buffer.as_ptr(), property.as_ptr()
+ ));
+ }
+ }
+
+ /// Get a property with the given `name` in this frame, if it exist.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Residue, Property};
+ /// let mut residue = Residue::new("ALA");
+ /// residue.set("foo", Property::Double(22.2));
+ ///
+ /// assert_eq!(residue.get("foo"), Some(Property::Double(22.2)));
+ /// assert_eq!(residue.get("Bar"), None);
+ /// ```
+ pub fn get(&self, name: &str) -> Option<Property> {
+ let buffer = strings::to_c(name);
+ unsafe {
+ let handle = chfl_residue_get_property(self.as_ptr(), buffer.as_ptr());
+ if handle.is_null() {
+ None
+ } else {
+ let raw = RawProperty::from_ptr(handle);
+ Some(Property::from_raw(raw))
+ }
+ }
+ }
+
+ /// Get an iterator over all (name, property) pairs for this frame
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Residue, Property};
+ /// let mut residue = Residue::new("ALA");
+ /// residue.set("foo", Property::Double(22.2));
+ /// residue.set("bar", Property::Bool(false));
+ ///
+ /// for (name, property) in residue.properties() {
+ /// if name == "foo" {
+ /// assert_eq!(property, Property::Double(22.2));
+ /// } else if name == "bar" {
+ /// assert_eq!(property, Property::Bool(false));
+ /// }
+ /// }
+ /// ```
+ pub fn properties(&self) -> PropertiesIter {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_residue_properties_count(self.as_ptr(), &mut count));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = count as usize;
+ let mut c_names = vec![ptr::null_mut(); size];
+ unsafe {
+ check_success(chfl_residue_list_properties(self.as_ptr(), c_names.as_mut_ptr(), count));
+ }
+
+ let mut names = Vec::new();
+ for ptr in c_names {
+ names.push(strings::from_c(ptr));
+ }
+
+ PropertiesIter {
+ names: names.into_iter(),
+ getter: Box::new(move |name| self.get(&*name).expect("failed to get property"))
+ }
+ }
+}
+
+impl Drop for Residue {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut residue = Residue::new("A");
+ assert_eq!(residue.size(), 0);
+
+ let copy = residue.clone();
+ assert_eq!(copy.size(), 0);
+
+ residue.add_atom(3);
+ residue.add_atom(7);
+ assert_eq!(residue.size(), 2);
+ assert_eq!(copy.size(), 0);
+ }
+
+ #[test]
+ fn name() {
+ let residue = Residue::new("A");
+ assert_eq!(residue.name(), "A");
+ }
+
+ #[test]
+ fn id() {
+ let residue = Residue::new("A");
+ assert_eq!(residue.id(), None);
+
+ let residue = Residue::with_id("A", 42);
+ assert_eq!(residue.id(), Some(42));
+
+ let residue = Residue::with_id("A", -3);
+ assert_eq!(residue.id(), Some(-3));
+ }
+
+ #[test]
+ fn atoms() {
+ let mut residue = Residue::new("A");
+ assert_eq!(residue.size(), 0);
+
+ residue.add_atom(0);
+ residue.add_atom(3);
+ residue.add_atom(45);
+ assert_eq!(residue.size(), 3);
+
+ assert!(residue.contains(3));
+ assert!(!residue.contains(5));
+
+ assert_eq!(residue.atoms(), vec![0, 3, 45]);
+ }
+
+ #[test]
+ fn property() {
+ let mut residue = Residue::new("ALA");
+
+ residue.set("foo", -22.0);
+ assert_eq!(residue.get("foo"), Some(Property::Double(-22.0)));
+ assert_eq!(residue.get("bar"), None);
+
+ residue.set("bar", Property::String("here".into()));
+ for (name, property) in residue.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(-22.0));
+ } else if name == "bar" {
+ assert_eq!(property, Property::String("here".into()));
+ }
+ }
+ }
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371 +372 +373 +374 +375 +376 +377 +378 +379 +380 +381 +382 +383 +384 +385 +386 +387 +388 +389 +390 +391 +392 +393 +394 +395 +396 +397 +398 +399 +400 +401 +402 +403 +404 +405 +406 +407 +408 +409 +410 +411 +412 +413 +414 +415 +416 +417 +418 +419 +420 +421 +422 +423 +424 +425 +426 +427 +428 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::{Drop, Index};
+use std::iter::IntoIterator;
+use std::slice::Iter;
+
+use chemfiles_sys::*;
+use errors::{check, check_not_null, check_success, Error, Status};
+use strings;
+use frame::Frame;
+
+#[derive(Debug, Clone, PartialEq, Eq)]
+/// A `Match` is a set of atomic indexes matching a given selection. It can
+/// mostly be used like a `&[usize]`.
+pub struct Match {
+ size: usize,
+ atoms: [usize; 4],
+}
+
+#[allow(clippy::len_without_is_empty)]
+impl Match {
+ /// Get the length of the Match.
+ ///
+ /// # Example
+ ///
+ /// ```
+ /// # use chemfiles::Match;
+ /// let atomic_match = Match::new(&[3, 4, 5]);
+ /// assert_eq!(atomic_match.len(), 3);
+ /// ```
+ pub fn len(&self) -> usize {
+ self.size
+ }
+
+ /// Create a new match containing the atoms in the `atoms` slice.
+ ///
+ /// # Panics
+ ///
+ /// If the slice contains more than 4 elements, which is the maximal size
+ /// of a match.
+ ///
+ /// # Example
+ ///
+ /// ```
+ /// # use chemfiles::Match;
+ /// let atomic_match = Match::new(&[3, 4, 5]);
+ /// assert_eq!(atomic_match.len(), 3);
+ /// assert_eq!(atomic_match[0], 3);
+ /// assert_eq!(atomic_match[1], 4);
+ /// assert_eq!(atomic_match[2], 5);
+ /// ```
+ pub fn new(atoms: &[usize]) -> Match {
+ assert!(atoms.len() <= 4);
+ let size = atoms.len();
+ let mut matches = [usize::max_value(); 4];
+ for (i, atom) in atoms.iter().enumerate() {
+ matches[i] = *atom;
+ }
+ Match {
+ size,
+ atoms: matches,
+ }
+ }
+
+ /// Iterate over the atomic indexes in the match.
+ ///
+ /// # Example
+ ///
+ /// ```
+ /// # use chemfiles::Match;
+ /// let atomic_match = Match::new(&[3, 4, 5]);
+ /// let mut iter = atomic_match.iter();
+ ///
+ /// assert_eq!(iter.next(), Some(&3));
+ /// assert_eq!(iter.next(), Some(&4));
+ /// assert_eq!(iter.next(), Some(&5));
+ /// assert_eq!(iter.next(), None);
+ /// ```
+ pub fn iter(&self) -> Iter<usize> {
+ self.atoms[..self.len()].iter()
+ }
+}
+
+impl Index<usize> for Match {
+ type Output = usize;
+ fn index(&self, i: usize) -> &Self::Output {
+ assert!(i < self.len());
+ &self.atoms[i]
+ }
+}
+
+impl<'a> IntoIterator for &'a Match {
+ type Item = &'a usize;
+ type IntoIter = Iter<'a, usize>;
+ fn into_iter(self) -> Iter<'a, usize> {
+ self.atoms[..self.len()].iter()
+ }
+}
+
+/// A `Selection` allow to select atoms in a `Frame`, from a selection
+/// language. The selection language is built by combining basic operations.
+/// Each basic operation follows the `<selector>[(<variable>)] <operator>
+/// <value>` structure, where `<operator>` is a comparison operator in
+/// `== != < <= > >=`.
+pub struct Selection {
+ handle: *mut CHFL_SELECTION,
+}
+
+impl Clone for Selection {
+ fn clone(&self) -> Selection {
+ unsafe {
+ let new_handle = chfl_selection_copy(self.as_ptr());
+ Selection::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Drop for Selection {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+impl Selection {
+ /// Create a `Selection` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_SELECTION) -> Selection {
+ check_not_null(ptr);
+ Selection {
+ handle: ptr
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_SELECTION {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_SELECTION {
+ self.handle
+ }
+
+ /// Create a new selection from the given selection string.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the selection string is invalid.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Selection;
+ /// let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+ /// ```
+ pub fn new<'a, S: Into<&'a str>>(selection: S) -> Result<Selection, Error> {
+ let buffer = strings::to_c(selection.into());
+ unsafe {
+ let handle = chfl_selection(buffer.as_ptr());
+ if handle.is_null() {
+ Err(Error {
+ status: Status::SelectionError,
+ message: Error::last_error()
+ })
+ } else {
+ Ok(Selection::from_ptr(handle))
+ }
+ }
+ }
+
+ /// Get the size of the selection, i.e. the number of atoms we are selecting
+ /// together.
+ ///
+ /// This value is 1 for the 'atom' context, 2 for the 'pair' and 'bond'
+ /// context, 3 for the 'three' and 'angles' context and 4 for the 'four'
+ /// and 'dihedral' context.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Selection;
+ /// let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+ /// assert_eq!(selection.size(), 2);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(chfl_selection_size(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Get the selection string used to create this selection.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Selection;
+ /// let selection = Selection::new("name H").unwrap();
+ /// assert_eq!(selection.string(), "name H");
+ /// ```
+ pub fn string(&self) -> String {
+ let get_string = |ptr, len| unsafe { chfl_selection_string(self.as_ptr(), ptr, len) };
+ let selection = strings::call_autogrow_buffer(1024, get_string).expect("failed to get selection string");
+ return strings::from_c(selection.as_ptr());
+ }
+
+ /// Evaluate a selection for a given frame, and return the corresponding
+ /// matches.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Selection, Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+ ///
+ /// let mut selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+ /// let matches = selection.evaluate(&frame);
+ ///
+ /// assert_eq!(matches.len(), 2);
+ ///
+ /// assert_eq!(matches[0].len(), 2);
+ /// assert_eq!(matches[0][0], 0);
+ /// assert_eq!(matches[0][1], 1);
+ ///
+ /// assert_eq!(matches[1].len(), 2);
+ /// assert_eq!(matches[1][0], 2);
+ /// assert_eq!(matches[1][1], 1);
+ /// ```
+ pub fn evaluate(&mut self, frame: &Frame) -> Vec<Match> {
+ #![allow(clippy::cast_possible_truncation)]
+ let mut count = 0;
+ unsafe {
+ check(chfl_selection_evaluate(
+ self.as_mut_ptr(), frame.as_ptr(), &mut count
+ )).expect("failed to evaluate selection");
+ }
+
+ let size = count as usize;
+ let mut chfl_matches = vec![chfl_match { size: 0, atoms: [0; 4] }; size];
+ unsafe {
+ check(chfl_selection_matches(
+ self.handle,
+ chfl_matches.as_mut_ptr(),
+ count
+ )).expect("failed to extract matches");
+ }
+
+ return chfl_matches.into_iter()
+ .map(|chfl_match| Match {
+ size: chfl_match.size as usize,
+ atoms: [
+ chfl_match.atoms[0] as usize,
+ chfl_match.atoms[1] as usize,
+ chfl_match.atoms[2] as usize,
+ chfl_match.atoms[3] as usize,
+ ],
+ })
+ .collect();
+ }
+
+ /// Evaluates a selection of size 1 on a given `frame`. This function
+ /// returns the list of atomic indexes in the frame matching this selection.
+ ///
+ /// # Panics
+ ///
+ /// If the selection size is not 1
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Selection, Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+ ///
+ /// let mut selection = Selection::new("name H").unwrap();
+ /// let matches = selection.list(&frame);
+ ///
+ /// assert_eq!(matches.len(), 2);
+ /// assert_eq!(matches[0], 0);
+ /// assert_eq!(matches[1], 2);
+ /// ```
+ pub fn list(&mut self, frame: &Frame) -> Vec<usize> {
+ if self.size() != 1 {
+ panic!("can not call `Selection::list` on a multiple selection");
+ }
+ return self.evaluate(frame)
+ .into_iter()
+ .map(|m| m[0] as usize)
+ .collect();
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ use super::*;
+ use Frame;
+ use Topology;
+ use Atom;
+
+ #[test]
+ fn clone() {
+ let selection = Selection::new("name H").unwrap();
+
+ let copy = selection.clone();
+ assert_eq!(selection.size(), 1);
+ assert_eq!(copy.size(), 1);
+ }
+
+ fn testing_frame() -> Frame {
+ let mut topology = Topology::new();
+
+ topology.add_atom(&Atom::new("H"));
+ topology.add_atom(&Atom::new("O"));
+ topology.add_atom(&Atom::new("O"));
+ topology.add_atom(&Atom::new("H"));
+
+ topology.add_bond(0, 1);
+ topology.add_bond(1, 2);
+ topology.add_bond(2, 3);
+
+ let mut frame = Frame::new();
+ frame.resize(4);
+ frame.set_topology(&topology).unwrap();
+ return frame;
+ }
+
+ mod matches {
+ use super::*;
+
+ #[test]
+ fn index() {
+ let m = Match::new(&[1, 2, 3, 4]);
+ assert_eq!(m[0], 1);
+ assert_eq!(m[1], 2);
+ assert_eq!(m[2], 3);
+ assert_eq!(m[3], 4);
+
+ let m = Match::new(&[1, 2]);
+ assert_eq!(m[0], 1);
+ assert_eq!(m[1], 2);
+ }
+
+ #[test]
+ fn iter() {
+ let match_ = Match::new(&[1, 2, 3, 4]);
+ assert_eq!(match_.iter().copied().collect::<Vec<usize>>(), vec![1, 2, 3, 4]);
+
+ let v = vec![1, 2, 3, 4];
+ for (i, &m) in match_.iter().enumerate() {
+ assert_eq!(v[i], m);
+ }
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bound() {
+ let m = Match::new(&[1, 2]);
+ let _ = m[2];
+ }
+
+ #[test]
+ #[should_panic]
+ fn too_big() {
+ let _ = Match::new(&[1, 2, 3, 5, 4]);
+ }
+ }
+
+ #[test]
+ fn size() {
+ let selection = Selection::new("name H").unwrap();
+ assert_eq!(selection.size(), 1);
+
+ let selection = Selection::new("angles: name(#1) H").unwrap();
+ assert_eq!(selection.size(), 3);
+
+ let selection = Selection::new("four: name(#1) H").unwrap();
+ assert_eq!(selection.size(), 4);
+ }
+
+ #[test]
+ fn string() {
+ let selection = Selection::new("name H").unwrap();
+ assert_eq!(selection.string(), "name H");
+
+ let selection = Selection::new("angles: name(#1) H").unwrap();
+ assert_eq!(selection.string(), "angles: name(#1) H");
+ }
+
+ #[test]
+ fn evaluate() {
+ let frame = testing_frame();
+
+ let mut selection = Selection::new("name H").unwrap();
+ let res = selection.evaluate(&frame);
+ assert_eq!(res, &[Match::new(&[0]), Match::new(&[3])]);
+
+ let mut selection = Selection::new("angles: all").unwrap();
+ let res = selection.evaluate(&frame);
+ for m in &[Match::new(&[0, 1, 2]), Match::new(&[1, 2, 3])] {
+ assert!(res.iter().any(|r| r == m));
+ }
+ }
+
+ #[test]
+ fn list() {
+ let frame = testing_frame();
+
+ let mut selection = Selection::new("name H").unwrap();
+ let res = selection.list(&frame);
+ assert_eq!(res, vec![0, 3]);
+ }
+
+ #[test]
+ #[should_panic = "can not call `Selection::list` on a multiple selection"]
+ fn list_on_size_1_selection() {
+ let frame = testing_frame();
+ let mut selection = Selection::new("pairs: name(#1) H").unwrap();
+ let _list = selection.list(&frame);
+ }
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+
+//! String conversions between C and Rust
+use std::ffi::{CStr, CString};
+
+use chemfiles_sys::chfl_status;
+use errors::{check, Error};
+
+/// Create a Rust string from a C string. Clones all characters in `buffer`.
+pub fn from_c(buffer: *const i8) -> String {
+ unsafe {
+ let rust_str = CStr::from_ptr(buffer)
+ .to_str()
+ .expect("Invalid Rust string from C");
+ return String::from(rust_str);
+ }
+}
+
+/// Create a C string from a Rust string.
+pub fn to_c(string: &str) -> CString {
+ CString::new(string).expect("Invalid C string from Rust")
+}
+
+/// Check if a string buffer was big enough when passed to a C function
+fn buffer_was_big_enough(buffer: &[i8]) -> bool {
+ let len = buffer.len();
+ if len < 2 {
+ false
+ } else {
+ // The C code should always set the last element to 0
+ debug_assert_eq!(buffer[len - 1], 0);
+ buffer[len - 2] == 0
+ }
+}
+
+/// Call `callback` C function with a string buffer and it length, using
+/// `initial` as the buffer initial size. If the buffer was filled and the
+/// result truncated by the C library, grow the buffer and try again until we
+/// get all the data. Then return the filled buffer to the caller.
+pub fn call_autogrow_buffer<F>(initial: usize, callback: F) -> Result<Vec<i8>, Error>
+where
+ F: Fn(*mut i8, u64) -> chfl_status,
+{
+ let mut size = initial;
+ let mut buffer = vec![0; size];
+ check(callback(buffer.as_mut_ptr(), buffer.len() as u64))?;
+
+ while !buffer_was_big_enough(&buffer) {
+ // Grow the buffer and retry
+ size *= 2;
+ buffer.resize(size, 0);
+ check(callback(buffer.as_mut_ptr(), buffer.len() as u64))?;
+ }
+
+ Ok(buffer)
+}
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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::{Drop, Deref};
+use std::marker::PhantomData;
+
+use chemfiles_sys::*;
+use errors::{check, check_not_null, check_success, Error};
+use super::{Atom, AtomRef, AtomMut};
+use super::{Residue, ResidueRef};
+
+/// Possible bond order associated with bonds
+#[repr(C)]
+#[non_exhaustive]
+#[derive(Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord)]
+pub enum BondOrder {
+ /// Unknown or unspecified bond order
+ Unknown = chfl_bond_order::CHFL_BOND_UNKNOWN as isize,
+ /// Single bond
+ Single = chfl_bond_order::CHFL_BOND_SINGLE as isize,
+ /// Double bond
+ Double = chfl_bond_order::CHFL_BOND_DOUBLE as isize,
+ /// Triple bond
+ Triple = chfl_bond_order::CHFL_BOND_TRIPLE as isize,
+ /// Quadruple bond (present in some metals)
+ Quadruple = chfl_bond_order::CHFL_BOND_QUADRUPLE as isize,
+ /// Quintuplet bond (present in some metals)
+ Quintuplet = chfl_bond_order::CHFL_BOND_QUINTUPLET as isize,
+ /// Amide bond (required by some file formats)
+ Amide = chfl_bond_order::CHFL_BOND_AMIDE as isize,
+ /// Aromatic bond (required by some file formats)
+ Aromatic = chfl_bond_order::CHFL_BOND_AROMATIC as isize,
+}
+
+impl BondOrder {
+ pub(crate) fn as_raw(self) -> chfl_bond_order {
+ match self {
+ BondOrder::Unknown => chfl_bond_order::CHFL_BOND_UNKNOWN,
+ BondOrder::Single => chfl_bond_order::CHFL_BOND_SINGLE,
+ BondOrder::Double => chfl_bond_order::CHFL_BOND_DOUBLE,
+ BondOrder::Triple => chfl_bond_order::CHFL_BOND_TRIPLE,
+ BondOrder::Quadruple => chfl_bond_order::CHFL_BOND_QUADRUPLE,
+ BondOrder::Quintuplet => chfl_bond_order::CHFL_BOND_QUINTUPLET,
+ BondOrder::Amide => chfl_bond_order::CHFL_BOND_AMIDE,
+ BondOrder::Aromatic => chfl_bond_order::CHFL_BOND_AROMATIC,
+ }
+ }
+}
+
+impl From<chfl_bond_order> for BondOrder {
+ fn from(order: chfl_bond_order) -> BondOrder {
+ match order {
+ chfl_bond_order::CHFL_BOND_UNKNOWN => BondOrder::Unknown,
+ chfl_bond_order::CHFL_BOND_SINGLE => BondOrder::Single,
+ chfl_bond_order::CHFL_BOND_DOUBLE => BondOrder::Double,
+ chfl_bond_order::CHFL_BOND_TRIPLE => BondOrder::Triple,
+ chfl_bond_order::CHFL_BOND_QUADRUPLE => BondOrder::Quadruple,
+ chfl_bond_order::CHFL_BOND_QUINTUPLET => BondOrder::Quintuplet,
+ chfl_bond_order::CHFL_BOND_AMIDE => BondOrder::Amide,
+ chfl_bond_order::CHFL_BOND_AROMATIC => BondOrder::Aromatic,
+ }
+ }
+}
+
+/// A `Topology` contains the definition of all the atoms in the system, and
+/// the liaisons between the atoms (bonds, angles, dihedrals, ...). It will
+/// also contain all the residues information if it is available.
+pub struct Topology {
+ handle: *mut CHFL_TOPOLOGY,
+}
+
+/// An analog to a reference to a topology (`&Topology`)
+pub struct TopologyRef<'a> {
+ inner: Topology,
+ marker: PhantomData<&'a Topology>
+}
+
+impl<'a> Deref for TopologyRef<'a> {
+ type Target = Topology;
+ fn deref(&self) -> &Topology {
+ &self.inner
+ }
+}
+
+impl Clone for Topology {
+ fn clone(&self) -> Topology {
+ unsafe {
+ let new_handle = chfl_topology_copy(self.as_ptr());
+ Topology::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Topology {
+ /// Create a `Topology` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer,
+ /// except for it being non-null.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_TOPOLOGY) -> Topology {
+ check_not_null(ptr);
+ Topology {
+ handle: ptr
+ }
+ }
+
+ /// Create a borrowed `Topology` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, except for it being non-null, and the caller is responsible
+ /// for setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_TOPOLOGY) -> TopologyRef<'a> {
+ TopologyRef {
+ inner: Topology::from_ptr(ptr as *mut CHFL_TOPOLOGY),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_TOPOLOGY {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_TOPOLOGY {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer FROM A SHARED REFERENCE.
+ ///
+ /// For uses with functions of the C API using mut pointers for both read
+ /// and write access. Users should check that this does not lead to multiple
+ /// mutable borrows
+ #[inline]
+ #[allow(non_snake_case)]
+ pub(crate) fn as_mut_ptr_MANUALLY_CHECKING_BORROW(&self) -> *mut CHFL_TOPOLOGY {
+ self.handle
+ }
+
+ /// Create a new empty topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let topology = Topology::new();
+ /// assert_eq!(topology.size(), 0);
+ /// ```
+ pub fn new() -> Topology {
+ unsafe {
+ Topology::from_ptr(chfl_topology())
+ }
+ }
+
+ /// Get a reference of the atom at the given `index` in this topology.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(6);
+ ///
+ /// let atom = topology.atom(4);
+ /// assert_eq!(atom.name(), "");
+ /// ```
+ pub fn atom(&self, index: usize) -> AtomRef {
+ unsafe {
+ let handle = chfl_atom_from_topology(
+ self.as_mut_ptr_MANUALLY_CHECKING_BORROW(), index as u64
+ );
+ Atom::ref_from_ptr(handle)
+ }
+ }
+
+ /// Get a mutable reference to the atom at the given `index` in this topology.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(6);
+ ///
+ /// assert_eq!(topology.atom(4).name(), "");
+ ///
+ /// topology.atom_mut(4).set_name("Fe");
+ /// assert_eq!(topology.atom(4).name(), "Fe");
+ /// ```
+ pub fn atom_mut(&mut self, index: usize) -> AtomMut {
+ unsafe {
+ let handle = chfl_atom_from_topology(
+ self.as_mut_ptr(), index as u64
+ );
+ Atom::ref_mut_from_ptr(handle)
+ }
+ }
+
+ /// Get the current number of atoms in this topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.size(), 0);
+ ///
+ /// topology.resize(6);
+ /// assert_eq!(topology.size(), 6);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(chfl_topology_atoms_count(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Resize this topology to hold `natoms` atoms, inserting dummy atoms if
+ /// the new size if bigger than the old one.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.size(), 0);
+ ///
+ /// topology.resize(6);
+ /// assert_eq!(topology.size(), 6);
+ /// ```
+ pub fn resize(&mut self, natoms: usize) {
+ unsafe {
+ check_success(chfl_topology_resize(self.as_mut_ptr(), natoms as u64));
+ }
+ }
+
+ /// Add an `Atom` at the end of this topology
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Atom};
+ /// let mut topology = Topology::new();
+ /// topology.add_atom(&Atom::new("Mg"));
+ ///
+ /// let atom = topology.atom(0);
+ /// assert_eq!(atom.name(), "Mg");
+ /// ```
+ pub fn add_atom(&mut self, atom: &Atom) {
+ unsafe {
+ check_success(chfl_topology_add_atom(self.as_mut_ptr(), atom.as_ptr()));
+ }
+ }
+
+ /// Remove an `Atom` from this topology by `index`. This modify all the
+ /// other atoms indexes.
+ ///
+ /// # Panics
+ ///
+ /// If the `index` is out of bounds
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(9);
+ /// assert_eq!(topology.size(), 9);
+ ///
+ /// topology.remove(7);
+ /// assert_eq!(topology.size(), 8);
+ /// ```
+ pub fn remove(&mut self, index: usize) {
+ unsafe {
+ check_success(chfl_topology_remove(self.as_mut_ptr(), index as u64));
+ }
+ }
+
+ /// Get the number of bonds in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.bonds_count(), 3);
+ /// ```
+ pub fn bonds_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_bonds_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the number of angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.angles_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.angles_count(), 2);
+ /// ```
+ pub fn angles_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_angles_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the number of dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.dihedrals_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.dihedrals_count(), 1);
+ /// ```
+ pub fn dihedrals_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_dihedrals_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the number of improper dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.dihedrals_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// topology.add_bond(0, 3);
+ /// assert_eq!(topology.impropers_count(), 1);
+ /// ```
+ pub fn impropers_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_impropers_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the list of bonds in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);
+ /// ```
+ pub fn bonds(&self) -> Vec<[usize; 2]> {
+ let size = self.bonds_count();
+ let count = size as u64;
+ let mut bonds = vec![[u64::max_value(); 2]; size];
+ unsafe {
+ check_success(chfl_topology_bonds(self.as_ptr(), bonds.as_mut_ptr(), count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return bonds
+ .into_iter()
+ .map(|bond| [bond[0] as usize, bond[1] as usize])
+ .collect();
+ }
+
+ /// Get the list of angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);
+ /// ```
+ pub fn angles(&self) -> Vec<[usize; 3]> {
+ let size = self.angles_count();
+ let count = size as u64;
+ let mut angles = vec![[u64::max_value(); 3]; size];
+ unsafe {
+ check_success(chfl_topology_angles(self.as_ptr(), angles.as_mut_ptr(), count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return angles
+ .into_iter()
+ .map(|angle| [angle[0] as usize, angle[1] as usize, angle[2] as usize])
+ .collect();
+ }
+
+ /// Get the list of dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ ///
+ /// assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);
+ /// ```
+ pub fn dihedrals(&self) -> Vec<[usize; 4]> {
+ let size = self.dihedrals_count();
+ let count = size as u64;
+ let mut dihedrals = vec![[u64::max_value(); 4]; size];
+ unsafe {
+ check_success(chfl_topology_dihedrals(
+ self.as_ptr(), dihedrals.as_mut_ptr(), count
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return dihedrals
+ .into_iter()
+ .map(|dihedral| {
+ [
+ dihedral[0] as usize,
+ dihedral[1] as usize,
+ dihedral[2] as usize,
+ dihedral[3] as usize,
+ ]
+ })
+ .collect();
+ }
+
+ /// Get the list of improper dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// topology.add_bond(0, 3);
+ ///
+ /// assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);
+ /// ```
+ pub fn impropers(&self) -> Vec<[usize; 4]> {
+ let size = self.impropers_count();
+ let count = size as u64;
+ let mut impropers = vec![[u64::max_value(); 4]; size];
+ unsafe {
+ check_success(chfl_topology_impropers(
+ self.as_ptr(), impropers.as_mut_ptr(), count
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return impropers
+ .into_iter()
+ .map(|improper| {
+ [
+ improper[0] as usize,
+ improper[1] as usize,
+ improper[2] as usize,
+ improper[3] as usize,
+ ]
+ })
+ .collect();
+ }
+
+ /// Remove all existing bonds, angles, dihedral angles and improper
+ /// dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// assert_eq!(topology.bonds_count(), 2);
+ /// assert_eq!(topology.angles().len(), 1);
+ ///
+ /// topology.clear_bonds();
+ /// assert!(topology.bonds().is_empty());
+ /// assert!(topology.angles().is_empty());
+ /// ```
+ pub fn clear_bonds(&mut self) {
+ unsafe {
+ check_success(chfl_topology_clear_bonds(self.as_mut_ptr()));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the topology.
+ ///
+ /// The bond order is set to `BondOrder::Unknown`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// assert_eq!(topology.bonds_count(), 2);
+ ///
+ /// assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);
+ /// ```
+ pub fn add_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(chfl_topology_add_bond(self.as_mut_ptr(), i as u64, j as u64));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the topology
+ /// with the given bond `order`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(2);
+ ///
+ /// topology.add_bond_with_order(0, 1, BondOrder::Double);
+ /// assert_eq!(topology.bond_order(0, 1), BondOrder::Double);
+ /// ```
+ pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder) {
+ unsafe {
+ check_success(chfl_topology_bond_with_order(
+ self.as_mut_ptr(), i as u64, j as u64, order.as_raw()
+ ));
+ }
+ }
+
+ /// Get the bond order for the bond between the atoms at indexes `i` and
+ /// `j`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(2);
+ ///
+ /// topology.add_bond_with_order(0, 1, BondOrder::Double);
+ /// assert_eq!(topology.bond_order(0, 1), BondOrder::Double);
+ /// ```
+ pub fn bond_order(&self, i: usize, j: usize) -> BondOrder {
+ let mut order = chfl_bond_order::CHFL_BOND_UNKNOWN;
+ unsafe {
+ check_success(chfl_topology_bond_order(
+ self.as_ptr(), i as u64, j as u64, &mut order
+ ));
+ }
+ return order.into()
+ }
+
+ /// Get the bond order for all the bonds in the topology
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(3);
+ ///
+ /// topology.add_bond_with_order(0, 1, BondOrder::Double);
+ /// topology.add_bond_with_order(0, 2, BondOrder::Single);
+ ///
+ /// assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);
+ /// ```
+ pub fn bond_orders(&self) -> Vec<BondOrder> {
+ let size = self.bonds_count();
+ let count = size as u64;
+ let mut bonds = vec![BondOrder::Unknown; size];
+ unsafe {
+ check_success(chfl_topology_bond_orders(
+ self.as_ptr(),
+ // Casting BondOrder to chfl_bond_order is safe, as they are
+ // both `repr(C)` enums with the same values.
+ bonds.as_mut_ptr().cast(),
+ count
+ ));
+ }
+ return bonds;
+ }
+
+ /// Remove any existing bond between the atoms at indexes `i` and `j` in
+ /// this topology.
+ ///
+ /// This function does nothing if there is no bond between `i` and `j`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(1, 2);
+ /// assert_eq!(topology.bonds_count(), 2);
+ ///
+ /// topology.remove_bond(0, 1);
+ /// assert_eq!(topology.bonds_count(), 1);
+ ///
+ /// // Removing a bond that does not exists is fine
+ /// topology.remove_bond(0, 2);
+ /// assert_eq!(topology.bonds_count(), 1);
+ /// ```
+ pub fn remove_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(chfl_topology_remove_bond(self.as_mut_ptr(), i as u64, j as u64));
+ }
+ }
+
+ /// Get a reference to the residue at index `index` from this topology.
+ ///
+ /// The residue index in the topology is not always the same as the residue
+ /// `id`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// topology.add_residue(&Residue::new("water")).unwrap();
+ ///
+ /// let residue = topology.residue(0).unwrap();
+ /// assert_eq!(residue.name(), "water");
+ /// ```
+ pub fn residue(&self, index: u64) -> Option<ResidueRef> {
+ unsafe {
+ let handle = chfl_residue_from_topology(self.as_ptr(), index as u64);
+ if handle.is_null() {
+ None
+ } else {
+ Some(Residue::ref_from_ptr(handle))
+ }
+ }
+ }
+
+ /// Get a copy of the residue containing the atom at index `index` in this
+ /// topology, if any.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// topology.resize(8);
+ ///
+ /// let mut residue = Residue::new("water");
+ /// residue.add_atom(0);
+ /// residue.add_atom(1);
+ /// residue.add_atom(2);
+ /// topology.add_residue(&residue).unwrap();
+ ///
+ /// let residue = topology.residue_for_atom(0).unwrap();
+ /// assert_eq!(residue.name(), "water");
+ ///
+ /// assert!(topology.residue_for_atom(6).is_none());
+ /// ```
+ pub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef> {
+ let handle = unsafe {
+ chfl_residue_for_atom(self.as_ptr(), index as u64)
+ };
+ if handle.is_null() {
+ None
+ } else {
+ unsafe {
+ Some(Residue::ref_from_ptr(handle))
+ }
+ }
+ }
+
+ /// Get the number of residues in this topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.residues_count(), 0);
+ ///
+ /// topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+ /// topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+ /// assert_eq!(topology.residues_count(), 2);
+ /// ```
+ pub fn residues_count(&self) -> u64 {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_residues_count(self.as_ptr(), &mut count));
+ }
+ return count;
+ }
+
+ /// Add a residue to this topology.
+ ///
+ /// # Errors
+ ///
+ /// This function fails is the residue `id` is not already in the topology,
+ /// or if the residue contains atoms that are already in another residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// topology.add_residue(&Residue::new("water")).unwrap();
+ ///
+ /// let residue = topology.residue(0).unwrap();
+ /// assert_eq!(residue.name(), "water");
+ /// ```
+ pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error> {
+ unsafe {
+ check(chfl_topology_add_residue(self.as_mut_ptr(), residue.as_ptr()))
+ }
+ }
+
+ /// Check if the two residues `first` and `second` from the `topology` are
+ /// linked together, *i.e.* if there is a bond between one atom in the
+ /// first residue and one atom in the second one.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ ///
+ /// topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+ /// topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+ ///
+ /// let first = topology.residue(0).unwrap();
+ /// let second = topology.residue(1).unwrap();
+ /// assert_eq!(topology.are_linked(&first, &second), false);
+ /// ```
+ pub fn are_linked(&self, first: &Residue, second: &Residue) -> bool {
+ let mut linked = 0;
+ unsafe {
+ check_success(chfl_topology_residues_linked(
+ self.as_ptr(),
+ first.as_ptr(),
+ second.as_ptr(),
+ &mut linked
+ ));
+ }
+ return linked != 0;
+ }
+}
+
+impl Drop for Topology {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+ use {Atom, Residue};
+
+ #[test]
+ fn clone() {
+ let mut topology = Topology::new();
+ assert_eq!(topology.size(), 0);
+
+ let copy = topology.clone();
+ assert_eq!(copy.size(), 0);
+
+ topology.resize(10);
+ assert_eq!(topology.size(), 10);
+ assert_eq!(copy.size(), 0);
+ }
+
+ #[test]
+ fn size() {
+ let mut topology = Topology::new();
+ assert_eq!(topology.size(), 0);
+
+ topology.resize(10);
+ assert_eq!(topology.size(), 10);
+
+ topology.remove(7);
+ assert_eq!(topology.size(), 9);
+
+ topology.add_atom(&Atom::new("Hg"));
+ assert_eq!(topology.size(), 10);
+ }
+
+ #[test]
+ fn atoms() {
+ let mut topology = Topology::new();
+
+ topology.add_atom(&Atom::new("Hg"));
+ topology.add_atom(&Atom::new("Mn"));
+ topology.add_atom(&Atom::new("W"));
+ topology.add_atom(&Atom::new("Fe"));
+
+ assert_eq!(topology.atom(0).name(), "Hg");
+ assert_eq!(topology.atom(3).name(), "Fe");
+ }
+
+ #[test]
+ fn remove() {
+ let mut topology = Topology::new();
+ topology.add_atom(&Atom::new("Hg"));
+ topology.add_atom(&Atom::new("Mn"));
+ topology.add_atom(&Atom::new("W"));
+ topology.add_atom(&Atom::new("Fe"));
+
+ assert_eq!(topology.atom(0).name(), "Hg");
+ assert_eq!(topology.atom(2).name(), "W");
+
+ topology.remove(1);
+ assert_eq!(topology.atom(0).name(), "Hg");
+ assert_eq!(topology.atom(2).name(), "Fe");
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_remove() {
+ let mut topology = Topology::new();
+ topology.resize(18);
+ topology.remove(33);
+ }
+
+
+ #[test]
+ fn bonds() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.bonds_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(9, 2);
+ topology.add_bond_with_order(3, 7, BondOrder::Aromatic);
+ assert_eq!(topology.bonds_count(), 3);
+
+ assert_eq!(topology.bonds(), vec![[0, 1], [2, 9], [3, 7]]);
+ let expected = vec![BondOrder::Unknown, BondOrder::Unknown, BondOrder::Aromatic];
+ assert_eq!(topology.bond_orders(), expected);
+
+ assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);
+ assert_eq!(topology.bond_order(3, 7), BondOrder::Aromatic);
+
+ topology.remove_bond(3, 7);
+ // Removing unexisting bond is OK if both indexes are in bounds
+ topology.remove_bond(8, 7);
+ assert_eq!(topology.bonds_count(), 2);
+
+ topology.clear_bonds();
+ assert_eq!(topology.bonds_count(), 0);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ topology.add_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_remove_bond() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ topology.remove_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds_with_order() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ topology.add_bond_with_order(300, 7, BondOrder::Unknown);
+ }
+
+ #[test]
+ fn angles() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.angles_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(1, 2);
+ topology.add_bond(3, 7);
+ topology.add_bond(3, 5);
+ assert_eq!(topology.angles_count(), 2);
+
+ assert_eq!(topology.angles(), vec![[0, 1, 2], [5, 3, 7]]);
+
+ topology.clear_bonds();
+ assert_eq!(topology.angles_count(), 0);
+ }
+
+ #[test]
+ fn dihedrals() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.dihedrals_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(1, 2);
+ topology.add_bond(3, 2);
+ topology.add_bond(4, 7);
+ topology.add_bond(4, 5);
+ topology.add_bond(7, 10);
+ assert_eq!(topology.dihedrals_count(), 2);
+
+ assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3], [5, 4, 7, 10]]);
+
+ topology.clear_bonds();
+ assert_eq!(topology.dihedrals_count(), 0);
+ }
+
+ #[test]
+ fn impropers() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.impropers_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(0, 2);
+ topology.add_bond(0, 3);
+ topology.add_bond(4, 7);
+ topology.add_bond(4, 5);
+ topology.add_bond(4, 8);
+ assert_eq!(topology.impropers_count(), 2);
+
+ assert_eq!(topology.impropers(), vec![[1, 0, 2, 3], [5, 4, 7, 8]]);
+
+ topology.clear_bonds();
+ assert_eq!(topology.impropers_count(), 0);
+ }
+
+ #[test]
+ fn residues() {
+ let mut topology = Topology::new();
+ topology.resize(4);
+ assert_eq!(topology.residues_count(), 0);
+
+ let mut residue = Residue::new("Foo");
+ residue.add_atom(0);
+ residue.add_atom(2);
+
+ topology.add_residue(&residue).unwrap();
+ assert_eq!(topology.residues_count(), 1);
+
+ assert_eq!(topology.residue(0).unwrap().name(), "Foo");
+ {
+ let residue = topology.residue_for_atom(2).unwrap();
+ assert_eq!(residue.name(), "Foo");
+ }
+
+ let mut residue = Residue::new("Bar");
+ residue.add_atom(3);
+ topology.add_residue(&residue).unwrap();
+ assert_eq!(topology.residues_count(), 2);
+
+ let first = topology.residue(0).unwrap();
+ let second = topology.residue(0).unwrap();
+ assert!(topology.are_linked(&first, &second));
+
+ // missing residue
+ assert!(topology.residue_for_atom(1).is_none());
+ // out of bounds
+ assert!(topology.residue_for_atom(67).is_none());
+ }
+}
+1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9 + 10 + 11 + 12 + 13 + 14 + 15 + 16 + 17 + 18 + 19 + 20 + 21 + 22 + 23 + 24 + 25 + 26 + 27 + 28 + 29 + 30 + 31 + 32 + 33 + 34 + 35 + 36 + 37 + 38 + 39 + 40 + 41 + 42 + 43 + 44 + 45 + 46 + 47 + 48 + 49 + 50 + 51 + 52 + 53 + 54 + 55 + 56 + 57 + 58 + 59 + 60 + 61 + 62 + 63 + 64 + 65 + 66 + 67 + 68 + 69 + 70 + 71 + 72 + 73 + 74 + 75 + 76 + 77 + 78 + 79 + 80 + 81 + 82 + 83 + 84 + 85 + 86 + 87 + 88 + 89 + 90 + 91 + 92 + 93 + 94 + 95 + 96 + 97 + 98 + 99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371 +372 +373 +374 +375 +376 +377 +378 +379 +380 +381 +382 +383 +384 +385 +386 +387 +388 +389 +390 +391 +392 +393 +394 +395 +396 +397 +398 +399 +400 +401 +402 +403 +404 +405 +406 +407 +408 +409 +410 +411 +412 +413 +414 +415 +416 +417 +418 +419 +420 +421 +422 +423 +424 +425 +426 +427 +428 +429 +430 +431 +432 +433 +434 +435 +436 +437 +438 +439 +440 +441 +442 +443 +444 +445 +446 +447 +448 +449 +450 +451 +452 +453 +454 +455 +456 +457 +458 +459 +460 +461 +462 +463 +464 +465 +466 +467 +468 +469 +470 +471 +472 +473 +474 +475 +476 +477 +478 +479 +480 +481 +482 +483 +484 +485 +486 +487 +488 +489 +490 +491 +492 +493 +494 +495 +496 +497 +498 +499 +500 +501 +502 +503 +504 +505 +506 +507 +508 +509 +510 +511 +512 +513 +514 +515 +516 +517 +518 +519 +520 +521 +522 +523 +524 +525 +526 +527 +528 +529 +530 +531 +532 +533 +534 +535 +536 +537 +538 +539 +540 +541 +542 +543 +544 +545 +546 +547 +548 +549 +550 +551 +552 +553 +554 +555 +556 +557 +558 +559 +560 +561 +562 +563 +564 +565 +566 +567 +568 +569 +570 +571 +572 +573 +574 +575 +576 +577 +578 +579 +580 +581 +582 +583 +584 +585 +586 +587 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::convert::TryInto;
+use std::path::Path;
+use std::ptr;
+
+use chemfiles_sys::*;
+use errors::{check, check_success, Error, Status};
+use strings;
+
+use {Frame, Topology, UnitCell};
+
+/// The `Trajectory` type is the main entry point when using chemfiles. A
+/// `Trajectory` behave a bit like a file, allowing to read and/or write
+/// `Frame`.
+pub struct Trajectory {
+ handle: *mut CHFL_TRAJECTORY,
+}
+
+impl Trajectory {
+ /// Create a `Trajectory` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_TRAJECTORY) -> Result<Trajectory, Error> {
+ if ptr.is_null() {
+ Err(Error {
+ status: Status::FileError,
+ message: Error::last_error()
+ })
+ } else {
+ Ok(Trajectory {
+ handle: ptr
+ })
+ }
+ }
+
+ /// Get the underlying C pointer as a pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_TRAJECTORY {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_TRAJECTORY {
+ self.handle
+ }
+
+ /// Open the file at the given `path` in the given `mode`.
+ ///
+ /// Valid modes are `'r'` for read, `'w'` for write and `'a'` for append.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the file is not accessible for the given mode, if
+ /// it is incorrectly formatted for the corresponding format, or in case of
+ /// I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// ```
+ pub fn open<P>(path: P, mode: char) -> Result<Trajectory, Error>
+ where
+ P: AsRef<Path>,
+ {
+ let path = path.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(path.as_ref()))?;
+
+ let path = strings::to_c(path);
+ unsafe {
+ #[allow(clippy::cast_possible_wrap)]
+ let handle = chfl_trajectory_open(path.as_ptr(), mode as i8);
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Open the file at the given `path` using a specific file `format` and the
+ /// given `mode`.
+ ///
+ /// Valid modes are `'r'` for read, `'w'` for write and `'a'` for append.
+ ///
+ /// Specifying a format is needed when the file format does not match the
+ /// extension, or when there is not standard extension for this format. If
+ /// `format` is an empty string, the format will be guessed from the
+ /// extension.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the file is not accessible for the given mode, if
+ /// it is incorrectly formatted for the corresponding format, or in case of
+ /// I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let trajectory = Trajectory::open_with_format("water.zeo", 'r', "XYZ").unwrap();
+ /// ```
+ pub fn open_with_format<'a, P, S>(filename: P, mode: char, format: S) -> Result<Trajectory, Error>
+ where
+ P: AsRef<Path>,
+ S: Into<&'a str>,
+ {
+ let filename =
+ filename.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(filename.as_ref()))?;
+
+ let filename = strings::to_c(filename);
+ let format = strings::to_c(format.into());
+ unsafe {
+ #[allow(clippy::cast_possible_wrap)]
+ let handle = chfl_trajectory_with_format(
+ filename.as_ptr(), mode as i8, format.as_ptr()
+ );
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Read a memory buffer as though it was a formatted file.
+ ///
+ /// The memory buffer used to store the file is given using the `data`
+ /// argument. The `format` parameter is required and should follow the same
+ /// rules as in the main `Trajectory` constructor.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format, or if the format do not support in-memory readers.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let aromatics = "c1ccccc1\nc1ccco1\nc1ccccn1\n";
+ /// let mut trajectory = Trajectory::memory_reader(aromatics, "SMI").unwrap();
+ /// let mut frame = Frame::new();
+ /// trajectory.read(&mut frame).unwrap();
+ /// assert_eq!(frame.size(), 6);
+ /// ```
+ pub fn memory_reader<'a, S>(data: S, format: S) -> Result<Trajectory, Error>
+ where S: Into<&'a str>,
+ {
+ let data = strings::to_c(data.into());
+ let format = strings::to_c(format.into());
+ unsafe {
+ let handle = chfl_trajectory_memory_reader(
+ data.as_ptr(), data.as_bytes().len() as u64, format.as_ptr()
+ );
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Write to a memory buffer as though it was a formatted file.
+ ///
+ /// The `format` parameter should follow the same rules as in the main
+ /// `Trajectory` constructor, except that compression specification
+ /// is not supported.
+ ///
+ /// The `memory_buffer` function can be used to retrieve the data written
+ /// to memory of the `Trajectory`.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the format do not support in-memory writers.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Trajectory;
+ /// let trajectory_memory = Trajectory::memory_writer("SMI");
+ ///
+ /// // Binary formats typically do not support this feature
+ /// assert!(Trajectory::memory_writer("XTC").is_err());
+ /// ```
+ pub fn memory_writer<'a, S>(format: S) -> Result<Trajectory, Error>
+ where S: Into<&'a str>,
+ {
+ let format = strings::to_c(format.into());
+ unsafe {
+ let handle = chfl_trajectory_memory_writer(format.as_ptr());
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Read the next step of this trajectory into a `frame`.
+ ///
+ /// If the number of atoms in frame does not correspond to the number of atom
+ /// in the next step, the frame is resized.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format, or in case of I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// let mut frame = Frame::new();
+ ///
+ /// trajectory.read(&mut frame).unwrap();
+ /// ```
+ pub fn read(&mut self, frame: &mut Frame) -> Result<(), Error> {
+ unsafe {
+ check(chfl_trajectory_read(self.as_mut_ptr(), frame.as_mut_ptr()))
+ }
+ }
+
+ /// Read a specific `step` of this trajectory into a `frame`.
+ ///
+ /// If the number of atoms in frame does not correspond to the number of
+ /// atom at this step, the frame is resized.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// let mut frame = Frame::new();
+ ///
+ /// trajectory.read_step(10, &mut frame).unwrap();
+ /// ```
+ pub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error> {
+ unsafe {
+ check(chfl_trajectory_read_step(self.as_mut_ptr(), step as u64, frame.as_mut_ptr()))
+ }
+ }
+
+ /// Write a `frame` to this trajectory.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let mut trajectory = Trajectory::open("water.pdb", 'w').unwrap();
+ /// let mut frame = Frame::new();
+ ///
+ /// trajectory.write(&mut frame).unwrap();
+ /// ```
+ pub fn write(&mut self, frame: &Frame) -> Result<(), Error> {
+ unsafe {
+ check(chfl_trajectory_write(self.as_mut_ptr(), frame.as_ptr()))
+ }
+ }
+
+ /// Set the `topology` associated with this trajectory. This topology will
+ /// be used when reading and writing the files, replacing any topology in
+ /// the frames or files.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Atom, Topology};
+ /// let mut topology = Topology::new();
+ /// topology.add_atom(&Atom::new("H"));
+ /// topology.add_atom(&Atom::new("O"));
+ /// topology.add_atom(&Atom::new("H"));
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(1, 2);
+ ///
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// trajectory.set_topology(&topology);
+ /// ```
+ pub fn set_topology(&mut self, topology: &Topology) {
+ unsafe {
+ check_success(chfl_trajectory_set_topology(self.as_mut_ptr(), topology.as_ptr()));
+ }
+ }
+
+ /// Set the topology associated with this trajectory by reading the first
+ /// frame of the file at the given `path` using the file format in `format`;
+ /// and extracting the topology of this frame.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the topology file is incorrectly formatted for
+ /// the corresponding format, or in case of I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+ /// trajectory.set_topology_file("topology.pdb").unwrap();
+ /// ```
+ pub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error>
+ where
+ P: AsRef<Path>,
+ {
+ let path = path.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(path.as_ref()))?;
+
+ let path = strings::to_c(path);
+ unsafe {
+ check(chfl_trajectory_topology_file(self.as_mut_ptr(), path.as_ptr(), ptr::null()))
+ }
+ }
+
+ /// Set the topology associated with this trajectory by reading the first
+ /// frame of the file at the given `path` using the file format in
+ /// `format`; and extracting the topology of this frame.
+ ///
+ /// If `format` is an empty string, the format will be guessed from the
+ /// `path` extension.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the topology file is incorrectly formatted for
+ /// the corresponding format, or in case of I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+ /// trajectory.set_topology_with_format("topology.mol", "PDB").unwrap();
+ /// ```
+ pub fn set_topology_with_format<'a, P, S>(&mut self, path: P, format: S) -> Result<(), Error>
+ where
+ P: AsRef<Path>,
+ S: Into<&'a str>,
+ {
+ let path = path.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(path.as_ref()))?;
+
+ let format = strings::to_c(format.into());
+ let path = strings::to_c(path);
+ unsafe {
+ check(chfl_trajectory_topology_file(self.as_mut_ptr(), path.as_ptr(), format.as_ptr()))
+ }
+ }
+
+ /// Set the unit `cell` associated with a trajectory. This cell will be
+ /// used when reading and writing the files, replacing any unit cell in the
+ /// frames or files.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, UnitCell};
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// trajectory.set_cell(&UnitCell::new([10.0, 11.0, 12.5]));
+ /// ```
+ pub fn set_cell(&mut self, cell: &UnitCell) {
+ unsafe {
+ check_success(chfl_trajectory_set_cell(self.as_mut_ptr(), cell.as_ptr()));
+ }
+ }
+
+ /// Get the number of steps (the number of frames) in a trajectory.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ ///
+ /// println!("This trajectory contains {} steps", trajectory.nsteps());
+ /// ```
+ // FIXME should this take &self instead? The file can be modified by this
+ // function, but the format should reset the state.
+ pub fn nsteps(&mut self) -> usize {
+ let mut res = 0;
+ unsafe {
+ check(chfl_trajectory_nsteps(self.as_mut_ptr(), &mut res)).expect(
+ "failed to get the number of steps in this trajectory"
+ );
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return res as usize;
+ }
+
+ /// Obtain the memory buffer written to by the trajectory.
+ ///
+ /// # Errors
+ ///
+ /// This fails if the trajectory was not opened with
+ /// `Trajectory::memory_writer`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Atom, BondOrder, Frame, Trajectory};
+ /// let mut trajectory_memory = Trajectory::memory_writer("SMI").unwrap();
+ ///
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+ /// frame.add_bond_with_order(0, 1, BondOrder::Single);
+ ///
+ /// trajectory_memory.write(&frame).unwrap();
+ ///
+ /// let result = trajectory_memory.memory_buffer();
+ /// assert_eq!(result.unwrap(), "CC\n");
+ /// ```
+ #[allow(clippy::cast_possible_truncation)]
+ pub fn memory_buffer(&self) -> Result<&str, Error> {
+ let mut ptr: *const i8 = std::ptr::null();
+ let mut count: u64 = 0;
+ let buffer = unsafe {
+ check(chfl_trajectory_memory_buffer(self.as_ptr(), &mut ptr, &mut count))?;
+ std::slice::from_raw_parts(
+ ptr.cast(), count.try_into().expect("failed to convert u64 to usize")
+ )
+ };
+
+ let string = std::str::from_utf8(buffer)?;
+ Ok(string)
+ }
+
+ /// Get file path for this trajectory.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ ///
+ /// assert_eq!(trajectory.path(), "water.xyz");
+ /// ```
+ pub fn path(&self) -> String {
+ let get_string = |ptr, len| unsafe { chfl_trajectory_path(self.as_ptr(), ptr, len) };
+ let path = strings::call_autogrow_buffer(1024, get_string).expect("failed to get path string");
+ return strings::from_c(path.as_ptr());
+ }
+}
+
+impl Drop for Trajectory {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_trajectory_close(self.as_ptr());
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ use std::fs;
+ use std::path::Path;
+ use std::io::Read;
+
+ use approx::assert_ulps_eq;
+
+ use {Atom, CellShape, Frame, Topology, UnitCell};
+
+ #[test]
+ fn read() {
+ let root = Path::new(file!()).parent().unwrap().join("..");
+ let filename = root.join("data").join("water.xyz");
+ let mut file = Trajectory::open(filename.to_str().unwrap(), 'r').unwrap();
+
+ if cfg!(target_family = "unix") {
+ assert_eq!(file.path(), "src/../data/water.xyz");
+ } else if cfg!(target_family = "windows") {
+ assert_eq!(file.path(), "src\\..\\data\\water.xyz");
+ } else {
+ panic!("please add test for this OS!");
+ }
+
+ assert_eq!(file.nsteps(), 100);
+
+ let mut frame = Frame::new();
+ assert!(file.read(&mut frame).is_ok());
+
+ assert_eq!(frame.size(), 297);
+ assert_ulps_eq!(frame.positions()[0][0], 0.417219);
+ assert_ulps_eq!(frame.positions()[0][1], 8.303366);
+ assert_ulps_eq!(frame.positions()[0][2], 11.737172);
+ assert_ulps_eq!(frame.positions()[124][0], 5.099554);
+ assert_ulps_eq!(frame.positions()[124][1], -0.045104);
+ assert_ulps_eq!(frame.positions()[124][2], 14.153846);
+
+ assert_eq!(frame.atom(0).name(), "O");
+
+ file.set_cell(&UnitCell::new([30.0, 30.0, 30.0]));
+ assert!(file.read_step(41, &mut frame).is_ok());
+ let cell = frame.cell().clone();
+ assert_eq!(cell.lengths(), [30.0, 30.0, 30.0]);
+
+
+ assert_ulps_eq!(frame.positions()[0][0], 0.761277);
+ assert_ulps_eq!(frame.positions()[0][1], 8.106125);
+ assert_ulps_eq!(frame.positions()[0][2], 10.622949);
+ assert_ulps_eq!(frame.positions()[124][0], 5.13242);
+ assert_ulps_eq!(frame.positions()[124][1], 0.079862);
+ assert_ulps_eq!(frame.positions()[124][2], 14.194161);
+
+ {
+ let topology = frame.topology();
+ assert_eq!(topology.size(), 297);
+ assert_eq!(topology.bonds_count(), 0);
+ }
+
+ assert!(frame.guess_bonds().is_ok());
+ {
+ let topology = frame.topology();
+ assert_eq!(topology.size(), 297);
+ assert_eq!(topology.bonds_count(), 180);
+ assert_eq!(topology.angles_count(), 84);
+ }
+
+ let mut topology = Topology::new();
+ let atom = Atom::new("Cs");
+ for _ in 0..297 {
+ topology.add_atom(&atom);
+ }
+
+ file.set_topology(&topology);
+ assert!(file.read_step(10, &mut frame).is_ok());
+ assert_eq!(frame.atom(42).name(), "Cs");
+
+ let filename = root.join("data").join("topology.xyz");
+ assert!(file.set_topology_file(filename.to_str().unwrap()).is_ok());
+ assert!(file.read(&mut frame).is_ok());
+ assert_eq!(frame.atom(100).name(), "Rd");
+
+ let filename = root.join("data").join("helium.xyz.but.not.really");
+ let filename = filename.to_str().unwrap();
+ let mut file = Trajectory::open_with_format(filename, 'r', "XYZ").unwrap();
+ assert!(file.read(&mut frame).is_ok());
+ assert_eq!(frame.size(), 125);
+ }
+
+ fn write_file(path: &str) {
+ let mut file = Trajectory::open(path, 'w').unwrap();
+ let mut frame = Frame::new();
+ frame.resize(4);
+
+ for position in frame.positions_mut() {
+ *position = [1.0, 2.0, 3.0];
+ }
+
+ let mut topology = Topology::new();
+ let atom = Atom::new("X");
+ for _ in 0..4 {
+ topology.add_atom(&atom);
+ }
+ frame.set_topology(&topology).unwrap();
+ assert!(file.write(&frame).is_ok());
+ }
+
+ #[test]
+ fn write() {
+ let filename = "test-tmp.xyz";
+ write_file(filename);
+
+ let expected_content = "4
+Properties=species:S:1:pos:R:3
+X 1 2 3
+X 1 2 3
+X 1 2 3
+X 1 2 3".lines().collect::<Vec<_>>();
+
+ let mut file = fs::File::open(filename).unwrap();
+ let mut content = String::new();
+ let _ = file.read_to_string(&mut content).unwrap();
+
+ assert_eq!(expected_content, content.lines().collect::<Vec<_>>());
+ fs::remove_file(filename).unwrap();
+ }
+
+ #[test]
+ fn memory() {
+ // formats in decreasing order of their memory buffer length to check null termination
+ for format in &["CSSR", "GRO", "XYZ"] {
+ let mut frame_write = Frame::new();
+ frame_write.add_atom(&Atom::new("H"), [1.5, 3.0, -10.0], None);
+ frame_write.add_atom(&Atom::new("O"), [2.3, -1.4, 50.0], None);
+ frame_write.add_atom(&Atom::new("H"), [-1.5, 10.0, 0.0], None);
+ let cell = UnitCell::new([10.0, 11.0, 12.5]);
+
+ let mut trajectory_write = Trajectory::memory_writer(*format).unwrap();
+ trajectory_write.set_cell(&cell);
+ trajectory_write.write(&frame_write).unwrap();
+
+ let buffer = trajectory_write.memory_buffer().unwrap();
+ let mut trajectory_read = Trajectory::memory_reader(buffer, *format).unwrap();
+ let mut frame_read = Frame::new();
+ trajectory_read.read(&mut frame_read).unwrap();
+
+ assert_eq!(trajectory_read.nsteps(), 1);
+ assert_eq!(frame_read.cell().shape(), CellShape::Orthorhombic);
+ assert_eq!(frame_read.size(), 3);
+ assert_eq!(frame_read.atom(1).name(), "O");
+ crate::assert_vector3d_eq(&frame_read.positions()[2], &[-1.5, 10.0, 0.0], 1e-4);
+ }
+ }
+}
+Redirecting to ../../chemfiles/struct.Atom.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/atom/struct.AtomMut.html b/0.10.3/chemfiles/atom/struct.AtomMut.html new file mode 100644 index 000000000..2843d6f36 --- /dev/null +++ b/0.10.3/chemfiles/atom/struct.AtomMut.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.AtomMut.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/atom/struct.AtomRef.html b/0.10.3/chemfiles/atom/struct.AtomRef.html new file mode 100644 index 000000000..fc21ff8b9 --- /dev/null +++ b/0.10.3/chemfiles/atom/struct.AtomRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.AtomRef.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/cell/enum.CellShape.html b/0.10.3/chemfiles/cell/enum.CellShape.html new file mode 100644 index 000000000..9d3d95dbc --- /dev/null +++ b/0.10.3/chemfiles/cell/enum.CellShape.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/enum.CellShape.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/cell/struct.UnitCell.html b/0.10.3/chemfiles/cell/struct.UnitCell.html new file mode 100644 index 000000000..c199c7635 --- /dev/null +++ b/0.10.3/chemfiles/cell/struct.UnitCell.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.UnitCell.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/cell/struct.UnitCellMut.html b/0.10.3/chemfiles/cell/struct.UnitCellMut.html new file mode 100644 index 000000000..a07e76605 --- /dev/null +++ b/0.10.3/chemfiles/cell/struct.UnitCellMut.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.UnitCellMut.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/cell/struct.UnitCellRef.html b/0.10.3/chemfiles/cell/struct.UnitCellRef.html new file mode 100644 index 000000000..7455c76ac --- /dev/null +++ b/0.10.3/chemfiles/cell/struct.UnitCellRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.UnitCellRef.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/enum.BondOrder.html b/0.10.3/chemfiles/enum.BondOrder.html new file mode 100644 index 000000000..afa60b69a --- /dev/null +++ b/0.10.3/chemfiles/enum.BondOrder.html @@ -0,0 +1,61 @@ +
#[repr(C)]
+#[non_exhaustive]
+pub enum BondOrder {
+ Unknown,
+ Single,
+ Double,
+ Triple,
+ Quadruple,
+ Quintuplet,
+ Amide,
+ Aromatic,
+}Expand description
Possible bond order associated with bonds
+Variants (Non-exhaustive)
This enum is marked as non-exhaustive
Non-exhaustive enums could have additional variants added in future. Therefore, when matching against variants of non-exhaustive enums, an extra wildcard arm must be added to account for any future variants.
Unknown
Unknown or unspecified bond order
+Single
Single bond
+Double
Double bond
+Triple
Triple bond
+Quadruple
Quadruple bond (present in some metals)
+Quintuplet
Quintuplet bond (present in some metals)
+Amide
Amide bond (required by some file formats)
+Aromatic
Aromatic bond (required by some file formats)
+Trait Implementations
sourceimpl Ord for BondOrder
impl Ord for BondOrder
sourceimpl PartialOrd<BondOrder> for BondOrder
impl PartialOrd<BondOrder> for BondOrder
sourcefn partial_cmp(&self, other: &BondOrder) -> Option<Ordering>
fn partial_cmp(&self, other: &BondOrder) -> Option<Ordering>
This method returns an ordering between self and other values if one exists. Read more
1.0.0 · sourcefn lt(&self, other: &Rhs) -> bool
fn lt(&self, other: &Rhs) -> bool
This method tests less than (for self and other) and is used by the < operator. Read more
1.0.0 · sourcefn le(&self, other: &Rhs) -> bool
fn le(&self, other: &Rhs) -> bool
This method tests less than or equal to (for self and other) and is used by the <=
+operator. Read more
impl Copy for BondOrder
impl Eq for BondOrder
impl StructuralEq for BondOrder
impl StructuralPartialEq for BondOrder
Auto Trait Implementations
impl RefUnwindSafe for BondOrder
impl Send for BondOrder
impl Sync for BondOrder
impl Unpin for BondOrder
impl UnwindSafe for BondOrder
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+pub enum CellShape {
+ Orthorhombic,
+ Triclinic,
+ Infinite,
+}Expand description
Available unit cell shapes.
+Variants
Orthorhombic
Orthorhombic cell, with the three angles equals to 90°.
+Triclinic
Triclinic cell, with any values for the angles.
+Infinite
Infinite cell, to use when there is no cell.
+Trait Implementations
impl Eq for CellShape
impl StructuralEq for CellShape
impl StructuralPartialEq for CellShape
Auto Trait Implementations
impl RefUnwindSafe for CellShape
impl Send for CellShape
impl Sync for CellShape
impl Unpin for CellShape
impl UnwindSafe for CellShape
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+Expand description
A Property is a piece of data that can be associated with an Atom or a
+Frame.
Variants
Bool(bool)
Boolean property
+Double(f64)
Floating point property
+String(String)
String property
+Vector3D([f64; 3])
3-dimensional vector property
+Trait Implementations
sourceimpl PartialOrd<Property> for Property
impl PartialOrd<Property> for Property
sourcefn partial_cmp(&self, other: &Property) -> Option<Ordering>
fn partial_cmp(&self, other: &Property) -> Option<Ordering>
This method returns an ordering between self and other values if one exists. Read more
1.0.0 · sourcefn lt(&self, other: &Rhs) -> bool
fn lt(&self, other: &Rhs) -> bool
This method tests less than (for self and other) and is used by the < operator. Read more
1.0.0 · sourcefn le(&self, other: &Rhs) -> bool
fn le(&self, other: &Rhs) -> bool
This method tests less than or equal to (for self and other) and is used by the <=
+operator. Read more
impl StructuralPartialEq for Property
Auto Trait Implementations
impl RefUnwindSafe for Property
impl Send for Property
impl Sync for Property
impl Unpin for Property
impl UnwindSafe for Property
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+#[repr(C)]
+#[non_exhaustive]
+pub enum Status {
+ Success,
+ MemoryError,
+ FileError,
+ FormatError,
+ SelectionError,
+ ConfigurationError,
+ OutOfBounds,
+ PropertyError,
+ ChemfilesError,
+ StdCppError,
+ UTF8PathError,
+}Expand description
Possible causes of error in chemfiles
+Variants (Non-exhaustive)
This enum is marked as non-exhaustive
Non-exhaustive enums could have additional variants added in future. Therefore, when matching against variants of non-exhaustive enums, an extra wildcard arm must be added to account for any future variants.
Success
No error
+MemoryError
Error in memory allocations
+FileError
Error while reading or writing a file
+FormatError
Error in file formatting, i.e. the file is invalid
+SelectionError
Error in selection string syntax
+ConfigurationError
Error in configuration files syntax
+OutOfBounds
Error for out of bounds indexing
+PropertyError
Error related to properties
+ChemfilesError
Exception in the C++ chemfiles library
+StdCppError
Exception in the C++ standard library
+UTF8PathError
The given path is not valid UTF8
+Trait Implementations
impl Eq for Status
impl StructuralEq for Status
impl StructuralPartialEq for Status
Auto Trait Implementations
impl RefUnwindSafe for Status
impl Send for Status
impl Sync for Status
impl Unpin for Status
impl UnwindSafe for Status
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+Redirecting to ../../chemfiles/enum.Status.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/errors/fn.set_warning_callback.html b/0.10.3/chemfiles/errors/fn.set_warning_callback.html new file mode 100644 index 000000000..97bc2a1ba --- /dev/null +++ b/0.10.3/chemfiles/errors/fn.set_warning_callback.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/fn.set_warning_callback.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/errors/struct.Error.html b/0.10.3/chemfiles/errors/struct.Error.html new file mode 100644 index 000000000..34339c749 --- /dev/null +++ b/0.10.3/chemfiles/errors/struct.Error.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Error.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/fn.add_configuration.html b/0.10.3/chemfiles/fn.add_configuration.html new file mode 100644 index 000000000..069ed3473 --- /dev/null +++ b/0.10.3/chemfiles/fn.add_configuration.html @@ -0,0 +1,20 @@ +
+ Function chemfiles::
source · [−]
Function chemfiles::add_configuration
source · [−]Expand description
Read configuration data from the file at path.
By default, chemfiles reads configuration from any file named
+.chemfiles.toml in the current directory or any parent directory. This
+function can be used to add data from another configuration file. Data from
+the new configuration file will overwrite any existing data.
Errors
+This function will fail if there is no file at path, or if the file is
+incorrectly formatted.
Example
+chemfiles::add_configuration("local-config.toml").unwrap();
+// from now on, the data from "local-config.toml" will be used
+ Function chemfiles::
source · [−]
Function chemfiles::formats_list
source · [−]pub fn formats_list() -> Vec<FormatMetadata>Expand description
Get the list of formats known by chemfiles, as well as all associated metadata.
+Example
+let formats = chemfiles::formats_list();
+println!("chemfiles supports {} formats:", formats.len());
+for format in &formats {
+ println!(
+ " {:<15} {}",
+ format.name,
+ format.extension.as_deref().unwrap_or("")
+ );
+}
+ Function chemfiles::
source · [−]
Function chemfiles::guess_format
source · [−]Expand description
Get the format that chemfiles would use to read a file at the given
+path.
The format is mostly guessed from the path extension, chemfiles only tries
+to read the file to distinguish between CIF and mmCIF files. Opening the
+file using the returned format string might still fail. For example, it will
+fail if the file is not actually formatted according to the guessed format;
+or the format/compression combination is not supported (e.g. XTC / GZ will
+not work since the XTC reader does not support compressed files).
The returned format is represented in a way compatible with the various
+Trajectory constructors, i.e. "<format name> [/ <compression>]", where
+compression is optional.
Examples
+let format = chemfiles::guess_format("trajectory.xyz.xz");
+assert_eq!(format, "XYZ / XZ");
+
+let format = chemfiles::guess_format("trajectory.nc");
+assert_eq!(format, "Amber NetCDF");
+ Function chemfiles::
source · [−]
Function chemfiles::set_warning_callback
source · [−]pub fn set_warning_callback<F>(callback: F) where
F: WarningCallback + 'static, Expand description
Use callback for every chemfiles warning. The callback will be passed
+the warning message. This will drop any previous warning callback.
Redirecting to ../../chemfiles/struct.Frame.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/index.html b/0.10.3/chemfiles/index.html new file mode 100644 index 000000000..d3622c468 --- /dev/null +++ b/0.10.3/chemfiles/index.html @@ -0,0 +1,69 @@ +Expand description
Chemfiles is a multi-language library written in modern C++ for reading and +writing from and to molecular trajectory files. These files are created by +your favorite theoretical chemistry program, and contains information about +atomic or residues names and positions. Some format also have additional +information, such as velocities, forces, energy, …
+This crate expose the C API of chemfiles to Rust, and make all the +functionalities accessible. For more information on the C++ library, +please see its documentation. Specifically, the following pages +are worth reading:
+-
+
- The overview of the classes organization; +
- The list of supported formats; +
- The documentation for the selection language; +
Structs
+An Atom is a particle in the current Frame. It stores the following
+atomic properties:
An analog to a mutable reference to an atom (&mut Atom)
An analog to a reference to an atom (&Atom)
Error type for Chemfiles.
+FormatMetadata contains metadata associated with one format.
A Frame contains data from one simulation step: the current unit
+cell, the topology, the positions, and the velocities of the particles in
+the system. If some information is missing (topology or velocity or unit
+cell), the corresponding data is filled with a default value.
A Match is a set of atomic indexes matching a given selection. It can
+mostly be used like a &[usize].
An iterator over the properties in an atom/frame/residue
+A Residue is a group of atoms belonging to the same logical unit. They
+can be small molecules, amino-acids in a protein, monomers in polymers,
+etc.
An analog to a reference to a residue (&Residue)
A Selection allow to select atoms in a Frame, from a selection
+language. The selection language is built by combining basic operations.
+Each basic operation follows the <selector>[(<variable>)] <operator> <value> structure, where <operator> is a comparison operator in
+== != < <= > >=.
A Topology contains the definition of all the atoms in the system, and
+the liaisons between the atoms (bonds, angles, dihedrals, …). It will
+also contain all the residues information if it is available.
An analog to a reference to a topology (&Topology)
The Trajectory type is the main entry point when using chemfiles. A
+Trajectory behave a bit like a file, allowing to read and/or write
+Frame.
An UnitCell represent the box containing the atoms, and its periodicity.
An analog to a mutable reference to an unit cell (&mut UnitCell)
An analog to a reference to an unit cell (&UnitCell)
Enums
+Possible bond order associated with bonds
+Available unit cell shapes.
+A Property is a piece of data that can be associated with an Atom or a
+Frame.
Possible causes of error in chemfiles
+Functions
+Read configuration data from the file at path.
Get the list of formats known by chemfiles, as well as all associated metadata.
+Get the format that chemfiles would use to read a file at the given
+path.
Use callback for every chemfiles warning. The callback will be passed
+the warning message. This will drop any previous warning callback.
Get the version of the chemfiles library.
+Redirecting to ../../chemfiles/fn.formats_list.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/misc/fn.guess_format.html b/0.10.3/chemfiles/misc/fn.guess_format.html new file mode 100644 index 000000000..681a66ce5 --- /dev/null +++ b/0.10.3/chemfiles/misc/fn.guess_format.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/fn.guess_format.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/misc/struct.FormatMetadata.html b/0.10.3/chemfiles/misc/struct.FormatMetadata.html new file mode 100644 index 000000000..10fda814b --- /dev/null +++ b/0.10.3/chemfiles/misc/struct.FormatMetadata.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.FormatMetadata.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/property/enum.Property.html b/0.10.3/chemfiles/property/enum.Property.html new file mode 100644 index 000000000..87bfc97da --- /dev/null +++ b/0.10.3/chemfiles/property/enum.Property.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/enum.Property.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/property/struct.PropertiesIter.html b/0.10.3/chemfiles/property/struct.PropertiesIter.html new file mode 100644 index 000000000..2faef8a54 --- /dev/null +++ b/0.10.3/chemfiles/property/struct.PropertiesIter.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.PropertiesIter.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/residue/struct.Residue.html b/0.10.3/chemfiles/residue/struct.Residue.html new file mode 100644 index 000000000..e8f25ad8a --- /dev/null +++ b/0.10.3/chemfiles/residue/struct.Residue.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Residue.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/residue/struct.ResidueRef.html b/0.10.3/chemfiles/residue/struct.ResidueRef.html new file mode 100644 index 000000000..9d26d5daa --- /dev/null +++ b/0.10.3/chemfiles/residue/struct.ResidueRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.ResidueRef.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/selection/struct.Match.html b/0.10.3/chemfiles/selection/struct.Match.html new file mode 100644 index 000000000..3c7b0b709 --- /dev/null +++ b/0.10.3/chemfiles/selection/struct.Match.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Match.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/selection/struct.Selection.html b/0.10.3/chemfiles/selection/struct.Selection.html new file mode 100644 index 000000000..8ed2b5d77 --- /dev/null +++ b/0.10.3/chemfiles/selection/struct.Selection.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Selection.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/sidebar-items.js b/0.10.3/chemfiles/sidebar-items.js new file mode 100644 index 000000000..341178b5a --- /dev/null +++ b/0.10.3/chemfiles/sidebar-items.js @@ -0,0 +1 @@ +window.SIDEBAR_ITEMS = {"enum":[["BondOrder","Possible bond order associated with bonds"],["CellShape","Available unit cell shapes."],["Property","A `Property` is a piece of data that can be associated with an `Atom` or a `Frame`."],["Status","Possible causes of error in chemfiles"]],"fn":[["add_configuration","Read configuration data from the file at `path`."],["formats_list","Get the list of formats known by chemfiles, as well as all associated metadata."],["guess_format","Get the format that chemfiles would use to read a file at the given `path`."],["set_warning_callback","Use `callback` for every chemfiles warning. The callback will be passed the warning message. This will drop any previous warning callback."],["version","Get the version of the chemfiles library."]],"struct":[["Atom","An `Atom` is a particle in the current `Frame`. It stores the following atomic properties:"],["AtomMut","An analog to a mutable reference to an atom (`&mut Atom`)"],["AtomRef","An analog to a reference to an atom (`&Atom`)"],["Error","Error type for Chemfiles."],["FormatMetadata","`FormatMetadata` contains metadata associated with one format."],["Frame","A `Frame` contains data from one simulation step: the current unit cell, the topology, the positions, and the velocities of the particles in the system. If some information is missing (topology or velocity or unit cell), the corresponding data is filled with a default value."],["Match","A `Match` is a set of atomic indexes matching a given selection. It can mostly be used like a `&[usize]`."],["PropertiesIter","An iterator over the properties in an atom/frame/residue"],["Residue","A `Residue` is a group of atoms belonging to the same logical unit. They can be small molecules, amino-acids in a protein, monomers in polymers, etc."],["ResidueRef","An analog to a reference to a residue (`&Residue`)"],["Selection","A `Selection` allow to select atoms in a `Frame`, from a selection language. The selection language is built by combining basic operations. Each basic operation follows the `pub struct Atom { /* private fields */ }Expand description
An Atom is a particle in the current Frame. It stores the following
+atomic properties:
-
+
- atom name; +
- atom type; +
- atom mass; +
- atom charge. +
The atom name is usually an unique identifier (H1, C_a) while the
+atom type will be shared between all particles of the same type: H,
+Ow, CH3.
Implementations
sourceimpl Atom
impl Atom
sourcepub fn new<'a>(name: impl Into<&'a str>) -> Atom
pub fn new<'a>(name: impl Into<&'a str>) -> Atom
Create an atom with the given name, and set the atom type to name.
Example
+let atom = Atom::new("He");
+assert_eq!(atom.name(), "He");sourcepub fn mass(&self) -> f64
pub fn mass(&self) -> f64
Get the atom mass, in atomic mass units.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.mass(), 4.002602);sourcepub fn set_mass(&mut self, mass: f64)
pub fn set_mass(&mut self, mass: f64)
Set the atom mass to mass, in atomic mass units.
Example
+let mut atom = Atom::new("He");
+
+atom.set_mass(34.9);
+assert_eq!(atom.mass(), 34.9);sourcepub fn charge(&self) -> f64
pub fn charge(&self) -> f64
Get the atom charge, in number of the electron charge e.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.charge(), 0.0);sourcepub fn set_charge(&mut self, charge: f64)
pub fn set_charge(&mut self, charge: f64)
Set the atom charge to charge, in number of the electron charge e.
Example
+let mut atom = Atom::new("He");
+
+atom.set_charge(-2.0);
+assert_eq!(atom.charge(), -2.0);sourcepub fn atomic_type(&self) -> String
pub fn atomic_type(&self) -> String
sourcepub fn set_name<'a>(&mut self, name: impl Into<&'a str>)
pub fn set_name<'a>(&mut self, name: impl Into<&'a str>)
Set the atom name to name.
Example
+let mut atom = Atom::new("He");
+
+atom.set_name("Zn3");
+assert_eq!(atom.name(), "Zn3");sourcepub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>)
pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>)
Set the atom type to atomic_type.
Example
+let mut atom = Atom::new("He");
+
+atom.set_atomic_type("F");
+assert_eq!(atom.atomic_type(), "F");sourcepub fn full_name(&self) -> String
pub fn full_name(&self) -> String
Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
+let atom = Atom::new("Zn");
+assert_eq!(atom.full_name(), "Zinc");sourcepub fn vdw_radius(&self) -> f64
pub fn vdw_radius(&self) -> f64
Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);sourcepub fn covalent_radius(&self) -> f64
pub fn covalent_radius(&self) -> f64
Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);sourcepub fn atomic_number(&self) -> u64
pub fn atomic_number(&self) -> u64
Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").atomic_number(), 2);
+assert_eq!(Atom::new("Xxx").atomic_number(), 0);sourcepub fn set(&mut self, name: &str, property: impl Into<Property>)
pub fn set(&mut self, name: &str, property: impl Into<Property>)
Add a new property with the given name to this atom.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut atom = Atom::new("He");
+atom.set("a bool", true);
+atom.set("a string", "test");
+
+assert_eq!(atom.get("a bool"), Some(Property::Bool(true)));
+assert_eq!(atom.get("a string"), Some(Property::String("test".into())));sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this atom, if it exist.
Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+
+assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(atom.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Get an iterator over all (name, property) pairs for this atom
+Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+atom.set("bar", Property::Bool(false));
+
+for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Atom
impl !Send for Atom
impl !Sync for Atom
impl Unpin for Atom
impl UnwindSafe for Atom
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+pub struct AtomMut<'a> { /* private fields */ }Expand description
An analog to a mutable reference to an atom (&mut Atom)
Methods from Deref<Target = Atom>
sourcepub fn mass(&self) -> f64
pub fn mass(&self) -> f64
Get the atom mass, in atomic mass units.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.mass(), 4.002602);sourcepub fn set_mass(&mut self, mass: f64)
pub fn set_mass(&mut self, mass: f64)
Set the atom mass to mass, in atomic mass units.
Example
+let mut atom = Atom::new("He");
+
+atom.set_mass(34.9);
+assert_eq!(atom.mass(), 34.9);sourcepub fn charge(&self) -> f64
pub fn charge(&self) -> f64
Get the atom charge, in number of the electron charge e.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.charge(), 0.0);sourcepub fn set_charge(&mut self, charge: f64)
pub fn set_charge(&mut self, charge: f64)
Set the atom charge to charge, in number of the electron charge e.
Example
+let mut atom = Atom::new("He");
+
+atom.set_charge(-2.0);
+assert_eq!(atom.charge(), -2.0);sourcepub fn atomic_type(&self) -> String
pub fn atomic_type(&self) -> String
sourcepub fn set_name<'a>(&mut self, name: impl Into<&'a str>)
pub fn set_name<'a>(&mut self, name: impl Into<&'a str>)
Set the atom name to name.
Example
+let mut atom = Atom::new("He");
+
+atom.set_name("Zn3");
+assert_eq!(atom.name(), "Zn3");sourcepub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>)
pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>)
Set the atom type to atomic_type.
Example
+let mut atom = Atom::new("He");
+
+atom.set_atomic_type("F");
+assert_eq!(atom.atomic_type(), "F");sourcepub fn full_name(&self) -> String
pub fn full_name(&self) -> String
Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
+let atom = Atom::new("Zn");
+assert_eq!(atom.full_name(), "Zinc");sourcepub fn vdw_radius(&self) -> f64
pub fn vdw_radius(&self) -> f64
Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);sourcepub fn covalent_radius(&self) -> f64
pub fn covalent_radius(&self) -> f64
Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);sourcepub fn atomic_number(&self) -> u64
pub fn atomic_number(&self) -> u64
Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").atomic_number(), 2);
+assert_eq!(Atom::new("Xxx").atomic_number(), 0);sourcepub fn set(&mut self, name: &str, property: impl Into<Property>)
pub fn set(&mut self, name: &str, property: impl Into<Property>)
Add a new property with the given name to this atom.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut atom = Atom::new("He");
+atom.set("a bool", true);
+atom.set("a string", "test");
+
+assert_eq!(atom.get("a bool"), Some(Property::Bool(true)));
+assert_eq!(atom.get("a string"), Some(Property::String("test".into())));sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this atom, if it exist.
Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+
+assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(atom.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Get an iterator over all (name, property) pairs for this atom
+Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+atom.set("bar", Property::Bool(false));
+
+for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for AtomMut<'a>
impl<'a> !Send for AtomMut<'a>
impl<'a> !Sync for AtomMut<'a>
impl<'a> Unpin for AtomMut<'a>
impl<'a> !UnwindSafe for AtomMut<'a>
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+pub struct AtomRef<'a> { /* private fields */ }Expand description
An analog to a reference to an atom (&Atom)
Methods from Deref<Target = Atom>
sourcepub fn mass(&self) -> f64
pub fn mass(&self) -> f64
Get the atom mass, in atomic mass units.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.mass(), 4.002602);sourcepub fn charge(&self) -> f64
pub fn charge(&self) -> f64
Get the atom charge, in number of the electron charge e.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.charge(), 0.0);sourcepub fn atomic_type(&self) -> String
pub fn atomic_type(&self) -> String
sourcepub fn full_name(&self) -> String
pub fn full_name(&self) -> String
Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
+let atom = Atom::new("Zn");
+assert_eq!(atom.full_name(), "Zinc");sourcepub fn vdw_radius(&self) -> f64
pub fn vdw_radius(&self) -> f64
Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);sourcepub fn covalent_radius(&self) -> f64
pub fn covalent_radius(&self) -> f64
Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);sourcepub fn atomic_number(&self) -> u64
pub fn atomic_number(&self) -> u64
Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").atomic_number(), 2);
+assert_eq!(Atom::new("Xxx").atomic_number(), 0);sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this atom, if it exist.
Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+
+assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(atom.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Get an iterator over all (name, property) pairs for this atom
+Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+atom.set("bar", Property::Bool(false));
+
+for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for AtomRef<'a>
impl<'a> !Send for AtomRef<'a>
impl<'a> !Sync for AtomRef<'a>
impl<'a> Unpin for AtomRef<'a>
impl<'a> UnwindSafe for AtomRef<'a>
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+Expand description
Error type for Chemfiles.
+Fields
status: StatusThe error status code
+message: StringA message describing the error cause
+Implementations
Trait Implementations
sourceimpl Error for Error
impl Error for Error
sourcefn description(&self) -> &str
fn description(&self) -> &str
👎 Deprecated since 1.42.0:
use the Display impl or to_string()
+1.30.0 · sourcefn source(&self) -> Option<&(dyn Error + 'static)>
fn source(&self) -> Option<&(dyn Error + 'static)>
The lower-level source of this error, if any. Read more
+impl Eq for Error
impl StructuralEq for Error
impl StructuralPartialEq for Error
Auto Trait Implementations
impl RefUnwindSafe for Error
impl Send for Error
impl Sync for Error
impl Unpin for Error
impl UnwindSafe for Error
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+
+ Struct chemfiles::
source · [−]
Struct chemfiles::FormatMetadata
source · [−]pub struct FormatMetadata {Show 13 fields
+ pub name: &'static str,
+ pub extension: Option<&'static str>,
+ pub description: &'static str,
+ pub reference: &'static str,
+ pub read: bool,
+ pub write: bool,
+ pub memory: bool,
+ pub positions: bool,
+ pub velocities: bool,
+ pub unit_cell: bool,
+ pub atoms: bool,
+ pub bonds: bool,
+ pub residues: bool,
+}Expand description
FormatMetadata contains metadata associated with one format.
Fields
name: &'static strName of the format.
+extension: Option<&'static str>Extension associated with the format.
+description: &'static strExtended, user-facing description of the format.
+reference: &'static strURL pointing to the format definition/reference.
+read: boolIs reading files in this format implemented?
+write: boolIs writing files in this format implemented?
+memory: boolDoes this format support in-memory IO?
+positions: boolDoes this format support storing atomic positions?
+velocities: boolDoes this format support storing atomic velocities?
+unit_cell: boolDoes this format support storing unit cell information?
+atoms: boolDoes this format support storing atom names or types?
+bonds: boolDoes this format support storing bonds between atoms?
+residues: boolDoes this format support storing residues?
+Trait Implementations
sourceimpl Clone for FormatMetadata
impl Clone for FormatMetadata
sourcefn clone(&self) -> FormatMetadata
fn clone(&self) -> FormatMetadata
Returns a copy of the value. Read more
+1.0.0 · sourcefn clone_from(&mut self, source: &Self)
fn clone_from(&mut self, source: &Self)
Performs copy-assignment from source. Read more
sourceimpl Debug for FormatMetadata
impl Debug for FormatMetadata
sourceimpl PartialEq<FormatMetadata> for FormatMetadata
impl PartialEq<FormatMetadata> for FormatMetadata
sourcefn eq(&self, other: &FormatMetadata) -> bool
fn eq(&self, other: &FormatMetadata) -> bool
This method tests for self and other values to be equal, and is used
+by ==. Read more
sourcefn ne(&self, other: &FormatMetadata) -> bool
fn ne(&self, other: &FormatMetadata) -> bool
This method tests for !=.
impl Eq for FormatMetadata
impl StructuralEq for FormatMetadata
impl StructuralPartialEq for FormatMetadata
Auto Trait Implementations
impl RefUnwindSafe for FormatMetadata
impl Send for FormatMetadata
impl Sync for FormatMetadata
impl Unpin for FormatMetadata
impl UnwindSafe for FormatMetadata
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+pub struct Frame { /* private fields */ }Expand description
A Frame contains data from one simulation step: the current unit
+cell, the topology, the positions, and the velocities of the particles in
+the system. If some information is missing (topology or velocity or unit
+cell), the corresponding data is filled with a default value.
Implementations
sourceimpl Frame
impl Frame
sourcepub fn new() -> Frame
pub fn new() -> Frame
Create an empty frame. It will be resized by the library as needed.
+Example
+let frame = Frame::new();
+
+assert_eq!(frame.size(), 0);sourcepub fn atom_mut(&mut self, index: usize) -> AtomMut<'_>
pub fn atom_mut(&mut self, index: usize) -> AtomMut<'_>
Get a mutable reference to the atom at the given index in this frame.
Panics
+If index is out of bounds.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+
+assert_eq!(frame.atom(0).name(), "Zn");
+
+frame.atom_mut(0).set_name("Fe");
+assert_eq!(frame.atom(0).name(), "Fe");sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the current number of atoms in this frame.
+Example
+let mut frame = Frame::new();
+assert_eq!(frame.size(), 0);
+
+frame.resize(67);
+assert_eq!(frame.size(), 67);sourcepub fn resize(&mut self, natoms: usize)
pub fn resize(&mut self, natoms: usize)
Resize the positions and the velocities in this frame, to make space for
+natoms atoms. Previous data is conserved, as well as the presence of
+absence of velocities.
Example
+let mut frame = Frame::new();
+frame.resize(67);
+assert_eq!(frame.size(), 67);sourcepub fn add_atom(
&mut self,
atom: &Atom,
position: [f64; 3],
velocity: impl Into<Option<[f64; 3]>>
)
pub fn add_atom(
&mut self,
atom: &Atom,
position: [f64; 3],
velocity: impl Into<Option<[f64; 3]>>
)
Add an Atom and the corresponding position and optionally velocity
+data to this frame.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("Zn"), [1.0, 1.0, 2.0], None);
+
+frame.add_velocities();
+frame.add_atom(&Atom::new("Zn"), [-1.0, 1.0, 2.0], [0.2, 0.1, 0.0]);sourcepub fn remove(&mut self, i: usize)
pub fn remove(&mut self, i: usize)
Remove the atom at index i in this frame.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+frame.add_atom(&Atom::new("Fe"), [0.0; 3], None);
+frame.add_atom(&Atom::new("Sn"), [0.0; 3], None);
+assert_eq!(frame.size(), 3);
+
+frame.remove(1);
+assert_eq!(frame.size(), 2);
+assert_eq!(frame.atom(1).name(), "Sn");sourcepub fn add_bond(&mut self, i: usize, j: usize)
pub fn add_bond(&mut self, i: usize, j: usize)
Add a bond between the atoms at indexes i and j in the frame.
The bond order is set to BondOrder::Unknown.
Example
+let mut frame = Frame::new();
+assert_eq!(frame.topology().bonds_count(), 0);
+frame.resize(5);
+
+frame.add_bond(0, 1);
+frame.add_bond(3, 1);
+frame.add_bond(2, 4);
+assert_eq!(frame.topology().bonds_count(), 3);
+
+assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown);
+assert_eq!(frame.topology().bonds(), vec![[0, 1], [1, 3], [2, 4]]);sourcepub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder)
pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder)
Add a bond between the atoms at indexes i and j in the frame
+with the given bond order.
Example
+let mut frame = Frame::new();
+assert_eq!(frame.topology().bonds_count(), 0);
+frame.resize(2);
+
+frame.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Double);sourcepub fn remove_bond(&mut self, i: usize, j: usize)
pub fn remove_bond(&mut self, i: usize, j: usize)
Remove any existing bond between the atoms at indexes i and j in
+the frame.
This function does nothing if there is no bond between i and j.
Example
+let mut frame = Frame::new();
+frame.resize(5);
+
+frame.add_bond(0, 1);
+frame.add_bond(3, 1);
+frame.add_bond(2, 4);
+
+let bonds = frame.topology().bonds();
+assert_eq!(bonds, vec![[0, 1], [1, 3], [2, 4]]);
+
+frame.remove_bond(2, 4);
+let bonds = frame.topology().bonds();
+assert_eq!(bonds, vec![[0, 1], [1, 3]]);sourcepub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error>
pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error>
Add a copy of residue to this frame.
Errors
+This function fails is the residue id is already in this frame’s +topology, or if the residue contain atoms that are already in another +residue.
+Example
+let mut frame = Frame::new();
+
+let residue = Residue::new("foo");
+frame.add_residue(&residue).unwrap();
+
+let topology = frame.topology();
+assert_eq!(topology.residues_count(), 1);
+assert_eq!(topology.residue(0).unwrap().name(), "foo");sourcepub fn distance(&self, i: usize, j: usize) -> f64
pub fn distance(&self, i: usize, j: usize) -> f64
Get the distance between the atoms at indexes i and j in this frame,
+accounting for periodic boundary conditions. The result is expressed in
+Angstroms.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [1.0, 2.0, 3.0], None);
+
+assert_eq!(frame.distance(0, 1), f64::sqrt(14.0));sourcepub fn angle(&self, i: usize, j: usize, k: usize) -> f64
pub fn angle(&self, i: usize, j: usize, k: usize) -> f64
Get the angle formed by the atoms at indexes i, j and k in this
+frame, accounting for periodic boundary conditions. The result is
+expressed in radians.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+
+assert_eq!(frame.angle(0, 1, 2), f64::consts::PI / 2.0);sourcepub fn dihedral(&self, i: usize, j: usize, k: usize, m: usize) -> f64
pub fn dihedral(&self, i: usize, j: usize, k: usize, m: usize) -> f64
Get the dihedral angle formed by the atoms at indexes i, j, k and
+m in this frame, accounting for periodic boundary conditions. The
+result is expressed in radians.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+frame.add_atom(&Atom::new("D"), [0.0, 1.0, 1.0], None);
+
+assert_eq!(frame.dihedral(0, 1, 2, 3), f64::consts::PI / 2.0);sourcepub fn out_of_plane(&self, i: usize, j: usize, k: usize, m: usize) -> f64
pub fn out_of_plane(&self, i: usize, j: usize, k: usize, m: usize) -> f64
Get the out of plane distance formed by the atoms at indexes i, j,
+k and m in this frame, accounting for periodic boundary conditions.
+The result is expressed in angstroms.
This is the distance between the atom j and the ikm plane. The j atom +is the center of the improper dihedral angle formed by i, j, k and m.
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [0.0, 0.0, 2.0], None);
+frame.add_atom(&Atom::new("C"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("D"), [0.0, 1.0, 0.0], None);
+
+assert_eq!(frame.out_of_plane(0, 1, 2, 3), 2.0);sourcepub fn positions(&self) -> &[[f64; 3]]
pub fn positions(&self) -> &[[f64; 3]]
Get a view into the positions of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+
+let positions = frame.positions();
+assert_eq!(positions.len(), 67);
+assert_eq!(positions[0], [0.0, 0.0, 0.0]);sourcepub fn positions_mut(&mut self) -> &mut [[f64; 3]]
pub fn positions_mut(&mut self) -> &mut [[f64; 3]]
Get a mutable view into the positions of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+{
+ let positions = frame.positions_mut();
+ assert_eq!(positions[0], [0.0, 0.0, 0.0]);
+ positions[0] = [1.0, 2.0, 3.0];
+}
+
+let positions = frame.positions();
+assert_eq!(positions[0], [1.0, 2.0, 3.0]);sourcepub fn velocities(&self) -> Option<&[[f64; 3]]>
pub fn velocities(&self) -> Option<&[[f64; 3]]>
Get a view into the velocities of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+frame.add_velocities();
+
+let velocities = frame.velocities().expect("missing velocities");
+assert_eq!(velocities.len(), 67);
+assert_eq!(velocities[0], [0.0, 0.0, 0.0]);sourcepub fn velocities_mut(&mut self) -> Option<&mut [[f64; 3]]>
pub fn velocities_mut(&mut self) -> Option<&mut [[f64; 3]]>
Get a mutable view into the velocities of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+frame.add_velocities();
+{
+ let velocities = frame.velocities_mut().expect("missing velocities");
+ assert_eq!(velocities[0], [0.0, 0.0, 0.0]);
+ velocities[0] = [1.0, 2.0, 3.0];
+}
+
+let velocities = frame.velocities().expect("missing velocities");
+assert_eq!(velocities[0], [1.0, 2.0, 3.0]);sourcepub fn has_velocities(&self) -> bool
pub fn has_velocities(&self) -> bool
Check if this frame contains velocity data.
+Example
+let mut frame = Frame::new();
+assert_eq!(frame.has_velocities(), false);
+
+frame.add_velocities();
+assert_eq!(frame.has_velocities(), true);sourcepub fn add_velocities(&mut self)
pub fn add_velocities(&mut self)
Add velocity data to this frame. If the frame already have velocities, +this does nothing.
+Example
+let mut frame = Frame::new();
+assert_eq!(frame.has_velocities(), false);
+
+frame.add_velocities();
+assert_eq!(frame.has_velocities(), true);sourcepub fn cell(&self) -> UnitCellRef<'_>
pub fn cell(&self) -> UnitCellRef<'_>
Get a reference to the UnitCell from this frame.
Example
+let frame = Frame::new();
+
+let cell = frame.cell();
+assert_eq!(cell.shape(), CellShape::Infinite);sourcepub fn cell_mut(&mut self) -> UnitCellMut<'_>
pub fn cell_mut(&mut self) -> UnitCellMut<'_>
Get a mutable reference to the UnitCell from this frame.
Example
+let mut frame = Frame::new();
+
+assert_eq!(frame.cell().shape(), CellShape::Infinite);
+
+frame.cell_mut().set_shape(CellShape::Triclinic).unwrap();
+assert_eq!(frame.cell().shape(), CellShape::Triclinic);sourcepub fn set_cell(&mut self, cell: &UnitCell)
pub fn set_cell(&mut self, cell: &UnitCell)
Set the UnitCell of this frame to cell.
Example
+let mut frame = Frame::new();
+
+frame.set_cell(&UnitCell::new([10.0, 10.0, 10.0]));
+
+let cell = frame.cell();
+assert_eq!(cell.shape(), CellShape::Orthorhombic);
+assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);sourcepub fn topology(&self) -> TopologyRef<'_>
pub fn topology(&self) -> TopologyRef<'_>
Get a reference to the Topology of this frame.
Example
+let mut frame = Frame::new();
+frame.resize(42);
+
+let topology = frame.topology();
+assert_eq!(topology.size(), 42);sourcepub fn set_topology(&mut self, topology: &Topology) -> Result<(), Error>
pub fn set_topology(&mut self, topology: &Topology) -> Result<(), Error>
Set the Topology of this frame to topology.
Errors
+This function fails if the topology contains a different number of atoms +than this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(2);
+
+let mut topology = Topology::new();
+topology.add_atom(&Atom::new("Cl"));
+topology.add_atom(&Atom::new("Cl"));
+topology.add_bond(0, 1);
+
+frame.set_topology(&topology).unwrap();
+assert_eq!(frame.atom(0).name(), "Cl");sourcepub fn step(&self) -> usize
pub fn step(&self) -> usize
Get this frame step, i.e. the frame number in the trajectory
+Example
+let frame = Frame::new();
+assert_eq!(frame.step(), 0);sourcepub fn set_step(&mut self, step: usize)
pub fn set_step(&mut self, step: usize)
Set this frame step to step.
Example
+let mut frame = Frame::new();
+assert_eq!(frame.step(), 0);
+
+frame.set_step(10);
+assert_eq!(frame.step(), 10);sourcepub fn guess_bonds(&mut self) -> Result<(), Error>
pub fn guess_bonds(&mut self) -> Result<(), Error>
Guess the bonds, angles and dihedrals in this frame.
The bonds are guessed using a distance-based algorithm, and then angles +and dihedrals are guessed from the bonds.
+Errors
+This function can fail if the covalent radius is unknown for some atoms +in the frame.
+Example
+let mut frame = Frame::new();
+
+frame.add_atom(&Atom::new("Cl"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("Cl"), [1.5, 0.0, 0.0], None);
+assert_eq!(frame.topology().bonds_count(), 0);
+
+frame.guess_bonds().unwrap();
+assert_eq!(frame.topology().bonds_count(), 1);sourcepub fn clear_bonds(&mut self)
pub fn clear_bonds(&mut self)
Remove all existing bonds, angles, dihedral angles and improper +dihedral angles in the topology of the frame.
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [0.0, 1.0, 0.0], None);
+
+frame.add_bond(0, 1);
+frame.add_bond(1, 2);
+
+assert_eq!(frame.topology().bonds().len(), 2);
+assert_eq!(frame.topology().angles().len(), 1);
+
+frame.clear_bonds();
+assert!(frame.topology().bonds().is_empty());
+assert!(frame.topology().angles().is_empty());sourcepub fn set(&mut self, name: &str, property: impl Into<Property>)
pub fn set(&mut self, name: &str, property: impl Into<Property>)
Add a new property with the given name to this frame.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut frame = Frame::new();
+frame.set("a string", "hello");
+frame.set("a double", 4.3);
+
+assert_eq!(frame.get("a string"), Some(Property::String("hello".into())));
+assert_eq!(frame.get("a double"), Some(Property::Double(4.3)));sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this frame, if it exist.
Examples
+let mut frame = Frame::new();
+frame.set("foo", Property::Double(22.2));
+
+assert_eq!(frame.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(frame.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Get an iterator over all (name, property) pairs for this frame
+Examples
+let mut frame = Frame::new();
+frame.set("foo", Property::Double(22.2));
+frame.set("bar", Property::Bool(false));
+
+for (name, property) in frame.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}sourcepub fn iter_atoms(&self) -> AtomIter<'_>
pub fn iter_atoms(&self) -> AtomIter<'_>
Gets an iterator over atoms
+Example
+let mut frame = Frame::new();
+
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+
+let mut atoms: Vec<AtomRef> = Vec::new();
+
+for atom in frame.iter_atoms() {
+ atoms.push(atom);
+}
+
+assert_eq!(atoms.len(), 2);Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Frame
impl !Send for Frame
impl !Sync for Frame
impl Unpin for Frame
impl UnwindSafe for Frame
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+pub struct Match { /* private fields */ }Expand description
A Match is a set of atomic indexes matching a given selection. It can
+mostly be used like a &[usize].
Implementations
sourceimpl Match
impl Match
sourcepub fn len(&self) -> usize
pub fn len(&self) -> usize
Get the length of the Match.
+Example
+let atomic_match = Match::new(&[3, 4, 5]);
+assert_eq!(atomic_match.len(), 3);sourcepub fn new(atoms: &[usize]) -> Match
pub fn new(atoms: &[usize]) -> Match
Create a new match containing the atoms in the atoms slice.
Panics
+If the slice contains more than 4 elements, which is the maximal size +of a match.
+Example
+let atomic_match = Match::new(&[3, 4, 5]);
+assert_eq!(atomic_match.len(), 3);
+assert_eq!(atomic_match[0], 3);
+assert_eq!(atomic_match[1], 4);
+assert_eq!(atomic_match[2], 5);sourcepub fn iter(&self) -> Iter<'_, usize>
pub fn iter(&self) -> Iter<'_, usize>
Iterate over the atomic indexes in the match.
+Example
+let atomic_match = Match::new(&[3, 4, 5]);
+let mut iter = atomic_match.iter();
+
+assert_eq!(iter.next(), Some(&3));
+assert_eq!(iter.next(), Some(&4));
+assert_eq!(iter.next(), Some(&5));
+assert_eq!(iter.next(), None);Trait Implementations
sourceimpl<'a> IntoIterator for &'a Match
impl<'a> IntoIterator for &'a Match
impl Eq for Match
impl StructuralEq for Match
impl StructuralPartialEq for Match
Auto Trait Implementations
impl RefUnwindSafe for Match
impl Send for Match
impl Sync for Match
impl Unpin for Match
impl UnwindSafe for Match
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+
+ Struct chemfiles::
source · [−]
Struct chemfiles::PropertiesIter
source · [−]pub struct PropertiesIter<'a> { /* private fields */ }Expand description
An iterator over the properties in an atom/frame/residue
+Trait Implementations
sourceimpl<'a> Iterator for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a>
sourcefn next(&mut self) -> Option<Self::Item>
fn next(&mut self) -> Option<Self::Item>
Advances the iterator and returns the next value. Read more
+sourcefn size_hint(&self) -> (usize, Option<usize>)
fn size_hint(&self) -> (usize, Option<usize>)
Returns the bounds on the remaining length of the iterator. Read more
+sourcefn count(self) -> usize
fn count(self) -> usize
Consumes the iterator, counting the number of iterations and returning it. Read more
+1.0.0 · sourcefn last(self) -> Option<Self::Item>
fn last(self) -> Option<Self::Item>
Consumes the iterator, returning the last element. Read more
+sourcefn advance_by(&mut self, n: usize) -> Result<(), usize>
fn advance_by(&mut self, n: usize) -> Result<(), usize>
🔬 This is a nightly-only experimental API. (
iter_advance_by)Advances the iterator by n elements. Read more
1.0.0 · sourcefn nth(&mut self, n: usize) -> Option<Self::Item>
fn nth(&mut self, n: usize) -> Option<Self::Item>
Returns the nth element of the iterator. Read more
1.28.0 · sourcefn step_by(self, step: usize) -> StepBy<Self>
fn step_by(self, step: usize) -> StepBy<Self>
Creates an iterator starting at the same point, but stepping by +the given amount at each iteration. Read more
+1.0.0 · sourcefn chain<U>(self, other: U) -> Chain<Self, <U as IntoIterator>::IntoIter> where
U: IntoIterator<Item = Self::Item>,
fn chain<U>(self, other: U) -> Chain<Self, <U as IntoIterator>::IntoIter> where
U: IntoIterator<Item = Self::Item>,
Takes two iterators and creates a new iterator over both in sequence. Read more
+1.0.0 · sourcefn zip<U>(self, other: U) -> Zip<Self, <U as IntoIterator>::IntoIter> where
U: IntoIterator,
fn zip<U>(self, other: U) -> Zip<Self, <U as IntoIterator>::IntoIter> where
U: IntoIterator,
‘Zips up’ two iterators into a single iterator of pairs. Read more
+sourcefn intersperse(self, separator: Self::Item) -> Intersperse<Self> where
Self::Item: Clone,
fn intersperse(self, separator: Self::Item) -> Intersperse<Self> where
Self::Item: Clone,
🔬 This is a nightly-only experimental API. (
iter_intersperse)Creates a new iterator which places a copy of separator between adjacent
+items of the original iterator. Read more
sourcefn intersperse_with<G>(self, separator: G) -> IntersperseWith<Self, G> where
G: FnMut() -> Self::Item,
fn intersperse_with<G>(self, separator: G) -> IntersperseWith<Self, G> where
G: FnMut() -> Self::Item,
🔬 This is a nightly-only experimental API. (
iter_intersperse)Creates a new iterator which places an item generated by separator
+between adjacent items of the original iterator. Read more
1.0.0 · sourcefn map<B, F>(self, f: F) -> Map<Self, F> where
F: FnMut(Self::Item) -> B,
fn map<B, F>(self, f: F) -> Map<Self, F> where
F: FnMut(Self::Item) -> B,
Takes a closure and creates an iterator which calls that closure on each +element. Read more
+1.21.0 · sourcefn for_each<F>(self, f: F) where
F: FnMut(Self::Item),
fn for_each<F>(self, f: F) where
F: FnMut(Self::Item),
Calls a closure on each element of an iterator. Read more
+1.0.0 · sourcefn filter<P>(self, predicate: P) -> Filter<Self, P> where
P: FnMut(&Self::Item) -> bool,
fn filter<P>(self, predicate: P) -> Filter<Self, P> where
P: FnMut(&Self::Item) -> bool,
Creates an iterator which uses a closure to determine if an element +should be yielded. Read more
+1.0.0 · sourcefn filter_map<B, F>(self, f: F) -> FilterMap<Self, F> where
F: FnMut(Self::Item) -> Option<B>,
fn filter_map<B, F>(self, f: F) -> FilterMap<Self, F> where
F: FnMut(Self::Item) -> Option<B>,
Creates an iterator that both filters and maps. Read more
+1.0.0 · sourcefn enumerate(self) -> Enumerate<Self>
fn enumerate(self) -> Enumerate<Self>
Creates an iterator which gives the current iteration count as well as +the next value. Read more
+1.0.0 · sourcefn skip_while<P>(self, predicate: P) -> SkipWhile<Self, P> where
P: FnMut(&Self::Item) -> bool,
fn skip_while<P>(self, predicate: P) -> SkipWhile<Self, P> where
P: FnMut(&Self::Item) -> bool,
1.0.0 · sourcefn take_while<P>(self, predicate: P) -> TakeWhile<Self, P> where
P: FnMut(&Self::Item) -> bool,
fn take_while<P>(self, predicate: P) -> TakeWhile<Self, P> where
P: FnMut(&Self::Item) -> bool,
Creates an iterator that yields elements based on a predicate. Read more
+1.57.0 · sourcefn map_while<B, P>(self, predicate: P) -> MapWhile<Self, P> where
P: FnMut(Self::Item) -> Option<B>,
fn map_while<B, P>(self, predicate: P) -> MapWhile<Self, P> where
P: FnMut(Self::Item) -> Option<B>,
Creates an iterator that both yields elements based on a predicate and maps. Read more
+1.0.0 · sourcefn skip(self, n: usize) -> Skip<Self>
fn skip(self, n: usize) -> Skip<Self>
Creates an iterator that skips the first n elements. Read more
1.0.0 · sourcefn take(self, n: usize) -> Take<Self>
fn take(self, n: usize) -> Take<Self>
Creates an iterator that yields the first n elements, or fewer
+if the underlying iterator ends sooner. Read more
1.0.0 · sourcefn scan<St, B, F>(self, initial_state: St, f: F) -> Scan<Self, St, F> where
F: FnMut(&mut St, Self::Item) -> Option<B>,
fn scan<St, B, F>(self, initial_state: St, f: F) -> Scan<Self, St, F> where
F: FnMut(&mut St, Self::Item) -> Option<B>,
1.0.0 · sourcefn flat_map<U, F>(self, f: F) -> FlatMap<Self, U, F> where
U: IntoIterator,
F: FnMut(Self::Item) -> U,
fn flat_map<U, F>(self, f: F) -> FlatMap<Self, U, F> where
U: IntoIterator,
F: FnMut(Self::Item) -> U,
Creates an iterator that works like map, but flattens nested structure. Read more
+1.29.0 · sourcefn flatten(self) -> Flatten<Self> where
Self::Item: IntoIterator,
fn flatten(self) -> Flatten<Self> where
Self::Item: IntoIterator,
Creates an iterator that flattens nested structure. Read more
+1.0.0 · sourcefn inspect<F>(self, f: F) -> Inspect<Self, F> where
F: FnMut(&Self::Item),
fn inspect<F>(self, f: F) -> Inspect<Self, F> where
F: FnMut(&Self::Item),
Does something with each element of an iterator, passing the value on. Read more
+1.0.0 · sourcefn by_ref(&mut self) -> &mut Self
fn by_ref(&mut self) -> &mut Self
Borrows an iterator, rather than consuming it. Read more
+1.0.0 · sourcefn collect<B>(self) -> B where
B: FromIterator<Self::Item>,
fn collect<B>(self) -> B where
B: FromIterator<Self::Item>,
Transforms an iterator into a collection. Read more
+sourcefn try_collect<B>(
&mut self
) -> <<Self::Item as Try>::Residual as Residual<B>>::TryType where
B: FromIterator<<Self::Item as Try>::Output>,
Self::Item: Try,
<Self::Item as Try>::Residual: Residual<B>,
fn try_collect<B>(
&mut self
) -> <<Self::Item as Try>::Residual as Residual<B>>::TryType where
B: FromIterator<<Self::Item as Try>::Output>,
Self::Item: Try,
<Self::Item as Try>::Residual: Residual<B>,
🔬 This is a nightly-only experimental API. (
iterator_try_collect)Fallibly transforms an iterator into a collection, short circuiting if +a failure is encountered. Read more
+sourcefn collect_into<E>(self, collection: &mut E) -> &mut E where
E: Extend<Self::Item>,
fn collect_into<E>(self, collection: &mut E) -> &mut E where
E: Extend<Self::Item>,
🔬 This is a nightly-only experimental API. (
iter_collect_into)Collects all the items from an iterator into a collection. Read more
+1.0.0 · sourcefn partition<B, F>(self, f: F) -> (B, B) where
B: Default + Extend<Self::Item>,
F: FnMut(&Self::Item) -> bool,
fn partition<B, F>(self, f: F) -> (B, B) where
B: Default + Extend<Self::Item>,
F: FnMut(&Self::Item) -> bool,
Consumes an iterator, creating two collections from it. Read more
+sourcefn partition_in_place<'a, T, P>(self, predicate: P) -> usize where
T: 'a,
Self: DoubleEndedIterator<Item = &'a mut T>,
P: FnMut(&T) -> bool,
fn partition_in_place<'a, T, P>(self, predicate: P) -> usize where
T: 'a,
Self: DoubleEndedIterator<Item = &'a mut T>,
P: FnMut(&T) -> bool,
🔬 This is a nightly-only experimental API. (
iter_partition_in_place)Reorders the elements of this iterator in-place according to the given predicate,
+such that all those that return true precede all those that return false.
+Returns the number of true elements found. Read more
sourcefn is_partitioned<P>(self, predicate: P) -> bool where
P: FnMut(Self::Item) -> bool,
fn is_partitioned<P>(self, predicate: P) -> bool where
P: FnMut(Self::Item) -> bool,
🔬 This is a nightly-only experimental API. (
iter_is_partitioned)Checks if the elements of this iterator are partitioned according to the given predicate,
+such that all those that return true precede all those that return false. Read more
1.27.0 · sourcefn try_fold<B, F, R>(&mut self, init: B, f: F) -> R where
F: FnMut(B, Self::Item) -> R,
R: Try<Output = B>,
fn try_fold<B, F, R>(&mut self, init: B, f: F) -> R where
F: FnMut(B, Self::Item) -> R,
R: Try<Output = B>,
An iterator method that applies a function as long as it returns +successfully, producing a single, final value. Read more
+1.27.0 · sourcefn try_for_each<F, R>(&mut self, f: F) -> R where
F: FnMut(Self::Item) -> R,
R: Try<Output = ()>,
fn try_for_each<F, R>(&mut self, f: F) -> R where
F: FnMut(Self::Item) -> R,
R: Try<Output = ()>,
An iterator method that applies a fallible function to each item in the +iterator, stopping at the first error and returning that error. Read more
+1.0.0 · sourcefn fold<B, F>(self, init: B, f: F) -> B where
F: FnMut(B, Self::Item) -> B,
fn fold<B, F>(self, init: B, f: F) -> B where
F: FnMut(B, Self::Item) -> B,
Folds every element into an accumulator by applying an operation, +returning the final result. Read more
+1.51.0 · sourcefn reduce<F>(self, f: F) -> Option<Self::Item> where
F: FnMut(Self::Item, Self::Item) -> Self::Item,
fn reduce<F>(self, f: F) -> Option<Self::Item> where
F: FnMut(Self::Item, Self::Item) -> Self::Item,
Reduces the elements to a single one, by repeatedly applying a reducing +operation. Read more
+sourcefn try_reduce<F, R>(
&mut self,
f: F
) -> <<R as Try>::Residual as Residual<Option<<R as Try>::Output>>>::TryType where
F: FnMut(Self::Item, Self::Item) -> R,
R: Try<Output = Self::Item>,
<R as Try>::Residual: Residual<Option<Self::Item>>,
fn try_reduce<F, R>(
&mut self,
f: F
) -> <<R as Try>::Residual as Residual<Option<<R as Try>::Output>>>::TryType where
F: FnMut(Self::Item, Self::Item) -> R,
R: Try<Output = Self::Item>,
<R as Try>::Residual: Residual<Option<Self::Item>>,
🔬 This is a nightly-only experimental API. (
iterator_try_reduce)Reduces the elements to a single one by repeatedly applying a reducing operation. If the +closure returns a failure, the failure is propagated back to the caller immediately. Read more
+1.0.0 · sourcefn all<F>(&mut self, f: F) -> bool where
F: FnMut(Self::Item) -> bool,
fn all<F>(&mut self, f: F) -> bool where
F: FnMut(Self::Item) -> bool,
Tests if every element of the iterator matches a predicate. Read more
+1.0.0 · sourcefn any<F>(&mut self, f: F) -> bool where
F: FnMut(Self::Item) -> bool,
fn any<F>(&mut self, f: F) -> bool where
F: FnMut(Self::Item) -> bool,
Tests if any element of the iterator matches a predicate. Read more
+1.0.0 · sourcefn find<P>(&mut self, predicate: P) -> Option<Self::Item> where
P: FnMut(&Self::Item) -> bool,
fn find<P>(&mut self, predicate: P) -> Option<Self::Item> where
P: FnMut(&Self::Item) -> bool,
Searches for an element of an iterator that satisfies a predicate. Read more
+1.30.0 · sourcefn find_map<B, F>(&mut self, f: F) -> Option<B> where
F: FnMut(Self::Item) -> Option<B>,
fn find_map<B, F>(&mut self, f: F) -> Option<B> where
F: FnMut(Self::Item) -> Option<B>,
Applies function to the elements of iterator and returns +the first non-none result. Read more
+sourcefn try_find<F, R>(
&mut self,
f: F
) -> <<R as Try>::Residual as Residual<Option<Self::Item>>>::TryType where
F: FnMut(&Self::Item) -> R,
R: Try<Output = bool>,
<R as Try>::Residual: Residual<Option<Self::Item>>,
fn try_find<F, R>(
&mut self,
f: F
) -> <<R as Try>::Residual as Residual<Option<Self::Item>>>::TryType where
F: FnMut(&Self::Item) -> R,
R: Try<Output = bool>,
<R as Try>::Residual: Residual<Option<Self::Item>>,
🔬 This is a nightly-only experimental API. (
try_find)Applies function to the elements of iterator and returns +the first true result or the first error. Read more
+1.0.0 · sourcefn position<P>(&mut self, predicate: P) -> Option<usize> where
P: FnMut(Self::Item) -> bool,
fn position<P>(&mut self, predicate: P) -> Option<usize> where
P: FnMut(Self::Item) -> bool,
Searches for an element in an iterator, returning its index. Read more
+1.0.0 · sourcefn rposition<P>(&mut self, predicate: P) -> Option<usize> where
P: FnMut(Self::Item) -> bool,
Self: ExactSizeIterator + DoubleEndedIterator,
fn rposition<P>(&mut self, predicate: P) -> Option<usize> where
P: FnMut(Self::Item) -> bool,
Self: ExactSizeIterator + DoubleEndedIterator,
Searches for an element in an iterator from the right, returning its +index. Read more
+1.0.0 · sourcefn max(self) -> Option<Self::Item> where
Self::Item: Ord,
fn max(self) -> Option<Self::Item> where
Self::Item: Ord,
Returns the maximum element of an iterator. Read more
+1.0.0 · sourcefn min(self) -> Option<Self::Item> where
Self::Item: Ord,
fn min(self) -> Option<Self::Item> where
Self::Item: Ord,
Returns the minimum element of an iterator. Read more
+1.6.0 · sourcefn max_by_key<B, F>(self, f: F) -> Option<Self::Item> where
B: Ord,
F: FnMut(&Self::Item) -> B,
fn max_by_key<B, F>(self, f: F) -> Option<Self::Item> where
B: Ord,
F: FnMut(&Self::Item) -> B,
Returns the element that gives the maximum value from the +specified function. Read more
+1.15.0 · sourcefn max_by<F>(self, compare: F) -> Option<Self::Item> where
F: FnMut(&Self::Item, &Self::Item) -> Ordering,
fn max_by<F>(self, compare: F) -> Option<Self::Item> where
F: FnMut(&Self::Item, &Self::Item) -> Ordering,
Returns the element that gives the maximum value with respect to the +specified comparison function. Read more
+1.6.0 · sourcefn min_by_key<B, F>(self, f: F) -> Option<Self::Item> where
B: Ord,
F: FnMut(&Self::Item) -> B,
fn min_by_key<B, F>(self, f: F) -> Option<Self::Item> where
B: Ord,
F: FnMut(&Self::Item) -> B,
Returns the element that gives the minimum value from the +specified function. Read more
+1.15.0 · sourcefn min_by<F>(self, compare: F) -> Option<Self::Item> where
F: FnMut(&Self::Item, &Self::Item) -> Ordering,
fn min_by<F>(self, compare: F) -> Option<Self::Item> where
F: FnMut(&Self::Item, &Self::Item) -> Ordering,
Returns the element that gives the minimum value with respect to the +specified comparison function. Read more
+1.0.0 · sourcefn rev(self) -> Rev<Self> where
Self: DoubleEndedIterator,
fn rev(self) -> Rev<Self> where
Self: DoubleEndedIterator,
Reverses an iterator’s direction. Read more
+1.0.0 · sourcefn unzip<A, B, FromA, FromB>(self) -> (FromA, FromB) where
FromA: Default + Extend<A>,
FromB: Default + Extend<B>,
Self: Iterator<Item = (A, B)>,
fn unzip<A, B, FromA, FromB>(self) -> (FromA, FromB) where
FromA: Default + Extend<A>,
FromB: Default + Extend<B>,
Self: Iterator<Item = (A, B)>,
Converts an iterator of pairs into a pair of containers. Read more
+1.36.0 · sourcefn copied<'a, T>(self) -> Copied<Self> where
T: 'a + Copy,
Self: Iterator<Item = &'a T>,
fn copied<'a, T>(self) -> Copied<Self> where
T: 'a + Copy,
Self: Iterator<Item = &'a T>,
Creates an iterator which copies all of its elements. Read more
+1.0.0 · sourcefn cloned<'a, T>(self) -> Cloned<Self> where
T: 'a + Clone,
Self: Iterator<Item = &'a T>,
fn cloned<'a, T>(self) -> Cloned<Self> where
T: 'a + Clone,
Self: Iterator<Item = &'a T>,
1.0.0 · sourcefn cycle(self) -> Cycle<Self> where
Self: Clone,
fn cycle(self) -> Cycle<Self> where
Self: Clone,
Repeats an iterator endlessly. Read more
+1.11.0 · sourcefn sum<S>(self) -> S where
S: Sum<Self::Item>,
fn sum<S>(self) -> S where
S: Sum<Self::Item>,
Sums the elements of an iterator. Read more
+1.11.0 · sourcefn product<P>(self) -> P where
P: Product<Self::Item>,
fn product<P>(self) -> P where
P: Product<Self::Item>,
Iterates over the entire iterator, multiplying all the elements Read more
+1.5.0 · sourcefn cmp<I>(self, other: I) -> Ordering where
I: IntoIterator<Item = Self::Item>,
Self::Item: Ord,
fn cmp<I>(self, other: I) -> Ordering where
I: IntoIterator<Item = Self::Item>,
Self::Item: Ord,
Lexicographically compares the elements of this Iterator with those
+of another. Read more
sourcefn cmp_by<I, F>(self, other: I, cmp: F) -> Ordering where
I: IntoIterator,
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,
fn cmp_by<I, F>(self, other: I, cmp: F) -> Ordering where
I: IntoIterator,
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,
🔬 This is a nightly-only experimental API. (
iter_order_by)Lexicographically compares the elements of this Iterator with those
+of another with respect to the specified comparison function. Read more
1.5.0 · sourcefn partial_cmp<I>(self, other: I) -> Option<Ordering> where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
fn partial_cmp<I>(self, other: I) -> Option<Ordering> where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
Lexicographically compares the elements of this Iterator with those
+of another. Read more
sourcefn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering> where
I: IntoIterator,
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,
fn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering> where
I: IntoIterator,
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,
🔬 This is a nightly-only experimental API. (
iter_order_by)Lexicographically compares the elements of this Iterator with those
+of another with respect to the specified comparison function. Read more
1.5.0 · sourcefn eq<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>,
fn eq<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>,
sourcefn eq_by<I, F>(self, other: I, eq: F) -> bool where
I: IntoIterator,
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> bool,
fn eq_by<I, F>(self, other: I, eq: F) -> bool where
I: IntoIterator,
F: FnMut(Self::Item, <I as IntoIterator>::Item) -> bool,
🔬 This is a nightly-only experimental API. (
iter_order_by)1.5.0 · sourcefn ne<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>,
fn ne<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialEq<<I as IntoIterator>::Item>,
1.5.0 · sourcefn lt<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
fn lt<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
Determines if the elements of this Iterator are lexicographically
+less than those of another. Read more
1.5.0 · sourcefn le<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
fn le<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
Determines if the elements of this Iterator are lexicographically
+less or equal to those of another. Read more
1.5.0 · sourcefn gt<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
fn gt<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
Determines if the elements of this Iterator are lexicographically
+greater than those of another. Read more
1.5.0 · sourcefn ge<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
fn ge<I>(self, other: I) -> bool where
I: IntoIterator,
Self::Item: PartialOrd<<I as IntoIterator>::Item>,
Determines if the elements of this Iterator are lexicographically
+greater than or equal to those of another. Read more
sourcefn is_sorted(self) -> bool where
Self::Item: PartialOrd<Self::Item>,
fn is_sorted(self) -> bool where
Self::Item: PartialOrd<Self::Item>,
🔬 This is a nightly-only experimental API. (
is_sorted)Checks if the elements of this iterator are sorted. Read more
+sourcefn is_sorted_by<F>(self, compare: F) -> bool where
F: FnMut(&Self::Item, &Self::Item) -> Option<Ordering>,
fn is_sorted_by<F>(self, compare: F) -> bool where
F: FnMut(&Self::Item, &Self::Item) -> Option<Ordering>,
🔬 This is a nightly-only experimental API. (
is_sorted)Checks if the elements of this iterator are sorted using the given comparator function. Read more
+sourcefn is_sorted_by_key<F, K>(self, f: F) -> bool where
F: FnMut(Self::Item) -> K,
K: PartialOrd<K>,
fn is_sorted_by_key<F, K>(self, f: F) -> bool where
F: FnMut(Self::Item) -> K,
K: PartialOrd<K>,
🔬 This is a nightly-only experimental API. (
is_sorted)Checks if the elements of this iterator are sorted using the given key extraction +function. Read more
+Auto Trait Implementations
impl<'a> !RefUnwindSafe for PropertiesIter<'a>
impl<'a> !Send for PropertiesIter<'a>
impl<'a> !Sync for PropertiesIter<'a>
impl<'a> Unpin for PropertiesIter<'a>
impl<'a> !UnwindSafe for PropertiesIter<'a>
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+sourceimpl<I> IntoIterator for I where
I: Iterator,
impl<I> IntoIterator for I where
I: Iterator,
pub struct Residue { /* private fields */ }Expand description
A Residue is a group of atoms belonging to the same logical unit. They
+can be small molecules, amino-acids in a protein, monomers in polymers,
+etc.
Implementations
sourceimpl Residue
impl Residue
sourcepub fn new<'a>(name: impl Into<&'a str>) -> Residue
pub fn new<'a>(name: impl Into<&'a str>) -> Residue
Create a new residue with the given name
Example
+let residue = Residue::new("ALA");
+assert_eq!(residue.name(), "ALA");
+assert_eq!(residue.id(), None);sourcepub fn with_id<'a>(name: impl Into<&'a str>, id: i64) -> Residue
pub fn with_id<'a>(name: impl Into<&'a str>, id: i64) -> Residue
Create a new residue with the given name and id as identifier.
Example
+let residue = Residue::with_id("ALA", 67);
+assert_eq!(residue.name(), "ALA");
+assert_eq!(residue.id(), Some(67));sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the number of atoms in this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.size(), 0);
+
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+assert_eq!(residue.size(), 3);sourcepub fn id(&self) -> Option<i64>
pub fn id(&self) -> Option<i64>
Get the identifier of this residue in the initial topology file.
+Example
+let residue = Residue::with_id("", 42);
+assert_eq!(residue.id(), Some(42));sourcepub fn name(&self) -> String
pub fn name(&self) -> String
Get the name of this residue.
+Example
+let residue = Residue::new("water");
+assert_eq!(residue.name(), "water");sourcepub fn add_atom(&mut self, atom: usize)
pub fn add_atom(&mut self, atom: usize)
Add the atom at index atom in this residue.
This will fail if the atom is already in the residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.size(), 0);
+assert_eq!(residue.contains(56), false);
+
+residue.add_atom(56);
+assert_eq!(residue.size(), 1);
+assert_eq!(residue.contains(56), true);
+
+// Adding the same atom twice is fine
+residue.add_atom(56);
+assert_eq!(residue.size(), 1);sourcepub fn contains(&self, atom: usize) -> bool
pub fn contains(&self, atom: usize) -> bool
Check if the atom at index i is in this residue
Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.contains(56), false);
+
+residue.add_atom(56);
+assert_eq!(residue.contains(56), true);sourcepub fn atoms(&self) -> Vec<usize>
pub fn atoms(&self) -> Vec<usize>
Get the list of atoms of this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.atoms(), vec![]);
+
+residue.add_atom(56);
+assert_eq!(residue.atoms(), vec![56]);sourcepub fn set(&mut self, name: &str, property: impl Into<Property>)
pub fn set(&mut self, name: &str, property: impl Into<Property>)
Add a new property with the given name to this residue.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut residue = Residue::new("ALA");
+residue.set("a string", "hello");
+residue.set("a double", 3.2);
+
+assert_eq!(residue.get("a string"), Some(Property::String("hello".into())));
+assert_eq!(residue.get("a double"), Some(Property::Double(3.2)));sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this frame, if it exist.
Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+
+assert_eq!(residue.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(residue.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Get an iterator over all (name, property) pairs for this frame
+Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+residue.set("bar", Property::Bool(false));
+
+for (name, property) in residue.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Residue
impl !Send for Residue
impl !Sync for Residue
impl Unpin for Residue
impl UnwindSafe for Residue
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+
+ Struct chemfiles::
source · [−]
Struct chemfiles::ResidueRef
source · [−]pub struct ResidueRef<'a> { /* private fields */ }Expand description
An analog to a reference to a residue (&Residue)
Methods from Deref<Target = Residue>
sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the number of atoms in this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.size(), 0);
+
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+assert_eq!(residue.size(), 3);sourcepub fn id(&self) -> Option<i64>
pub fn id(&self) -> Option<i64>
Get the identifier of this residue in the initial topology file.
+Example
+let residue = Residue::with_id("", 42);
+assert_eq!(residue.id(), Some(42));sourcepub fn name(&self) -> String
pub fn name(&self) -> String
Get the name of this residue.
+Example
+let residue = Residue::new("water");
+assert_eq!(residue.name(), "water");sourcepub fn contains(&self, atom: usize) -> bool
pub fn contains(&self, atom: usize) -> bool
Check if the atom at index i is in this residue
Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.contains(56), false);
+
+residue.add_atom(56);
+assert_eq!(residue.contains(56), true);sourcepub fn atoms(&self) -> Vec<usize>
pub fn atoms(&self) -> Vec<usize>
Get the list of atoms of this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.atoms(), vec![]);
+
+residue.add_atom(56);
+assert_eq!(residue.atoms(), vec![56]);sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this frame, if it exist.
Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+
+assert_eq!(residue.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(residue.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
pub fn properties(&self) -> PropertiesIter<'_>ⓘNotable traits for PropertiesIter<'a>impl<'a> Iterator for PropertiesIter<'a> type Item = (String, Property);
Get an iterator over all (name, property) pairs for this frame
+Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+residue.set("bar", Property::Bool(false));
+
+for (name, property) in residue.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for ResidueRef<'a>
impl<'a> !Send for ResidueRef<'a>
impl<'a> !Sync for ResidueRef<'a>
impl<'a> Unpin for ResidueRef<'a>
impl<'a> UnwindSafe for ResidueRef<'a>
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+pub struct Selection { /* private fields */ }Expand description
A Selection allow to select atoms in a Frame, from a selection
+language. The selection language is built by combining basic operations.
+Each basic operation follows the <selector>[(<variable>)] <operator> <value> structure, where <operator> is a comparison operator in
+== != < <= > >=.
Implementations
sourceimpl Selection
impl Selection
sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the size of the selection, i.e. the number of atoms we are selecting +together.
+This value is 1 for the ‘atom’ context, 2 for the ‘pair’ and ‘bond’ +context, 3 for the ‘three’ and ‘angles’ context and 4 for the ‘four’ +and ‘dihedral’ context.
+Example
+let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+assert_eq!(selection.size(), 2);sourcepub fn string(&self) -> String
pub fn string(&self) -> String
Get the selection string used to create this selection.
+Example
+let selection = Selection::new("name H").unwrap();
+assert_eq!(selection.string(), "name H");sourcepub fn evaluate(&mut self, frame: &Frame) -> Vec<Match>
pub fn evaluate(&mut self, frame: &Frame) -> Vec<Match>
Evaluate a selection for a given frame, and return the corresponding +matches.
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+
+let mut selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+let matches = selection.evaluate(&frame);
+
+assert_eq!(matches.len(), 2);
+
+assert_eq!(matches[0].len(), 2);
+assert_eq!(matches[0][0], 0);
+assert_eq!(matches[0][1], 1);
+
+assert_eq!(matches[1].len(), 2);
+assert_eq!(matches[1][0], 2);
+assert_eq!(matches[1][1], 1);sourcepub fn list(&mut self, frame: &Frame) -> Vec<usize>
pub fn list(&mut self, frame: &Frame) -> Vec<usize>
Evaluates a selection of size 1 on a given frame. This function
+returns the list of atomic indexes in the frame matching this selection.
Panics
+If the selection size is not 1
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+
+let mut selection = Selection::new("name H").unwrap();
+let matches = selection.list(&frame);
+
+assert_eq!(matches.len(), 2);
+assert_eq!(matches[0], 0);
+assert_eq!(matches[1], 2);Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Selection
impl !Send for Selection
impl !Sync for Selection
impl Unpin for Selection
impl UnwindSafe for Selection
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+pub struct Topology { /* private fields */ }Expand description
A Topology contains the definition of all the atoms in the system, and
+the liaisons between the atoms (bonds, angles, dihedrals, …). It will
+also contain all the residues information if it is available.
Implementations
sourceimpl Topology
impl Topology
sourcepub fn new() -> Topology
pub fn new() -> Topology
Create a new empty topology.
+Example
+let topology = Topology::new();
+assert_eq!(topology.size(), 0);sourcepub fn atom_mut(&mut self, index: usize) -> AtomMut<'_>
pub fn atom_mut(&mut self, index: usize) -> AtomMut<'_>
Get a mutable reference to the atom at the given index in this topology.
Panics
+If index is out of bounds.
Example
+let mut topology = Topology::new();
+topology.resize(6);
+
+assert_eq!(topology.atom(4).name(), "");
+
+topology.atom_mut(4).set_name("Fe");
+assert_eq!(topology.atom(4).name(), "Fe");sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the current number of atoms in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.size(), 0);
+
+topology.resize(6);
+assert_eq!(topology.size(), 6);sourcepub fn resize(&mut self, natoms: usize)
pub fn resize(&mut self, natoms: usize)
Resize this topology to hold natoms atoms, inserting dummy atoms if
+the new size if bigger than the old one.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.size(), 0);
+
+topology.resize(6);
+assert_eq!(topology.size(), 6);sourcepub fn add_atom(&mut self, atom: &Atom)
pub fn add_atom(&mut self, atom: &Atom)
Add an Atom at the end of this topology
Example
+let mut topology = Topology::new();
+topology.add_atom(&Atom::new("Mg"));
+
+let atom = topology.atom(0);
+assert_eq!(atom.name(), "Mg");sourcepub fn bonds_count(&self) -> usize
pub fn bonds_count(&self) -> usize
Get the number of bonds in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds_count(), 3);sourcepub fn angles_count(&self) -> usize
pub fn angles_count(&self) -> usize
Get the number of angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.angles_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles_count(), 2);sourcepub fn dihedrals_count(&self) -> usize
pub fn dihedrals_count(&self) -> usize
Get the number of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.dihedrals_count(), 1);sourcepub fn impropers_count(&self) -> usize
pub fn impropers_count(&self) -> usize
Get the number of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+assert_eq!(topology.impropers_count(), 1);sourcepub fn bonds(&self) -> Vec<[usize; 2]>
pub fn bonds(&self) -> Vec<[usize; 2]>
Get the list of bonds in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);sourcepub fn angles(&self) -> Vec<[usize; 3]>
pub fn angles(&self) -> Vec<[usize; 3]>
Get the list of angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);sourcepub fn dihedrals(&self) -> Vec<[usize; 4]>
pub fn dihedrals(&self) -> Vec<[usize; 4]>
Get the list of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+
+assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);sourcepub fn impropers(&self) -> Vec<[usize; 4]>
pub fn impropers(&self) -> Vec<[usize; 4]>
Get the list of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+
+assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);sourcepub fn clear_bonds(&mut self)
pub fn clear_bonds(&mut self)
Remove all existing bonds, angles, dihedral angles and improper +dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+assert_eq!(topology.bonds_count(), 2);
+assert_eq!(topology.angles().len(), 1);
+
+topology.clear_bonds();
+assert!(topology.bonds().is_empty());
+assert!(topology.angles().is_empty());sourcepub fn add_bond(&mut self, i: usize, j: usize)
pub fn add_bond(&mut self, i: usize, j: usize)
Add a bond between the atoms at indexes i and j in the topology.
The bond order is set to BondOrder::Unknown.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+assert_eq!(topology.bonds_count(), 2);
+
+assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);sourcepub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder)
pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder)
Add a bond between the atoms at indexes i and j in the topology
+with the given bond order.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(2);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(topology.bond_order(0, 1), BondOrder::Double);sourcepub fn bond_order(&self, i: usize, j: usize) -> BondOrder
pub fn bond_order(&self, i: usize, j: usize) -> BondOrder
Get the bond order for the bond between the atoms at indexes i and
+j.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(2);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(topology.bond_order(0, 1), BondOrder::Double);sourcepub fn bond_orders(&self) -> Vec<BondOrder>
pub fn bond_orders(&self) -> Vec<BondOrder>
Get the bond order for all the bonds in the topology
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(3);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+topology.add_bond_with_order(0, 2, BondOrder::Single);
+
+assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);sourcepub fn remove_bond(&mut self, i: usize, j: usize)
pub fn remove_bond(&mut self, i: usize, j: usize)
Remove any existing bond between the atoms at indexes i and j in
+this topology.
This function does nothing if there is no bond between i and j.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(1, 2);
+assert_eq!(topology.bonds_count(), 2);
+
+topology.remove_bond(0, 1);
+assert_eq!(topology.bonds_count(), 1);
+
+// Removing a bond that does not exists is fine
+topology.remove_bond(0, 2);
+assert_eq!(topology.bonds_count(), 1);sourcepub fn residue(&self, index: u64) -> Option<ResidueRef<'_>>
pub fn residue(&self, index: u64) -> Option<ResidueRef<'_>>
Get a reference to the residue at index index from this topology.
The residue index in the topology is not always the same as the residue
+id.
Example
+let mut topology = Topology::new();
+topology.add_residue(&Residue::new("water")).unwrap();
+
+let residue = topology.residue(0).unwrap();
+assert_eq!(residue.name(), "water");sourcepub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef<'_>>
pub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef<'_>>
Get a copy of the residue containing the atom at index index in this
+topology, if any.
Example
+let mut topology = Topology::new();
+topology.resize(8);
+
+let mut residue = Residue::new("water");
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+topology.add_residue(&residue).unwrap();
+
+let residue = topology.residue_for_atom(0).unwrap();
+assert_eq!(residue.name(), "water");
+
+assert!(topology.residue_for_atom(6).is_none());sourcepub fn residues_count(&self) -> u64
pub fn residues_count(&self) -> u64
Get the number of residues in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.residues_count(), 0);
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+assert_eq!(topology.residues_count(), 2);sourcepub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error>
pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error>
Add a residue to this topology.
+Errors
+This function fails is the residue id is not already in the topology,
+or if the residue contains atoms that are already in another residue.
Example
+let mut topology = Topology::new();
+topology.add_residue(&Residue::new("water")).unwrap();
+
+let residue = topology.residue(0).unwrap();
+assert_eq!(residue.name(), "water");sourcepub fn are_linked(&self, first: &Residue, second: &Residue) -> bool
pub fn are_linked(&self, first: &Residue, second: &Residue) -> bool
Check if the two residues first and second from the topology are
+linked together, i.e. if there is a bond between one atom in the
+first residue and one atom in the second one.
Example
+let mut topology = Topology::new();
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+
+let first = topology.residue(0).unwrap();
+let second = topology.residue(1).unwrap();
+assert_eq!(topology.are_linked(&first, &second), false);Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Topology
impl !Send for Topology
impl !Sync for Topology
impl Unpin for Topology
impl UnwindSafe for Topology
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+
+ Struct chemfiles::
source · [−]
Struct chemfiles::TopologyRef
source · [−]pub struct TopologyRef<'a> { /* private fields */ }Expand description
An analog to a reference to a topology (&Topology)
Methods from Deref<Target = Topology>
sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the current number of atoms in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.size(), 0);
+
+topology.resize(6);
+assert_eq!(topology.size(), 6);sourcepub fn bonds_count(&self) -> usize
pub fn bonds_count(&self) -> usize
Get the number of bonds in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds_count(), 3);sourcepub fn angles_count(&self) -> usize
pub fn angles_count(&self) -> usize
Get the number of angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.angles_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles_count(), 2);sourcepub fn dihedrals_count(&self) -> usize
pub fn dihedrals_count(&self) -> usize
Get the number of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.dihedrals_count(), 1);sourcepub fn impropers_count(&self) -> usize
pub fn impropers_count(&self) -> usize
Get the number of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+assert_eq!(topology.impropers_count(), 1);sourcepub fn bonds(&self) -> Vec<[usize; 2]>
pub fn bonds(&self) -> Vec<[usize; 2]>
Get the list of bonds in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);sourcepub fn angles(&self) -> Vec<[usize; 3]>
pub fn angles(&self) -> Vec<[usize; 3]>
Get the list of angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);sourcepub fn dihedrals(&self) -> Vec<[usize; 4]>
pub fn dihedrals(&self) -> Vec<[usize; 4]>
Get the list of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+
+assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);sourcepub fn impropers(&self) -> Vec<[usize; 4]>
pub fn impropers(&self) -> Vec<[usize; 4]>
Get the list of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+
+assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);sourcepub fn bond_order(&self, i: usize, j: usize) -> BondOrder
pub fn bond_order(&self, i: usize, j: usize) -> BondOrder
Get the bond order for the bond between the atoms at indexes i and
+j.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(2);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(topology.bond_order(0, 1), BondOrder::Double);sourcepub fn bond_orders(&self) -> Vec<BondOrder>
pub fn bond_orders(&self) -> Vec<BondOrder>
Get the bond order for all the bonds in the topology
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(3);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+topology.add_bond_with_order(0, 2, BondOrder::Single);
+
+assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);sourcepub fn residue(&self, index: u64) -> Option<ResidueRef<'_>>
pub fn residue(&self, index: u64) -> Option<ResidueRef<'_>>
Get a reference to the residue at index index from this topology.
The residue index in the topology is not always the same as the residue
+id.
Example
+let mut topology = Topology::new();
+topology.add_residue(&Residue::new("water")).unwrap();
+
+let residue = topology.residue(0).unwrap();
+assert_eq!(residue.name(), "water");sourcepub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef<'_>>
pub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef<'_>>
Get a copy of the residue containing the atom at index index in this
+topology, if any.
Example
+let mut topology = Topology::new();
+topology.resize(8);
+
+let mut residue = Residue::new("water");
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+topology.add_residue(&residue).unwrap();
+
+let residue = topology.residue_for_atom(0).unwrap();
+assert_eq!(residue.name(), "water");
+
+assert!(topology.residue_for_atom(6).is_none());sourcepub fn residues_count(&self) -> u64
pub fn residues_count(&self) -> u64
Get the number of residues in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.residues_count(), 0);
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+assert_eq!(topology.residues_count(), 2);sourcepub fn are_linked(&self, first: &Residue, second: &Residue) -> bool
pub fn are_linked(&self, first: &Residue, second: &Residue) -> bool
Check if the two residues first and second from the topology are
+linked together, i.e. if there is a bond between one atom in the
+first residue and one atom in the second one.
Example
+let mut topology = Topology::new();
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+
+let first = topology.residue(0).unwrap();
+let second = topology.residue(1).unwrap();
+assert_eq!(topology.are_linked(&first, &second), false);Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for TopologyRef<'a>
impl<'a> !Send for TopologyRef<'a>
impl<'a> !Sync for TopologyRef<'a>
impl<'a> Unpin for TopologyRef<'a>
impl<'a> UnwindSafe for TopologyRef<'a>
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+
+ Struct chemfiles::
source · [−]
Struct chemfiles::Trajectory
source · [−]pub struct Trajectory { /* private fields */ }Expand description
The Trajectory type is the main entry point when using chemfiles. A
+Trajectory behave a bit like a file, allowing to read and/or write
+Frame.
Implementations
sourceimpl Trajectory
impl Trajectory
sourcepub fn open<P>(path: P, mode: char) -> Result<Trajectory, Error> where
P: AsRef<Path>,
pub fn open<P>(path: P, mode: char) -> Result<Trajectory, Error> where
P: AsRef<Path>,
Open the file at the given path in the given mode.
Valid modes are 'r' for read, 'w' for write and 'a' for append.
Errors
+This function fails if the file is not accessible for the given mode, if +it is incorrectly formatted for the corresponding format, or in case of +I/O errors from the OS.
+Example
+let trajectory = Trajectory::open("water.xyz", 'r').unwrap();sourcepub fn open_with_format<'a, P, S>(
filename: P,
mode: char,
format: S
) -> Result<Trajectory, Error> where
P: AsRef<Path>,
S: Into<&'a str>,
pub fn open_with_format<'a, P, S>(
filename: P,
mode: char,
format: S
) -> Result<Trajectory, Error> where
P: AsRef<Path>,
S: Into<&'a str>,
Open the file at the given path using a specific file format and the
+given mode.
Valid modes are 'r' for read, 'w' for write and 'a' for append.
Specifying a format is needed when the file format does not match the
+extension, or when there is not standard extension for this format. If
+format is an empty string, the format will be guessed from the
+extension.
Errors
+This function fails if the file is not accessible for the given mode, if +it is incorrectly formatted for the corresponding format, or in case of +I/O errors from the OS.
+Example
+let trajectory = Trajectory::open_with_format("water.zeo", 'r', "XYZ").unwrap();sourcepub fn memory_reader<'a, S>(data: S, format: S) -> Result<Trajectory, Error> where
S: Into<&'a str>,
pub fn memory_reader<'a, S>(data: S, format: S) -> Result<Trajectory, Error> where
S: Into<&'a str>,
Read a memory buffer as though it was a formatted file.
+The memory buffer used to store the file is given using the data
+argument. The format parameter is required and should follow the same
+rules as in the main Trajectory constructor.
Errors
+This function fails if the data is incorrectly formatted for the +corresponding format, or if the format do not support in-memory readers.
+Example
+let aromatics = "c1ccccc1\nc1ccco1\nc1ccccn1\n";
+let mut trajectory = Trajectory::memory_reader(aromatics, "SMI").unwrap();
+let mut frame = Frame::new();
+trajectory.read(&mut frame).unwrap();
+assert_eq!(frame.size(), 6);sourcepub fn memory_writer<'a, S>(format: S) -> Result<Trajectory, Error> where
S: Into<&'a str>,
pub fn memory_writer<'a, S>(format: S) -> Result<Trajectory, Error> where
S: Into<&'a str>,
Write to a memory buffer as though it was a formatted file.
+The format parameter should follow the same rules as in the main
+Trajectory constructor, except that compression specification
+is not supported.
The memory_buffer function can be used to retrieve the data written
+to memory of the Trajectory.
Errors
+This function fails if the format do not support in-memory writers.
+Example
+let trajectory_memory = Trajectory::memory_writer("SMI");
+
+// Binary formats typically do not support this feature
+assert!(Trajectory::memory_writer("XTC").is_err());sourcepub fn read(&mut self, frame: &mut Frame) -> Result<(), Error>
pub fn read(&mut self, frame: &mut Frame) -> Result<(), Error>
Read the next step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of atom +in the next step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+let mut frame = Frame::new();
+
+trajectory.read(&mut frame).unwrap();sourcepub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error>
pub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error>
Read a specific step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of +atom at this step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+let mut frame = Frame::new();
+
+trajectory.read_step(10, &mut frame).unwrap();sourcepub fn set_topology(&mut self, topology: &Topology)
pub fn set_topology(&mut self, topology: &Topology)
Set the topology associated with this trajectory. This topology will
+be used when reading and writing the files, replacing any topology in
+the frames or files.
Example
+let mut topology = Topology::new();
+topology.add_atom(&Atom::new("H"));
+topology.add_atom(&Atom::new("O"));
+topology.add_atom(&Atom::new("H"));
+topology.add_bond(0, 1);
+topology.add_bond(1, 2);
+
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+trajectory.set_topology(&topology);sourcepub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error> where
P: AsRef<Path>,
pub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error> where
P: AsRef<Path>,
Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in format;
+and extracting the topology of this frame.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+trajectory.set_topology_file("topology.pdb").unwrap();sourcepub fn set_topology_with_format<'a, P, S>(
&mut self,
path: P,
format: S
) -> Result<(), Error> where
P: AsRef<Path>,
S: Into<&'a str>,
pub fn set_topology_with_format<'a, P, S>(
&mut self,
path: P,
format: S
) -> Result<(), Error> where
P: AsRef<Path>,
S: Into<&'a str>,
Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in
+format; and extracting the topology of this frame.
If format is an empty string, the format will be guessed from the
+path extension.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+trajectory.set_topology_with_format("topology.mol", "PDB").unwrap();sourcepub fn set_cell(&mut self, cell: &UnitCell)
pub fn set_cell(&mut self, cell: &UnitCell)
Set the unit cell associated with a trajectory. This cell will be
+used when reading and writing the files, replacing any unit cell in the
+frames or files.
Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+trajectory.set_cell(&UnitCell::new([10.0, 11.0, 12.5]));sourcepub fn nsteps(&mut self) -> usize
pub fn nsteps(&mut self) -> usize
Get the number of steps (the number of frames) in a trajectory.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+
+println!("This trajectory contains {} steps", trajectory.nsteps());sourcepub fn memory_buffer(&self) -> Result<&str, Error>
pub fn memory_buffer(&self) -> Result<&str, Error>
Obtain the memory buffer written to by the trajectory.
+Errors
+This fails if the trajectory was not opened with
+Trajectory::memory_writer.
Example
+let mut trajectory_memory = Trajectory::memory_writer("SMI").unwrap();
+
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+frame.add_bond_with_order(0, 1, BondOrder::Single);
+
+trajectory_memory.write(&frame).unwrap();
+
+let result = trajectory_memory.memory_buffer();
+assert_eq!(result.unwrap(), "CC\n");Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Trajectory
impl !Send for Trajectory
impl !Sync for Trajectory
impl Unpin for Trajectory
impl UnwindSafe for Trajectory
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+pub struct UnitCell { /* private fields */ }Expand description
An UnitCell represent the box containing the atoms, and its periodicity.
An unit cell is fully represented by three lengths (a, b, c); and three +angles (alpha, beta, gamma). The angles are stored in degrees, and the +lengths in Angstroms.
+A cell also has a matricial representation, by projecting the three base +vector into an orthonormal base. We choose to represent such matrix as an +upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |Implementations
sourceimpl UnitCell
impl UnitCell
sourcepub fn new(lengths: [f64; 3]) -> UnitCell
pub fn new(lengths: [f64; 3]) -> UnitCell
Create an Orthorhombic UnitCell from the three lengths, in Angstroms.
Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);sourcepub fn infinite() -> UnitCell
pub fn infinite() -> UnitCell
Create an Infinite UnitCell.
Example
+let cell = UnitCell::infinite();
+
+assert_eq!(cell.lengths(), [0.0, 0.0, 0.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+assert_eq!(cell.shape(), CellShape::Infinite);sourcepub fn triclinic(lengths: [f64; 3], angles: [f64; 3]) -> UnitCell
pub fn triclinic(lengths: [f64; 3], angles: [f64; 3]) -> UnitCell
Create an Triclinic UnitCell from the three lengths (in Angstroms)
+and three angles (in degree). alpha is the angle between the vectors
+b and c; beta is the between the vectors a and c and gamma
+is the angle between the vectors a and b.
Example
+let cell = UnitCell::triclinic([10.0, 10.0, 10.0], [98.0, 99.0, 90.0]);
+
+assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);
+assert_eq!(cell.angles()[0], 98.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 99.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);
+assert_eq!(cell.shape(), CellShape::Triclinic);sourcepub fn from_matrix(matrix: [[f64; 3]; 3]) -> UnitCell
pub fn from_matrix(matrix: [[f64; 3]; 3]) -> UnitCell
Create an UnitCell from a cell matrix. If matrix contains only
+zeros, then an Infinite cell is created. If only the diagonal of the
+matrix is non-zero, then the cell is Orthorhombic. Else a
+Triclinic cell is created. The matrix entries should be in Angstroms.
Panics
+If the matrix has a negative determinant, or more generally is not +representing a unit cell.
+Example
+let cell = UnitCell::from_matrix([
+ [1.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]
+]);
+
+assert_eq!(cell.lengths(), [1.0, 2.0, 3.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);sourcepub fn lengths(&self) -> [f64; 3]
pub fn lengths(&self) -> [f64; 3]
Get the three lengths of the cell, in Angstroms.
+Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);sourcepub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error>
pub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error>
Set the three lengths of the cell, in Angstroms.
+Errors
+This function fails if the unit cell is infinite, or if one of the +lengths is negative.
+Example
+let mut cell = UnitCell::new([30.0, 30.0, 23.0]);
+
+cell.set_lengths([10.0, 30.0, 42.0]).unwrap();
+assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]);
+
+assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());sourcepub fn angles(&self) -> [f64; 3]
pub fn angles(&self) -> [f64; 3]
Get the three angles of the cell, in degrees.
+Example
+let cell = UnitCell::new([20.0, 20.0, 20.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+
+let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);sourcepub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error>
pub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error>
Set the three angles of the cell, in degrees.
+Errors
+This function fails if the unit cell is not Triclinic.
Example
+let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);
+
+cell.set_angles([90.0, 90.0, 90.0]).unwrap();
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);sourcepub fn matrix(&self) -> [[f64; 3]; 3]
pub fn matrix(&self) -> [[f64; 3]; 3]
Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+
+let matrix = cell.matrix();
+
+assert_eq!(matrix[0][0], 10.0);
+assert_eq!(matrix[1][1], 20.0);
+assert_eq!(matrix[2][2], 30.0);
+
+assert!(matrix[1][2].abs() < 1e-9);sourcepub fn shape(&self) -> CellShape
pub fn shape(&self) -> CellShape
Get the shape of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);sourcepub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error>
pub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error>
Set the shape of the unit cell to shape.
Errors
+This can fail if the cell length or angles are incompatible with the +new shape.
+Example
+let mut cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);
+
+cell.set_shape(CellShape::Triclinic).unwrap();
+assert_eq!(cell.shape(), CellShape::Triclinic);Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for UnitCell
impl !Send for UnitCell
impl !Sync for UnitCell
impl Unpin for UnitCell
impl UnwindSafe for UnitCell
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+
+ Struct chemfiles::
source · [−]
Struct chemfiles::UnitCellMut
source · [−]pub struct UnitCellMut<'a> { /* private fields */ }Expand description
An analog to a mutable reference to an unit cell (&mut UnitCell)
Methods from Deref<Target = UnitCell>
sourcepub fn lengths(&self) -> [f64; 3]
pub fn lengths(&self) -> [f64; 3]
Get the three lengths of the cell, in Angstroms.
+Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);sourcepub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error>
pub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error>
Set the three lengths of the cell, in Angstroms.
+Errors
+This function fails if the unit cell is infinite, or if one of the +lengths is negative.
+Example
+let mut cell = UnitCell::new([30.0, 30.0, 23.0]);
+
+cell.set_lengths([10.0, 30.0, 42.0]).unwrap();
+assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]);
+
+assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());sourcepub fn angles(&self) -> [f64; 3]
pub fn angles(&self) -> [f64; 3]
Get the three angles of the cell, in degrees.
+Example
+let cell = UnitCell::new([20.0, 20.0, 20.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+
+let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);sourcepub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error>
pub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error>
Set the three angles of the cell, in degrees.
+Errors
+This function fails if the unit cell is not Triclinic.
Example
+let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);
+
+cell.set_angles([90.0, 90.0, 90.0]).unwrap();
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);sourcepub fn matrix(&self) -> [[f64; 3]; 3]
pub fn matrix(&self) -> [[f64; 3]; 3]
Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+
+let matrix = cell.matrix();
+
+assert_eq!(matrix[0][0], 10.0);
+assert_eq!(matrix[1][1], 20.0);
+assert_eq!(matrix[2][2], 30.0);
+
+assert!(matrix[1][2].abs() < 1e-9);sourcepub fn shape(&self) -> CellShape
pub fn shape(&self) -> CellShape
Get the shape of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);sourcepub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error>
pub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error>
Set the shape of the unit cell to shape.
Errors
+This can fail if the cell length or angles are incompatible with the +new shape.
+Example
+let mut cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);
+
+cell.set_shape(CellShape::Triclinic).unwrap();
+assert_eq!(cell.shape(), CellShape::Triclinic);Trait Implementations
sourceimpl<'a> Deref for UnitCellMut<'a>
impl<'a> Deref for UnitCellMut<'a>
Auto Trait Implementations
impl<'a> RefUnwindSafe for UnitCellMut<'a>
impl<'a> !Send for UnitCellMut<'a>
impl<'a> !Sync for UnitCellMut<'a>
impl<'a> Unpin for UnitCellMut<'a>
impl<'a> !UnwindSafe for UnitCellMut<'a>
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+
+ Struct chemfiles::
source · [−]
Struct chemfiles::UnitCellRef
source · [−]pub struct UnitCellRef<'a> { /* private fields */ }Expand description
An analog to a reference to an unit cell (&UnitCell)
Methods from Deref<Target = UnitCell>
sourcepub fn lengths(&self) -> [f64; 3]
pub fn lengths(&self) -> [f64; 3]
Get the three lengths of the cell, in Angstroms.
+Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);sourcepub fn angles(&self) -> [f64; 3]
pub fn angles(&self) -> [f64; 3]
Get the three angles of the cell, in degrees.
+Example
+let cell = UnitCell::new([20.0, 20.0, 20.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+
+let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);sourcepub fn matrix(&self) -> [[f64; 3]; 3]
pub fn matrix(&self) -> [[f64; 3]; 3]
Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+
+let matrix = cell.matrix();
+
+assert_eq!(matrix[0][0], 10.0);
+assert_eq!(matrix[1][1], 20.0);
+assert_eq!(matrix[2][2], 30.0);
+
+assert!(matrix[1][2].abs() < 1e-9);sourcepub fn shape(&self) -> CellShape
pub fn shape(&self) -> CellShape
Get the shape of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);Trait Implementations
Auto Trait Implementations
impl<'a> RefUnwindSafe for UnitCellRef<'a>
impl<'a> !Send for UnitCellRef<'a>
impl<'a> !Sync for UnitCellRef<'a>
impl<'a> Unpin for UnitCellRef<'a>
impl<'a> UnwindSafe for UnitCellRef<'a>
Blanket Implementations
sourceimpl<T> BorrowMut<T> for T where
T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
+Redirecting to ../../chemfiles/enum.BondOrder.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/topology/struct.Topology.html b/0.10.3/chemfiles/topology/struct.Topology.html new file mode 100644 index 000000000..1215dacfd --- /dev/null +++ b/0.10.3/chemfiles/topology/struct.Topology.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Topology.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/topology/struct.TopologyRef.html b/0.10.3/chemfiles/topology/struct.TopologyRef.html new file mode 100644 index 000000000..7cdec6164 --- /dev/null +++ b/0.10.3/chemfiles/topology/struct.TopologyRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.TopologyRef.html...
+ + + \ No newline at end of file diff --git a/0.10.3/chemfiles/trajectory/struct.Trajectory.html b/0.10.3/chemfiles/trajectory/struct.Trajectory.html new file mode 100644 index 000000000..bab83ffc9 --- /dev/null +++ b/0.10.3/chemfiles/trajectory/struct.Trajectory.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Trajectory.html...
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Status","synthetic":false,"types":["chemfiles::errors::Status"]},{"text":"impl Eq for CellShape","synthetic":false,"types":["chemfiles::cell::CellShape"]},{"text":"impl Eq for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]},{"text":"impl Eq for Match","synthetic":false,"types":["chemfiles::selection::Match"]},{"text":"impl Eq for FormatMetadata","synthetic":false,"types":["chemfiles::misc::FormatMetadata"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.3/implementors/core/cmp/trait.Ord.js b/0.10.3/implementors/core/cmp/trait.Ord.js new file mode 100644 index 000000000..4bdf98353 --- /dev/null +++ b/0.10.3/implementors/core/cmp/trait.Ord.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Ord for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.3/implementors/core/cmp/trait.PartialEq.js b/0.10.3/implementors/core/cmp/trait.PartialEq.js new file mode 100644 index 000000000..9b4c7c34b --- /dev/null +++ b/0.10.3/implementors/core/cmp/trait.PartialEq.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl PartialEq<Error> for Error","synthetic":false,"types":["chemfiles::errors::Error"]},{"text":"impl PartialEq<Status> for Status","synthetic":false,"types":["chemfiles::errors::Status"]},{"text":"impl PartialEq<CellShape> for CellShape","synthetic":false,"types":["chemfiles::cell::CellShape"]},{"text":"impl PartialEq<BondOrder> for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]},{"text":"impl PartialEq<Match> for Match","synthetic":false,"types":["chemfiles::selection::Match"]},{"text":"impl PartialEq<Property> for Property","synthetic":false,"types":["chemfiles::property::Property"]},{"text":"impl PartialEq<FormatMetadata> for FormatMetadata","synthetic":false,"types":["chemfiles::misc::FormatMetadata"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.3/implementors/core/cmp/trait.PartialOrd.js b/0.10.3/implementors/core/cmp/trait.PartialOrd.js new file mode 100644 index 000000000..119bcde74 --- /dev/null +++ b/0.10.3/implementors/core/cmp/trait.PartialOrd.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl PartialOrd<BondOrder> for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]},{"text":"impl PartialOrd<Property> for Property","synthetic":false,"types":["chemfiles::property::Property"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.3/implementors/core/convert/trait.From.js b/0.10.3/implementors/core/convert/trait.From.js new file mode 100644 index 000000000..90f239b11 --- /dev/null +++ b/0.10.3/implementors/core/convert/trait.From.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl From<chfl_status> for Error","synthetic":false,"types":["chemfiles::errors::Error"]},{"text":"impl From<Utf8Error> for Error","synthetic":false,"types":["chemfiles::errors::Error"]},{"text":"impl From<chfl_cellshape> for CellShape","synthetic":false,"types":["chemfiles::cell::CellShape"]},{"text":"impl From<CellShape> for chfl_cellshape","synthetic":false,"types":["chemfiles_sys::chfl_cellshape"]},{"text":"impl From<chfl_bond_order> for 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implementors = {}; +implementors["chemfiles"] = [{"text":"impl Debug for Error","synthetic":false,"types":["chemfiles::errors::Error"]},{"text":"impl Debug for Status","synthetic":false,"types":["chemfiles::errors::Status"]},{"text":"impl Debug for CellShape","synthetic":false,"types":["chemfiles::cell::CellShape"]},{"text":"impl Debug for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]},{"text":"impl Debug for Match","synthetic":false,"types":["chemfiles::selection::Match"]},{"text":"impl Debug for Property","synthetic":false,"types":["chemfiles::property::Property"]},{"text":"impl Debug for FormatMetadata","synthetic":false,"types":["chemfiles::misc::FormatMetadata"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.3/implementors/core/fmt/trait.Display.js b/0.10.3/implementors/core/fmt/trait.Display.js new file mode 100644 index 000000000..7b6a05cce --- /dev/null +++ b/0.10.3/implementors/core/fmt/trait.Display.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Display for Error","synthetic":false,"types":["chemfiles::errors::Error"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.3/implementors/core/iter/traits/collect/trait.IntoIterator.js b/0.10.3/implementors/core/iter/traits/collect/trait.IntoIterator.js new file mode 100644 index 000000000..eecd9d68f --- /dev/null +++ b/0.10.3/implementors/core/iter/traits/collect/trait.IntoIterator.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl<'a> IntoIterator for &'a Match","synthetic":false,"types":["chemfiles::selection::Match"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.3/implementors/core/iter/traits/iterator/trait.Iterator.js b/0.10.3/implementors/core/iter/traits/iterator/trait.Iterator.js new file mode 100644 index 000000000..284ee309a --- /dev/null +++ b/0.10.3/implementors/core/iter/traits/iterator/trait.Iterator.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl<'a> Iterator for PropertiesIter<'a>","synthetic":false,"types":["chemfiles::property::PropertiesIter"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.3/implementors/core/marker/trait.Copy.js b/0.10.3/implementors/core/marker/trait.Copy.js new file mode 100644 index 000000000..22cf88f0d --- /dev/null +++ b/0.10.3/implementors/core/marker/trait.Copy.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Copy for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.3/implementors/core/marker/trait.Freeze.js b/0.10.3/implementors/core/marker/trait.Freeze.js new file mode 100644 index 000000000..7a6ceb43d --- /dev/null +++ b/0.10.3/implementors/core/marker/trait.Freeze.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Freeze for Error","synthetic":true,"types":["chemfiles::errors::Error"]},{"text":"impl Freeze for Status","synthetic":true,"types":["chemfiles::errors::Status"]},{"text":"impl Freeze for Atom","synthetic":true,"types":["chemfiles::atom::Atom"]},{"text":"impl<'a> Freeze for AtomRef<'a>","synthetic":true,"types":["chemfiles::atom::AtomRef"]},{"text":"impl<'a> Freeze for AtomMut<'a>","synthetic":true,"types":["chemfiles::atom::AtomMut"]},{"text":"impl Freeze for CellShape","synthetic":true,"types":["chemfiles::cell::CellShape"]},{"text":"impl Freeze for UnitCell","synthetic":true,"types":["chemfiles::cell::UnitCell"]},{"text":"impl<'a> Freeze for UnitCellRef<'a>","synthetic":true,"types":["chemfiles::cell::UnitCellRef"]},{"text":"impl<'a> Freeze for UnitCellMut<'a>","synthetic":true,"types":["chemfiles::cell::UnitCellMut"]},{"text":"impl Freeze for Residue","synthetic":true,"types":["chemfiles::residue::Residue"]},{"text":"impl<'a> Freeze for ResidueRef<'a>","synthetic":true,"types":["chemfiles::residue::ResidueRef"]},{"text":"impl Freeze for BondOrder","synthetic":true,"types":["chemfiles::topology::BondOrder"]},{"text":"impl Freeze for Topology","synthetic":true,"types":["chemfiles::topology::Topology"]},{"text":"impl<'a> Freeze for TopologyRef<'a>","synthetic":true,"types":["chemfiles::topology::TopologyRef"]},{"text":"impl Freeze for 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+++ b/0.10.3/implementors/core/marker/trait.Send.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Send for Error","synthetic":true,"types":["chemfiles::errors::Error"]},{"text":"impl Send for Status","synthetic":true,"types":["chemfiles::errors::Status"]},{"text":"impl !Send for Atom","synthetic":true,"types":["chemfiles::atom::Atom"]},{"text":"impl<'a> !Send for AtomRef<'a>","synthetic":true,"types":["chemfiles::atom::AtomRef"]},{"text":"impl<'a> !Send for AtomMut<'a>","synthetic":true,"types":["chemfiles::atom::AtomMut"]},{"text":"impl Send for CellShape","synthetic":true,"types":["chemfiles::cell::CellShape"]},{"text":"impl !Send for UnitCell","synthetic":true,"types":["chemfiles::cell::UnitCell"]},{"text":"impl<'a> !Send for UnitCellRef<'a>","synthetic":true,"types":["chemfiles::cell::UnitCellRef"]},{"text":"impl<'a> !Send for UnitCellMut<'a>","synthetic":true,"types":["chemfiles::cell::UnitCellMut"]},{"text":"impl !Send for 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PropertiesIter<'a>","synthetic":true,"types":["chemfiles::property::PropertiesIter"]},{"text":"impl Send for FormatMetadata","synthetic":true,"types":["chemfiles::misc::FormatMetadata"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.3/implementors/core/marker/trait.StructuralEq.js b/0.10.3/implementors/core/marker/trait.StructuralEq.js new file mode 100644 index 000000000..4639cdd07 --- /dev/null +++ b/0.10.3/implementors/core/marker/trait.StructuralEq.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl StructuralEq for Error","synthetic":false,"types":["chemfiles::errors::Error"]},{"text":"impl StructuralEq for Status","synthetic":false,"types":["chemfiles::errors::Status"]},{"text":"impl StructuralEq for CellShape","synthetic":false,"types":["chemfiles::cell::CellShape"]},{"text":"impl StructuralEq for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]},{"text":"impl StructuralEq for Match","synthetic":false,"types":["chemfiles::selection::Match"]},{"text":"impl StructuralEq for FormatMetadata","synthetic":false,"types":["chemfiles::misc::FormatMetadata"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.3/implementors/core/marker/trait.StructuralPartialEq.js b/0.10.3/implementors/core/marker/trait.StructuralPartialEq.js new file mode 100644 index 000000000..88336d06d --- /dev/null +++ b/0.10.3/implementors/core/marker/trait.StructuralPartialEq.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl StructuralPartialEq for Error","synthetic":false,"types":["chemfiles::errors::Error"]},{"text":"impl StructuralPartialEq for Status","synthetic":false,"types":["chemfiles::errors::Status"]},{"text":"impl StructuralPartialEq for CellShape","synthetic":false,"types":["chemfiles::cell::CellShape"]},{"text":"impl StructuralPartialEq for BondOrder","synthetic":false,"types":["chemfiles::topology::BondOrder"]},{"text":"impl StructuralPartialEq for Match","synthetic":false,"types":["chemfiles::selection::Match"]},{"text":"impl StructuralPartialEq for Property","synthetic":false,"types":["chemfiles::property::Property"]},{"text":"impl StructuralPartialEq for FormatMetadata","synthetic":false,"types":["chemfiles::misc::FormatMetadata"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.3/implementors/core/marker/trait.Sync.js b/0.10.3/implementors/core/marker/trait.Sync.js new file mode 100644 index 000000000..f899722b8 --- /dev/null +++ b/0.10.3/implementors/core/marker/trait.Sync.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Sync for Error","synthetic":true,"types":["chemfiles::errors::Error"]},{"text":"impl Sync for Status","synthetic":true,"types":["chemfiles::errors::Status"]},{"text":"impl !Sync for Atom","synthetic":true,"types":["chemfiles::atom::Atom"]},{"text":"impl<'a> !Sync for AtomRef<'a>","synthetic":true,"types":["chemfiles::atom::AtomRef"]},{"text":"impl<'a> !Sync for AtomMut<'a>","synthetic":true,"types":["chemfiles::atom::AtomMut"]},{"text":"impl Sync for CellShape","synthetic":true,"types":["chemfiles::cell::CellShape"]},{"text":"impl !Sync for UnitCell","synthetic":true,"types":["chemfiles::cell::UnitCell"]},{"text":"impl<'a> !Sync for UnitCellRef<'a>","synthetic":true,"types":["chemfiles::cell::UnitCellRef"]},{"text":"impl<'a> !Sync for UnitCellMut<'a>","synthetic":true,"types":["chemfiles::cell::UnitCellMut"]},{"text":"impl !Sync for 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PropertiesIter<'a>","synthetic":true,"types":["chemfiles::property::PropertiesIter"]},{"text":"impl Sync for FormatMetadata","synthetic":true,"types":["chemfiles::misc::FormatMetadata"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.3/implementors/core/marker/trait.Unpin.js b/0.10.3/implementors/core/marker/trait.Unpin.js new file mode 100644 index 000000000..c32cfa86c --- /dev/null +++ b/0.10.3/implementors/core/marker/trait.Unpin.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Unpin for Error","synthetic":true,"types":["chemfiles::errors::Error"]},{"text":"impl Unpin for Status","synthetic":true,"types":["chemfiles::errors::Status"]},{"text":"impl Unpin for Atom","synthetic":true,"types":["chemfiles::atom::Atom"]},{"text":"impl<'a> Unpin for 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100644 index 000000000..ff396c5ca --- /dev/null +++ b/0.10.3/implementors/core/ops/index/trait.Index.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl Index<usize> for Match","synthetic":false,"types":["chemfiles::selection::Match"]}]; +if (window.register_implementors) {window.register_implementors(implementors);} else {window.pending_implementors = implementors;}})() \ No newline at end of file diff --git a/0.10.3/implementors/core/panic/unwind_safe/trait.RefUnwindSafe.js b/0.10.3/implementors/core/panic/unwind_safe/trait.RefUnwindSafe.js new file mode 100644 index 000000000..de625538a --- /dev/null +++ b/0.10.3/implementors/core/panic/unwind_safe/trait.RefUnwindSafe.js @@ -0,0 +1,3 @@ +(function() {var implementors = {}; +implementors["chemfiles"] = [{"text":"impl RefUnwindSafe for Error","synthetic":true,"types":["chemfiles::errors::Error"]},{"text":"impl RefUnwindSafe for 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It stores the …","An analog to a mutable reference to an atom (&mut Atom)","An analog to a reference to an atom (&Atom)","Possible bond order associated with bonds","Boolean property","Available unit cell shapes.","Exception in the C++ chemfiles library","Error in configuration files syntax","Double bond","Floating point property","Error type for Chemfiles.","Error while reading or writing a file","Error in file formatting, i.e. the file is invalid","FormatMetadata contains metadata associated with one …","A Frame contains data from one simulation step: the …","Infinite cell, to use when there is no cell.","A Match is a set of atomic indexes matching a given …","Error in memory allocations","Orthorhombic cell, with the three angles equals to 90°.","Error for out of bounds indexing","An iterator over the properties in an atom/frame/residue","A Property is a piece of data that can be associated with …","Error related to properties","Quadruple bond (present in some metals)","Quintuplet bond (present in some metals)","A Residue is a group of atoms belonging to the same …","An analog to a reference to a residue (&Residue)","A Selection allow to select atoms in a Frame, from a …","Error in selection string syntax","Single bond","Possible causes of error in chemfiles","Exception in the C++ standard library","String property","No error","A Topology contains the definition of all the atoms in the …","An analog to a reference to a topology (&Topology)","The Trajectory type is the main entry point when using …","Triclinic cell, with any values for the angles.","Triple bond","The given path is not valid UTF8","An UnitCell represent the box containing the atoms, and …","An analog to a mutable reference to an unit cell (…","An analog to a reference to an unit cell (&UnitCell)","Unknown or unspecified bond order","3-dimensional vector property","Add the atom at index atom in this residue.","Add an Atom at the end of this topology","Add an Atom and the corresponding position and optionally …","Add a bond between the atoms at indexes i and j in the …","Add a bond between the atoms at indexes i and j in the …","Add a bond between the atoms at indexes i and j in the …","Add a bond between the atoms at indexes i and j in the …","Read configuration data from the file at path.","Add a residue to this topology.","Add a copy of residue to this frame.","Add velocity data to this frame. If the frame already have …","Get the angle formed by the atoms at indexes i, j and k in …","Get the three angles of the cell, in degrees.","Get the list of angles in the topology.","Get the number of angles in the topology.","Check if the two residues first and second from the …","Get a reference of the atom at the given index in this …","Get a reference to the atom at the given index in this …","Get a mutable reference to the atom at the given index in …","Get a mutable reference to the atom at the given index in …","Try to get the atomic number of the atom from the atomic …","Get the atom type.","Get the list of atoms of this residue.","Does this format support storing atom names or types?","Get the bond order for the bond between the atoms at …","Get the bond order for all the bonds in the topology","Get the list of bonds in the topology.","Does this format support storing bonds between atoms?","Get the number of bonds in the topology.","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","Get a reference to the UnitCell from this frame.","Get a mutable reference to the UnitCell from this frame.","Get the atom charge, in number of the electron charge e.","Clear any error from the C++ library","Remove all existing bonds, angles, dihedral angles and …","Remove all existing bonds, angles, dihedral angles and …","","","","","","","","","","","","","","","","","","","","","","","","","","","","Check if the atom at index i is in this residue","","Try to get the covalent radius of the atom from the atomic …","","","","","","","","","","Extended, user-facing description of the format.","Get the dihedral angle formed by the atoms at indexes i, j…","Get the list of dihedral angles in the topology.","Get the number of dihedral angles in the topology.","Get the distance between the atoms at indexes i and j in …","","","","","","","","","","","","","","","Evaluate a selection for a given frame, and return the …","Extension associated with the format.","","","","","","","","","Get the list of formats known by chemfiles, as well as all …","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","","Returns the argument unchanged.","","Returns the argument unchanged.","Returns the argument unchanged.","","","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","","","","","","Returns the argument unchanged.","Create an UnitCell from a cell matrix. If matrix contains …","Try to get the full name of the atom from the atomic type. …","Get a property with the given name in this atom, if it …","Get a property with the given name in this frame, if it …","Get a property with the given name in this frame, if it …","Guess the bonds, angles and dihedrals in this frame.","Get the format that chemfiles would use to read a file at …","Check if this frame contains velocity data.","Get the identifier of this residue in the initial topology …","Get the list of improper dihedral angles in the topology.","Get the number of improper dihedral angles in the topology.","","Create an Infinite UnitCell.","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","","","Iterate over the atomic indexes in the match.","Gets an iterator over atoms","Get the last error message from the C++ library.","Get the length of the Match.","Get the three lengths of the cell, in Angstroms.","Evaluates a selection of size 1 on a given frame. This …","Get the atom mass, in atomic mass units.","Get the unit cell matricial representation.","Does this format support in-memory IO?","Obtain the memory buffer written to by the trajectory.","Read a memory buffer as though it was a formatted file.","Write to a memory buffer as though it was a formatted file.","A message describing the error cause","Get the atom name.","Get the name of this residue.","Name of the format.","","","","","Create an atom with the given name, and set the atom type …","Create an Orthorhombic UnitCell from the three lengths, in …","Create a new residue with the given name","Create a new empty topology.","Create an empty frame. It will be resized by the library …","Create a new selection from the given selection string.","Create a new match containing the atoms in the atoms slice.","","Get the number of steps (the number of frames) in a …","Open the file at the given path in the given mode.","Open the file at the given path using a specific file …","Get the out of plane distance formed by the atoms at …","","","Get file path for this trajectory.","Get a view into the positions of this frame.","Does this format support storing atomic positions?","Get a mutable view into the positions of this frame.","Get an iterator over all (name, property) pairs for this …","Get an iterator over all (name, property) pairs for this …","Get an iterator over all (name, property) pairs for this …","Read the next step of this trajectory into a frame.","Is reading files in this format implemented?","Read a specific step of this trajectory into a frame.","URL pointing to the format definition/reference.","Remove an Atom from this topology by index. This modify …","Remove the atom at index i in this frame.","Remove any existing bond between the atoms at indexes i …","Remove any existing bond between the atoms at indexes i …","Get a reference to the residue at index index from this …","Get a copy of the residue containing the atom at index …","Does this format support storing residues?","Get the number of residues in this topology.","Resize this topology to hold natoms atoms, inserting dummy …","Resize the positions and the velocities in this frame, to …","Add a new property with the given name to this atom.","Add a new property with the given name to this residue.","Add a new property with the given name to this frame.","Set the three angles of the cell, in degrees.","Set the atom type to atomic_type.","Set the UnitCell of this frame to cell.","Set the unit cell associated with a trajectory. This cell …","Set the atom charge to charge, in number of the electron …","Set the three lengths of the cell, in Angstroms.","Set the atom mass to mass, in atomic mass units.","Set the atom name to name.","Set the shape of the unit cell to shape.","Set this frame step to step.","Set the Topology of this frame to topology.","Set the topology associated with this trajectory. This …","Set the topology associated with this trajectory by …","Set the topology associated with this trajectory by …","Use callback for every chemfiles warning. 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+}');
+if (typeof window !== 'undefined' && window.initSearch) {window.initSearch(searchIndex)};
+if (typeof exports !== 'undefined') {exports.searchIndex = searchIndex};
diff --git a/0.10.3/search.js b/0.10.3/search.js
new file mode 100644
index 000000000..8fd46df61
--- /dev/null
+++ b/0.10.3/search.js
@@ -0,0 +1 @@
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"+"Or try looking in one of these:
- The Rust Reference "+" for technical details about the language.
- Rust By "+"Example for expository code examples.
- The Rust Book for "+"introductions to language features and the language itself.
- Docs.rs for documentation of crates released on"+" crates.io.
"+`
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";currentTab=0}else if(results.query.foundElems<=1&&results.query.returned.length===0){output+=""+makeTabHeader(0,"In Names",ret_others[1])+makeTabHeader(1,"In Parameters",ret_in_args[1])+makeTabHeader(2,"In Return Types",ret_returned[1])+"
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diff --git a/0.10.3/source-files.js b/0.10.3/source-files.js
new file mode 100644
index 000000000..99e415e09
--- /dev/null
+++ b/0.10.3/source-files.js
@@ -0,0 +1,3 @@
+var sourcesIndex = {};
+sourcesIndex["chemfiles"] = {"name":"","files":["atom.rs","cell.rs","errors.rs","frame.rs","lib.rs","misc.rs","property.rs","residue.rs","selection.rs","strings.rs","topology.rs","trajectory.rs"]};
+createSourceSidebar();
diff --git a/0.10.3/source-script.js b/0.10.3/source-script.js
new file mode 100644
index 000000000..c8856707a
--- /dev/null
+++ b/0.10.3/source-script.js
@@ -0,0 +1 @@
+"use strict";(function(){const rootPath=document.getElementById("rustdoc-vars").attributes["data-root-path"].value;function createDirEntry(elem,parent,fullPath,hasFoundFile){const name=document.createElement("div");name.className="name";fullPath+=elem["name"]+"/";name.onclick=ev=>{if(hasClass(ev.target,"expand")){removeClass(ev.target,"expand")}else{addClass(ev.target,"expand")}};name.innerText=elem["name"];const children=document.createElement("div");children.className="children";const folders=document.createElement("div");folders.className="folders";if(elem.dirs){for(const dir of elem.dirs){if(createDirEntry(dir,folders,fullPath,hasFoundFile)){addClass(name,"expand");hasFoundFile=true}}}children.appendChild(folders);const files=document.createElement("div");files.className="files";if(elem.files){for(const file_text of elem.files){const file=document.createElement("a");file.innerText=file_text;file.href=rootPath+"src/"+fullPath+file_text+".html";const w=window.location.href.split("#")[0];if(!hasFoundFile&&w===file.href){file.className="selected";addClass(name,"expand");hasFoundFile=true}files.appendChild(file)}}children.appendChild(files);parent.appendChild(name);parent.appendChild(children);return hasFoundFile}function toggleSidebar(){const child=this.children[0];if(child.innerText===">"){addClass(document.documentElement,"source-sidebar-expanded");child.innerText="<";updateLocalStorage("source-sidebar-show","true")}else{removeClass(document.documentElement,"source-sidebar-expanded");child.innerText=">";updateLocalStorage("source-sidebar-show","false")}}function createSidebarToggle(){const sidebarToggle=document.createElement("div");sidebarToggle.id="sidebar-toggle";sidebarToggle.onclick=toggleSidebar;const inner=document.createElement("div");if(getCurrentValue("source-sidebar-show")==="true"){inner.innerText="<"}else{inner.innerText=">"}sidebarToggle.appendChild(inner);return sidebarToggle}function createSourceSidebar(){const container=document.querySelector("nav.sidebar");const sidebarToggle=createSidebarToggle();container.insertBefore(sidebarToggle,container.firstChild);const sidebar=document.createElement("div");sidebar.id="source-sidebar";let hasFoundFile=false;const title=document.createElement("div");title.className="title";title.innerText="Files";sidebar.appendChild(title);Object.keys(sourcesIndex).forEach(key=>{sourcesIndex[key].name=key;hasFoundFile=createDirEntry(sourcesIndex[key],sidebar,"",hasFoundFile)});container.appendChild(sidebar);const selected_elem=sidebar.getElementsByClassName("selected")[0];if(typeof selected_elem!=="undefined"){selected_elem.focus()}}const lineNumbersRegex=/^#?(\d+)(?:-(\d+))?$/;function highlightSourceLines(match){if(typeof match==="undefined"){match=window.location.hash.match(lineNumbersRegex)}if(!match){return}let from=parseInt(match[1],10);let to=from;if(typeof match[2]!=="undefined"){to=parseInt(match[2],10)}if(to
1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371 +372 +373 +374 +375 +376 +377 +378 +379 +380 +381 +382 +383 +384 +385 +386 +387 +388 +389 +390 +391 +392 +393 +394 +395 +396 +397 +398 +399 +400 +401 +402 +403 +404 +405 +406 +407 +408 +409 +410 +411 +412 +413 +414 +415 +416 +417 +418 +419 +420 +421 +422 +423 +424 +425 +426 +427 +428 +429 +430 +431 +432 +433 +434 +435 +436 +437 +438 +439 +440 +441 +442 +443 +444 +445 +446 +447 +448 +449 +450 +451 +452 +453 +454 +455 +456 +457 +458 +459 +460 +461 +462 +463 +464 +465 +466 +467 +468 +469 +470 +471 +472 +473 +474 +475 +476 +477 +478 +479 +480 +481 +482 +483 +484 +485 +486 +487 +488 +489 +490 +491 +492 +493 +494 +495 +496 +497 +498 +499 +500 +501 +502 +503 +504 +505 +506 +507 +508 +509 +510 +511 +512 +513 +514 +515 +516 +517 +518 +519 +520 +521 +522 +523 +524 +525 +526 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::{Drop, Deref, DerefMut};
+use std::marker::PhantomData;
+use std::ptr;
+
+use chemfiles_sys::*;
+use errors::{check_success, check_not_null};
+use strings;
+
+use property::{Property, RawProperty, PropertiesIter};
+
+/// An `Atom` is a particle in the current `Frame`. It stores the following
+/// atomic properties:
+///
+/// - atom name;
+/// - atom type;
+/// - atom mass;
+/// - atom charge.
+///
+/// The atom name is usually an unique identifier (`H1`, `C_a`) while the
+/// atom type will be shared between all particles of the same type: `H`,
+/// `Ow`, `CH3`.
+pub struct Atom {
+ handle: *mut CHFL_ATOM,
+}
+
+/// An analog to a reference to an atom (`&Atom`)
+pub struct AtomRef<'a> {
+ inner: Atom,
+ marker: PhantomData<&'a Atom>
+}
+
+impl<'a> Deref for AtomRef<'a> {
+ type Target = Atom;
+ fn deref(&self) -> &Atom {
+ &self.inner
+ }
+}
+
+/// An analog to a mutable reference to an atom (`&mut Atom`)
+pub struct AtomMut<'a> {
+ inner: Atom,
+ marker: PhantomData<&'a mut Atom>
+}
+
+impl<'a> Deref for AtomMut<'a> {
+ type Target = Atom;
+ fn deref(&self) -> &Atom {
+ &self.inner
+ }
+}
+
+impl<'a> DerefMut for AtomMut<'a> {
+ fn deref_mut(&mut self) -> &mut Atom {
+ &mut self.inner
+ }
+}
+
+impl Clone for Atom {
+ fn clone(&self) -> Atom {
+ unsafe {
+ let new_handle = chfl_atom_copy(self.as_ptr());
+ Atom::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Atom {
+ /// Create an owned `Atom` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_ATOM) -> Atom {
+ check_not_null(ptr);
+ Atom {
+ handle: ptr
+ }
+ }
+
+ /// Create a borrowed `Atom` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, and the caller is responsible for setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_ATOM) -> AtomRef<'a> {
+ AtomRef {
+ inner: Atom::from_ptr(ptr as *mut CHFL_ATOM),
+ marker: PhantomData,
+ }
+ }
+
+ /// Create a mutably borrowed `Atom` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, and the caller is responsible for setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_mut_from_ptr<'a>(ptr: *mut CHFL_ATOM) -> AtomMut<'a> {
+ AtomMut {
+ inner: Atom::from_ptr(ptr),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_ATOM {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_ATOM {
+ self.handle
+ }
+
+ /// Create an atom with the given `name`, and set the atom type to `name`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.name(), "He");
+ /// ```
+ pub fn new<'a>(name: impl Into<&'a str>) -> Atom {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ let handle = chfl_atom(buffer.as_ptr());
+ Atom::from_ptr(handle)
+ }
+ }
+
+ /// Get the atom mass, in atomic mass units.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.mass(), 4.002602);
+ /// ```
+ pub fn mass(&self) -> f64 {
+ let mut mass = 0.0;
+ unsafe {
+ check_success(chfl_atom_mass(self.as_ptr(), &mut mass));
+ }
+ return mass;
+ }
+
+ /// Set the atom mass to `mass`, in atomic mass units.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_mass(34.9);
+ /// assert_eq!(atom.mass(), 34.9);
+ /// ```
+ pub fn set_mass(&mut self, mass: f64) {
+ unsafe {
+ check_success(chfl_atom_set_mass(self.as_mut_ptr(), mass));
+ }
+ }
+
+ /// Get the atom charge, in number of the electron charge *e*.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.charge(), 0.0);
+ /// ```
+ pub fn charge(&self) -> f64 {
+ let mut charge = 0.0;
+ unsafe {
+ check_success(chfl_atom_charge(self.as_ptr(), &mut charge));
+ }
+ return charge;
+ }
+
+ /// Set the atom charge to `charge`, in number of the electron charge *e*.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_charge(-2.0);
+ /// assert_eq!(atom.charge(), -2.0);
+ /// ```
+ pub fn set_charge(&mut self, charge: f64) {
+ unsafe {
+ check_success(chfl_atom_set_charge(self.as_mut_ptr(), charge));
+ }
+ }
+
+ /// Get the atom name.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.name(), "He");
+ /// ```
+ pub fn name(&self) -> String {
+ let get_name = |ptr, len| unsafe { chfl_atom_name(self.as_ptr(), ptr, len) };
+ let name = strings::call_autogrow_buffer(10, get_name).expect("getting name failed");
+ return strings::from_c(name.as_ptr());
+ }
+
+ /// Get the atom type.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.atomic_type(), "He");
+ /// ```
+ pub fn atomic_type(&self) -> String {
+ let get_type = |ptr, len| unsafe { chfl_atom_type(self.as_ptr(), ptr, len) };
+ let buffer = strings::call_autogrow_buffer(10, get_type).expect("getting type failed");
+ return strings::from_c(buffer.as_ptr());
+ }
+
+ /// Set the atom name to `name`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_name("Zn3");
+ /// assert_eq!(atom.name(), "Zn3");
+ /// ```
+ pub fn set_name<'a>(&mut self, name: impl Into<&'a str>) {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ check_success(chfl_atom_set_name(self.as_mut_ptr(), buffer.as_ptr()));
+ }
+ }
+
+ /// Set the atom type to `atomic_type`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_atomic_type("F");
+ /// assert_eq!(atom.atomic_type(), "F");
+ /// ```
+ pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>) {
+ let buffer = strings::to_c(atomic_type.into());
+ unsafe {
+ check_success(chfl_atom_set_type(self.as_mut_ptr(), buffer.as_ptr()));
+ }
+ }
+
+ /// Try to get the full name of the atom from the atomic type. For example,
+ /// the full name of "He" is "Helium", and so on. If the name can not be
+ /// found, this function returns the empty string.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("Zn");
+ /// assert_eq!(atom.full_name(), "Zinc");
+ /// ```
+ pub fn full_name(&self) -> String {
+ let get_full_name = |ptr, len| unsafe { chfl_atom_full_name(self.as_ptr(), ptr, len) };
+ let name = strings::call_autogrow_buffer(10, get_full_name).expect("getting full name failed");
+ return strings::from_c(name.as_ptr());
+ }
+
+ /// Try to get the Van der Waals radius of the atom from the atomic type.
+ /// If the radius can not be found, returns 0.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+ /// assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);
+ /// ```
+ pub fn vdw_radius(&self) -> f64 {
+ let mut radius: f64 = 0.0;
+ unsafe {
+ check_success(chfl_atom_vdw_radius(self.as_ptr(), &mut radius));
+ }
+ return radius;
+ }
+
+ /// Try to get the covalent radius of the atom from the atomic type. If the
+ /// radius can not be found, returns 0.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+ /// assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);
+ /// ```
+ pub fn covalent_radius(&self) -> f64 {
+ let mut radius: f64 = 0.0;
+ unsafe {
+ check_success(chfl_atom_covalent_radius(self.as_ptr(), &mut radius));
+ }
+ return radius;
+ }
+
+ /// Try to get the atomic number of the atom from the atomic type. If the
+ /// number can not be found, returns 0.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// assert_eq!(Atom::new("He").atomic_number(), 2);
+ /// assert_eq!(Atom::new("Xxx").atomic_number(), 0);
+ /// ```
+ pub fn atomic_number(&self) -> u64 {
+ let mut number = 0;
+ unsafe {
+ check_success(chfl_atom_atomic_number(self.as_ptr(), &mut number));
+ }
+ return number;
+ }
+
+ /// Add a new `property` with the given `name` to this atom.
+ ///
+ /// If a property with the same name already exists, this function override
+ /// the existing property with the new one.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Atom, Property};
+ /// let mut atom = Atom::new("He");
+ /// atom.set("a bool", true);
+ /// atom.set("a string", "test");
+ ///
+ /// assert_eq!(atom.get("a bool"), Some(Property::Bool(true)));
+ /// assert_eq!(atom.get("a string"), Some(Property::String("test".into())));
+ /// ```
+ pub fn set(&mut self, name: &str, property: impl Into<Property>) {
+ let buffer = strings::to_c(name);
+ let property = property.into().as_raw();
+ unsafe {
+ check_success(chfl_atom_set_property(
+ self.as_mut_ptr(), buffer.as_ptr(), property.as_ptr()
+ ));
+ }
+ }
+
+
+ /// Get a property with the given `name` in this atom, if it exist.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Atom, Property};
+ /// let mut atom = Atom::new("He");
+ /// atom.set("foo", Property::Double(22.2));
+ ///
+ /// assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+ /// assert_eq!(atom.get("Bar"), None);
+ /// ```
+ pub fn get(&self, name: &str) -> Option<Property> {
+ let buffer = strings::to_c(name);
+ unsafe {
+ let handle = chfl_atom_get_property(self.as_ptr(), buffer.as_ptr());
+ if handle.is_null() {
+ None
+ } else {
+ let raw = RawProperty::from_ptr(handle);
+ let property = Property::from_raw(raw);
+ Some(property)
+ }
+ }
+ }
+
+ /// Get an iterator over all (name, property) pairs for this atom
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Atom, Property};
+ /// let mut atom = Atom::new("He");
+ /// atom.set("foo", Property::Double(22.2));
+ /// atom.set("bar", Property::Bool(false));
+ ///
+ /// for (name, property) in atom.properties() {
+ /// if name == "foo" {
+ /// assert_eq!(property, Property::Double(22.2));
+ /// } else if name == "bar" {
+ /// assert_eq!(property, Property::Bool(false));
+ /// }
+ /// }
+ /// ```
+ pub fn properties(&self) -> PropertiesIter {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_atom_properties_count(self.as_ptr(), &mut count));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = count as usize;
+ let mut c_names = vec![ptr::null_mut(); size];
+ unsafe {
+ check_success(chfl_atom_list_properties(self.as_ptr(), c_names.as_mut_ptr(), count));
+ }
+
+ let mut names = Vec::new();
+ for ptr in c_names {
+ names.push(strings::from_c(ptr));
+ }
+
+ PropertiesIter {
+ names: names.into_iter(),
+ getter: Box::new(move |name| self.get(name).expect("failed to get property"))
+ }
+ }
+}
+
+impl Drop for Atom {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.name(), "He");
+
+ let copy = atom.clone();
+ assert_eq!(copy.name(), "He");
+
+ atom.set_name("Na");
+ assert_eq!(atom.name(), "Na");
+ assert_eq!(copy.name(), "He");
+ }
+
+ #[test]
+ fn mass() {
+ let mut atom = Atom::new("He");
+ assert_ulps_eq!(atom.mass(), 4.002602);
+ atom.set_mass(15.0);
+ assert_eq!(atom.mass(), 15.0);
+ }
+
+ #[test]
+ fn charge() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.charge(), 0.0);
+ atom.set_charge(-1.5);
+ assert_eq!(atom.charge(), -1.5);
+ }
+
+ #[test]
+ fn name() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.name(), "He");
+ atom.set_name("Zn-12");
+ assert_eq!(atom.name(), "Zn-12");
+ }
+
+ #[test]
+ fn atomic_type() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.atomic_type(), "He");
+ atom.set_atomic_type("Zn");
+ assert_eq!(atom.atomic_type(), "Zn");
+ }
+
+ #[test]
+ fn full_name() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.full_name(), "Helium");
+
+ atom.set_atomic_type("Zn");
+ assert_eq!(atom.full_name(), "Zinc");
+
+ let atom = Atom::new("Unknown");
+ assert_eq!(atom.full_name(), "");
+ }
+
+ #[test]
+ fn radii() {
+ let atom = Atom::new("He");
+ assert_ulps_eq!(atom.vdw_radius(), 1.4);
+ assert_ulps_eq!(atom.covalent_radius(), 0.32);
+
+ let atom = Atom::new("Unknown");
+ assert_eq!(atom.vdw_radius(), 0.0);
+ assert_eq!(atom.covalent_radius(), 0.0);
+ }
+
+ #[test]
+ fn atomic_number() {
+ let atom = Atom::new("He");
+ assert_eq!(atom.atomic_number(), 2);
+
+ let atom = Atom::new("Unknown");
+ assert_eq!(atom.atomic_number(), 0);
+ }
+
+ #[test]
+ fn property() {
+ let mut atom = Atom::new("F");
+
+ atom.set("foo", -22.0);
+ assert_eq!(atom.get("foo"), Some(Property::Double(-22.0)));
+ assert_eq!(atom.get("bar"), None);
+
+ atom.set("bar", Property::String("here".into()));
+ for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(-22.0));
+ } else if name == "bar" {
+ assert_eq!(property, Property::String("here".into()));
+ }
+ }
+ }
+}
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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::{Drop, Deref, DerefMut};
+use std::marker::PhantomData;
+use std::ptr;
+
+use chemfiles_sys::*;
+use errors::{check_success, check_not_null, check, Error};
+
+/// Available unit cell shapes.
+#[derive(Clone, Debug, PartialEq, Eq)]
+pub enum CellShape {
+ /// Orthorhombic cell, with the three angles equals to 90°.
+ Orthorhombic,
+ /// Triclinic cell, with any values for the angles.
+ Triclinic,
+ /// Infinite cell, to use when there is no cell.
+ Infinite,
+}
+
+impl From<chfl_cellshape> for CellShape {
+ fn from(celltype: chfl_cellshape) -> CellShape {
+ match celltype {
+ chfl_cellshape::CHFL_CELL_ORTHORHOMBIC => CellShape::Orthorhombic,
+ chfl_cellshape::CHFL_CELL_TRICLINIC => CellShape::Triclinic,
+ chfl_cellshape::CHFL_CELL_INFINITE => CellShape::Infinite,
+ }
+ }
+}
+
+impl From<CellShape> for chfl_cellshape {
+ fn from(celltype: CellShape) -> chfl_cellshape {
+ match celltype {
+ CellShape::Orthorhombic => chfl_cellshape::CHFL_CELL_ORTHORHOMBIC,
+ CellShape::Triclinic => chfl_cellshape::CHFL_CELL_TRICLINIC,
+ CellShape::Infinite => chfl_cellshape::CHFL_CELL_INFINITE,
+ }
+ }
+}
+
+/// An `UnitCell` represent the box containing the atoms, and its periodicity.
+///
+/// An unit cell is fully represented by three lengths (a, b, c); and three
+/// angles (alpha, beta, gamma). The angles are stored in degrees, and the
+/// lengths in Angstroms.
+///
+/// A cell also has a matricial representation, by projecting the three base
+/// vector into an orthonormal base. We choose to represent such matrix as an
+/// upper triangular matrix:
+///
+/// ```text
+/// | a_x b_x c_x |
+/// | 0 b_y c_y |
+/// | 0 0 c_z |
+/// ```
+pub struct UnitCell {
+ handle: *mut CHFL_CELL,
+}
+
+/// An analog to a reference to an unit cell (`&UnitCell`)
+pub struct UnitCellRef<'a> {
+ inner: UnitCell,
+ marker: PhantomData<&'a UnitCell>
+}
+
+impl<'a> Deref for UnitCellRef<'a> {
+ type Target = UnitCell;
+ fn deref(&self) -> &UnitCell {
+ &self.inner
+ }
+}
+
+/// An analog to a mutable reference to an unit cell (`&mut UnitCell`)
+pub struct UnitCellMut<'a> {
+ inner: UnitCell,
+ marker: PhantomData<&'a mut UnitCell>
+}
+
+impl<'a> Deref for UnitCellMut<'a> {
+ type Target = UnitCell;
+ fn deref(&self) -> &UnitCell {
+ &self.inner
+ }
+}
+
+impl<'a> DerefMut for UnitCellMut<'a> {
+ fn deref_mut(&mut self) -> &mut UnitCell {
+ &mut self.inner
+ }
+}
+
+impl Clone for UnitCell {
+ fn clone(&self) -> UnitCell {
+ unsafe {
+ let new_handle = chfl_cell_copy(self.as_ptr());
+ UnitCell::from_ptr(new_handle)
+ }
+ }
+}
+
+impl UnitCell {
+ /// Create an owned `UnitCell` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_CELL) -> UnitCell {
+ check_not_null(ptr);
+ UnitCell {
+ handle: ptr
+ }
+ }
+
+ /// Create a borrowed `UnitCell` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, and the caller is responsible for setting the right lifetime.
+ #[inline]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_CELL) -> UnitCellRef<'a> {
+ UnitCellRef {
+ inner: UnitCell::from_ptr(ptr as *mut CHFL_CELL),
+ marker: PhantomData,
+ }
+ }
+
+ /// Create a borrowed `UnitCell` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, except for it being non-null, and the caller is responsible for
+ /// setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_mut_from_ptr<'a>(ptr: *mut CHFL_CELL) -> UnitCellMut<'a> {
+ UnitCellMut {
+ inner: UnitCell::from_ptr(ptr),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_CELL {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_CELL {
+ self.handle
+ }
+
+ /// Create an `Orthorhombic` `UnitCell` from the three lengths, in Angstroms.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::new([30.0, 30.0, 23.0]);
+ ///
+ /// assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// ```
+ pub fn new(lengths: [f64; 3]) -> UnitCell {
+ unsafe {
+ let handle = chfl_cell(lengths.as_ptr(), ptr::null());
+ UnitCell::from_ptr(handle)
+ }
+ }
+
+ /// Create an `Infinite` `UnitCell`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::infinite();
+ ///
+ /// assert_eq!(cell.lengths(), [0.0, 0.0, 0.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// assert_eq!(cell.shape(), CellShape::Infinite);
+ /// ```
+ pub fn infinite() -> UnitCell {
+ let mut cell = UnitCell::new([0.0, 0.0, 0.0]);
+ cell.set_shape(CellShape::Infinite).expect("could not set cell shape");
+ return cell;
+ }
+
+ /// Create an `Triclinic` `UnitCell` from the three lengths (in Angstroms)
+ /// and three angles (in degree). `alpha` is the angle between the vectors
+ /// `b` and `c`; `beta` is the between the vectors `a` and `c` and `gamma`
+ /// is the angle between the vectors `a` and `b`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::triclinic([10.0, 10.0, 10.0], [98.0, 99.0, 90.0]);
+ ///
+ /// assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);
+ /// assert_eq!(cell.angles()[0], 98.0);
+ /// // Rounding errors might occur due to internal representation
+ /// assert!((cell.angles()[1] - 99.0).abs() < 1e-12);
+ /// assert_eq!(cell.angles()[2], 90.0);
+ /// assert_eq!(cell.shape(), CellShape::Triclinic);
+ /// ```
+ pub fn triclinic(lengths: [f64; 3], angles: [f64; 3]) -> UnitCell {
+ unsafe {
+ let handle = chfl_cell(lengths.as_ptr(), angles.as_ptr());
+ UnitCell::from_ptr(handle)
+ }
+ }
+
+ /// Create an `UnitCell` from a cell matrix. If `matrix` contains only
+ /// zeros, then an `Infinite` cell is created. If only the diagonal of the
+ /// matrix is non-zero, then the cell is `Orthorhombic`. Else a
+ /// `Triclinic` cell is created. The matrix entries should be in Angstroms.
+ ///
+ /// # Panics
+ ///
+ /// If the matrix has a negative determinant, or more generally is not
+ /// representing a unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::from_matrix([
+ /// [1.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]
+ /// ]);
+ ///
+ /// assert_eq!(cell.lengths(), [1.0, 2.0, 3.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// ```
+ pub fn from_matrix(mut matrix: [[f64; 3]; 3]) -> UnitCell {
+ unsafe {
+ let handle = chfl_cell_from_matrix(matrix.as_mut_ptr());
+ UnitCell::from_ptr(handle)
+ }
+ }
+
+ /// Get the three lengths of the cell, in Angstroms.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([30.0, 30.0, 23.0]);
+ /// assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
+ /// ```
+ pub fn lengths(&self) -> [f64; 3] {
+ let mut lengths = [0.0; 3];
+ unsafe {
+ check_success(chfl_cell_lengths(self.as_ptr(), lengths.as_mut_ptr()));
+ }
+ return lengths;
+ }
+
+ /// Set the three lengths of the cell, in Angstroms.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the unit cell is infinite, or if one of the
+ /// lengths is negative.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let mut cell = UnitCell::new([30.0, 30.0, 23.0]);
+ ///
+ /// cell.set_lengths([10.0, 30.0, 42.0]).unwrap();
+ /// assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]);
+ ///
+ /// assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());
+ /// ```
+ pub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error> {
+ unsafe {
+ check(chfl_cell_set_lengths(self.as_mut_ptr(), lengths.as_ptr()))
+ }
+ }
+
+ /// Get the three angles of the cell, in degrees.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([20.0, 20.0, 20.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ ///
+ /// let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+ /// assert_eq!(cell.angles()[0], 100.0);
+ /// // Rounding errors might occur due to internal representation
+ /// assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+ /// assert_eq!(cell.angles()[2], 90.0);
+ /// ```
+ pub fn angles(&self) -> [f64; 3] {
+ let mut angles = [0.0; 3];
+ unsafe {
+ check_success(chfl_cell_angles(self.as_ptr(), angles.as_mut_ptr()));
+ }
+ return angles;
+ }
+
+ /// Set the three angles of the cell, in degrees.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the unit cell is not `Triclinic`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+ /// assert_eq!(cell.angles()[0], 100.0);
+ /// // Rounding errors might occur due to internal representation
+ /// assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+ /// assert_eq!(cell.angles()[2], 90.0);
+ ///
+ /// cell.set_angles([90.0, 90.0, 90.0]).unwrap();
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// ```
+ pub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error> {
+ unsafe {
+ check(chfl_cell_set_angles(self.as_mut_ptr(), angles.as_ptr()))
+ }
+ }
+
+ /// Get the unit cell matricial representation.
+ ///
+ /// The unit cell representation is obtained by aligning the a vector along
+ /// the *x* axis and putting the b vector in the *xy* plane. This make the
+ /// matrix an upper triangular matrix:
+ ///
+ /// ```text
+ /// | a_x b_x c_x |
+ /// | 0 b_y c_y |
+ /// | 0 0 c_z |
+ /// ```
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ ///
+ /// let matrix = cell.matrix();
+ ///
+ /// assert_eq!(matrix[0][0], 10.0);
+ /// assert_eq!(matrix[1][1], 20.0);
+ /// assert_eq!(matrix[2][2], 30.0);
+ ///
+ /// assert!(matrix[1][2].abs() < 1e-9);
+ /// ```
+ pub fn matrix(&self) -> [[f64; 3]; 3] {
+ let mut matrix = [[0.0; 3]; 3];
+ unsafe {
+ check_success(chfl_cell_matrix(self.as_ptr(), matrix.as_mut_ptr()));
+ }
+ return matrix;
+ }
+
+ /// Get the shape of the unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// ```
+ pub fn shape(&self) -> CellShape {
+ let mut shape = chfl_cellshape::CHFL_CELL_INFINITE;
+ unsafe {
+ check_success(chfl_cell_shape(self.as_ptr(), &mut shape));
+ }
+ return CellShape::from(shape);
+ }
+
+ /// Set the shape of the unit cell to `shape`.
+ ///
+ /// # Errors
+ ///
+ /// This can fail if the cell length or angles are incompatible with the
+ /// new shape.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let mut cell = UnitCell::new([10.0, 20.0, 30.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ ///
+ /// cell.set_shape(CellShape::Triclinic).unwrap();
+ /// assert_eq!(cell.shape(), CellShape::Triclinic);
+ /// ```
+ pub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error> {
+ unsafe {
+ check(chfl_cell_set_shape(self.as_mut_ptr(), shape.into()))
+ }
+ }
+
+ /// Get the volume of the unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ /// assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0);
+ /// ```
+ pub fn volume(&self) -> f64 {
+ let mut volume = 0.0;
+ unsafe {
+ check_success(chfl_cell_volume(self.as_ptr(), &mut volume));
+ }
+ return volume;
+ }
+
+ /// Wrap a `vector` in this unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ ///
+ /// let mut vector = [12.0, 5.2, -45.3];
+ /// cell.wrap(&mut vector);
+ /// assert_eq!(vector, [2.0, 5.2, 14.700000000000003]);
+ /// ```
+ pub fn wrap(&self, vector: &mut [f64; 3]) {
+ unsafe {
+ check_success(chfl_cell_wrap(self.as_ptr(), vector.as_mut_ptr()));
+ }
+ }
+}
+
+impl Drop for UnitCell {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.lengths(), [2.0, 3.0, 4.0]);
+
+ let copy = cell.clone();
+ assert_eq!(copy.lengths(), [2.0, 3.0, 4.0]);
+
+ cell.set_lengths([10.0, 12.0, 11.0]).unwrap();
+ assert_eq!(cell.lengths(), [10.0, 12.0, 11.0]);
+ assert_eq!(copy.lengths(), [2.0, 3.0, 4.0]);
+ }
+
+ #[test]
+ fn lengths() {
+ let mut cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.lengths(), [2.0, 3.0, 4.0]);
+ cell.set_lengths([10.0, 12.0, 11.0]).unwrap();
+ assert_eq!(cell.lengths(), [10.0, 12.0, 11.0]);
+ }
+
+ #[test]
+ fn angles() {
+ let mut cell = UnitCell::new([2.0, 3.0, 4.0]);
+ crate::assert_vector3d_eq(&cell.angles(), &[90.0, 90.0, 90.0], 1e-6);
+
+ cell.set_shape(CellShape::Triclinic).unwrap();
+ cell.set_angles([80.0, 89.0, 100.0]).unwrap();
+
+ crate::assert_vector3d_eq(&cell.angles(), &[80.0, 89.0, 100.0], 1e-6);
+
+ let cell = UnitCell::triclinic([1., 2., 3.], [80., 90., 100.]);
+ crate::assert_vector3d_eq(&cell.angles(), &[80.0, 90.0, 100.0], 1e-6);
+ }
+
+ #[test]
+ fn volume() {
+ let cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.volume(), 2.0 * 3.0 * 4.0);
+ }
+
+ #[test]
+ fn wrap() {
+ let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ let mut vector = [12.0, 5.2, -45.3];
+ cell.wrap(&mut vector);
+ crate::assert_vector3d_eq(&vector, &[2.0, 5.2, 14.7], 1e-6);
+ }
+
+ #[test]
+ fn matrix() {
+ let cell = UnitCell::new([2.0, 3.0, 4.0]);
+
+ let matrix = cell.matrix();
+ let result = [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]];
+
+ for i in 0..3 {
+ for j in 0..3 {
+ assert_ulps_eq!(matrix[i][j], result[i][j], epsilon = 1e-12);
+ }
+ }
+ }
+
+ #[test]
+ fn from_matrix() {
+ let cell = UnitCell::from_matrix([[10.0, 0.0, 0.0], [0.0, 21.0, 0.0], [0.0, 0.0, 32.0]]);
+ assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ assert_eq!(cell.lengths(), [10.0, 21.0, 32.0]);
+
+ let result_matrix = [
+ [123.0, 4.08386, 71.7295],
+ [0.0, 233.964, 133.571],
+ [0.0, 0.0, 309.901],
+ ];
+ let cell = UnitCell::from_matrix(result_matrix);
+
+ assert_eq!(cell.shape(), CellShape::Triclinic);
+ for i in 0..3 {
+ assert_ulps_eq!(
+ cell.lengths()[i],
+ [123.0, 234.0, 345.0][i],
+ epsilon = 1e-3
+ );
+ assert_ulps_eq!(cell.angles()[i], [67.0, 78.0, 89.0][i], epsilon = 1e-3);
+ }
+
+ let matrix = cell.matrix();
+ for i in 0..3 {
+ for j in 0..3 {
+ assert_ulps_eq!(matrix[i][j], result_matrix[i][j], epsilon = 1e-12);
+ }
+ }
+ }
+
+ #[test]
+ fn shape() {
+ let cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.shape(), CellShape::Orthorhombic);
+
+ let cell = UnitCell::infinite();
+ assert_eq!(cell.shape(), CellShape::Infinite);
+
+ let cell = UnitCell::triclinic([1.0, 2.0, 3.0], [80.0, 90.0, 100.0]);
+ assert_eq!(cell.shape(), CellShape::Triclinic);
+
+ let mut cell = UnitCell::new([10.0, 10.0, 10.0]);
+ assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ cell.set_shape(CellShape::Triclinic).unwrap();
+ assert_eq!(cell.shape(), CellShape::Triclinic);
+ }
+}
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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+extern crate libc;
+
+use std::error;
+use std::fmt;
+use std::panic::{self, RefUnwindSafe};
+use std::path::Path;
+
+use self::libc::c_char;
+
+use chemfiles_sys::*;
+use strings;
+
+#[derive(Clone, Debug, PartialEq, Eq)]
+/// Error type for Chemfiles.
+pub struct Error {
+ /// The error status code
+ pub status: Status,
+ /// A message describing the error cause
+ pub message: String,
+}
+
+#[repr(C)]
+#[non_exhaustive]
+#[derive(Clone, Debug, PartialEq, Eq)]
+/// Possible causes of error in chemfiles
+pub enum Status {
+ /// No error
+ Success = chfl_status::CHFL_SUCCESS as isize,
+ /// Error in memory allocations
+ MemoryError = chfl_status::CHFL_MEMORY_ERROR as isize,
+ /// Error while reading or writing a file
+ FileError = chfl_status::CHFL_FILE_ERROR as isize,
+ /// Error in file formatting, *i.e.* the file is invalid
+ FormatError = chfl_status::CHFL_FORMAT_ERROR as isize,
+ /// Error in selection string syntax
+ SelectionError = chfl_status::CHFL_SELECTION_ERROR as isize,
+ /// Error in configuration files syntax
+ ConfigurationError = chfl_status::CHFL_CONFIGURATION_ERROR as isize,
+ /// Error for out of bounds indexing
+ OutOfBounds = chfl_status::CHFL_OUT_OF_BOUNDS as isize,
+ /// Error related to properties
+ PropertyError = chfl_status::CHFL_PROPERTY_ERROR as isize,
+ /// Exception in the C++ chemfiles library
+ ChemfilesError = chfl_status::CHFL_GENERIC_ERROR as isize,
+ /// Exception in the C++ standard library
+ StdCppError = chfl_status::CHFL_CXX_ERROR as isize,
+ /// The given path is not valid UTF8
+ // TODO: rename this to UTF8Error in the next breaking release
+ UTF8PathError,
+}
+
+impl From<chfl_status> for Error {
+ fn from(status: chfl_status) -> Error {
+ let status = match status {
+ chfl_status::CHFL_SUCCESS => Status::Success,
+ chfl_status::CHFL_CXX_ERROR => Status::StdCppError,
+ chfl_status::CHFL_GENERIC_ERROR => Status::ChemfilesError,
+ chfl_status::CHFL_MEMORY_ERROR => Status::MemoryError,
+ chfl_status::CHFL_FILE_ERROR => Status::FileError,
+ chfl_status::CHFL_FORMAT_ERROR => Status::FormatError,
+ chfl_status::CHFL_SELECTION_ERROR => Status::SelectionError,
+ chfl_status::CHFL_CONFIGURATION_ERROR => Status::ConfigurationError,
+ chfl_status::CHFL_OUT_OF_BOUNDS => Status::OutOfBounds,
+ chfl_status::CHFL_PROPERTY_ERROR => Status::PropertyError,
+ };
+
+ let message = Error::last_error();
+ Error {
+ status,
+ message,
+ }
+ }
+}
+
+impl From<std::str::Utf8Error> for Error {
+ fn from(_: std::str::Utf8Error) -> Self {
+ Error {
+ status: Status::UTF8PathError,
+ message: "failed to convert data to UTF8 string".into(),
+ }
+ }
+}
+
+impl Error {
+ /// Create a new error because the given `path` is invalid UTF-8 data
+ pub(crate) fn utf8_path_error(path: &Path) -> Error {
+ Error {
+ status: Status::UTF8PathError,
+ message: format!("Could not convert '{}' to UTF8", path.display()),
+ }
+ }
+
+ /// Get the last error message from the C++ library.
+ pub fn last_error() -> String {
+ unsafe { strings::from_c(chfl_last_error()) }
+ }
+
+ /// Clear any error from the C++ library
+ pub fn cleanup() {
+ unsafe {
+ check(chfl_clear_errors()).expect("error in chfl_clear_errors. Things went very bad");
+ }
+ }
+}
+
+/// Check return value of a C function, and get the error if needed.
+pub(crate) fn check(status: chfl_status) -> Result<(), Error> {
+ if status == chfl_status::CHFL_SUCCESS {
+ Ok(())
+ } else {
+ Err(Error::from(status))
+ }
+}
+
+/// Check return value of a C function, panic if it failed.
+pub(crate) fn check_success(status: chfl_status) {
+ assert!(status == chfl_status::CHFL_SUCCESS, "unexpected failure: {}", Error::last_error());
+}
+
+/// Check a pointer for null.
+pub(crate) fn check_not_null<T>(ptr: *const T) {
+ assert!(!ptr.is_null(), "unexpected null pointer: {}", Error::last_error());
+}
+
+pub trait WarningCallback: RefUnwindSafe + Fn(&str) {}
+impl<T> WarningCallback for T
+where
+ T: RefUnwindSafe + Fn(&str),
+{
+}
+
+static mut LOGGING_CALLBACK: Option<*mut dyn WarningCallback<Output = ()>> = None;
+
+extern "C" fn warning_callback(message: *const c_char) {
+ unsafe {
+ let callback = &*LOGGING_CALLBACK.expect("No callback provided, this is an internal bug");
+ // ignore result. If a panic happened, everything is going badly anyway
+ let _result = panic::catch_unwind(|| {
+ callback(&strings::from_c(message));
+ });
+ }
+}
+
+/// Use `callback` for every chemfiles warning. The callback will be passed
+/// the warning message. This will drop any previous warning callback.
+pub fn set_warning_callback<F>(callback: F) where F: WarningCallback + 'static {
+ // box callback to ensure it stays accessible
+ let callback = Box::into_raw(Box::new(callback));
+ unsafe {
+ if let Some(previous) = LOGGING_CALLBACK {
+ // drop the previous callback
+ let previous = Box::from_raw(previous);
+ std::mem::drop(previous);
+ // set the LOGGING_CALLBACK to the new one
+ LOGGING_CALLBACK = Some(callback);
+ } else {
+ // set the LOGGING_CALLBACK
+ LOGGING_CALLBACK = Some(callback);
+ // Tell C code to use Rust-provided callback
+ check_success(chfl_set_warning_callback(warning_callback));
+ }
+ }
+}
+
+
+impl fmt::Display for Error {
+ fn fmt(&self, fmt: &mut fmt::Formatter) -> Result<(), fmt::Error> {
+ write!(fmt, "{}", self.message)
+ }
+}
+
+impl error::Error for Error {
+ fn description(&self) -> &str {
+ match self.status {
+ Status::Success => "Success",
+ Status::StdCppError => "Exception from the C++ standard library",
+ Status::ChemfilesError => "Exception from the chemfiles library",
+ Status::MemoryError => "Error in memory allocations",
+ Status::FileError => "Error while reading or writing a file",
+ Status::FormatError => "Error in file formatting, i.e. the file is invalid",
+ Status::SelectionError => "Error in selection string syntax",
+ Status::UTF8PathError => "A string is not valid UTF8",
+ Status::ConfigurationError => "Error in configuration files",
+ Status::OutOfBounds => "Out of bounds indexing",
+ Status::PropertyError => "Error in property",
+ }
+ }
+}
+
+
+#[cfg(test)]
+mod test {
+ use super::*;
+ use Trajectory;
+
+ #[test]
+ fn errors() {
+ Error::cleanup();
+ assert_eq!(Error::last_error(), "");
+ assert!(Trajectory::open("nope", 'r').is_err());
+ assert_eq!(
+ Error::last_error(),
+ "file at \'nope\' does not have an extension, provide a format name to read it"
+ );
+ Error::cleanup();
+ assert_eq!(Error::last_error(), "");
+ }
+
+ #[test]
+ fn codes() {
+ assert_eq!(Error::from(chfl_status::CHFL_SUCCESS).status, Status::Success);
+ assert_eq!(Error::from(chfl_status::CHFL_CXX_ERROR).status, Status::StdCppError);
+ assert_eq!(Error::from(chfl_status::CHFL_GENERIC_ERROR).status, Status::ChemfilesError);
+ assert_eq!(Error::from(chfl_status::CHFL_MEMORY_ERROR).status, Status::MemoryError);
+ assert_eq!(Error::from(chfl_status::CHFL_FILE_ERROR).status, Status::FileError);
+ assert_eq!(Error::from(chfl_status::CHFL_FORMAT_ERROR).status, Status::FormatError);
+ assert_eq!(Error::from(chfl_status::CHFL_SELECTION_ERROR).status, Status::SelectionError);
+ assert_eq!(Error::from(chfl_status::CHFL_OUT_OF_BOUNDS).status, Status::OutOfBounds);
+ assert_eq!(Error::from(chfl_status::CHFL_PROPERTY_ERROR).status, Status::PropertyError);
+ }
+}
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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::Drop;
+use std::ptr;
+use std::slice;
+
+use super::{Atom, AtomMut, AtomRef};
+use super::{BondOrder, Residue, Topology, TopologyRef};
+use super::{UnitCell, UnitCellMut, UnitCellRef};
+use chemfiles_sys::*;
+use errors::{check, check_not_null, check_success, Error};
+use property::{PropertiesIter, Property, RawProperty};
+use strings;
+
+/// A `Frame` contains data from one simulation step: the current unit
+/// cell, the topology, the positions, and the velocities of the particles in
+/// the system. If some information is missing (topology or velocity or unit
+/// cell), the corresponding data is filled with a default value.
+pub struct Frame {
+ handle: *mut CHFL_FRAME,
+}
+
+impl Clone for Frame {
+ fn clone(&self) -> Frame {
+ unsafe {
+ let new_handle = chfl_frame_copy(self.as_ptr());
+ Frame::from_ptr(new_handle)
+ }
+ }
+}
+
+pub struct AtomIter<'a> {
+ frame: &'a Frame,
+ index: usize,
+ size: usize,
+}
+
+impl Frame {
+ /// Create a `Frame` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer,
+ /// except for it being non-null.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_FRAME) -> Frame {
+ check_not_null(ptr);
+ Frame { handle: ptr }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_FRAME {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_FRAME {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer FROM A SHARED REFERENCE.
+ ///
+ /// For uses with functions of the C API using mut pointers for both read
+ /// and write access. Users should check that this does not lead to multiple
+ /// mutable borrows
+ #[inline]
+ #[allow(non_snake_case)]
+ pub(crate) fn as_mut_ptr_MANUALLY_CHECKING_BORROW(&self) -> *mut CHFL_FRAME {
+ self.handle
+ }
+
+ /// Create an empty frame. It will be resized by the library as needed.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let frame = Frame::new();
+ ///
+ /// assert_eq!(frame.size(), 0);
+ /// ```
+ pub fn new() -> Frame {
+ unsafe { Frame::from_ptr(chfl_frame()) }
+ }
+
+ /// Get a reference to the atom at the given `index` in this frame.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+ ///
+ /// let atom = frame.atom(0);
+ /// assert_eq!(atom.name(), "Zn");
+ /// ```
+ pub fn atom(&self, index: usize) -> AtomRef {
+ unsafe {
+ let handle =
+ chfl_atom_from_frame(self.as_mut_ptr_MANUALLY_CHECKING_BORROW(), index as u64);
+ Atom::ref_from_ptr(handle)
+ }
+ }
+
+ /// Get a mutable reference to the atom at the given `index` in this frame.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+ ///
+ /// assert_eq!(frame.atom(0).name(), "Zn");
+ ///
+ /// frame.atom_mut(0).set_name("Fe");
+ /// assert_eq!(frame.atom(0).name(), "Fe");
+ /// ```
+ pub fn atom_mut(&mut self, index: usize) -> AtomMut {
+ unsafe {
+ let handle = chfl_atom_from_frame(self.as_mut_ptr(), index as u64);
+ Atom::ref_mut_from_ptr(handle)
+ }
+ }
+
+ /// Get the current number of atoms in this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.size(), 0);
+ ///
+ /// frame.resize(67);
+ /// assert_eq!(frame.size(), 67);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(chfl_frame_atoms_count(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Resize the positions and the velocities in this frame, to make space for
+ /// `natoms` atoms. Previous data is conserved, as well as the presence of
+ /// absence of velocities.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// assert_eq!(frame.size(), 67);
+ /// ```
+ pub fn resize(&mut self, natoms: usize) {
+ unsafe {
+ check_success(chfl_frame_resize(self.as_mut_ptr(), natoms as u64));
+ }
+ }
+
+ /// Add an `Atom` and the corresponding position and optionally velocity
+ /// data to this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [1.0, 1.0, 2.0], None);
+ ///
+ /// frame.add_velocities();
+ /// frame.add_atom(&Atom::new("Zn"), [-1.0, 1.0, 2.0], [0.2, 0.1, 0.0]);
+ /// ```
+ pub fn add_atom(
+ &mut self,
+ atom: &Atom,
+ position: [f64; 3],
+ velocity: impl Into<Option<[f64; 3]>>,
+ ) {
+ let velocity = velocity.into();
+ let velocity_ptr = match velocity {
+ Some(ref data) => data.as_ptr(),
+ None => ptr::null(),
+ };
+
+ unsafe {
+ check_success(chfl_frame_add_atom(
+ self.as_mut_ptr(),
+ atom.as_ptr(),
+ position.as_ptr(),
+ velocity_ptr,
+ ));
+ }
+ }
+
+ /// Remove the atom at index `i` in this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+ /// frame.add_atom(&Atom::new("Fe"), [0.0; 3], None);
+ /// frame.add_atom(&Atom::new("Sn"), [0.0; 3], None);
+ /// assert_eq!(frame.size(), 3);
+ ///
+ /// frame.remove(1);
+ /// assert_eq!(frame.size(), 2);
+ /// assert_eq!(frame.atom(1).name(), "Sn");
+ /// ```
+ pub fn remove(&mut self, i: usize) {
+ unsafe {
+ check_success(chfl_frame_remove(self.as_mut_ptr(), i as u64));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the frame.
+ ///
+ /// The bond order is set to `BondOrder::Unknown`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, BondOrder};
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.topology().bonds_count(), 0);
+ /// frame.resize(5);
+ ///
+ /// frame.add_bond(0, 1);
+ /// frame.add_bond(3, 1);
+ /// frame.add_bond(2, 4);
+ /// assert_eq!(frame.topology().bonds_count(), 3);
+ ///
+ /// assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown);
+ /// assert_eq!(frame.topology().bonds(), vec![[0, 1], [1, 3], [2, 4]]);
+ /// ```
+ pub fn add_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(chfl_frame_add_bond(self.as_mut_ptr(), i as u64, j as u64));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the frame
+ /// with the given bond `order`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, BondOrder};
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.topology().bonds_count(), 0);
+ /// frame.resize(2);
+ ///
+ /// frame.add_bond_with_order(0, 1, BondOrder::Double);
+ /// assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Double);
+ /// ```
+ pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder) {
+ unsafe {
+ check_success(chfl_frame_bond_with_order(
+ self.as_mut_ptr(),
+ i as u64,
+ j as u64,
+ order.as_raw(),
+ ));
+ }
+ }
+
+ /// Remove any existing bond between the atoms at indexes `i` and `j` in
+ /// the frame.
+ ///
+ /// This function does nothing if there is no bond between `i` and `j`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(5);
+ ///
+ /// frame.add_bond(0, 1);
+ /// frame.add_bond(3, 1);
+ /// frame.add_bond(2, 4);
+ ///
+ /// let bonds = frame.topology().bonds();
+ /// assert_eq!(bonds, vec![[0, 1], [1, 3], [2, 4]]);
+ ///
+ /// frame.remove_bond(2, 4);
+ /// let bonds = frame.topology().bonds();
+ /// assert_eq!(bonds, vec![[0, 1], [1, 3]]);
+ /// ```
+ pub fn remove_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(chfl_frame_remove_bond(
+ self.as_mut_ptr(),
+ i as u64,
+ j as u64,
+ ));
+ }
+ }
+
+ /// Add a copy of `residue` to this frame.
+ ///
+ /// # Errors
+ ///
+ /// This function fails is the residue id is already in this frame's
+ /// topology, or if the residue contain atoms that are already in another
+ /// residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Residue};
+ /// let mut frame = Frame::new();
+ ///
+ /// let residue = Residue::new("foo");
+ /// frame.add_residue(&residue).unwrap();
+ ///
+ /// let topology = frame.topology();
+ /// assert_eq!(topology.residues_count(), 1);
+ /// assert_eq!(topology.residue(0).unwrap().name(), "foo");
+ /// ```
+ pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error> {
+ unsafe { check(chfl_frame_add_residue(self.as_mut_ptr(), residue.as_ptr())) }
+ }
+
+ /// Get the distance between the atoms at indexes `i` and `j` in this frame,
+ /// accounting for periodic boundary conditions. The result is expressed in
+ /// Angstroms.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [1.0, 2.0, 3.0], None);
+ ///
+ /// assert_eq!(frame.distance(0, 1), f64::sqrt(14.0));
+ /// ```
+ pub fn distance(&self, i: usize, j: usize) -> f64 {
+ let mut distance = 0.0;
+ unsafe {
+ check_success(chfl_frame_distance(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ &mut distance,
+ ));
+ }
+ return distance;
+ }
+
+ /// Get the angle formed by the atoms at indexes `i`, `j` and `k` in this
+ /// frame, accounting for periodic boundary conditions. The result is
+ /// expressed in radians.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// # use std::f64;
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+ ///
+ /// assert_eq!(frame.angle(0, 1, 2), f64::consts::PI / 2.0);
+ /// ```
+ pub fn angle(&self, i: usize, j: usize, k: usize) -> f64 {
+ let mut angle = 0.0;
+ unsafe {
+ check_success(chfl_frame_angle(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ k as u64,
+ &mut angle,
+ ));
+ }
+ return angle;
+ }
+
+ /// Get the dihedral angle formed by the atoms at indexes `i`, `j`, `k` and
+ /// `m` in this frame, accounting for periodic boundary conditions. The
+ /// result is expressed in radians.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// # use std::f64;
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("D"), [0.0, 1.0, 1.0], None);
+ ///
+ /// assert_eq!(frame.dihedral(0, 1, 2, 3), f64::consts::PI / 2.0);
+ /// ```
+ pub fn dihedral(&self, i: usize, j: usize, k: usize, m: usize) -> f64 {
+ let mut dihedral = 0.0;
+ unsafe {
+ check_success(chfl_frame_dihedral(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ k as u64,
+ m as u64,
+ &mut dihedral,
+ ));
+ }
+ return dihedral;
+ }
+
+ /// Get the out of plane distance formed by the atoms at indexes `i`, `j`,
+ /// `k` and `m` in this frame, accounting for periodic boundary conditions.
+ /// The result is expressed in angstroms.
+ ///
+ /// This is the distance between the atom j and the ikm plane. The j atom
+ /// is the center of the improper dihedral angle formed by i, j, k and m.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 2.0], None);
+ /// frame.add_atom(&Atom::new("C"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("D"), [0.0, 1.0, 0.0], None);
+ ///
+ /// assert_eq!(frame.out_of_plane(0, 1, 2, 3), 2.0);
+ /// ```
+ pub fn out_of_plane(&self, i: usize, j: usize, k: usize, m: usize) -> f64 {
+ let mut distance = 0.0;
+ unsafe {
+ check_success(chfl_frame_out_of_plane(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ k as u64,
+ m as u64,
+ &mut distance,
+ ));
+ }
+ return distance;
+ }
+
+ /// Get a view into the positions of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ ///
+ /// let positions = frame.positions();
+ /// assert_eq!(positions.len(), 67);
+ /// assert_eq!(positions[0], [0.0, 0.0, 0.0]);
+ /// ```
+ pub fn positions(&self) -> &[[f64; 3]] {
+ let mut ptr = ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(chfl_frame_positions(
+ self.as_mut_ptr_MANUALLY_CHECKING_BORROW(),
+ &mut ptr,
+ &mut natoms,
+ ));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return slice::from_raw_parts(ptr, size);
+ }
+ }
+
+ /// Get a mutable view into the positions of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// {
+ /// let positions = frame.positions_mut();
+ /// assert_eq!(positions[0], [0.0, 0.0, 0.0]);
+ /// positions[0] = [1.0, 2.0, 3.0];
+ /// }
+ ///
+ /// let positions = frame.positions();
+ /// assert_eq!(positions[0], [1.0, 2.0, 3.0]);
+ /// ```
+ pub fn positions_mut(&mut self) -> &mut [[f64; 3]] {
+ let mut ptr = ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(chfl_frame_positions(
+ self.as_mut_ptr(),
+ &mut ptr,
+ &mut natoms,
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return slice::from_raw_parts_mut(ptr, size);
+ }
+ }
+
+ /// Get a view into the velocities of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// frame.add_velocities();
+ ///
+ /// let velocities = frame.velocities().expect("missing velocities");
+ /// assert_eq!(velocities.len(), 67);
+ /// assert_eq!(velocities[0], [0.0, 0.0, 0.0]);
+ /// ```
+ pub fn velocities(&self) -> Option<&[[f64; 3]]> {
+ if !self.has_velocities() {
+ return None;
+ }
+
+ let mut ptr = ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(chfl_frame_velocities(
+ self.as_mut_ptr_MANUALLY_CHECKING_BORROW(),
+ &mut ptr,
+ &mut natoms,
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return Some(slice::from_raw_parts(ptr, size));
+ }
+ }
+
+ /// Get a mutable view into the velocities of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// frame.add_velocities();
+ /// {
+ /// let velocities = frame.velocities_mut().expect("missing velocities");
+ /// assert_eq!(velocities[0], [0.0, 0.0, 0.0]);
+ /// velocities[0] = [1.0, 2.0, 3.0];
+ /// }
+ ///
+ /// let velocities = frame.velocities().expect("missing velocities");
+ /// assert_eq!(velocities[0], [1.0, 2.0, 3.0]);
+ /// ```
+ pub fn velocities_mut(&mut self) -> Option<&mut [[f64; 3]]> {
+ if !self.has_velocities() {
+ return None;
+ }
+
+ let mut ptr = ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(chfl_frame_velocities(
+ self.as_mut_ptr(),
+ &mut ptr,
+ &mut natoms,
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return Some(slice::from_raw_parts_mut(ptr, size));
+ }
+ }
+
+ /// Check if this frame contains velocity data.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.has_velocities(), false);
+ ///
+ /// frame.add_velocities();
+ /// assert_eq!(frame.has_velocities(), true);
+ /// ```
+ pub fn has_velocities(&self) -> bool {
+ let mut res = 0;
+ unsafe {
+ check_success(chfl_frame_has_velocities(self.as_ptr(), &mut res));
+ }
+ return res != 0;
+ }
+
+ /// Add velocity data to this frame. If the frame already have velocities,
+ /// this does nothing.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.has_velocities(), false);
+ ///
+ /// frame.add_velocities();
+ /// assert_eq!(frame.has_velocities(), true);
+ /// ```
+ pub fn add_velocities(&mut self) {
+ unsafe {
+ check_success(chfl_frame_add_velocities(self.as_mut_ptr()));
+ }
+ }
+
+ /// Get a reference to the `UnitCell` from this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, CellShape};
+ /// let frame = Frame::new();
+ ///
+ /// let cell = frame.cell();
+ /// assert_eq!(cell.shape(), CellShape::Infinite);
+ /// ```
+ pub fn cell(&self) -> UnitCellRef {
+ unsafe {
+ let handle = chfl_cell_from_frame(self.as_mut_ptr_MANUALLY_CHECKING_BORROW());
+ UnitCell::ref_from_ptr(handle)
+ }
+ }
+
+ /// Get a mutable reference to the `UnitCell` from this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, CellShape};
+ /// let mut frame = Frame::new();
+ ///
+ /// assert_eq!(frame.cell().shape(), CellShape::Infinite);
+ ///
+ /// frame.cell_mut().set_shape(CellShape::Triclinic).unwrap();
+ /// assert_eq!(frame.cell().shape(), CellShape::Triclinic);
+ /// ```
+ pub fn cell_mut(&mut self) -> UnitCellMut {
+ unsafe {
+ let handle = chfl_cell_from_frame(self.as_mut_ptr());
+ UnitCell::ref_mut_from_ptr(handle)
+ }
+ }
+
+ /// Set the `UnitCell` of this frame to `cell`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, UnitCell, CellShape};
+ /// let mut frame = Frame::new();
+ ///
+ /// frame.set_cell(&UnitCell::new([10.0, 10.0, 10.0]));
+ ///
+ /// let cell = frame.cell();
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);
+ /// ```
+ pub fn set_cell(&mut self, cell: &UnitCell) {
+ unsafe {
+ check_success(chfl_frame_set_cell(self.as_mut_ptr(), cell.as_ptr()));
+ }
+ }
+
+ /// Get a reference to the `Topology` of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(42);
+ ///
+ /// let topology = frame.topology();
+ /// assert_eq!(topology.size(), 42);
+ /// ```
+ pub fn topology(&self) -> TopologyRef {
+ unsafe {
+ let handle = chfl_topology_from_frame(self.as_ptr());
+ Topology::ref_from_ptr(handle)
+ }
+ }
+
+ /// Set the `Topology` of this frame to `topology`.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the topology contains a different number of atoms
+ /// than this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Topology, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.resize(2);
+ ///
+ /// let mut topology = Topology::new();
+ /// topology.add_atom(&Atom::new("Cl"));
+ /// topology.add_atom(&Atom::new("Cl"));
+ /// topology.add_bond(0, 1);
+ ///
+ /// frame.set_topology(&topology).unwrap();
+ /// assert_eq!(frame.atom(0).name(), "Cl");
+ /// ```
+ pub fn set_topology(&mut self, topology: &Topology) -> Result<(), Error> {
+ unsafe {
+ check(chfl_frame_set_topology(
+ self.as_mut_ptr(),
+ topology.as_ptr(),
+ ))
+ }
+ }
+
+ /// Get this frame step, i.e. the frame number in the trajectory
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let frame = Frame::new();
+ /// assert_eq!(frame.step(), 0);
+ /// ```
+ pub fn step(&self) -> usize {
+ let mut step = 0;
+ unsafe {
+ check_success(chfl_frame_step(self.as_ptr(), &mut step));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return step as usize;
+ }
+
+ /// Set this frame step to `step`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.step(), 0);
+ ///
+ /// frame.set_step(10);
+ /// assert_eq!(frame.step(), 10);
+ /// ```
+ pub fn set_step(&mut self, step: usize) {
+ unsafe {
+ check_success(chfl_frame_set_step(self.as_mut_ptr(), step as u64));
+ }
+ }
+
+ /// Guess the bonds, angles and dihedrals in this `frame`.
+ ///
+ /// The bonds are guessed using a distance-based algorithm, and then angles
+ /// and dihedrals are guessed from the bonds.
+ ///
+ /// # Errors
+ ////
+ /// This function can fail if the covalent radius is unknown for some atoms
+ /// in the frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ ///
+ /// frame.add_atom(&Atom::new("Cl"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("Cl"), [1.5, 0.0, 0.0], None);
+ /// assert_eq!(frame.topology().bonds_count(), 0);
+ ///
+ /// frame.guess_bonds().unwrap();
+ /// assert_eq!(frame.topology().bonds_count(), 1);
+ /// ```
+ pub fn guess_bonds(&mut self) -> Result<(), Error> {
+ unsafe { check(chfl_frame_guess_bonds(self.as_mut_ptr())) }
+ }
+
+ /// Remove all existing bonds, angles, dihedral angles and improper
+ /// dihedral angles in the topology of the frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Atom, Frame};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [0.0, 1.0, 0.0], None);
+ ///
+ /// frame.add_bond(0, 1);
+ /// frame.add_bond(1, 2);
+ ///
+ /// assert_eq!(frame.topology().bonds().len(), 2);
+ /// assert_eq!(frame.topology().angles().len(), 1);
+ ///
+ /// frame.clear_bonds();
+ /// assert!(frame.topology().bonds().is_empty());
+ /// assert!(frame.topology().angles().is_empty());
+ /// ```
+ pub fn clear_bonds(&mut self) {
+ unsafe {
+ check_success(chfl_frame_clear_bonds(self.as_mut_ptr()));
+ }
+ }
+
+ /// Add a new `property` with the given `name` to this frame.
+ ///
+ /// If a property with the same name already exists, this function override
+ /// the existing property with the new one.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Frame, Property};
+ /// let mut frame = Frame::new();
+ /// frame.set("a string", "hello");
+ /// frame.set("a double", 4.3);
+ ///
+ /// assert_eq!(frame.get("a string"), Some(Property::String("hello".into())));
+ /// assert_eq!(frame.get("a double"), Some(Property::Double(4.3)));
+ /// ```
+ pub fn set(&mut self, name: &str, property: impl Into<Property>) {
+ let buffer = strings::to_c(name);
+ let property = property.into().as_raw();
+ unsafe {
+ check_success(chfl_frame_set_property(
+ self.as_mut_ptr(),
+ buffer.as_ptr(),
+ property.as_ptr(),
+ ));
+ }
+ }
+
+ /// Get a property with the given `name` in this frame, if it exist.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Frame, Property};
+ /// let mut frame = Frame::new();
+ /// frame.set("foo", Property::Double(22.2));
+ ///
+ /// assert_eq!(frame.get("foo"), Some(Property::Double(22.2)));
+ /// assert_eq!(frame.get("Bar"), None);
+ /// ```
+ pub fn get(&self, name: &str) -> Option<Property> {
+ let buffer = strings::to_c(name);
+ unsafe {
+ let handle = chfl_frame_get_property(self.as_ptr(), buffer.as_ptr());
+ if handle.is_null() {
+ None
+ } else {
+ let raw = RawProperty::from_ptr(handle);
+ Some(Property::from_raw(raw))
+ }
+ }
+ }
+
+ /// Get an iterator over all (name, property) pairs for this frame
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Frame, Property};
+ /// let mut frame = Frame::new();
+ /// frame.set("foo", Property::Double(22.2));
+ /// frame.set("bar", Property::Bool(false));
+ ///
+ /// for (name, property) in frame.properties() {
+ /// if name == "foo" {
+ /// assert_eq!(property, Property::Double(22.2));
+ /// } else if name == "bar" {
+ /// assert_eq!(property, Property::Bool(false));
+ /// }
+ /// }
+ /// ```
+ pub fn properties(&self) -> PropertiesIter {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_frame_properties_count(self.as_ptr(), &mut count));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = count as usize;
+ let mut c_names = vec![ptr::null_mut(); size];
+ unsafe {
+ check_success(chfl_frame_list_properties(
+ self.as_ptr(),
+ c_names.as_mut_ptr(),
+ count,
+ ));
+ }
+
+ let mut names = Vec::new();
+ for ptr in c_names {
+ names.push(strings::from_c(ptr));
+ }
+
+ PropertiesIter {
+ names: names.into_iter(),
+ getter: Box::new(move |name| self.get(name).expect("failed to get property")),
+ }
+ }
+
+ /// Gets an iterator over atoms
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Atom, AtomRef, Frame};
+ /// let mut frame = Frame::new();
+ ///
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ ///
+ /// let mut atoms: Vec<AtomRef> = Vec::new();
+ ///
+ /// for atom in frame.iter_atoms() {
+ /// atoms.push(atom);
+ /// }
+ ///
+ /// assert_eq!(atoms.len(), 2);
+ /// ```
+ pub fn iter_atoms(&self) -> AtomIter<'_> {
+ AtomIter {
+ frame: self,
+ index: 0,
+ size: self.size(),
+ }
+ }
+}
+
+impl Drop for Frame {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+impl<'a> Iterator for AtomIter<'a> {
+ type Item = AtomRef<'a>;
+
+ fn next(&mut self) -> Option<Self::Item> {
+ if self.size <= self.index {
+ return None;
+ }
+ let atom = self.frame.atom(self.index);
+ self.index += 1;
+ Some(atom)
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+ use {Atom, Topology, UnitCell};
+
+ #[test]
+ fn clone() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.size(), 0);
+ let copy = frame.clone();
+ assert_eq!(copy.size(), 0);
+
+ frame.resize(42);
+ assert_eq!(frame.size(), 42);
+ assert_eq!(copy.size(), 0);
+ }
+
+ #[test]
+ fn size() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.size(), 0);
+
+ frame.resize(12);
+ assert_eq!(frame.size(), 12);
+ }
+
+ #[test]
+ fn add_atom() {
+ let mut frame = Frame::new();
+
+ frame.add_atom(&Atom::new("U"), [1.0, 1.0, 2.0], None);
+ assert_eq!(frame.size(), 1);
+ assert_eq!(frame.atom(0).name(), "U");
+
+ let positions = &[[1.0, 1.0, 2.0]];
+ assert_eq!(frame.positions(), positions);
+
+ frame.add_velocities();
+ frame.add_atom(&Atom::new("F"), [1.0, 1.0, 2.0], [4.0, 3.0, 2.0]);
+ assert_eq!(frame.size(), 2);
+ assert_eq!(frame.atom(0).name(), "U");
+ assert_eq!(frame.atom(1).name(), "F");
+
+ let positions = &[[1.0, 1.0, 2.0], [1.0, 1.0, 2.0]];
+ assert_eq!(frame.positions(), positions);
+
+ let velocities = &[[0.0, 0.0, 0.0], [4.0, 3.0, 2.0]];
+ assert_eq!(frame.velocities().unwrap(), velocities);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_atom() {
+ let mut frame = Frame::new();
+ frame.resize(22);
+ let _atom = frame.atom(23);
+ }
+
+ #[test]
+ fn remove_atom() {
+ let mut frame = Frame::new();
+ frame.add_atom(&Atom::new("U"), [1.0, 1.0, 2.0], None);
+ frame.add_atom(&Atom::new("F"), [1.0, 1.0, 2.0], None);
+
+ assert_eq!(frame.size(), 2);
+ assert_eq!(frame.atom(0).name(), "U");
+
+ frame.remove(0);
+ assert_eq!(frame.size(), 1);
+ assert_eq!(frame.atom(0).name(), "F");
+ }
+
+ #[test]
+ #[should_panic]
+ fn remove_out_of_bounds() {
+ let mut frame = Frame::new();
+ frame.resize(32);
+
+ frame.remove(100);
+ }
+
+ #[test]
+ fn positions() {
+ let mut frame = Frame::new();
+ frame.resize(4);
+ let expected = &[
+ [1.0, 2.0, 3.0],
+ [4.0, 5.0, 6.0],
+ [7.0, 8.0, 9.0],
+ [10.0, 11.0, 12.0],
+ ];
+
+ frame.positions_mut().clone_from_slice(expected);
+ assert_eq!(frame.positions(), expected);
+ }
+
+ #[test]
+ fn velocities() {
+ let mut frame = Frame::new();
+ frame.resize(4);
+ assert!(!frame.has_velocities());
+ frame.add_velocities();
+ assert!(frame.has_velocities());
+
+ let expected = &[
+ [1.0, 2.0, 3.0],
+ [4.0, 5.0, 6.0],
+ [7.0, 8.0, 9.0],
+ [10.0, 11.0, 12.0],
+ ];
+
+ frame.velocities_mut().unwrap().clone_from_slice(expected);
+ assert_eq!(frame.velocities().unwrap(), expected);
+ }
+
+ #[test]
+ fn cell() {
+ let mut frame = Frame::new();
+ frame.set_cell(&UnitCell::new([3.0, 4.0, 5.0]));
+ let cell = frame.cell();
+ assert_eq!(cell.lengths(), [3.0, 4.0, 5.0]);
+ }
+
+ #[test]
+ fn topology() {
+ let mut frame = Frame::new();
+ frame.resize(2);
+ let mut topology = Topology::new();
+
+ topology.add_atom(&Atom::new("Zn"));
+ topology.add_atom(&Atom::new("Ar"));
+
+ assert!(frame.set_topology(&topology).is_ok());
+
+ let topology = frame.topology();
+
+ assert_eq!(topology.atom(0).name(), "Zn");
+ assert_eq!(topology.atom(1).name(), "Ar");
+
+ assert_eq!(frame.atom(0).name(), "Zn");
+ assert_eq!(frame.atom(1).name(), "Ar");
+ }
+
+ #[test]
+ fn bonds() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ assert_eq!(frame.topology().bonds_count(), 0);
+
+ frame.add_bond(0, 1);
+ frame.add_bond(9, 2);
+ frame.add_bond_with_order(3, 7, BondOrder::Aromatic);
+ assert_eq!(frame.topology().bonds_count(), 3);
+
+ assert_eq!(frame.topology().bonds(), vec![[0, 1], [2, 9], [3, 7]]);
+ let expected = vec![BondOrder::Unknown, BondOrder::Unknown, BondOrder::Aromatic];
+ assert_eq!(frame.topology().bond_orders(), expected);
+
+ assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown);
+ assert_eq!(frame.topology().bond_order(3, 7), BondOrder::Aromatic);
+
+ frame.remove_bond(3, 7);
+ // Removing unexisting bond is OK if both indexes are in bounds
+ frame.remove_bond(8, 7);
+ assert_eq!(frame.topology().bonds_count(), 2);
+
+ frame.clear_bonds();
+ assert_eq!(frame.topology().bonds_count(), 0);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ frame.add_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_remove_bond() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ frame.remove_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds_with_order() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ frame.add_bond_with_order(300, 7, BondOrder::Unknown);
+ }
+
+ #[test]
+ fn residues() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.topology().residues_count(), 0);
+
+ let residue = &Residue::new("foobar");
+ frame.add_residue(residue).unwrap();
+ frame.add_residue(residue).unwrap();
+ frame.add_residue(residue).unwrap();
+
+ assert_eq!(frame.topology().residues_count(), 3);
+ assert_eq!(frame.topology().residue(0).unwrap().name(), "foobar");
+ }
+
+ #[test]
+ fn step() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.step(), 0);
+ frame.set_step(42);
+ assert_eq!(frame.step(), 42);
+ }
+
+ #[test]
+ fn property() {
+ let mut frame = Frame::new();
+ frame.set("foo", -22.0);
+ assert_eq!(frame.get("foo"), Some(Property::Double(-22.0)));
+ assert_eq!(frame.get("bar"), None);
+
+ frame.set("bar", Property::String("here".into()));
+ for (name, property) in frame.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(-22.0));
+ } else if name == "bar" {
+ assert_eq!(property, Property::String("here".into()));
+ }
+ }
+ }
+
+ #[test]
+ fn pbc_geometry() {
+ use std::f64::consts::PI;
+
+ let mut frame = Frame::new();
+ let atom = &Atom::new("");
+
+ frame.add_atom(atom, [1.0, 0.0, 0.0], None);
+ frame.add_atom(atom, [0.0, 0.0, 0.0], None);
+ frame.add_atom(atom, [0.0, 1.0, 0.0], None);
+ frame.add_atom(atom, [0.0, 1.0, 1.0], None);
+ frame.add_atom(atom, [0.0, 0.0, 2.0], None);
+
+ assert_eq!(frame.distance(0, 2), f64::sqrt(2.0));
+ assert_eq!(frame.angle(0, 1, 2), PI / 2.0);
+ assert_eq!(frame.dihedral(0, 1, 2, 3), PI / 2.0);
+ assert_eq!(frame.out_of_plane(1, 4, 0, 2), 2.0);
+ }
+
+ #[test]
+ fn atom_iterator() {
+ let mut frame = Frame::new();
+
+ frame.add_atom(&Atom::new("H1"), [1.0, 0.0, 0.0], None);
+ frame.add_atom(&Atom::new("H2"), [0.0, 1.0, 0.0], None);
+ frame.add_atom(&Atom::new("H3"), [0.0, 0.0, 1.0], None);
+ frame.add_atom(&Atom::new("H4"), [1.0, 1.0, 1.0], None);
+
+ let mut items: Vec<(AtomRef, &[f64; 3])> = Vec::new();
+
+ for item in frame.iter_atoms().zip(frame.positions()) {
+ items.push(item);
+ }
+
+ assert_eq!(items[0].0.name(), "H1");
+ assert_eq!(items[2].0.name(), "H3");
+
+ assert_eq!(items[1].1, &[0.0_f64, 1.0_f64, 0.0_f64]);
+ assert_eq!(items[3].1, &[1.0_f64, 1.0_f64, 1.0_f64]);
+ }
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+
+//! Chemfiles is a multi-language library written in modern C++ for reading and
+//! writing from and to molecular trajectory files. These files are created by
+//! your favorite theoretical chemistry program, and contains information about
+//! atomic or residues names and positions. Some format also have additional
+//! information, such as velocities, forces, energy, …
+//!
+//! This crate expose the C API of chemfiles to Rust, and make all the
+//! functionalities accessible. For more information on the C++ library,
+//! please see its [documentation][cxx_doc]. Specifically, the following pages
+//! are worth reading:
+//!
+//! - The [overview][overview] of the classes organization;
+//! - The list of [supported formats][formats];
+//! - The documentation for the [selection language][selections];
+//!
+//! [cxx_doc]: https://chemfiles.org/chemfiles
+//! [overview]: https://chemfiles.org/chemfiles/latest/overview.html
+//! [formats]: https://chemfiles.org/chemfiles/latest/formats.html
+//! [selections]: https://chemfiles.org/chemfiles/latest/selections.html
+
+#![deny(missing_docs)]
+#![warn(trivial_casts, unused_import_braces, variant_size_differences)]
+#![warn(unused_results)]
+// Configuration for clippy lints
+#![warn(clippy::all, clippy::pedantic)]
+#![allow(clippy::needless_return, clippy::module_name_repetitions)]
+#![allow(clippy::must_use_candidate, clippy::wildcard_imports)]
+
+// Allow a few more clippy lints in test mode
+#![cfg_attr(test, allow(clippy::float_cmp, clippy::unreadable_literal, clippy::shadow_unrelated))]
+
+// deny(warnings) in doc tests
+#![doc(test(attr(deny(warnings))))]
+#![doc(test(attr(allow(unused_variables))))]
+
+#[cfg(test)]
+#[macro_use]
+extern crate approx;
+
+extern crate chemfiles_sys;
+use chemfiles_sys::{chfl_add_configuration, chfl_version};
+
+mod strings;
+
+mod errors;
+pub use errors::{Error, Status};
+pub use errors::set_warning_callback;
+
+mod atom;
+pub use atom::Atom;
+pub use atom::AtomRef;
+pub use atom::AtomMut;
+
+mod cell;
+pub use cell::UnitCell;
+pub use cell::UnitCellRef;
+pub use cell::UnitCellMut;
+pub use cell::CellShape;
+
+mod residue;
+pub use residue::Residue;
+pub use residue::ResidueRef;
+
+mod topology;
+pub use topology::Topology;
+pub use topology::TopologyRef;
+pub use topology::BondOrder;
+
+mod frame;
+pub use frame::Frame;
+
+mod trajectory;
+pub use trajectory::Trajectory;
+
+mod selection;
+pub use selection::{Match, Selection};
+
+mod property;
+pub use property::Property;
+pub use property::PropertiesIter;
+
+mod misc;
+pub use misc::{FormatMetadata, formats_list, guess_format};
+
+/// Get the version of the chemfiles library.
+///
+/// # Example
+/// ```
+/// let version = chemfiles::version();
+/// assert!(version.starts_with("0.10"));
+/// ```
+pub fn version() -> String {
+ unsafe { strings::from_c(chfl_version()) }
+}
+
+/// Read configuration data from the file at `path`.
+///
+/// By default, chemfiles reads configuration from any file named
+/// `.chemfiles.toml` in the current directory or any parent directory. This
+/// function can be used to add data from another configuration file. Data from
+/// the new configuration file will overwrite any existing data.
+///
+/// # Errors
+///
+/// This function will fail if there is no file at `path`, or if the file is
+/// incorrectly formatted.
+///
+/// # Example
+/// ```no_run
+/// chemfiles::add_configuration("local-config.toml").unwrap();
+/// // from now on, the data from "local-config.toml" will be used
+/// ```
+pub fn add_configuration<S>(path: S) -> Result<(), Error>
+where
+ S: AsRef<str>,
+{
+ let buffer = strings::to_c(path.as_ref());
+ unsafe {
+ errors::check(chfl_add_configuration(buffer.as_ptr()))
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ #[test]
+ fn version() {
+ assert!(!crate::version().is_empty());
+ assert!(crate::version().starts_with("0.10"));
+ }
+}
+
+#[cfg(test)]
+fn assert_vector3d_eq(lhs: &[f64; 3], rhs: &[f64; 3], eps: f64) {
+ lhs.iter()
+ .zip(rhs)
+ .for_each(|(l, r)| assert_ulps_eq!(l, r, epsilon = eps));
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2020 Guillaume Fraux -- BSD licensed
+
+use std::convert::TryInto;
+use std::ffi::CStr;
+
+use chemfiles_sys::{chfl_format_metadata, chfl_formats_list, chfl_free, chfl_guess_format};
+use errors::check_success;
+
+/// `FormatMetadata` contains metadata associated with one format.
+#[allow(clippy::struct_excessive_bools)]
+#[derive(Debug, Clone, PartialEq, Eq)]
+pub struct FormatMetadata {
+ /// Name of the format.
+ pub name: &'static str,
+ /// Extension associated with the format.
+ pub extension: Option<&'static str>,
+ /// Extended, user-facing description of the format.
+ pub description: &'static str,
+ /// URL pointing to the format definition/reference.
+ pub reference: &'static str,
+ /// Is reading files in this format implemented?
+ pub read: bool,
+ /// Is writing files in this format implemented?
+ pub write: bool,
+ /// Does this format support in-memory IO?
+ pub memory: bool,
+ /// Does this format support storing atomic positions?
+ pub positions: bool,
+ /// Does this format support storing atomic velocities?
+ pub velocities: bool,
+ /// Does this format support storing unit cell information?
+ pub unit_cell: bool,
+ /// Does this format support storing atom names or types?
+ pub atoms: bool,
+ /// Does this format support storing bonds between atoms?
+ pub bonds: bool,
+ /// Does this format support storing residues?
+ pub residues: bool,
+}
+
+impl FormatMetadata {
+ pub(crate) fn from_raw(raw: &chfl_format_metadata) -> Self {
+ let str_from_ptr = |ptr| unsafe {
+ CStr::from_ptr(ptr)
+ .to_str()
+ .expect("Invalid Rust str from C")
+ };
+ let extension = if raw.extension.is_null() {
+ None
+ } else {
+ Some(str_from_ptr(raw.extension))
+ };
+ Self {
+ name: str_from_ptr(raw.name),
+ extension,
+ description: str_from_ptr(raw.description),
+ reference: str_from_ptr(raw.reference),
+ read: raw.read,
+ write: raw.write,
+ memory: raw.memory,
+ positions: raw.positions,
+ velocities: raw.velocities,
+ unit_cell: raw.unit_cell,
+ atoms: raw.atoms,
+ bonds: raw.bonds,
+ residues: raw.residues,
+ }
+ }
+}
+
+/// Get the list of formats known by chemfiles, as well as all associated metadata.
+///
+/// # Example
+/// ```
+/// let formats = chemfiles::formats_list();
+/// println!("chemfiles supports {} formats:", formats.len());
+/// for format in &formats {
+/// println!(
+/// " {:<15} {}",
+/// format.name,
+/// format.extension.as_deref().unwrap_or("")
+/// );
+/// }
+/// ```
+#[must_use]
+pub fn formats_list() -> Vec<FormatMetadata> {
+ let mut formats = std::ptr::null_mut();
+ let mut count: u64 = 0;
+ let formats_slice = unsafe {
+ check_success(chfl_formats_list(&mut formats, &mut count));
+ std::slice::from_raw_parts(formats, count.try_into().expect("failed to convert u64 to usize"))
+ };
+ let formats_vec = formats_slice
+ .iter()
+ .map(FormatMetadata::from_raw)
+ .collect();
+ unsafe {
+ let _ = chfl_free(formats as *const _);
+ }
+ return formats_vec;
+}
+
+#[allow(clippy::doc_markdown)]
+/// Get the format that chemfiles would use to read a file at the given
+/// ``path``.
+///
+/// The format is mostly guessed from the path extension, chemfiles only tries
+/// to read the file to distinguish between CIF and mmCIF files. Opening the
+/// file using the returned format string might still fail. For example, it will
+/// fail if the file is not actually formatted according to the guessed format;
+/// or the format/compression combination is not supported (e.g. `XTC / GZ` will
+/// not work since the XTC reader does not support compressed files).
+///
+/// The returned format is represented in a way compatible with the various
+/// `Trajectory` constructors, i.e. `"<format name> [/ <compression>]"`, where
+/// compression is optional.
+///
+/// # Examples
+/// ```
+/// let format = chemfiles::guess_format("trajectory.xyz.xz");
+/// assert_eq!(format, "XYZ / XZ");
+///
+/// let format = chemfiles::guess_format("trajectory.nc");
+/// assert_eq!(format, "Amber NetCDF");
+/// ```
+pub fn guess_format(path: &str) -> String {
+ let path = crate::strings::to_c(path);
+ let mut buffer = vec![0; 128];
+ unsafe {
+ check_success(chfl_guess_format(
+ path.as_ptr(), buffer.as_mut_ptr(), buffer.len() as u64
+ ));
+ }
+ return crate::strings::from_c(buffer.as_ptr());
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::Drop;
+use std::vec::IntoIter;
+
+use chemfiles_sys::*;
+use errors::{check, check_not_null, check_success, Error};
+use strings;
+
+/// A thin wrapper around `CHFL_PROPERTY`
+pub(crate) struct RawProperty {
+ handle: *mut CHFL_PROPERTY,
+}
+
+impl RawProperty {
+ /// Create a `RawProperty` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ pub unsafe fn from_ptr(ptr: *mut CHFL_PROPERTY) -> RawProperty {
+ check_not_null(ptr);
+ RawProperty {
+ handle: ptr
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ pub fn as_ptr(&self) -> *const CHFL_PROPERTY {
+ self.handle
+ }
+
+ fn double(value: f64) -> RawProperty {
+ unsafe {
+ let handle = chfl_property_double(value);
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn bool(value: bool) -> RawProperty {
+ let value = if value { 1 } else { 0 };
+ unsafe {
+ let handle = chfl_property_bool(value);
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn vector3d(value: [f64; 3]) -> RawProperty {
+ unsafe {
+ let handle = chfl_property_vector3d(value.as_ptr());
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn string(value: &str) -> RawProperty {
+ let buffer = strings::to_c(value);
+ unsafe {
+ let handle = chfl_property_string(buffer.as_ptr());
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn get_kind(&self) -> chfl_property_kind {
+ let mut kind = chfl_property_kind::CHFL_PROPERTY_BOOL;
+ unsafe {
+ check_success(chfl_property_get_kind(self.as_ptr(), &mut kind));
+ }
+ return kind;
+ }
+
+ fn get_bool(&self) -> Result<bool, Error> {
+ let mut value = 0;
+ unsafe {
+ check(chfl_property_get_bool(self.as_ptr(), &mut value))?;
+ }
+ return Ok(value != 0);
+ }
+
+ fn get_double(&self) -> Result<f64, Error> {
+ let mut value = 0.0;
+ unsafe {
+ check(chfl_property_get_double(self.as_ptr(), &mut value))?;
+ }
+ return Ok(value);
+ }
+
+ fn get_string(&self) -> Result<String, Error> {
+ let get_string = |ptr, len| unsafe { chfl_property_get_string(self.as_ptr(), ptr, len) };
+ let value = strings::call_autogrow_buffer(64, get_string)?;
+ return Ok(strings::from_c(value.as_ptr()));
+ }
+
+ fn get_vector3d(&self) -> Result<[f64; 3], Error> {
+ let mut value = [0.0; 3];
+ unsafe {
+ check(chfl_property_get_vector3d(self.as_ptr(), value.as_mut_ptr()))?;
+ }
+ return Ok(value);
+ }
+}
+
+impl Drop for RawProperty {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+/// A `Property` is a piece of data that can be associated with an `Atom` or a
+/// `Frame`.
+#[derive(Debug, Clone, PartialEq, PartialOrd)]
+pub enum Property {
+ /// Boolean property
+ Bool(bool),
+ /// Floating point property
+ Double(f64),
+ /// String property
+ String(String),
+ /// 3-dimensional vector property
+ Vector3D([f64; 3]),
+}
+
+impl From<bool> for Property {
+ fn from(value: bool) -> Self {
+ Property::Bool(value)
+ }
+}
+
+impl From<f64> for Property {
+ fn from(value: f64) -> Self {
+ Property::Double(value)
+ }
+}
+
+impl From<String> for Property {
+ fn from(value: String) -> Self {
+ Property::String(value)
+ }
+}
+
+impl<'a> From<&'a str> for Property {
+ fn from(value: &'a str) -> Self {
+ Property::String(value.into())
+ }
+}
+
+impl From<[f64; 3]> for Property {
+ fn from(value: [f64; 3]) -> Self {
+ Property::Vector3D(value)
+ }
+}
+
+impl Property {
+ pub(crate) fn as_raw(&self) -> RawProperty {
+ match *self {
+ Property::Bool(value) => RawProperty::bool(value),
+ Property::Double(value) => RawProperty::double(value),
+ Property::String(ref value) => RawProperty::string(value),
+ Property::Vector3D(value) => RawProperty::vector3d(value),
+ }
+ }
+
+ #[allow(clippy::needless_pass_by_value)] // raw property
+ pub(crate) fn from_raw(raw: RawProperty) -> Property {
+ match raw.get_kind() {
+ chfl_property_kind::CHFL_PROPERTY_BOOL => {
+ Property::Bool(raw.get_bool().expect("shoudl be a bool"))
+ }
+ chfl_property_kind::CHFL_PROPERTY_DOUBLE => {
+ Property::Double(raw.get_double().expect("should be a double"))
+ }
+ chfl_property_kind::CHFL_PROPERTY_STRING => {
+ Property::String(raw.get_string().expect("should be a string"))
+ }
+ chfl_property_kind::CHFL_PROPERTY_VECTOR3D => {
+ Property::Vector3D(raw.get_vector3d().expect("should be a vector3d"))
+ }
+ }
+ }
+}
+
+/// An iterator over the properties in an atom/frame/residue
+pub struct PropertiesIter<'a> where {
+ pub(crate) names: IntoIter<String>,
+ pub(crate) getter: Box<dyn Fn(&str) -> Property + 'a>,
+}
+
+impl<'a> Iterator for PropertiesIter<'a> {
+ type Item = (String, Property);
+ fn next(&mut self) -> Option<Self::Item> {
+ self.names.next().map(|name| {
+ let property = (self.getter)(&*name);
+ (name, property)
+ })
+ }
+
+ fn size_hint(&self) -> (usize, Option<usize>) {
+ self.names.size_hint()
+ }
+
+ fn count(self) -> usize {
+ self.names.count()
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ mod raw {
+ use super::super::*;
+
+ #[test]
+ fn bool() {
+ let property = RawProperty::bool(false);
+ assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_BOOL);
+ assert_eq!(property.get_bool(), Ok(false));
+ }
+
+ #[test]
+ fn double() {
+ let property = RawProperty::double(45.0);
+ assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_DOUBLE);
+ assert_eq!(property.get_double(), Ok(45.0));
+ }
+
+ #[test]
+ fn string() {
+ let property = RawProperty::string("test");
+ assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_STRING);
+ assert_eq!(property.get_string(), Ok("test".into()));
+ }
+
+ #[test]
+ fn vector3d() {
+ let property = RawProperty::vector3d([1.2, 3.4, 5.6]);
+ assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_VECTOR3D);
+ assert_eq!(property.get_vector3d(), Ok([1.2, 3.4, 5.6]));
+ }
+ }
+
+ mod rust {
+ use super::super::*;
+
+ #[test]
+ fn bool() {
+ let property = Property::Bool(false);
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_BOOL);
+ assert_eq!(raw.get_bool(), Ok(false));
+
+ assert_eq!(Property::from_raw(raw), property);
+ }
+
+ #[test]
+ fn double() {
+ let property = Property::Double(45.0);
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_DOUBLE);
+ assert_eq!(raw.get_double(), Ok(45.0));
+
+ assert_eq!(Property::from_raw(raw), property);
+ }
+
+ #[test]
+ fn string() {
+ let property = Property::String("test".into());
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_STRING);
+ assert_eq!(raw.get_string(), Ok("test".into()));
+
+ assert_eq!(Property::from_raw(raw), property);
+
+ let property = Property::String("long string ".repeat(128));
+ let raw = property.as_raw();
+ assert_eq!(raw.get_string(), Ok("long string ".repeat(128)));
+ }
+
+ #[test]
+ fn vector3d() {
+ let property = Property::Vector3D([1.2, 3.4, 5.6]);
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_VECTOR3D);
+ assert_eq!(raw.get_vector3d(), Ok([1.2, 3.4, 5.6]));
+
+ assert_eq!(Property::from_raw(raw), property);
+ }
+ }
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371 +372 +373 +374 +375 +376 +377 +378 +379 +380 +381 +382 +383 +384 +385 +386 +387 +388 +389 +390 +391 +392 +393 +394 +395 +396 +397 +398 +399 +400 +401 +402 +403 +404 +405 +406 +407 +408 +409 +410 +411 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::{Drop, Deref};
+use std::marker::PhantomData;
+use std::ptr;
+
+use chemfiles_sys::*;
+use errors::{check_not_null, check_success};
+use property::{Property, RawProperty, PropertiesIter};
+use strings;
+
+/// A `Residue` is a group of atoms belonging to the same logical unit. They
+/// can be small molecules, amino-acids in a protein, monomers in polymers,
+/// *etc.*
+pub struct Residue {
+ handle: *mut CHFL_RESIDUE,
+}
+
+/// An analog to a reference to a residue (`&Residue`)
+pub struct ResidueRef<'a> {
+ inner: Residue,
+ marker: PhantomData<&'a Residue>
+}
+
+impl<'a> Deref for ResidueRef<'a> {
+ type Target = Residue;
+ fn deref(&self) -> &Residue {
+ &self.inner
+ }
+}
+
+impl Clone for Residue {
+ fn clone(&self) -> Residue {
+ unsafe {
+ let new_handle = chfl_residue_copy(self.as_ptr());
+ Residue::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Residue {
+ /// Create a `Residue` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_RESIDUE) -> Residue {
+ check_not_null(ptr);
+ Residue {
+ handle: ptr
+ }
+ }
+
+ /// Create a borrowed `Residue` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, except for it being non-null, and the caller is responsible
+ /// for setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_RESIDUE) -> ResidueRef<'a> {
+ ResidueRef {
+ inner: Residue::from_ptr(ptr as *mut CHFL_RESIDUE),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_RESIDUE {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_RESIDUE {
+ self.handle
+ }
+
+ /// Create a new residue with the given `name`
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::new("ALA");
+ /// assert_eq!(residue.name(), "ALA");
+ /// assert_eq!(residue.id(), None);
+ /// ```
+ pub fn new<'a>(name: impl Into<&'a str>) -> Residue {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ let handle = chfl_residue(buffer.as_ptr());
+ Residue::from_ptr(handle)
+ }
+ }
+
+ /// Create a new residue with the given `name` and `id` as identifier.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::with_id("ALA", 67);
+ /// assert_eq!(residue.name(), "ALA");
+ /// assert_eq!(residue.id(), Some(67));
+ /// ```
+ pub fn with_id<'a>(name: impl Into<&'a str>, id: i64) -> Residue {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ let handle = chfl_residue_with_id(buffer.as_ptr(), id);
+ Residue::from_ptr(handle)
+ }
+ }
+
+ /// Get the number of atoms in this residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.size(), 0);
+ ///
+ /// residue.add_atom(0);
+ /// residue.add_atom(1);
+ /// residue.add_atom(2);
+ /// assert_eq!(residue.size(), 3);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(chfl_residue_atoms_count(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Get the identifier of this residue in the initial topology file.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::with_id("", 42);
+ /// assert_eq!(residue.id(), Some(42));
+ /// ```
+ pub fn id(&self) -> Option<i64> {
+ let mut resid = 0;
+ let status = unsafe {
+ chfl_residue_id(self.as_ptr(), &mut resid)
+ };
+
+ if status == chfl_status::CHFL_SUCCESS {
+ return Some(resid);
+ } else if status == chfl_status::CHFL_GENERIC_ERROR {
+ return None;
+ }
+
+ // call check_success to panic in case of error
+ check_success(status);
+ unreachable!();
+ }
+
+ /// Get the name of this residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::new("water");
+ /// assert_eq!(residue.name(), "water");
+ /// ```
+ pub fn name(&self) -> String {
+ let get_name = |ptr, len| unsafe { chfl_residue_name(self.as_ptr(), ptr, len) };
+ let name = strings::call_autogrow_buffer(64, get_name).expect("getting residue name failed");
+ return strings::from_c(name.as_ptr());
+ }
+
+ /// Add the atom at index `atom` in this residue.
+ ///
+ /// This will fail if the atom is already in the residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.size(), 0);
+ /// assert_eq!(residue.contains(56), false);
+ ///
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.size(), 1);
+ /// assert_eq!(residue.contains(56), true);
+ ///
+ /// // Adding the same atom twice is fine
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.size(), 1);
+ /// ```
+ pub fn add_atom(&mut self, atom: usize) {
+ unsafe {
+ check_success(chfl_residue_add_atom(self.as_mut_ptr(), atom as u64));
+ }
+ }
+
+ /// Check if the atom at index `i` is in this residue
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.contains(56), false);
+ ///
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.contains(56), true);
+ /// ```
+ pub fn contains(&self, atom: usize) -> bool {
+ let mut inside = 0;
+ unsafe {
+ check_success(chfl_residue_contains(self.as_ptr(), atom as u64, &mut inside));
+ }
+ return inside != 0;
+ }
+
+ /// Get the list of atoms of this residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.atoms(), vec![]);
+ ///
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.atoms(), vec![56]);
+ /// ```
+ pub fn atoms(&self) -> Vec<usize> {
+ let size = self.size();
+ let count = size as u64;
+ let mut indices = vec![u64::max_value(); size];
+ unsafe {
+ check_success(chfl_residue_atoms(
+ self.as_ptr(),
+ indices.as_mut_ptr(),
+ count,
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return indices.into_iter().map(|idx| idx as usize).collect();
+ }
+
+ /// Add a new `property` with the given `name` to this residue.
+ ///
+ /// If a property with the same name already exists, this function override
+ /// the existing property with the new one.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Residue, Property};
+ /// let mut residue = Residue::new("ALA");
+ /// residue.set("a string", "hello");
+ /// residue.set("a double", 3.2);
+ ///
+ /// assert_eq!(residue.get("a string"), Some(Property::String("hello".into())));
+ /// assert_eq!(residue.get("a double"), Some(Property::Double(3.2)));
+ /// ```
+ pub fn set(&mut self, name: &str, property: impl Into<Property>) {
+ let buffer = strings::to_c(name);
+ let property = property.into().as_raw();
+ unsafe {
+ check_success(chfl_residue_set_property(
+ self.as_mut_ptr(), buffer.as_ptr(), property.as_ptr()
+ ));
+ }
+ }
+
+ /// Get a property with the given `name` in this frame, if it exist.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Residue, Property};
+ /// let mut residue = Residue::new("ALA");
+ /// residue.set("foo", Property::Double(22.2));
+ ///
+ /// assert_eq!(residue.get("foo"), Some(Property::Double(22.2)));
+ /// assert_eq!(residue.get("Bar"), None);
+ /// ```
+ pub fn get(&self, name: &str) -> Option<Property> {
+ let buffer = strings::to_c(name);
+ unsafe {
+ let handle = chfl_residue_get_property(self.as_ptr(), buffer.as_ptr());
+ if handle.is_null() {
+ None
+ } else {
+ let raw = RawProperty::from_ptr(handle);
+ Some(Property::from_raw(raw))
+ }
+ }
+ }
+
+ /// Get an iterator over all (name, property) pairs for this frame
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Residue, Property};
+ /// let mut residue = Residue::new("ALA");
+ /// residue.set("foo", Property::Double(22.2));
+ /// residue.set("bar", Property::Bool(false));
+ ///
+ /// for (name, property) in residue.properties() {
+ /// if name == "foo" {
+ /// assert_eq!(property, Property::Double(22.2));
+ /// } else if name == "bar" {
+ /// assert_eq!(property, Property::Bool(false));
+ /// }
+ /// }
+ /// ```
+ pub fn properties(&self) -> PropertiesIter {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_residue_properties_count(self.as_ptr(), &mut count));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = count as usize;
+ let mut c_names = vec![ptr::null_mut(); size];
+ unsafe {
+ check_success(chfl_residue_list_properties(self.as_ptr(), c_names.as_mut_ptr(), count));
+ }
+
+ let mut names = Vec::new();
+ for ptr in c_names {
+ names.push(strings::from_c(ptr));
+ }
+
+ PropertiesIter {
+ names: names.into_iter(),
+ getter: Box::new(move |name| self.get(name).expect("failed to get property"))
+ }
+ }
+}
+
+impl Drop for Residue {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut residue = Residue::new("A");
+ assert_eq!(residue.size(), 0);
+
+ let copy = residue.clone();
+ assert_eq!(copy.size(), 0);
+
+ residue.add_atom(3);
+ residue.add_atom(7);
+ assert_eq!(residue.size(), 2);
+ assert_eq!(copy.size(), 0);
+ }
+
+ #[test]
+ fn name() {
+ let residue = Residue::new("A");
+ assert_eq!(residue.name(), "A");
+ }
+
+ #[test]
+ fn id() {
+ let residue = Residue::new("A");
+ assert_eq!(residue.id(), None);
+
+ let residue = Residue::with_id("A", 42);
+ assert_eq!(residue.id(), Some(42));
+
+ let residue = Residue::with_id("A", -3);
+ assert_eq!(residue.id(), Some(-3));
+ }
+
+ #[test]
+ fn atoms() {
+ let mut residue = Residue::new("A");
+ assert_eq!(residue.size(), 0);
+
+ residue.add_atom(0);
+ residue.add_atom(3);
+ residue.add_atom(45);
+ assert_eq!(residue.size(), 3);
+
+ assert!(residue.contains(3));
+ assert!(!residue.contains(5));
+
+ assert_eq!(residue.atoms(), vec![0, 3, 45]);
+ }
+
+ #[test]
+ fn property() {
+ let mut residue = Residue::new("ALA");
+
+ residue.set("foo", -22.0);
+ assert_eq!(residue.get("foo"), Some(Property::Double(-22.0)));
+ assert_eq!(residue.get("bar"), None);
+
+ residue.set("bar", Property::String("here".into()));
+ for (name, property) in residue.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(-22.0));
+ } else if name == "bar" {
+ assert_eq!(property, Property::String("here".into()));
+ }
+ }
+ }
+}
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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::{Drop, Index};
+use std::iter::IntoIterator;
+use std::slice::Iter;
+
+use chemfiles_sys::*;
+use errors::{check, check_not_null, check_success, Error, Status};
+use strings;
+use frame::Frame;
+
+#[derive(Debug, Clone, PartialEq, Eq)]
+/// A `Match` is a set of atomic indexes matching a given selection. It can
+/// mostly be used like a `&[usize]`.
+pub struct Match {
+ size: usize,
+ atoms: [usize; 4],
+}
+
+#[allow(clippy::len_without_is_empty)]
+impl Match {
+ /// Get the length of the Match.
+ ///
+ /// # Example
+ ///
+ /// ```
+ /// # use chemfiles::Match;
+ /// let atomic_match = Match::new(&[3, 4, 5]);
+ /// assert_eq!(atomic_match.len(), 3);
+ /// ```
+ pub fn len(&self) -> usize {
+ self.size
+ }
+
+ /// Create a new match containing the atoms in the `atoms` slice.
+ ///
+ /// # Panics
+ ///
+ /// If the slice contains more than 4 elements, which is the maximal size
+ /// of a match.
+ ///
+ /// # Example
+ ///
+ /// ```
+ /// # use chemfiles::Match;
+ /// let atomic_match = Match::new(&[3, 4, 5]);
+ /// assert_eq!(atomic_match.len(), 3);
+ /// assert_eq!(atomic_match[0], 3);
+ /// assert_eq!(atomic_match[1], 4);
+ /// assert_eq!(atomic_match[2], 5);
+ /// ```
+ pub fn new(atoms: &[usize]) -> Match {
+ assert!(atoms.len() <= 4);
+ let size = atoms.len();
+ let mut matches = [usize::max_value(); 4];
+ for (i, atom) in atoms.iter().enumerate() {
+ matches[i] = *atom;
+ }
+ Match {
+ size,
+ atoms: matches,
+ }
+ }
+
+ /// Iterate over the atomic indexes in the match.
+ ///
+ /// # Example
+ ///
+ /// ```
+ /// # use chemfiles::Match;
+ /// let atomic_match = Match::new(&[3, 4, 5]);
+ /// let mut iter = atomic_match.iter();
+ ///
+ /// assert_eq!(iter.next(), Some(&3));
+ /// assert_eq!(iter.next(), Some(&4));
+ /// assert_eq!(iter.next(), Some(&5));
+ /// assert_eq!(iter.next(), None);
+ /// ```
+ pub fn iter(&self) -> Iter<usize> {
+ self.atoms[..self.len()].iter()
+ }
+}
+
+impl Index<usize> for Match {
+ type Output = usize;
+ fn index(&self, i: usize) -> &Self::Output {
+ assert!(i < self.len());
+ &self.atoms[i]
+ }
+}
+
+impl<'a> IntoIterator for &'a Match {
+ type Item = &'a usize;
+ type IntoIter = Iter<'a, usize>;
+ fn into_iter(self) -> Iter<'a, usize> {
+ self.atoms[..self.len()].iter()
+ }
+}
+
+/// A `Selection` allow to select atoms in a `Frame`, from a selection
+/// language. The selection language is built by combining basic operations.
+/// Each basic operation follows the `<selector>[(<variable>)] <operator>
+/// <value>` structure, where `<operator>` is a comparison operator in
+/// `== != < <= > >=`.
+pub struct Selection {
+ handle: *mut CHFL_SELECTION,
+}
+
+impl Clone for Selection {
+ fn clone(&self) -> Selection {
+ unsafe {
+ let new_handle = chfl_selection_copy(self.as_ptr());
+ Selection::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Drop for Selection {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+impl Selection {
+ /// Create a `Selection` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_SELECTION) -> Selection {
+ check_not_null(ptr);
+ Selection {
+ handle: ptr
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_SELECTION {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_SELECTION {
+ self.handle
+ }
+
+ /// Create a new selection from the given selection string.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the selection string is invalid.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Selection;
+ /// let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+ /// ```
+ pub fn new<'a, S: Into<&'a str>>(selection: S) -> Result<Selection, Error> {
+ let buffer = strings::to_c(selection.into());
+ unsafe {
+ let handle = chfl_selection(buffer.as_ptr());
+ if handle.is_null() {
+ Err(Error {
+ status: Status::SelectionError,
+ message: Error::last_error()
+ })
+ } else {
+ Ok(Selection::from_ptr(handle))
+ }
+ }
+ }
+
+ /// Get the size of the selection, i.e. the number of atoms we are selecting
+ /// together.
+ ///
+ /// This value is 1 for the 'atom' context, 2 for the 'pair' and 'bond'
+ /// context, 3 for the 'three' and 'angles' context and 4 for the 'four'
+ /// and 'dihedral' context.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Selection;
+ /// let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+ /// assert_eq!(selection.size(), 2);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(chfl_selection_size(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Get the selection string used to create this selection.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Selection;
+ /// let selection = Selection::new("name H").unwrap();
+ /// assert_eq!(selection.string(), "name H");
+ /// ```
+ pub fn string(&self) -> String {
+ let get_string = |ptr, len| unsafe { chfl_selection_string(self.as_ptr(), ptr, len) };
+ let selection = strings::call_autogrow_buffer(1024, get_string).expect("failed to get selection string");
+ return strings::from_c(selection.as_ptr());
+ }
+
+ /// Evaluate a selection for a given frame, and return the corresponding
+ /// matches.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Selection, Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+ ///
+ /// let mut selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+ /// let matches = selection.evaluate(&frame);
+ ///
+ /// assert_eq!(matches.len(), 2);
+ ///
+ /// assert_eq!(matches[0].len(), 2);
+ /// assert_eq!(matches[0][0], 0);
+ /// assert_eq!(matches[0][1], 1);
+ ///
+ /// assert_eq!(matches[1].len(), 2);
+ /// assert_eq!(matches[1][0], 2);
+ /// assert_eq!(matches[1][1], 1);
+ /// ```
+ pub fn evaluate(&mut self, frame: &Frame) -> Vec<Match> {
+ #![allow(clippy::cast_possible_truncation)]
+ let mut count = 0;
+ unsafe {
+ check(chfl_selection_evaluate(
+ self.as_mut_ptr(), frame.as_ptr(), &mut count
+ )).expect("failed to evaluate selection");
+ }
+
+ let size = count as usize;
+ let mut chfl_matches = vec![chfl_match { size: 0, atoms: [0; 4] }; size];
+ unsafe {
+ check(chfl_selection_matches(
+ self.handle,
+ chfl_matches.as_mut_ptr(),
+ count
+ )).expect("failed to extract matches");
+ }
+
+ return chfl_matches.into_iter()
+ .map(|chfl_match| Match {
+ size: chfl_match.size as usize,
+ atoms: [
+ chfl_match.atoms[0] as usize,
+ chfl_match.atoms[1] as usize,
+ chfl_match.atoms[2] as usize,
+ chfl_match.atoms[3] as usize,
+ ],
+ })
+ .collect();
+ }
+
+ /// Evaluates a selection of size 1 on a given `frame`. This function
+ /// returns the list of atomic indexes in the frame matching this selection.
+ ///
+ /// # Panics
+ ///
+ /// If the selection size is not 1
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Selection, Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+ ///
+ /// let mut selection = Selection::new("name H").unwrap();
+ /// let matches = selection.list(&frame);
+ ///
+ /// assert_eq!(matches.len(), 2);
+ /// assert_eq!(matches[0], 0);
+ /// assert_eq!(matches[1], 2);
+ /// ```
+ pub fn list(&mut self, frame: &Frame) -> Vec<usize> {
+ if self.size() != 1 {
+ panic!("can not call `Selection::list` on a multiple selection");
+ }
+ return self.evaluate(frame)
+ .into_iter()
+ .map(|m| m[0] as usize)
+ .collect();
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ use super::*;
+ use Frame;
+ use Topology;
+ use Atom;
+
+ #[test]
+ fn clone() {
+ let selection = Selection::new("name H").unwrap();
+
+ let copy = selection.clone();
+ assert_eq!(selection.size(), 1);
+ assert_eq!(copy.size(), 1);
+ }
+
+ fn testing_frame() -> Frame {
+ let mut topology = Topology::new();
+
+ topology.add_atom(&Atom::new("H"));
+ topology.add_atom(&Atom::new("O"));
+ topology.add_atom(&Atom::new("O"));
+ topology.add_atom(&Atom::new("H"));
+
+ topology.add_bond(0, 1);
+ topology.add_bond(1, 2);
+ topology.add_bond(2, 3);
+
+ let mut frame = Frame::new();
+ frame.resize(4);
+ frame.set_topology(&topology).unwrap();
+ return frame;
+ }
+
+ mod matches {
+ use super::*;
+
+ #[test]
+ fn index() {
+ let m = Match::new(&[1, 2, 3, 4]);
+ assert_eq!(m[0], 1);
+ assert_eq!(m[1], 2);
+ assert_eq!(m[2], 3);
+ assert_eq!(m[3], 4);
+
+ let m = Match::new(&[1, 2]);
+ assert_eq!(m[0], 1);
+ assert_eq!(m[1], 2);
+ }
+
+ #[test]
+ fn iter() {
+ let match_ = Match::new(&[1, 2, 3, 4]);
+ assert_eq!(match_.iter().copied().collect::<Vec<usize>>(), vec![1, 2, 3, 4]);
+
+ let v = vec![1, 2, 3, 4];
+ for (i, &m) in match_.iter().enumerate() {
+ assert_eq!(v[i], m);
+ }
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bound() {
+ let m = Match::new(&[1, 2]);
+ let _ = m[2];
+ }
+
+ #[test]
+ #[should_panic]
+ fn too_big() {
+ let _ = Match::new(&[1, 2, 3, 5, 4]);
+ }
+ }
+
+ #[test]
+ fn size() {
+ let selection = Selection::new("name H").unwrap();
+ assert_eq!(selection.size(), 1);
+
+ let selection = Selection::new("angles: name(#1) H").unwrap();
+ assert_eq!(selection.size(), 3);
+
+ let selection = Selection::new("four: name(#1) H").unwrap();
+ assert_eq!(selection.size(), 4);
+ }
+
+ #[test]
+ fn string() {
+ let selection = Selection::new("name H").unwrap();
+ assert_eq!(selection.string(), "name H");
+
+ let selection = Selection::new("angles: name(#1) H").unwrap();
+ assert_eq!(selection.string(), "angles: name(#1) H");
+ }
+
+ #[test]
+ fn evaluate() {
+ let frame = testing_frame();
+
+ let mut selection = Selection::new("name H").unwrap();
+ let res = selection.evaluate(&frame);
+ assert_eq!(res, &[Match::new(&[0]), Match::new(&[3])]);
+
+ let mut selection = Selection::new("angles: all").unwrap();
+ let res = selection.evaluate(&frame);
+ for m in &[Match::new(&[0, 1, 2]), Match::new(&[1, 2, 3])] {
+ assert!(res.iter().any(|r| r == m));
+ }
+ }
+
+ #[test]
+ fn list() {
+ let frame = testing_frame();
+
+ let mut selection = Selection::new("name H").unwrap();
+ let res = selection.list(&frame);
+ assert_eq!(res, vec![0, 3]);
+ }
+
+ #[test]
+ #[should_panic = "can not call `Selection::list` on a multiple selection"]
+ fn list_on_size_1_selection() {
+ let frame = testing_frame();
+ let mut selection = Selection::new("pairs: name(#1) H").unwrap();
+ let _list = selection.list(&frame);
+ }
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+
+//! String conversions between C and Rust
+use std::ffi::{CStr, CString};
+use std::os::raw::c_char;
+
+use chemfiles_sys::chfl_status;
+use errors::{check, Error};
+
+/// Create a Rust string from a C string. Clones all characters in `buffer`.
+pub fn from_c(buffer: *const c_char) -> String {
+ unsafe {
+ let rust_str = CStr::from_ptr(buffer)
+ .to_str()
+ .expect("Invalid Rust string from C");
+ return String::from(rust_str);
+ }
+}
+
+/// Create a C string from a Rust string.
+pub fn to_c(string: &str) -> CString {
+ CString::new(string).expect("Invalid C string from Rust")
+}
+
+/// Check if a string buffer was big enough when passed to a C function
+fn buffer_was_big_enough(buffer: &[c_char]) -> bool {
+ let len = buffer.len();
+ if len < 2 {
+ false
+ } else {
+ // The C code should always set the last element to 0
+ debug_assert_eq!(buffer[len - 1], 0);
+ buffer[len - 2] == 0
+ }
+}
+
+/// Call `callback` C function with a string buffer and it length, using
+/// `initial` as the buffer initial size. If the buffer was filled and the
+/// result truncated by the C library, grow the buffer and try again until we
+/// get all the data. Then return the filled buffer to the caller.
+pub fn call_autogrow_buffer<F>(initial: usize, callback: F) -> Result<Vec<c_char>, Error>
+where
+ F: Fn(*mut c_char, u64) -> chfl_status,
+{
+ let mut size = initial;
+ let mut buffer = vec![0; size];
+ check(callback(buffer.as_mut_ptr(), buffer.len() as u64))?;
+
+ while !buffer_was_big_enough(&buffer) {
+ // Grow the buffer and retry
+ size *= 2;
+ buffer.resize(size, 0);
+ check(callback(buffer.as_mut_ptr(), buffer.len() as u64))?;
+ }
+
+ Ok(buffer)
+}
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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::ops::{Drop, Deref};
+use std::marker::PhantomData;
+
+use chemfiles_sys::*;
+use errors::{check, check_not_null, check_success, Error};
+use super::{Atom, AtomRef, AtomMut};
+use super::{Residue, ResidueRef};
+
+/// Possible bond order associated with bonds
+#[repr(C)]
+#[non_exhaustive]
+#[derive(Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord)]
+pub enum BondOrder {
+ /// Unknown or unspecified bond order
+ Unknown = chfl_bond_order::CHFL_BOND_UNKNOWN as isize,
+ /// Single bond
+ Single = chfl_bond_order::CHFL_BOND_SINGLE as isize,
+ /// Double bond
+ Double = chfl_bond_order::CHFL_BOND_DOUBLE as isize,
+ /// Triple bond
+ Triple = chfl_bond_order::CHFL_BOND_TRIPLE as isize,
+ /// Quadruple bond (present in some metals)
+ Quadruple = chfl_bond_order::CHFL_BOND_QUADRUPLE as isize,
+ /// Quintuplet bond (present in some metals)
+ Quintuplet = chfl_bond_order::CHFL_BOND_QUINTUPLET as isize,
+ /// Amide bond (required by some file formats)
+ Amide = chfl_bond_order::CHFL_BOND_AMIDE as isize,
+ /// Aromatic bond (required by some file formats)
+ Aromatic = chfl_bond_order::CHFL_BOND_AROMATIC as isize,
+}
+
+impl BondOrder {
+ pub(crate) fn as_raw(self) -> chfl_bond_order {
+ match self {
+ BondOrder::Unknown => chfl_bond_order::CHFL_BOND_UNKNOWN,
+ BondOrder::Single => chfl_bond_order::CHFL_BOND_SINGLE,
+ BondOrder::Double => chfl_bond_order::CHFL_BOND_DOUBLE,
+ BondOrder::Triple => chfl_bond_order::CHFL_BOND_TRIPLE,
+ BondOrder::Quadruple => chfl_bond_order::CHFL_BOND_QUADRUPLE,
+ BondOrder::Quintuplet => chfl_bond_order::CHFL_BOND_QUINTUPLET,
+ BondOrder::Amide => chfl_bond_order::CHFL_BOND_AMIDE,
+ BondOrder::Aromatic => chfl_bond_order::CHFL_BOND_AROMATIC,
+ }
+ }
+}
+
+impl From<chfl_bond_order> for BondOrder {
+ fn from(order: chfl_bond_order) -> BondOrder {
+ match order {
+ chfl_bond_order::CHFL_BOND_UNKNOWN => BondOrder::Unknown,
+ chfl_bond_order::CHFL_BOND_SINGLE => BondOrder::Single,
+ chfl_bond_order::CHFL_BOND_DOUBLE => BondOrder::Double,
+ chfl_bond_order::CHFL_BOND_TRIPLE => BondOrder::Triple,
+ chfl_bond_order::CHFL_BOND_QUADRUPLE => BondOrder::Quadruple,
+ chfl_bond_order::CHFL_BOND_QUINTUPLET => BondOrder::Quintuplet,
+ chfl_bond_order::CHFL_BOND_AMIDE => BondOrder::Amide,
+ chfl_bond_order::CHFL_BOND_AROMATIC => BondOrder::Aromatic,
+ }
+ }
+}
+
+/// A `Topology` contains the definition of all the atoms in the system, and
+/// the liaisons between the atoms (bonds, angles, dihedrals, ...). It will
+/// also contain all the residues information if it is available.
+pub struct Topology {
+ handle: *mut CHFL_TOPOLOGY,
+}
+
+/// An analog to a reference to a topology (`&Topology`)
+pub struct TopologyRef<'a> {
+ inner: Topology,
+ marker: PhantomData<&'a Topology>
+}
+
+impl<'a> Deref for TopologyRef<'a> {
+ type Target = Topology;
+ fn deref(&self) -> &Topology {
+ &self.inner
+ }
+}
+
+impl Clone for Topology {
+ fn clone(&self) -> Topology {
+ unsafe {
+ let new_handle = chfl_topology_copy(self.as_ptr());
+ Topology::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Topology {
+ /// Create a `Topology` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer,
+ /// except for it being non-null.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_TOPOLOGY) -> Topology {
+ check_not_null(ptr);
+ Topology {
+ handle: ptr
+ }
+ }
+
+ /// Create a borrowed `Topology` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, except for it being non-null, and the caller is responsible
+ /// for setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_TOPOLOGY) -> TopologyRef<'a> {
+ TopologyRef {
+ inner: Topology::from_ptr(ptr as *mut CHFL_TOPOLOGY),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_TOPOLOGY {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_TOPOLOGY {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer FROM A SHARED REFERENCE.
+ ///
+ /// For uses with functions of the C API using mut pointers for both read
+ /// and write access. Users should check that this does not lead to multiple
+ /// mutable borrows
+ #[inline]
+ #[allow(non_snake_case)]
+ pub(crate) fn as_mut_ptr_MANUALLY_CHECKING_BORROW(&self) -> *mut CHFL_TOPOLOGY {
+ self.handle
+ }
+
+ /// Create a new empty topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let topology = Topology::new();
+ /// assert_eq!(topology.size(), 0);
+ /// ```
+ pub fn new() -> Topology {
+ unsafe {
+ Topology::from_ptr(chfl_topology())
+ }
+ }
+
+ /// Get a reference of the atom at the given `index` in this topology.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(6);
+ ///
+ /// let atom = topology.atom(4);
+ /// assert_eq!(atom.name(), "");
+ /// ```
+ pub fn atom(&self, index: usize) -> AtomRef {
+ unsafe {
+ let handle = chfl_atom_from_topology(
+ self.as_mut_ptr_MANUALLY_CHECKING_BORROW(), index as u64
+ );
+ Atom::ref_from_ptr(handle)
+ }
+ }
+
+ /// Get a mutable reference to the atom at the given `index` in this topology.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(6);
+ ///
+ /// assert_eq!(topology.atom(4).name(), "");
+ ///
+ /// topology.atom_mut(4).set_name("Fe");
+ /// assert_eq!(topology.atom(4).name(), "Fe");
+ /// ```
+ pub fn atom_mut(&mut self, index: usize) -> AtomMut {
+ unsafe {
+ let handle = chfl_atom_from_topology(
+ self.as_mut_ptr(), index as u64
+ );
+ Atom::ref_mut_from_ptr(handle)
+ }
+ }
+
+ /// Get the current number of atoms in this topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.size(), 0);
+ ///
+ /// topology.resize(6);
+ /// assert_eq!(topology.size(), 6);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(chfl_topology_atoms_count(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Resize this topology to hold `natoms` atoms, inserting dummy atoms if
+ /// the new size if bigger than the old one.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.size(), 0);
+ ///
+ /// topology.resize(6);
+ /// assert_eq!(topology.size(), 6);
+ /// ```
+ pub fn resize(&mut self, natoms: usize) {
+ unsafe {
+ check_success(chfl_topology_resize(self.as_mut_ptr(), natoms as u64));
+ }
+ }
+
+ /// Add an `Atom` at the end of this topology
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Atom};
+ /// let mut topology = Topology::new();
+ /// topology.add_atom(&Atom::new("Mg"));
+ ///
+ /// let atom = topology.atom(0);
+ /// assert_eq!(atom.name(), "Mg");
+ /// ```
+ pub fn add_atom(&mut self, atom: &Atom) {
+ unsafe {
+ check_success(chfl_topology_add_atom(self.as_mut_ptr(), atom.as_ptr()));
+ }
+ }
+
+ /// Remove an `Atom` from this topology by `index`. This modify all the
+ /// other atoms indexes.
+ ///
+ /// # Panics
+ ///
+ /// If the `index` is out of bounds
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(9);
+ /// assert_eq!(topology.size(), 9);
+ ///
+ /// topology.remove(7);
+ /// assert_eq!(topology.size(), 8);
+ /// ```
+ pub fn remove(&mut self, index: usize) {
+ unsafe {
+ check_success(chfl_topology_remove(self.as_mut_ptr(), index as u64));
+ }
+ }
+
+ /// Get the number of bonds in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.bonds_count(), 3);
+ /// ```
+ pub fn bonds_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_bonds_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the number of angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.angles_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.angles_count(), 2);
+ /// ```
+ pub fn angles_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_angles_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the number of dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.dihedrals_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.dihedrals_count(), 1);
+ /// ```
+ pub fn dihedrals_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_dihedrals_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the number of improper dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.dihedrals_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// topology.add_bond(0, 3);
+ /// assert_eq!(topology.impropers_count(), 1);
+ /// ```
+ pub fn impropers_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_impropers_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the list of bonds in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);
+ /// ```
+ pub fn bonds(&self) -> Vec<[usize; 2]> {
+ let size = self.bonds_count();
+ let count = size as u64;
+ let mut bonds = vec![[u64::max_value(); 2]; size];
+ unsafe {
+ check_success(chfl_topology_bonds(self.as_ptr(), bonds.as_mut_ptr(), count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return bonds
+ .into_iter()
+ .map(|bond| [bond[0] as usize, bond[1] as usize])
+ .collect();
+ }
+
+ /// Get the list of angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);
+ /// ```
+ pub fn angles(&self) -> Vec<[usize; 3]> {
+ let size = self.angles_count();
+ let count = size as u64;
+ let mut angles = vec![[u64::max_value(); 3]; size];
+ unsafe {
+ check_success(chfl_topology_angles(self.as_ptr(), angles.as_mut_ptr(), count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return angles
+ .into_iter()
+ .map(|angle| [angle[0] as usize, angle[1] as usize, angle[2] as usize])
+ .collect();
+ }
+
+ /// Get the list of dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ ///
+ /// assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);
+ /// ```
+ pub fn dihedrals(&self) -> Vec<[usize; 4]> {
+ let size = self.dihedrals_count();
+ let count = size as u64;
+ let mut dihedrals = vec![[u64::max_value(); 4]; size];
+ unsafe {
+ check_success(chfl_topology_dihedrals(
+ self.as_ptr(), dihedrals.as_mut_ptr(), count
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return dihedrals
+ .into_iter()
+ .map(|dihedral| {
+ [
+ dihedral[0] as usize,
+ dihedral[1] as usize,
+ dihedral[2] as usize,
+ dihedral[3] as usize,
+ ]
+ })
+ .collect();
+ }
+
+ /// Get the list of improper dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// topology.add_bond(0, 3);
+ ///
+ /// assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);
+ /// ```
+ pub fn impropers(&self) -> Vec<[usize; 4]> {
+ let size = self.impropers_count();
+ let count = size as u64;
+ let mut impropers = vec![[u64::max_value(); 4]; size];
+ unsafe {
+ check_success(chfl_topology_impropers(
+ self.as_ptr(), impropers.as_mut_ptr(), count
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return impropers
+ .into_iter()
+ .map(|improper| {
+ [
+ improper[0] as usize,
+ improper[1] as usize,
+ improper[2] as usize,
+ improper[3] as usize,
+ ]
+ })
+ .collect();
+ }
+
+ /// Remove all existing bonds, angles, dihedral angles and improper
+ /// dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// assert_eq!(topology.bonds_count(), 2);
+ /// assert_eq!(topology.angles().len(), 1);
+ ///
+ /// topology.clear_bonds();
+ /// assert!(topology.bonds().is_empty());
+ /// assert!(topology.angles().is_empty());
+ /// ```
+ pub fn clear_bonds(&mut self) {
+ unsafe {
+ check_success(chfl_topology_clear_bonds(self.as_mut_ptr()));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the topology.
+ ///
+ /// The bond order is set to `BondOrder::Unknown`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// assert_eq!(topology.bonds_count(), 2);
+ ///
+ /// assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);
+ /// ```
+ pub fn add_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(chfl_topology_add_bond(self.as_mut_ptr(), i as u64, j as u64));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the topology
+ /// with the given bond `order`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(2);
+ ///
+ /// topology.add_bond_with_order(0, 1, BondOrder::Double);
+ /// assert_eq!(topology.bond_order(0, 1), BondOrder::Double);
+ /// ```
+ pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder) {
+ unsafe {
+ check_success(chfl_topology_bond_with_order(
+ self.as_mut_ptr(), i as u64, j as u64, order.as_raw()
+ ));
+ }
+ }
+
+ /// Get the bond order for the bond between the atoms at indexes `i` and
+ /// `j`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(2);
+ ///
+ /// topology.add_bond_with_order(0, 1, BondOrder::Double);
+ /// assert_eq!(topology.bond_order(0, 1), BondOrder::Double);
+ /// ```
+ pub fn bond_order(&self, i: usize, j: usize) -> BondOrder {
+ let mut order = chfl_bond_order::CHFL_BOND_UNKNOWN;
+ unsafe {
+ check_success(chfl_topology_bond_order(
+ self.as_ptr(), i as u64, j as u64, &mut order
+ ));
+ }
+ return order.into()
+ }
+
+ /// Get the bond order for all the bonds in the topology
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(3);
+ ///
+ /// topology.add_bond_with_order(0, 1, BondOrder::Double);
+ /// topology.add_bond_with_order(0, 2, BondOrder::Single);
+ ///
+ /// assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);
+ /// ```
+ pub fn bond_orders(&self) -> Vec<BondOrder> {
+ let size = self.bonds_count();
+ let count = size as u64;
+ let mut bonds = vec![BondOrder::Unknown; size];
+ unsafe {
+ check_success(chfl_topology_bond_orders(
+ self.as_ptr(),
+ // Casting BondOrder to chfl_bond_order is safe, as they are
+ // both `repr(C)` enums with the same values.
+ bonds.as_mut_ptr().cast(),
+ count
+ ));
+ }
+ return bonds;
+ }
+
+ /// Remove any existing bond between the atoms at indexes `i` and `j` in
+ /// this topology.
+ ///
+ /// This function does nothing if there is no bond between `i` and `j`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(1, 2);
+ /// assert_eq!(topology.bonds_count(), 2);
+ ///
+ /// topology.remove_bond(0, 1);
+ /// assert_eq!(topology.bonds_count(), 1);
+ ///
+ /// // Removing a bond that does not exists is fine
+ /// topology.remove_bond(0, 2);
+ /// assert_eq!(topology.bonds_count(), 1);
+ /// ```
+ pub fn remove_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(chfl_topology_remove_bond(self.as_mut_ptr(), i as u64, j as u64));
+ }
+ }
+
+ /// Get a reference to the residue at index `index` from this topology.
+ ///
+ /// The residue index in the topology is not always the same as the residue
+ /// `id`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// topology.add_residue(&Residue::new("water")).unwrap();
+ ///
+ /// let residue = topology.residue(0).unwrap();
+ /// assert_eq!(residue.name(), "water");
+ /// ```
+ pub fn residue(&self, index: u64) -> Option<ResidueRef> {
+ unsafe {
+ let handle = chfl_residue_from_topology(self.as_ptr(), index as u64);
+ if handle.is_null() {
+ None
+ } else {
+ Some(Residue::ref_from_ptr(handle))
+ }
+ }
+ }
+
+ /// Get a copy of the residue containing the atom at index `index` in this
+ /// topology, if any.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// topology.resize(8);
+ ///
+ /// let mut residue = Residue::new("water");
+ /// residue.add_atom(0);
+ /// residue.add_atom(1);
+ /// residue.add_atom(2);
+ /// topology.add_residue(&residue).unwrap();
+ ///
+ /// let residue = topology.residue_for_atom(0).unwrap();
+ /// assert_eq!(residue.name(), "water");
+ ///
+ /// assert!(topology.residue_for_atom(6).is_none());
+ /// ```
+ pub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef> {
+ let handle = unsafe {
+ chfl_residue_for_atom(self.as_ptr(), index as u64)
+ };
+ if handle.is_null() {
+ None
+ } else {
+ unsafe {
+ Some(Residue::ref_from_ptr(handle))
+ }
+ }
+ }
+
+ /// Get the number of residues in this topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.residues_count(), 0);
+ ///
+ /// topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+ /// topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+ /// assert_eq!(topology.residues_count(), 2);
+ /// ```
+ pub fn residues_count(&self) -> u64 {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_residues_count(self.as_ptr(), &mut count));
+ }
+ return count;
+ }
+
+ /// Add a residue to this topology.
+ ///
+ /// # Errors
+ ///
+ /// This function fails is the residue `id` is not already in the topology,
+ /// or if the residue contains atoms that are already in another residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// topology.add_residue(&Residue::new("water")).unwrap();
+ ///
+ /// let residue = topology.residue(0).unwrap();
+ /// assert_eq!(residue.name(), "water");
+ /// ```
+ pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error> {
+ unsafe {
+ check(chfl_topology_add_residue(self.as_mut_ptr(), residue.as_ptr()))
+ }
+ }
+
+ /// Check if the two residues `first` and `second` from the `topology` are
+ /// linked together, *i.e.* if there is a bond between one atom in the
+ /// first residue and one atom in the second one.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ ///
+ /// topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+ /// topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+ ///
+ /// let first = topology.residue(0).unwrap();
+ /// let second = topology.residue(1).unwrap();
+ /// assert_eq!(topology.are_linked(&first, &second), false);
+ /// ```
+ pub fn are_linked(&self, first: &Residue, second: &Residue) -> bool {
+ let mut linked = 0;
+ unsafe {
+ check_success(chfl_topology_residues_linked(
+ self.as_ptr(),
+ first.as_ptr(),
+ second.as_ptr(),
+ &mut linked
+ ));
+ }
+ return linked != 0;
+ }
+}
+
+impl Drop for Topology {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+ use {Atom, Residue};
+
+ #[test]
+ fn clone() {
+ let mut topology = Topology::new();
+ assert_eq!(topology.size(), 0);
+
+ let copy = topology.clone();
+ assert_eq!(copy.size(), 0);
+
+ topology.resize(10);
+ assert_eq!(topology.size(), 10);
+ assert_eq!(copy.size(), 0);
+ }
+
+ #[test]
+ fn size() {
+ let mut topology = Topology::new();
+ assert_eq!(topology.size(), 0);
+
+ topology.resize(10);
+ assert_eq!(topology.size(), 10);
+
+ topology.remove(7);
+ assert_eq!(topology.size(), 9);
+
+ topology.add_atom(&Atom::new("Hg"));
+ assert_eq!(topology.size(), 10);
+ }
+
+ #[test]
+ fn atoms() {
+ let mut topology = Topology::new();
+
+ topology.add_atom(&Atom::new("Hg"));
+ topology.add_atom(&Atom::new("Mn"));
+ topology.add_atom(&Atom::new("W"));
+ topology.add_atom(&Atom::new("Fe"));
+
+ assert_eq!(topology.atom(0).name(), "Hg");
+ assert_eq!(topology.atom(3).name(), "Fe");
+ }
+
+ #[test]
+ fn remove() {
+ let mut topology = Topology::new();
+ topology.add_atom(&Atom::new("Hg"));
+ topology.add_atom(&Atom::new("Mn"));
+ topology.add_atom(&Atom::new("W"));
+ topology.add_atom(&Atom::new("Fe"));
+
+ assert_eq!(topology.atom(0).name(), "Hg");
+ assert_eq!(topology.atom(2).name(), "W");
+
+ topology.remove(1);
+ assert_eq!(topology.atom(0).name(), "Hg");
+ assert_eq!(topology.atom(2).name(), "Fe");
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_remove() {
+ let mut topology = Topology::new();
+ topology.resize(18);
+ topology.remove(33);
+ }
+
+
+ #[test]
+ fn bonds() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.bonds_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(9, 2);
+ topology.add_bond_with_order(3, 7, BondOrder::Aromatic);
+ assert_eq!(topology.bonds_count(), 3);
+
+ assert_eq!(topology.bonds(), vec![[0, 1], [2, 9], [3, 7]]);
+ let expected = vec![BondOrder::Unknown, BondOrder::Unknown, BondOrder::Aromatic];
+ assert_eq!(topology.bond_orders(), expected);
+
+ assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);
+ assert_eq!(topology.bond_order(3, 7), BondOrder::Aromatic);
+
+ topology.remove_bond(3, 7);
+ // Removing unexisting bond is OK if both indexes are in bounds
+ topology.remove_bond(8, 7);
+ assert_eq!(topology.bonds_count(), 2);
+
+ topology.clear_bonds();
+ assert_eq!(topology.bonds_count(), 0);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ topology.add_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_remove_bond() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ topology.remove_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds_with_order() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ topology.add_bond_with_order(300, 7, BondOrder::Unknown);
+ }
+
+ #[test]
+ fn angles() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.angles_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(1, 2);
+ topology.add_bond(3, 7);
+ topology.add_bond(3, 5);
+ assert_eq!(topology.angles_count(), 2);
+
+ assert_eq!(topology.angles(), vec![[0, 1, 2], [5, 3, 7]]);
+
+ topology.clear_bonds();
+ assert_eq!(topology.angles_count(), 0);
+ }
+
+ #[test]
+ fn dihedrals() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.dihedrals_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(1, 2);
+ topology.add_bond(3, 2);
+ topology.add_bond(4, 7);
+ topology.add_bond(4, 5);
+ topology.add_bond(7, 10);
+ assert_eq!(topology.dihedrals_count(), 2);
+
+ assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3], [5, 4, 7, 10]]);
+
+ topology.clear_bonds();
+ assert_eq!(topology.dihedrals_count(), 0);
+ }
+
+ #[test]
+ fn impropers() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.impropers_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(0, 2);
+ topology.add_bond(0, 3);
+ topology.add_bond(4, 7);
+ topology.add_bond(4, 5);
+ topology.add_bond(4, 8);
+ assert_eq!(topology.impropers_count(), 2);
+
+ assert_eq!(topology.impropers(), vec![[1, 0, 2, 3], [5, 4, 7, 8]]);
+
+ topology.clear_bonds();
+ assert_eq!(topology.impropers_count(), 0);
+ }
+
+ #[test]
+ fn residues() {
+ let mut topology = Topology::new();
+ topology.resize(4);
+ assert_eq!(topology.residues_count(), 0);
+
+ let mut residue = Residue::new("Foo");
+ residue.add_atom(0);
+ residue.add_atom(2);
+
+ topology.add_residue(&residue).unwrap();
+ assert_eq!(topology.residues_count(), 1);
+
+ assert_eq!(topology.residue(0).unwrap().name(), "Foo");
+ {
+ let residue = topology.residue_for_atom(2).unwrap();
+ assert_eq!(residue.name(), "Foo");
+ }
+
+ let mut residue = Residue::new("Bar");
+ residue.add_atom(3);
+ topology.add_residue(&residue).unwrap();
+ assert_eq!(topology.residues_count(), 2);
+
+ let first = topology.residue(0).unwrap();
+ let second = topology.residue(0).unwrap();
+ assert!(topology.are_linked(&first, &second));
+
+ // missing residue
+ assert!(topology.residue_for_atom(1).is_none());
+ // out of bounds
+ assert!(topology.residue_for_atom(67).is_none());
+ }
+}
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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::convert::TryInto;
+use std::path::Path;
+use std::ptr;
+use std::os::raw::c_char;
+
+use chemfiles_sys::*;
+use errors::{check, check_success, Error, Status};
+use strings;
+
+use {Frame, Topology, UnitCell};
+
+/// The `Trajectory` type is the main entry point when using chemfiles. A
+/// `Trajectory` behave a bit like a file, allowing to read and/or write
+/// `Frame`.
+pub struct Trajectory {
+ handle: *mut CHFL_TRAJECTORY,
+}
+
+impl Trajectory {
+ /// Create a `Trajectory` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_TRAJECTORY) -> Result<Trajectory, Error> {
+ if ptr.is_null() {
+ Err(Error {
+ status: Status::FileError,
+ message: Error::last_error()
+ })
+ } else {
+ Ok(Trajectory {
+ handle: ptr
+ })
+ }
+ }
+
+ /// Get the underlying C pointer as a pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_TRAJECTORY {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_TRAJECTORY {
+ self.handle
+ }
+
+ /// Open the file at the given `path` in the given `mode`.
+ ///
+ /// Valid modes are `'r'` for read, `'w'` for write and `'a'` for append.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the file is not accessible for the given mode, if
+ /// it is incorrectly formatted for the corresponding format, or in case of
+ /// I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// ```
+ pub fn open<P>(path: P, mode: char) -> Result<Trajectory, Error>
+ where
+ P: AsRef<Path>,
+ {
+ let path = path.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(path.as_ref()))?;
+
+ let path = strings::to_c(path);
+ unsafe {
+ #[allow(clippy::cast_possible_wrap)]
+ let handle = chfl_trajectory_open(path.as_ptr(), mode as c_char);
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Open the file at the given `path` using a specific file `format` and the
+ /// given `mode`.
+ ///
+ /// Valid modes are `'r'` for read, `'w'` for write and `'a'` for append.
+ ///
+ /// Specifying a format is needed when the file format does not match the
+ /// extension, or when there is not standard extension for this format. If
+ /// `format` is an empty string, the format will be guessed from the
+ /// extension.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the file is not accessible for the given mode, if
+ /// it is incorrectly formatted for the corresponding format, or in case of
+ /// I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let trajectory = Trajectory::open_with_format("water.zeo", 'r', "XYZ").unwrap();
+ /// ```
+ pub fn open_with_format<'a, P, S>(filename: P, mode: char, format: S) -> Result<Trajectory, Error>
+ where
+ P: AsRef<Path>,
+ S: Into<&'a str>,
+ {
+ let filename =
+ filename.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(filename.as_ref()))?;
+
+ let filename = strings::to_c(filename);
+ let format = strings::to_c(format.into());
+ unsafe {
+ #[allow(clippy::cast_possible_wrap)]
+ let handle = chfl_trajectory_with_format(
+ filename.as_ptr(), mode as c_char, format.as_ptr()
+ );
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Read a memory buffer as though it was a formatted file.
+ ///
+ /// The memory buffer used to store the file is given using the `data`
+ /// argument. The `format` parameter is required and should follow the same
+ /// rules as in the main `Trajectory` constructor.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format, or if the format do not support in-memory readers.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let aromatics = "c1ccccc1\nc1ccco1\nc1ccccn1\n";
+ /// let mut trajectory = Trajectory::memory_reader(aromatics, "SMI").unwrap();
+ /// let mut frame = Frame::new();
+ /// trajectory.read(&mut frame).unwrap();
+ /// assert_eq!(frame.size(), 6);
+ /// ```
+ pub fn memory_reader<'a, S>(data: S, format: S) -> Result<Trajectory, Error>
+ where S: Into<&'a str>,
+ {
+ let data = strings::to_c(data.into());
+ let format = strings::to_c(format.into());
+ unsafe {
+ let handle = chfl_trajectory_memory_reader(
+ data.as_ptr(), data.as_bytes().len() as u64, format.as_ptr()
+ );
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Write to a memory buffer as though it was a formatted file.
+ ///
+ /// The `format` parameter should follow the same rules as in the main
+ /// `Trajectory` constructor, except that compression specification
+ /// is not supported.
+ ///
+ /// The `memory_buffer` function can be used to retrieve the data written
+ /// to memory of the `Trajectory`.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the format do not support in-memory writers.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Trajectory;
+ /// let trajectory_memory = Trajectory::memory_writer("SMI");
+ ///
+ /// // Binary formats typically do not support this feature
+ /// assert!(Trajectory::memory_writer("XTC").is_err());
+ /// ```
+ pub fn memory_writer<'a, S>(format: S) -> Result<Trajectory, Error>
+ where S: Into<&'a str>,
+ {
+ let format = strings::to_c(format.into());
+ unsafe {
+ let handle = chfl_trajectory_memory_writer(format.as_ptr());
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Read the next step of this trajectory into a `frame`.
+ ///
+ /// If the number of atoms in frame does not correspond to the number of atom
+ /// in the next step, the frame is resized.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format, or in case of I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// let mut frame = Frame::new();
+ ///
+ /// trajectory.read(&mut frame).unwrap();
+ /// ```
+ pub fn read(&mut self, frame: &mut Frame) -> Result<(), Error> {
+ unsafe {
+ check(chfl_trajectory_read(self.as_mut_ptr(), frame.as_mut_ptr()))
+ }
+ }
+
+ /// Read a specific `step` of this trajectory into a `frame`.
+ ///
+ /// If the number of atoms in frame does not correspond to the number of
+ /// atom at this step, the frame is resized.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// let mut frame = Frame::new();
+ ///
+ /// trajectory.read_step(10, &mut frame).unwrap();
+ /// ```
+ pub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error> {
+ unsafe {
+ check(chfl_trajectory_read_step(self.as_mut_ptr(), step as u64, frame.as_mut_ptr()))
+ }
+ }
+
+ /// Write a `frame` to this trajectory.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let mut trajectory = Trajectory::open("water.pdb", 'w').unwrap();
+ /// let mut frame = Frame::new();
+ ///
+ /// trajectory.write(&mut frame).unwrap();
+ /// ```
+ pub fn write(&mut self, frame: &Frame) -> Result<(), Error> {
+ unsafe {
+ check(chfl_trajectory_write(self.as_mut_ptr(), frame.as_ptr()))
+ }
+ }
+
+ /// Set the `topology` associated with this trajectory. This topology will
+ /// be used when reading and writing the files, replacing any topology in
+ /// the frames or files.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Atom, Topology};
+ /// let mut topology = Topology::new();
+ /// topology.add_atom(&Atom::new("H"));
+ /// topology.add_atom(&Atom::new("O"));
+ /// topology.add_atom(&Atom::new("H"));
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(1, 2);
+ ///
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// trajectory.set_topology(&topology);
+ /// ```
+ pub fn set_topology(&mut self, topology: &Topology) {
+ unsafe {
+ check_success(chfl_trajectory_set_topology(self.as_mut_ptr(), topology.as_ptr()));
+ }
+ }
+
+ /// Set the topology associated with this trajectory by reading the first
+ /// frame of the file at the given `path` using the file format in `format`;
+ /// and extracting the topology of this frame.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the topology file is incorrectly formatted for
+ /// the corresponding format, or in case of I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+ /// trajectory.set_topology_file("topology.pdb").unwrap();
+ /// ```
+ pub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error>
+ where
+ P: AsRef<Path>,
+ {
+ let path = path.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(path.as_ref()))?;
+
+ let path = strings::to_c(path);
+ unsafe {
+ check(chfl_trajectory_topology_file(self.as_mut_ptr(), path.as_ptr(), ptr::null()))
+ }
+ }
+
+ /// Set the topology associated with this trajectory by reading the first
+ /// frame of the file at the given `path` using the file format in
+ /// `format`; and extracting the topology of this frame.
+ ///
+ /// If `format` is an empty string, the format will be guessed from the
+ /// `path` extension.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the topology file is incorrectly formatted for
+ /// the corresponding format, or in case of I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+ /// trajectory.set_topology_with_format("topology.mol", "PDB").unwrap();
+ /// ```
+ pub fn set_topology_with_format<'a, P, S>(&mut self, path: P, format: S) -> Result<(), Error>
+ where
+ P: AsRef<Path>,
+ S: Into<&'a str>,
+ {
+ let path = path.as_ref().to_str().ok_or_else(|| Error::utf8_path_error(path.as_ref()))?;
+
+ let format = strings::to_c(format.into());
+ let path = strings::to_c(path);
+ unsafe {
+ check(chfl_trajectory_topology_file(self.as_mut_ptr(), path.as_ptr(), format.as_ptr()))
+ }
+ }
+
+ /// Set the unit `cell` associated with a trajectory. This cell will be
+ /// used when reading and writing the files, replacing any unit cell in the
+ /// frames or files.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, UnitCell};
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// trajectory.set_cell(&UnitCell::new([10.0, 11.0, 12.5]));
+ /// ```
+ pub fn set_cell(&mut self, cell: &UnitCell) {
+ unsafe {
+ check_success(chfl_trajectory_set_cell(self.as_mut_ptr(), cell.as_ptr()));
+ }
+ }
+
+ /// Get the number of steps (the number of frames) in a trajectory.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ ///
+ /// println!("This trajectory contains {} steps", trajectory.nsteps());
+ /// ```
+ // FIXME should this take &self instead? The file can be modified by this
+ // function, but the format should reset the state.
+ pub fn nsteps(&mut self) -> usize {
+ let mut res = 0;
+ unsafe {
+ check(chfl_trajectory_nsteps(self.as_mut_ptr(), &mut res)).expect(
+ "failed to get the number of steps in this trajectory"
+ );
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return res as usize;
+ }
+
+ /// Obtain the memory buffer written to by the trajectory.
+ ///
+ /// # Errors
+ ///
+ /// This fails if the trajectory was not opened with
+ /// `Trajectory::memory_writer`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Atom, BondOrder, Frame, Trajectory};
+ /// let mut trajectory_memory = Trajectory::memory_writer("SMI").unwrap();
+ ///
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+ /// frame.add_bond_with_order(0, 1, BondOrder::Single);
+ ///
+ /// trajectory_memory.write(&frame).unwrap();
+ ///
+ /// let result = trajectory_memory.memory_buffer();
+ /// assert_eq!(result.unwrap(), "CC\n");
+ /// ```
+ #[allow(clippy::cast_possible_truncation)]
+ pub fn memory_buffer(&self) -> Result<&str, Error> {
+ let mut ptr: *const c_char = std::ptr::null();
+ let mut count: u64 = 0;
+ let buffer = unsafe {
+ check(chfl_trajectory_memory_buffer(self.as_ptr(), &mut ptr, &mut count))?;
+ std::slice::from_raw_parts(
+ ptr.cast(), count.try_into().expect("failed to convert u64 to usize")
+ )
+ };
+
+ let string = std::str::from_utf8(buffer)?;
+ Ok(string)
+ }
+
+ /// Get file path for this trajectory.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ ///
+ /// assert_eq!(trajectory.path(), "water.xyz");
+ /// ```
+ pub fn path(&self) -> String {
+ let get_string = |ptr, len| unsafe { chfl_trajectory_path(self.as_ptr(), ptr, len) };
+ let path = strings::call_autogrow_buffer(1024, get_string).expect("failed to get path string");
+ return strings::from_c(path.as_ptr());
+ }
+}
+
+impl Drop for Trajectory {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_trajectory_close(self.as_ptr());
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ use std::fs;
+ use std::path::Path;
+ use std::io::Read;
+
+ use approx::assert_ulps_eq;
+
+ use {Atom, CellShape, Frame, Topology, UnitCell};
+
+ #[test]
+ fn read() {
+ let root = Path::new(file!()).parent().unwrap().join("..");
+ let filename = root.join("data").join("water.xyz");
+ let mut file = Trajectory::open(filename.to_str().unwrap(), 'r').unwrap();
+
+ if cfg!(target_family = "unix") {
+ assert_eq!(file.path(), "src/../data/water.xyz");
+ } else if cfg!(target_family = "windows") {
+ assert_eq!(file.path(), "src\\..\\data\\water.xyz");
+ } else {
+ panic!("please add test for this OS!");
+ }
+
+ assert_eq!(file.nsteps(), 100);
+
+ let mut frame = Frame::new();
+ assert!(file.read(&mut frame).is_ok());
+
+ assert_eq!(frame.size(), 297);
+ assert_ulps_eq!(frame.positions()[0][0], 0.417219);
+ assert_ulps_eq!(frame.positions()[0][1], 8.303366);
+ assert_ulps_eq!(frame.positions()[0][2], 11.737172);
+ assert_ulps_eq!(frame.positions()[124][0], 5.099554);
+ assert_ulps_eq!(frame.positions()[124][1], -0.045104);
+ assert_ulps_eq!(frame.positions()[124][2], 14.153846);
+
+ assert_eq!(frame.atom(0).name(), "O");
+
+ file.set_cell(&UnitCell::new([30.0, 30.0, 30.0]));
+ assert!(file.read_step(41, &mut frame).is_ok());
+ let cell = frame.cell().clone();
+ assert_eq!(cell.lengths(), [30.0, 30.0, 30.0]);
+
+
+ assert_ulps_eq!(frame.positions()[0][0], 0.761277);
+ assert_ulps_eq!(frame.positions()[0][1], 8.106125);
+ assert_ulps_eq!(frame.positions()[0][2], 10.622949);
+ assert_ulps_eq!(frame.positions()[124][0], 5.13242);
+ assert_ulps_eq!(frame.positions()[124][1], 0.079862);
+ assert_ulps_eq!(frame.positions()[124][2], 14.194161);
+
+ {
+ let topology = frame.topology();
+ assert_eq!(topology.size(), 297);
+ assert_eq!(topology.bonds_count(), 0);
+ }
+
+ assert!(frame.guess_bonds().is_ok());
+ {
+ let topology = frame.topology();
+ assert_eq!(topology.size(), 297);
+ assert_eq!(topology.bonds_count(), 180);
+ assert_eq!(topology.angles_count(), 84);
+ }
+
+ let mut topology = Topology::new();
+ let atom = Atom::new("Cs");
+ for _ in 0..297 {
+ topology.add_atom(&atom);
+ }
+
+ file.set_topology(&topology);
+ assert!(file.read_step(10, &mut frame).is_ok());
+ assert_eq!(frame.atom(42).name(), "Cs");
+
+ let filename = root.join("data").join("topology.xyz");
+ assert!(file.set_topology_file(filename.to_str().unwrap()).is_ok());
+ assert!(file.read(&mut frame).is_ok());
+ assert_eq!(frame.atom(100).name(), "Rd");
+
+ let filename = root.join("data").join("helium.xyz.but.not.really");
+ let filename = filename.to_str().unwrap();
+ let mut file = Trajectory::open_with_format(filename, 'r', "XYZ").unwrap();
+ assert!(file.read(&mut frame).is_ok());
+ assert_eq!(frame.size(), 125);
+ }
+
+ fn write_file(path: &str) {
+ let mut file = Trajectory::open(path, 'w').unwrap();
+ let mut frame = Frame::new();
+ frame.resize(4);
+
+ for position in frame.positions_mut() {
+ *position = [1.0, 2.0, 3.0];
+ }
+
+ let mut topology = Topology::new();
+ let atom = Atom::new("X");
+ for _ in 0..4 {
+ topology.add_atom(&atom);
+ }
+ frame.set_topology(&topology).unwrap();
+ assert!(file.write(&frame).is_ok());
+ }
+
+ #[test]
+ fn write() {
+ let filename = "test-tmp.xyz";
+ write_file(filename);
+
+ let expected_content = "4
+Properties=species:S:1:pos:R:3
+X 1 2 3
+X 1 2 3
+X 1 2 3
+X 1 2 3".lines().collect::<Vec<_>>();
+
+ let mut file = fs::File::open(filename).unwrap();
+ let mut content = String::new();
+ let _ = file.read_to_string(&mut content).unwrap();
+
+ assert_eq!(expected_content, content.lines().collect::<Vec<_>>());
+ fs::remove_file(filename).unwrap();
+ }
+
+ #[test]
+ fn memory() {
+ // formats in decreasing order of their memory buffer length to check null termination
+ for format in &["CSSR", "GRO", "XYZ"] {
+ let mut frame_write = Frame::new();
+ frame_write.add_atom(&Atom::new("H"), [1.5, 3.0, -10.0], None);
+ frame_write.add_atom(&Atom::new("O"), [2.3, -1.4, 50.0], None);
+ frame_write.add_atom(&Atom::new("H"), [-1.5, 10.0, 0.0], None);
+ let cell = UnitCell::new([10.0, 11.0, 12.5]);
+
+ let mut trajectory_write = Trajectory::memory_writer(*format).unwrap();
+ trajectory_write.set_cell(&cell);
+ trajectory_write.write(&frame_write).unwrap();
+
+ let buffer = trajectory_write.memory_buffer().unwrap();
+ let mut trajectory_read = Trajectory::memory_reader(buffer, *format).unwrap();
+ let mut frame_read = Frame::new();
+ trajectory_read.read(&mut frame_read).unwrap();
+
+ assert_eq!(trajectory_read.nsteps(), 1);
+ assert_eq!(frame_read.cell().shape(), CellShape::Orthorhombic);
+ assert_eq!(frame_read.size(), 3);
+ assert_eq!(frame_read.atom(1).name(), "O");
+ crate::assert_vector3d_eq(&frame_read.positions()[2], &[-1.5, 10.0, 0.0], 1e-4);
+ }
+ }
+}
+Redirecting to ../../chemfiles/struct.Atom.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/atom/struct.AtomMut.html b/0.10.4/chemfiles/atom/struct.AtomMut.html new file mode 100644 index 000000000..2843d6f36 --- /dev/null +++ b/0.10.4/chemfiles/atom/struct.AtomMut.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.AtomMut.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/atom/struct.AtomRef.html b/0.10.4/chemfiles/atom/struct.AtomRef.html new file mode 100644 index 000000000..fc21ff8b9 --- /dev/null +++ b/0.10.4/chemfiles/atom/struct.AtomRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.AtomRef.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/cell/enum.CellShape.html b/0.10.4/chemfiles/cell/enum.CellShape.html new file mode 100644 index 000000000..9d3d95dbc --- /dev/null +++ b/0.10.4/chemfiles/cell/enum.CellShape.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/enum.CellShape.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/cell/struct.UnitCell.html b/0.10.4/chemfiles/cell/struct.UnitCell.html new file mode 100644 index 000000000..c199c7635 --- /dev/null +++ b/0.10.4/chemfiles/cell/struct.UnitCell.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.UnitCell.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/cell/struct.UnitCellMut.html b/0.10.4/chemfiles/cell/struct.UnitCellMut.html new file mode 100644 index 000000000..a07e76605 --- /dev/null +++ b/0.10.4/chemfiles/cell/struct.UnitCellMut.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.UnitCellMut.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/cell/struct.UnitCellRef.html b/0.10.4/chemfiles/cell/struct.UnitCellRef.html new file mode 100644 index 000000000..7455c76ac --- /dev/null +++ b/0.10.4/chemfiles/cell/struct.UnitCellRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.UnitCellRef.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/enum.BondOrder.html b/0.10.4/chemfiles/enum.BondOrder.html new file mode 100644 index 000000000..2d168517d --- /dev/null +++ b/0.10.4/chemfiles/enum.BondOrder.html @@ -0,0 +1,39 @@ +#[repr(C)]
+#[non_exhaustive]
+pub enum BondOrder {
+ Unknown,
+ Single,
+ Double,
+ Triple,
+ Quadruple,
+ Quintuplet,
+ Amide,
+ Aromatic,
+}Expand description
Possible bond order associated with bonds
+Variants (Non-exhaustive)§
This enum is marked as non-exhaustive
Non-exhaustive enums could have additional variants added in future. Therefore, when matching against variants of non-exhaustive enums, an extra wildcard arm must be added to account for any future variants.
Unknown
Unknown or unspecified bond order
+Single
Single bond
+Double
Double bond
+Triple
Triple bond
+Quadruple
Quadruple bond (present in some metals)
+Quintuplet
Quintuplet bond (present in some metals)
+Amide
Amide bond (required by some file formats)
+Aromatic
Aromatic bond (required by some file formats)
+Trait Implementations§
source§impl Ord for BondOrder
impl Ord for BondOrder
1.21.0 · source§fn max(self, other: Self) -> Selfwhere
+ Self: Sized,
fn max(self, other: Self) -> Selfwhere + Self: Sized,
Compares and returns the maximum of two values. Read more
source§impl PartialEq<BondOrder> for BondOrder
impl PartialEq<BondOrder> for BondOrder
source§impl PartialOrd<BondOrder> for BondOrder
impl PartialOrd<BondOrder> for BondOrder
1.0.0 · source§fn le(&self, other: &Rhs) -> bool
fn le(&self, other: &Rhs) -> bool
This method tests less than or equal to (for
self and other) and is used by the <=
+operator. Read moreimpl Copy for BondOrder
impl Eq for BondOrder
impl StructuralEq for BondOrder
impl StructuralPartialEq for BondOrder
Auto Trait Implementations§
impl RefUnwindSafe for BondOrder
impl Send for BondOrder
impl Sync for BondOrder
impl Unpin for BondOrder
impl UnwindSafe for BondOrder
Blanket Implementations§
pub enum CellShape {
+ Orthorhombic,
+ Triclinic,
+ Infinite,
+}Expand description
Available unit cell shapes.
+Variants§
Orthorhombic
Orthorhombic cell, with the three angles equals to 90°.
+Triclinic
Triclinic cell, with any values for the angles.
+Infinite
Infinite cell, to use when there is no cell.
+Trait Implementations§
source§impl PartialEq<CellShape> for CellShape
impl PartialEq<CellShape> for CellShape
impl Eq for CellShape
impl StructuralEq for CellShape
impl StructuralPartialEq for CellShape
Auto Trait Implementations§
impl RefUnwindSafe for CellShape
impl Send for CellShape
impl Sync for CellShape
impl Unpin for CellShape
impl UnwindSafe for CellShape
Blanket Implementations§
pub enum Property {
+ Bool(bool),
+ Double(f64),
+ String(String),
+ Vector3D([f64; 3]),
+}Expand description
A Property is a piece of data that can be associated with an Atom or a
+Frame.
Variants§
Bool(bool)
Boolean property
+Double(f64)
Floating point property
+String(String)
String property
+Vector3D([f64; 3])
3-dimensional vector property
+Trait Implementations§
source§impl PartialEq<Property> for Property
impl PartialEq<Property> for Property
source§impl PartialOrd<Property> for Property
impl PartialOrd<Property> for Property
1.0.0 · source§fn le(&self, other: &Rhs) -> bool
fn le(&self, other: &Rhs) -> bool
This method tests less than or equal to (for
self and other) and is used by the <=
+operator. Read moreimpl StructuralPartialEq for Property
Auto Trait Implementations§
impl RefUnwindSafe for Property
impl Send for Property
impl Sync for Property
impl Unpin for Property
impl UnwindSafe for Property
Blanket Implementations§
#[repr(C)]
+#[non_exhaustive]
+pub enum Status {
+ Success,
+ MemoryError,
+ FileError,
+ FormatError,
+ SelectionError,
+ ConfigurationError,
+ OutOfBounds,
+ PropertyError,
+ ChemfilesError,
+ StdCppError,
+ UTF8PathError,
+}Expand description
Possible causes of error in chemfiles
+Variants (Non-exhaustive)§
This enum is marked as non-exhaustive
Non-exhaustive enums could have additional variants added in future. Therefore, when matching against variants of non-exhaustive enums, an extra wildcard arm must be added to account for any future variants.
Success
No error
+MemoryError
Error in memory allocations
+FileError
Error while reading or writing a file
+FormatError
Error in file formatting, i.e. the file is invalid
+SelectionError
Error in selection string syntax
+ConfigurationError
Error in configuration files syntax
+OutOfBounds
Error for out of bounds indexing
+PropertyError
Error related to properties
+ChemfilesError
Exception in the C++ chemfiles library
+StdCppError
Exception in the C++ standard library
+UTF8PathError
The given path is not valid UTF8
+Trait Implementations§
source§impl PartialEq<Status> for Status
impl PartialEq<Status> for Status
impl Eq for Status
impl StructuralEq for Status
impl StructuralPartialEq for Status
Auto Trait Implementations§
impl RefUnwindSafe for Status
impl Send for Status
impl Sync for Status
impl Unpin for Status
impl UnwindSafe for Status
Blanket Implementations§
Redirecting to ../../chemfiles/enum.Status.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/errors/fn.set_warning_callback.html b/0.10.4/chemfiles/errors/fn.set_warning_callback.html new file mode 100644 index 000000000..97bc2a1ba --- /dev/null +++ b/0.10.4/chemfiles/errors/fn.set_warning_callback.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/fn.set_warning_callback.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/errors/struct.Error.html b/0.10.4/chemfiles/errors/struct.Error.html new file mode 100644 index 000000000..34339c749 --- /dev/null +++ b/0.10.4/chemfiles/errors/struct.Error.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Error.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/fn.add_configuration.html b/0.10.4/chemfiles/fn.add_configuration.html new file mode 100644 index 000000000..9922d5c74 --- /dev/null +++ b/0.10.4/chemfiles/fn.add_configuration.html @@ -0,0 +1,13 @@ +Function chemfiles::add_configuration
source · pub fn add_configuration<S>(path: S) -> Result<(), Error>where
+ S: AsRef<str>,Expand description
Read configuration data from the file at path.
By default, chemfiles reads configuration from any file named
+.chemfiles.toml in the current directory or any parent directory. This
+function can be used to add data from another configuration file. Data from
+the new configuration file will overwrite any existing data.
Errors
+This function will fail if there is no file at path, or if the file is
+incorrectly formatted.
Example
+chemfiles::add_configuration("local-config.toml").unwrap();
+// from now on, the data from "local-config.toml" will be usedFunction chemfiles::formats_list
source · pub fn formats_list() -> Vec<FormatMetadata>Expand description
Get the list of formats known by chemfiles, as well as all associated metadata.
+Example
+let formats = chemfiles::formats_list();
+println!("chemfiles supports {} formats:", formats.len());
+for format in &formats {
+ println!(
+ " {:<15} {}",
+ format.name,
+ format.extension.as_deref().unwrap_or("")
+ );
+}Function chemfiles::guess_format
source · pub fn guess_format<P>(path: P) -> Result<String, Error>where
+ P: AsRef<Path>,Expand description
Get the format that chemfiles would use to read a file at the given
+path.
The format is mostly guessed from the path extension, chemfiles only tries
+to read the file to distinguish between CIF and mmCIF files. Opening the
+file using the returned format string might still fail. For example, it will
+fail if the file is not actually formatted according to the guessed format;
+or the format/compression combination is not supported (e.g. XTC / GZ will
+not work since the XTC reader does not support compressed files).
The returned format is represented in a way compatible with the various
+Trajectory constructors, i.e. "<format name> [/ <compression>]", where
+compression is optional.
Errors
+This function returns an error if the file format couldn’t be guessed.
+Panics
+This function panics if the path can’t be converted to a Unicode string.
+Examples
+let format = chemfiles::guess_format("trajectory.xyz.xz").unwrap();
+assert_eq!(format, "XYZ / XZ");
+
+let format = chemfiles::guess_format("trajectory.nc").unwrap();
+assert_eq!(format, "Amber NetCDF");
+
+let format = chemfiles::guess_format("trajectory.unknown.format");
+assert!(format.is_err());Function chemfiles::set_warning_callback
source · pub fn set_warning_callback<F>(callback: F)where
+ F: WarningCallback + 'static,Expand description
Use callback for every chemfiles warning. The callback will be passed
+the warning message. This will drop any previous warning callback.
Redirecting to ../../chemfiles/struct.Frame.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/index.html b/0.10.4/chemfiles/index.html new file mode 100644 index 000000000..a272193f0 --- /dev/null +++ b/0.10.4/chemfiles/index.html @@ -0,0 +1,32 @@ +Expand description
Chemfiles is a multi-language library written in modern C++ for reading and +writing from and to molecular trajectory files. These files are created by +your favorite theoretical chemistry program, and contains information about +atomic or residues names and positions. Some format also have additional +information, such as velocities, forces, energy, …
+This crate expose the C API of chemfiles to Rust, and make all the +functionalities accessible. For more information on the C++ library, +please see its documentation. Specifically, the following pages +are worth reading:
+-
+
- The overview of the classes organization; +
- The list of supported formats; +
- The documentation for the selection language; +
Structs
- An
Atomis a particle in the currentFrame. It stores the following +atomic properties: - An analog to a mutable reference to an atom (
&mut Atom) - An analog to a reference to an atom (
&Atom) - Error type for Chemfiles.
FormatMetadatacontains metadata associated with one format.- A
Framecontains data from one simulation step: the current unit +cell, the topology, the positions, and the velocities of the particles in +the system. If some information is missing (topology or velocity or unit +cell), the corresponding data is filled with a default value. - A
Matchis a set of atomic indexes matching a given selection. It can +mostly be used like a&[usize]. MemoryTrajectoryReaderis a handle for aTrajectoryin memory.- An iterator over the properties in an atom/frame/residue
- A
Residueis a group of atoms belonging to the same logical unit. They +can be small molecules, amino-acids in a protein, monomers in polymers, +etc. - An analog to a reference to a residue (
&Residue) - A
Selectionallow to select atoms in aFrame, from a selection +language. The selection language is built by combining basic operations. +Each basic operation follows the<selector>[(<variable>)] <operator> <value>structure, where<operator>is a comparison operator in +== != < <= > >=. - A
Topologycontains the definition of all the atoms in the system, and +the liaisons between the atoms (bonds, angles, dihedrals, …). It will +also contain all the residues information if it is available. - An analog to a reference to a topology (
&Topology) - The
Trajectorytype is the main entry point when using chemfiles. A +Trajectorybehave a bit like a file, allowing to read and/or write +Frame. - An
UnitCellrepresent the box containing the atoms, and its periodicity. - An analog to a mutable reference to an unit cell (
&mut UnitCell) - An analog to a reference to an unit cell (
&UnitCell)
Enums
- Possible bond order associated with bonds
- Available unit cell shapes.
- A
Propertyis a piece of data that can be associated with anAtomor a +Frame. - Possible causes of error in chemfiles
Functions
- Read configuration data from the file at
path. - Get the list of formats known by chemfiles, as well as all associated metadata.
- Get the format that chemfiles would use to read a file at the given +
path. - Use
callbackfor every chemfiles warning. The callback will be passed +the warning message. This will drop any previous warning callback. - Get the version of the chemfiles library.
Redirecting to ../../chemfiles/fn.formats_list.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/misc/fn.guess_format.html b/0.10.4/chemfiles/misc/fn.guess_format.html new file mode 100644 index 000000000..681a66ce5 --- /dev/null +++ b/0.10.4/chemfiles/misc/fn.guess_format.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/fn.guess_format.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/misc/struct.FormatMetadata.html b/0.10.4/chemfiles/misc/struct.FormatMetadata.html new file mode 100644 index 000000000..10fda814b --- /dev/null +++ b/0.10.4/chemfiles/misc/struct.FormatMetadata.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.FormatMetadata.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/property/enum.Property.html b/0.10.4/chemfiles/property/enum.Property.html new file mode 100644 index 000000000..87bfc97da --- /dev/null +++ b/0.10.4/chemfiles/property/enum.Property.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/enum.Property.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/property/struct.PropertiesIter.html b/0.10.4/chemfiles/property/struct.PropertiesIter.html new file mode 100644 index 000000000..2faef8a54 --- /dev/null +++ b/0.10.4/chemfiles/property/struct.PropertiesIter.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.PropertiesIter.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/residue/struct.Residue.html b/0.10.4/chemfiles/residue/struct.Residue.html new file mode 100644 index 000000000..e8f25ad8a --- /dev/null +++ b/0.10.4/chemfiles/residue/struct.Residue.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Residue.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/residue/struct.ResidueRef.html b/0.10.4/chemfiles/residue/struct.ResidueRef.html new file mode 100644 index 000000000..9d26d5daa --- /dev/null +++ b/0.10.4/chemfiles/residue/struct.ResidueRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.ResidueRef.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/selection/struct.Match.html b/0.10.4/chemfiles/selection/struct.Match.html new file mode 100644 index 000000000..3c7b0b709 --- /dev/null +++ b/0.10.4/chemfiles/selection/struct.Match.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Match.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/selection/struct.Selection.html b/0.10.4/chemfiles/selection/struct.Selection.html new file mode 100644 index 000000000..8ed2b5d77 --- /dev/null +++ b/0.10.4/chemfiles/selection/struct.Selection.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Selection.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/sidebar-items.js b/0.10.4/chemfiles/sidebar-items.js new file mode 100644 index 000000000..99ded65b4 --- /dev/null +++ b/0.10.4/chemfiles/sidebar-items.js @@ -0,0 +1 @@ +window.SIDEBAR_ITEMS = {"enum":["BondOrder","CellShape","Property","Status"],"fn":["add_configuration","formats_list","guess_format","set_warning_callback","version"],"struct":["Atom","AtomMut","AtomRef","Error","FormatMetadata","Frame","Match","MemoryTrajectoryReader","PropertiesIter","Residue","ResidueRef","Selection","Topology","TopologyRef","Trajectory","UnitCell","UnitCellMut","UnitCellRef"]}; \ No newline at end of file diff --git a/0.10.4/chemfiles/struct.Atom.html b/0.10.4/chemfiles/struct.Atom.html new file mode 100644 index 000000000..971735be0 --- /dev/null +++ b/0.10.4/chemfiles/struct.Atom.html @@ -0,0 +1,118 @@ +pub struct Atom { /* private fields */ }Expand description
An Atom is a particle in the current Frame. It stores the following
+atomic properties:
-
+
- atom name; +
- atom type; +
- atom mass; +
- atom charge. +
The atom name is usually an unique identifier (H1, C_a) while the
+atom type will be shared between all particles of the same type: H,
+Ow, CH3.
Implementations§
source§impl Atom
impl Atom
sourcepub fn new<'a>(name: impl Into<&'a str>) -> Atom
pub fn new<'a>(name: impl Into<&'a str>) -> Atom
Create an atom with the given name, and set the atom type to name.
Example
+let atom = Atom::new("He");
+assert_eq!(atom.name(), "He");sourcepub fn mass(&self) -> f64
pub fn mass(&self) -> f64
Get the atom mass, in atomic mass units.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.mass(), 4.002602);sourcepub fn set_mass(&mut self, mass: f64)
pub fn set_mass(&mut self, mass: f64)
Set the atom mass to mass, in atomic mass units.
Example
+let mut atom = Atom::new("He");
+
+atom.set_mass(34.9);
+assert_eq!(atom.mass(), 34.9);sourcepub fn charge(&self) -> f64
pub fn charge(&self) -> f64
Get the atom charge, in number of the electron charge e.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.charge(), 0.0);sourcepub fn set_charge(&mut self, charge: f64)
pub fn set_charge(&mut self, charge: f64)
Set the atom charge to charge, in number of the electron charge e.
Example
+let mut atom = Atom::new("He");
+
+atom.set_charge(-2.0);
+assert_eq!(atom.charge(), -2.0);sourcepub fn atomic_type(&self) -> String
pub fn atomic_type(&self) -> String
sourcepub fn set_name<'a>(&mut self, name: impl Into<&'a str>)
pub fn set_name<'a>(&mut self, name: impl Into<&'a str>)
Set the atom name to name.
Example
+let mut atom = Atom::new("He");
+
+atom.set_name("Zn3");
+assert_eq!(atom.name(), "Zn3");sourcepub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>)
pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>)
Set the atom type to atomic_type.
Example
+let mut atom = Atom::new("He");
+
+atom.set_atomic_type("F");
+assert_eq!(atom.atomic_type(), "F");sourcepub fn full_name(&self) -> String
pub fn full_name(&self) -> String
Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
+let atom = Atom::new("Zn");
+assert_eq!(atom.full_name(), "Zinc");sourcepub fn vdw_radius(&self) -> f64
pub fn vdw_radius(&self) -> f64
Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);sourcepub fn covalent_radius(&self) -> f64
pub fn covalent_radius(&self) -> f64
Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);sourcepub fn atomic_number(&self) -> u64
pub fn atomic_number(&self) -> u64
Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").atomic_number(), 2);
+assert_eq!(Atom::new("Xxx").atomic_number(), 0);sourcepub fn set(&mut self, name: &str, property: impl Into<Property>)
pub fn set(&mut self, name: &str, property: impl Into<Property>)
Add a new property with the given name to this atom.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut atom = Atom::new("He");
+atom.set("a bool", true);
+atom.set("a string", "test");
+
+assert_eq!(atom.get("a bool"), Some(Property::Bool(true)));
+assert_eq!(atom.get("a string"), Some(Property::String("test".into())));sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this atom, if it exist.
Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+
+assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(atom.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_> ⓘ
pub fn properties(&self) -> PropertiesIter<'_> ⓘ
Get an iterator over all (name, property) pairs for this atom
+Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+atom.set("bar", Property::Bool(false));
+
+for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations§
Auto Trait Implementations§
impl RefUnwindSafe for Atom
impl !Send for Atom
impl !Sync for Atom
impl Unpin for Atom
impl UnwindSafe for Atom
Blanket Implementations§
pub struct AtomMut<'a> { /* private fields */ }Expand description
An analog to a mutable reference to an atom (&mut Atom)
Methods from Deref<Target = Atom>§
sourcepub fn mass(&self) -> f64
pub fn mass(&self) -> f64
Get the atom mass, in atomic mass units.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.mass(), 4.002602);sourcepub fn set_mass(&mut self, mass: f64)
pub fn set_mass(&mut self, mass: f64)
Set the atom mass to mass, in atomic mass units.
Example
+let mut atom = Atom::new("He");
+
+atom.set_mass(34.9);
+assert_eq!(atom.mass(), 34.9);sourcepub fn charge(&self) -> f64
pub fn charge(&self) -> f64
Get the atom charge, in number of the electron charge e.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.charge(), 0.0);sourcepub fn set_charge(&mut self, charge: f64)
pub fn set_charge(&mut self, charge: f64)
Set the atom charge to charge, in number of the electron charge e.
Example
+let mut atom = Atom::new("He");
+
+atom.set_charge(-2.0);
+assert_eq!(atom.charge(), -2.0);sourcepub fn atomic_type(&self) -> String
pub fn atomic_type(&self) -> String
sourcepub fn set_name<'a>(&mut self, name: impl Into<&'a str>)
pub fn set_name<'a>(&mut self, name: impl Into<&'a str>)
Set the atom name to name.
Example
+let mut atom = Atom::new("He");
+
+atom.set_name("Zn3");
+assert_eq!(atom.name(), "Zn3");sourcepub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>)
pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>)
Set the atom type to atomic_type.
Example
+let mut atom = Atom::new("He");
+
+atom.set_atomic_type("F");
+assert_eq!(atom.atomic_type(), "F");sourcepub fn full_name(&self) -> String
pub fn full_name(&self) -> String
Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
+let atom = Atom::new("Zn");
+assert_eq!(atom.full_name(), "Zinc");sourcepub fn vdw_radius(&self) -> f64
pub fn vdw_radius(&self) -> f64
Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);sourcepub fn covalent_radius(&self) -> f64
pub fn covalent_radius(&self) -> f64
Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);sourcepub fn atomic_number(&self) -> u64
pub fn atomic_number(&self) -> u64
Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").atomic_number(), 2);
+assert_eq!(Atom::new("Xxx").atomic_number(), 0);sourcepub fn set(&mut self, name: &str, property: impl Into<Property>)
pub fn set(&mut self, name: &str, property: impl Into<Property>)
Add a new property with the given name to this atom.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut atom = Atom::new("He");
+atom.set("a bool", true);
+atom.set("a string", "test");
+
+assert_eq!(atom.get("a bool"), Some(Property::Bool(true)));
+assert_eq!(atom.get("a string"), Some(Property::String("test".into())));sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this atom, if it exist.
Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+
+assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(atom.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_> ⓘ
pub fn properties(&self) -> PropertiesIter<'_> ⓘ
Get an iterator over all (name, property) pairs for this atom
+Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+atom.set("bar", Property::Bool(false));
+
+for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations§
Auto Trait Implementations§
impl<'a> RefUnwindSafe for AtomMut<'a>
impl<'a> !Send for AtomMut<'a>
impl<'a> !Sync for AtomMut<'a>
impl<'a> Unpin for AtomMut<'a>
impl<'a> !UnwindSafe for AtomMut<'a>
Blanket Implementations§
pub struct AtomRef<'a> { /* private fields */ }Expand description
An analog to a reference to an atom (&Atom)
Methods from Deref<Target = Atom>§
sourcepub fn mass(&self) -> f64
pub fn mass(&self) -> f64
Get the atom mass, in atomic mass units.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.mass(), 4.002602);sourcepub fn charge(&self) -> f64
pub fn charge(&self) -> f64
Get the atom charge, in number of the electron charge e.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.charge(), 0.0);sourcepub fn atomic_type(&self) -> String
pub fn atomic_type(&self) -> String
sourcepub fn full_name(&self) -> String
pub fn full_name(&self) -> String
Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
+let atom = Atom::new("Zn");
+assert_eq!(atom.full_name(), "Zinc");sourcepub fn vdw_radius(&self) -> f64
pub fn vdw_radius(&self) -> f64
Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);sourcepub fn covalent_radius(&self) -> f64
pub fn covalent_radius(&self) -> f64
Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);sourcepub fn atomic_number(&self) -> u64
pub fn atomic_number(&self) -> u64
Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").atomic_number(), 2);
+assert_eq!(Atom::new("Xxx").atomic_number(), 0);sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this atom, if it exist.
Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+
+assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(atom.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_> ⓘ
pub fn properties(&self) -> PropertiesIter<'_> ⓘ
Get an iterator over all (name, property) pairs for this atom
+Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+atom.set("bar", Property::Bool(false));
+
+for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations§
Auto Trait Implementations§
impl<'a> RefUnwindSafe for AtomRef<'a>
impl<'a> !Send for AtomRef<'a>
impl<'a> !Sync for AtomRef<'a>
impl<'a> Unpin for AtomRef<'a>
impl<'a> UnwindSafe for AtomRef<'a>
Blanket Implementations§
pub struct Error {
+ pub status: Status,
+ pub message: String,
+}Expand description
Error type for Chemfiles.
+Fields§
§status: StatusThe error status code
+message: StringA message describing the error cause
+Implementations§
Trait Implementations§
source§impl Error for Error
impl Error for Error
source§fn description(&self) -> &str
fn description(&self) -> &str
👎Deprecated since 1.42.0: use the Display impl or to_string()
1.30.0 · source§fn source(&self) -> Option<&(dyn Error + 'static)>
fn source(&self) -> Option<&(dyn Error + 'static)>
The lower-level source of this error, if any. Read more
source§impl PartialEq<Error> for Error
impl PartialEq<Error> for Error
impl Eq for Error
impl StructuralEq for Error
impl StructuralPartialEq for Error
Auto Trait Implementations§
impl RefUnwindSafe for Error
impl Send for Error
impl Sync for Error
impl Unpin for Error
impl UnwindSafe for Error
Blanket Implementations§
Struct chemfiles::FormatMetadata
source · pub struct FormatMetadata {Show 13 fields
+ pub name: &'static str,
+ pub extension: Option<&'static str>,
+ pub description: &'static str,
+ pub reference: &'static str,
+ pub read: bool,
+ pub write: bool,
+ pub memory: bool,
+ pub positions: bool,
+ pub velocities: bool,
+ pub unit_cell: bool,
+ pub atoms: bool,
+ pub bonds: bool,
+ pub residues: bool,
+}Expand description
FormatMetadata contains metadata associated with one format.
Fields§
§name: &'static strName of the format.
+extension: Option<&'static str>Extension associated with the format.
+description: &'static strExtended, user-facing description of the format.
+reference: &'static strURL pointing to the format definition/reference.
+read: boolIs reading files in this format implemented?
+write: boolIs writing files in this format implemented?
+memory: boolDoes this format support in-memory IO?
+positions: boolDoes this format support storing atomic positions?
+velocities: boolDoes this format support storing atomic velocities?
+unit_cell: boolDoes this format support storing unit cell information?
+atoms: boolDoes this format support storing atom names or types?
+bonds: boolDoes this format support storing bonds between atoms?
+residues: boolDoes this format support storing residues?
+Trait Implementations§
source§impl Clone for FormatMetadata
impl Clone for FormatMetadata
source§fn clone(&self) -> FormatMetadata
fn clone(&self) -> FormatMetadata
Returns a copy of the value. Read more
1.0.0 · source§fn clone_from(&mut self, source: &Self)
fn clone_from(&mut self, source: &Self)
Performs copy-assignment from
source. Read moresource§impl Debug for FormatMetadata
impl Debug for FormatMetadata
source§impl PartialEq<FormatMetadata> for FormatMetadata
impl PartialEq<FormatMetadata> for FormatMetadata
source§fn eq(&self, other: &FormatMetadata) -> bool
fn eq(&self, other: &FormatMetadata) -> bool
This method tests for
self and other values to be equal, and is used
+by ==.impl Eq for FormatMetadata
impl StructuralEq for FormatMetadata
impl StructuralPartialEq for FormatMetadata
Auto Trait Implementations§
impl RefUnwindSafe for FormatMetadata
impl Send for FormatMetadata
impl Sync for FormatMetadata
impl Unpin for FormatMetadata
impl UnwindSafe for FormatMetadata
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pub struct Frame { /* private fields */ }Expand description
A Frame contains data from one simulation step: the current unit
+cell, the topology, the positions, and the velocities of the particles in
+the system. If some information is missing (topology or velocity or unit
+cell), the corresponding data is filled with a default value.
Implementations§
source§impl Frame
impl Frame
sourcepub fn new() -> Frame
pub fn new() -> Frame
Create an empty frame. It will be resized by the library as needed.
+Example
+let frame = Frame::new();
+
+assert_eq!(frame.size(), 0);sourcepub fn atom_mut(&mut self, index: usize) -> AtomMut<'_>
pub fn atom_mut(&mut self, index: usize) -> AtomMut<'_>
Get a mutable reference to the atom at the given index in this frame.
Panics
+If index is out of bounds.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+
+assert_eq!(frame.atom(0).name(), "Zn");
+
+frame.atom_mut(0).set_name("Fe");
+assert_eq!(frame.atom(0).name(), "Fe");sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the current number of atoms in this frame.
+Example
+let mut frame = Frame::new();
+assert_eq!(frame.size(), 0);
+
+frame.resize(67);
+assert_eq!(frame.size(), 67);sourcepub fn resize(&mut self, natoms: usize)
pub fn resize(&mut self, natoms: usize)
Resize the positions and the velocities in this frame, to make space for
+natoms atoms. Previous data is conserved, as well as the presence of
+absence of velocities.
Example
+let mut frame = Frame::new();
+frame.resize(67);
+assert_eq!(frame.size(), 67);sourcepub fn add_atom(
+ &mut self,
+ atom: &Atom,
+ position: [f64; 3],
+ velocity: impl Into<Option<[f64; 3]>>
+)
pub fn add_atom( + &mut self, + atom: &Atom, + position: [f64; 3], + velocity: impl Into<Option<[f64; 3]>> +)
Add an Atom and the corresponding position and optionally velocity
+data to this frame.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("Zn"), [1.0, 1.0, 2.0], None);
+
+frame.add_velocities();
+frame.add_atom(&Atom::new("Zn"), [-1.0, 1.0, 2.0], [0.2, 0.1, 0.0]);sourcepub fn remove(&mut self, i: usize)
pub fn remove(&mut self, i: usize)
Remove the atom at index i in this frame.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+frame.add_atom(&Atom::new("Fe"), [0.0; 3], None);
+frame.add_atom(&Atom::new("Sn"), [0.0; 3], None);
+assert_eq!(frame.size(), 3);
+
+frame.remove(1);
+assert_eq!(frame.size(), 2);
+assert_eq!(frame.atom(1).name(), "Sn");sourcepub fn add_bond(&mut self, i: usize, j: usize)
pub fn add_bond(&mut self, i: usize, j: usize)
Add a bond between the atoms at indexes i and j in the frame.
The bond order is set to BondOrder::Unknown.
Example
+let mut frame = Frame::new();
+assert_eq!(frame.topology().bonds_count(), 0);
+frame.resize(5);
+
+frame.add_bond(0, 1);
+frame.add_bond(3, 1);
+frame.add_bond(2, 4);
+assert_eq!(frame.topology().bonds_count(), 3);
+
+assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown);
+assert_eq!(frame.topology().bonds(), vec![[0, 1], [1, 3], [2, 4]]);sourcepub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder)
pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder)
Add a bond between the atoms at indexes i and j in the frame
+with the given bond order.
Example
+let mut frame = Frame::new();
+assert_eq!(frame.topology().bonds_count(), 0);
+frame.resize(2);
+
+frame.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Double);sourcepub fn remove_bond(&mut self, i: usize, j: usize)
pub fn remove_bond(&mut self, i: usize, j: usize)
Remove any existing bond between the atoms at indexes i and j in
+the frame.
This function does nothing if there is no bond between i and j.
Example
+let mut frame = Frame::new();
+frame.resize(5);
+
+frame.add_bond(0, 1);
+frame.add_bond(3, 1);
+frame.add_bond(2, 4);
+
+let bonds = frame.topology().bonds();
+assert_eq!(bonds, vec![[0, 1], [1, 3], [2, 4]]);
+
+frame.remove_bond(2, 4);
+let bonds = frame.topology().bonds();
+assert_eq!(bonds, vec![[0, 1], [1, 3]]);sourcepub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error>
pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error>
Add a copy of residue to this frame.
Errors
+This function fails is the residue id is already in this frame’s +topology, or if the residue contain atoms that are already in another +residue.
+Example
+let mut frame = Frame::new();
+
+let residue = Residue::new("foo");
+frame.add_residue(&residue).unwrap();
+
+let topology = frame.topology();
+assert_eq!(topology.residues_count(), 1);
+assert_eq!(topology.residue(0).unwrap().name(), "foo");sourcepub fn distance(&self, i: usize, j: usize) -> f64
pub fn distance(&self, i: usize, j: usize) -> f64
Get the distance between the atoms at indexes i and j in this frame,
+accounting for periodic boundary conditions. The result is expressed in
+Angstroms.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [1.0, 2.0, 3.0], None);
+
+assert_eq!(frame.distance(0, 1), f64::sqrt(14.0));sourcepub fn angle(&self, i: usize, j: usize, k: usize) -> f64
pub fn angle(&self, i: usize, j: usize, k: usize) -> f64
Get the angle formed by the atoms at indexes i, j and k in this
+frame, accounting for periodic boundary conditions. The result is
+expressed in radians.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+
+assert_eq!(frame.angle(0, 1, 2), f64::consts::PI / 2.0);sourcepub fn dihedral(&self, i: usize, j: usize, k: usize, m: usize) -> f64
pub fn dihedral(&self, i: usize, j: usize, k: usize, m: usize) -> f64
Get the dihedral angle formed by the atoms at indexes i, j, k and
+m in this frame, accounting for periodic boundary conditions. The
+result is expressed in radians.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+frame.add_atom(&Atom::new("D"), [0.0, 1.0, 1.0], None);
+
+assert_eq!(frame.dihedral(0, 1, 2, 3), f64::consts::PI / 2.0);sourcepub fn out_of_plane(&self, i: usize, j: usize, k: usize, m: usize) -> f64
pub fn out_of_plane(&self, i: usize, j: usize, k: usize, m: usize) -> f64
Get the out of plane distance formed by the atoms at indexes i, j,
+k and m in this frame, accounting for periodic boundary conditions.
+The result is expressed in angstroms.
This is the distance between the atom j and the ikm plane. The j atom +is the center of the improper dihedral angle formed by i, j, k and m.
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [0.0, 0.0, 2.0], None);
+frame.add_atom(&Atom::new("C"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("D"), [0.0, 1.0, 0.0], None);
+
+assert_eq!(frame.out_of_plane(0, 1, 2, 3), 2.0);sourcepub fn positions(&self) -> &[[f64; 3]]
pub fn positions(&self) -> &[[f64; 3]]
Get a view into the positions of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+
+let positions = frame.positions();
+assert_eq!(positions.len(), 67);
+assert_eq!(positions[0], [0.0, 0.0, 0.0]);sourcepub fn positions_mut(&mut self) -> &mut [[f64; 3]]
pub fn positions_mut(&mut self) -> &mut [[f64; 3]]
Get a mutable view into the positions of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+{
+ let positions = frame.positions_mut();
+ assert_eq!(positions[0], [0.0, 0.0, 0.0]);
+ positions[0] = [1.0, 2.0, 3.0];
+}
+
+let positions = frame.positions();
+assert_eq!(positions[0], [1.0, 2.0, 3.0]);sourcepub fn velocities(&self) -> Option<&[[f64; 3]]>
pub fn velocities(&self) -> Option<&[[f64; 3]]>
Get a view into the velocities of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+frame.add_velocities();
+
+let velocities = frame.velocities().expect("missing velocities");
+assert_eq!(velocities.len(), 67);
+assert_eq!(velocities[0], [0.0, 0.0, 0.0]);sourcepub fn velocities_mut(&mut self) -> Option<&mut [[f64; 3]]>
pub fn velocities_mut(&mut self) -> Option<&mut [[f64; 3]]>
Get a mutable view into the velocities of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+frame.add_velocities();
+{
+ let velocities = frame.velocities_mut().expect("missing velocities");
+ assert_eq!(velocities[0], [0.0, 0.0, 0.0]);
+ velocities[0] = [1.0, 2.0, 3.0];
+}
+
+let velocities = frame.velocities().expect("missing velocities");
+assert_eq!(velocities[0], [1.0, 2.0, 3.0]);sourcepub fn has_velocities(&self) -> bool
pub fn has_velocities(&self) -> bool
Check if this frame contains velocity data.
+Example
+let mut frame = Frame::new();
+assert_eq!(frame.has_velocities(), false);
+
+frame.add_velocities();
+assert_eq!(frame.has_velocities(), true);sourcepub fn add_velocities(&mut self)
pub fn add_velocities(&mut self)
Add velocity data to this frame. If the frame already have velocities, +this does nothing.
+Example
+let mut frame = Frame::new();
+assert_eq!(frame.has_velocities(), false);
+
+frame.add_velocities();
+assert_eq!(frame.has_velocities(), true);sourcepub fn cell(&self) -> UnitCellRef<'_>
pub fn cell(&self) -> UnitCellRef<'_>
Get a reference to the UnitCell from this frame.
Example
+let frame = Frame::new();
+
+let cell = frame.cell();
+assert_eq!(cell.shape(), CellShape::Infinite);sourcepub fn cell_mut(&mut self) -> UnitCellMut<'_>
pub fn cell_mut(&mut self) -> UnitCellMut<'_>
Get a mutable reference to the UnitCell from this frame.
Example
+let mut frame = Frame::new();
+
+assert_eq!(frame.cell().shape(), CellShape::Infinite);
+
+frame.cell_mut().set_shape(CellShape::Triclinic).unwrap();
+assert_eq!(frame.cell().shape(), CellShape::Triclinic);sourcepub fn set_cell(&mut self, cell: &UnitCell)
pub fn set_cell(&mut self, cell: &UnitCell)
Set the UnitCell of this frame to cell.
Example
+let mut frame = Frame::new();
+
+frame.set_cell(&UnitCell::new([10.0, 10.0, 10.0]));
+
+let cell = frame.cell();
+assert_eq!(cell.shape(), CellShape::Orthorhombic);
+assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);sourcepub fn topology(&self) -> TopologyRef<'_>
pub fn topology(&self) -> TopologyRef<'_>
Get a reference to the Topology of this frame.
Example
+let mut frame = Frame::new();
+frame.resize(42);
+
+let topology = frame.topology();
+assert_eq!(topology.size(), 42);sourcepub fn set_topology(&mut self, topology: &Topology) -> Result<(), Error>
pub fn set_topology(&mut self, topology: &Topology) -> Result<(), Error>
Set the Topology of this frame to topology.
Errors
+This function fails if the topology contains a different number of atoms +than this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(2);
+
+let mut topology = Topology::new();
+topology.add_atom(&Atom::new("Cl"));
+topology.add_atom(&Atom::new("Cl"));
+topology.add_bond(0, 1);
+
+frame.set_topology(&topology).unwrap();
+assert_eq!(frame.atom(0).name(), "Cl");sourcepub fn step(&self) -> usize
pub fn step(&self) -> usize
Get this frame step, i.e. the frame number in the trajectory
+Example
+let frame = Frame::new();
+assert_eq!(frame.step(), 0);sourcepub fn set_step(&mut self, step: usize)
pub fn set_step(&mut self, step: usize)
Set this frame step to step.
Example
+let mut frame = Frame::new();
+assert_eq!(frame.step(), 0);
+
+frame.set_step(10);
+assert_eq!(frame.step(), 10);sourcepub fn guess_bonds(&mut self) -> Result<(), Error>
pub fn guess_bonds(&mut self) -> Result<(), Error>
Guess the bonds, angles and dihedrals in this frame.
The bonds are guessed using a distance-based algorithm, and then angles +and dihedrals are guessed from the bonds.
+Errors
+This function can fail if the covalent radius is unknown for some atoms +in the frame.
+Example
+let mut frame = Frame::new();
+
+frame.add_atom(&Atom::new("Cl"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("Cl"), [1.5, 0.0, 0.0], None);
+assert_eq!(frame.topology().bonds_count(), 0);
+
+frame.guess_bonds().unwrap();
+assert_eq!(frame.topology().bonds_count(), 1);sourcepub fn clear_bonds(&mut self)
pub fn clear_bonds(&mut self)
Remove all existing bonds, angles, dihedral angles and improper +dihedral angles in the topology of the frame.
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [0.0, 1.0, 0.0], None);
+
+frame.add_bond(0, 1);
+frame.add_bond(1, 2);
+
+assert_eq!(frame.topology().bonds().len(), 2);
+assert_eq!(frame.topology().angles().len(), 1);
+
+frame.clear_bonds();
+assert!(frame.topology().bonds().is_empty());
+assert!(frame.topology().angles().is_empty());sourcepub fn set(&mut self, name: &str, property: impl Into<Property>)
pub fn set(&mut self, name: &str, property: impl Into<Property>)
Add a new property with the given name to this frame.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut frame = Frame::new();
+frame.set("a string", "hello");
+frame.set("a double", 4.3);
+
+assert_eq!(frame.get("a string"), Some(Property::String("hello".into())));
+assert_eq!(frame.get("a double"), Some(Property::Double(4.3)));sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this frame, if it exist.
Examples
+let mut frame = Frame::new();
+frame.set("foo", Property::Double(22.2));
+
+assert_eq!(frame.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(frame.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_> ⓘ
pub fn properties(&self) -> PropertiesIter<'_> ⓘ
Get an iterator over all (name, property) pairs for this frame
+Examples
+let mut frame = Frame::new();
+frame.set("foo", Property::Double(22.2));
+frame.set("bar", Property::Bool(false));
+
+for (name, property) in frame.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}sourcepub fn iter_atoms(&self) -> AtomIter<'_>
pub fn iter_atoms(&self) -> AtomIter<'_>
Gets an iterator over atoms
+Example
+let mut frame = Frame::new();
+
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+
+let mut atoms: Vec<AtomRef> = Vec::new();
+
+for atom in frame.iter_atoms() {
+ atoms.push(atom);
+}
+
+assert_eq!(atoms.len(), 2);Trait Implementations§
Auto Trait Implementations§
impl RefUnwindSafe for Frame
impl !Send for Frame
impl !Sync for Frame
impl Unpin for Frame
impl UnwindSafe for Frame
Blanket Implementations§
pub struct Match { /* private fields */ }Expand description
A Match is a set of atomic indexes matching a given selection. It can
+mostly be used like a &[usize].
Implementations§
source§impl Match
impl Match
sourcepub fn len(&self) -> usize
pub fn len(&self) -> usize
Get the length of the Match.
+Example
+let atomic_match = Match::new(&[3, 4, 5]);
+assert_eq!(atomic_match.len(), 3);sourcepub fn new(atoms: &[usize]) -> Match
pub fn new(atoms: &[usize]) -> Match
Create a new match containing the atoms in the atoms slice.
Panics
+If the slice contains more than 4 elements, which is the maximal size +of a match.
+Example
+let atomic_match = Match::new(&[3, 4, 5]);
+assert_eq!(atomic_match.len(), 3);
+assert_eq!(atomic_match[0], 3);
+assert_eq!(atomic_match[1], 4);
+assert_eq!(atomic_match[2], 5);sourcepub fn iter(&self) -> Iter<'_, usize>
pub fn iter(&self) -> Iter<'_, usize>
Iterate over the atomic indexes in the match.
+Example
+let atomic_match = Match::new(&[3, 4, 5]);
+let mut iter = atomic_match.iter();
+
+assert_eq!(iter.next(), Some(&3));
+assert_eq!(iter.next(), Some(&4));
+assert_eq!(iter.next(), Some(&5));
+assert_eq!(iter.next(), None);Trait Implementations§
source§impl<'a> IntoIterator for &'a Match
impl<'a> IntoIterator for &'a Match
source§impl PartialEq<Match> for Match
impl PartialEq<Match> for Match
impl Eq for Match
impl StructuralEq for Match
impl StructuralPartialEq for Match
Auto Trait Implementations§
impl RefUnwindSafe for Match
impl Send for Match
impl Sync for Match
impl Unpin for Match
impl UnwindSafe for Match
Blanket Implementations§
Struct chemfiles::MemoryTrajectoryReader
source · pub struct MemoryTrajectoryReader<'data> { /* private fields */ }Expand description
MemoryTrajectoryReader is a handle for a Trajectory in memory.
Implementations§
source§impl<'data> MemoryTrajectoryReader<'data>
impl<'data> MemoryTrajectoryReader<'data>
sourcepub fn new<Data, Format>(
+ data: Data,
+ format: Format
+) -> Result<MemoryTrajectoryReader<'data>, Error>where
+ Data: Into<&'data [u8]>,
+ Format: AsRef<str>,
pub fn new<Data, Format>( + data: Data, + format: Format +) -> Result<MemoryTrajectoryReader<'data>, Error>where + Data: Into<&'data [u8]>, + Format: AsRef<str>,
Read a memory buffer as though it was a formatted file.
+The memory buffer used to store the file is given using the data
+argument. The format parameter is required and should follow the same
+rules as in the main Trajectory constructor.
Errors
+This function fails if the data is incorrectly formatted for the +corresponding format, or if the format do not support in-memory readers.
+Example
+let aromatics = "c1ccccc1\nc1ccco1\nc1ccccn1\n";
+let mut trajectory = MemoryTrajectoryReader::new(aromatics.as_bytes(), "SMI").unwrap();
+let mut frame = Frame::new();
+trajectory.read(&mut frame).unwrap();
+assert_eq!(frame.size(), 6);Methods from Deref<Target = Trajectory>§
sourcepub fn read(&mut self, frame: &mut Frame) -> Result<(), Error>
pub fn read(&mut self, frame: &mut Frame) -> Result<(), Error>
Read the next step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of atom +in the next step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+let mut frame = Frame::new();
+
+trajectory.read(&mut frame).unwrap();sourcepub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error>
pub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error>
Read a specific step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of +atom at this step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+let mut frame = Frame::new();
+
+trajectory.read_step(10, &mut frame).unwrap();sourcepub fn set_topology(&mut self, topology: &Topology)
pub fn set_topology(&mut self, topology: &Topology)
Set the topology associated with this trajectory. This topology will
+be used when reading and writing the files, replacing any topology in
+the frames or files.
Example
+let mut topology = Topology::new();
+topology.add_atom(&Atom::new("H"));
+topology.add_atom(&Atom::new("O"));
+topology.add_atom(&Atom::new("H"));
+topology.add_bond(0, 1);
+topology.add_bond(1, 2);
+
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+trajectory.set_topology(&topology);sourcepub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error>where
+ P: AsRef<Path>,
pub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error>where + P: AsRef<Path>,
Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in format;
+and extracting the topology of this frame.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+trajectory.set_topology_file("topology.pdb").unwrap();sourcepub fn set_topology_with_format<'a, P, S>(
+ &mut self,
+ path: P,
+ format: S
+) -> Result<(), Error>where
+ P: AsRef<Path>,
+ S: Into<&'a str>,
pub fn set_topology_with_format<'a, P, S>( + &mut self, + path: P, + format: S +) -> Result<(), Error>where + P: AsRef<Path>, + S: Into<&'a str>,
Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in
+format; and extracting the topology of this frame.
If format is an empty string, the format will be guessed from the
+path extension.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+trajectory.set_topology_with_format("topology.mol", "PDB").unwrap();sourcepub fn set_cell(&mut self, cell: &UnitCell)
pub fn set_cell(&mut self, cell: &UnitCell)
Set the unit cell associated with a trajectory. This cell will be
+used when reading and writing the files, replacing any unit cell in the
+frames or files.
Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+trajectory.set_cell(&UnitCell::new([10.0, 11.0, 12.5]));sourcepub fn nsteps(&mut self) -> usize
pub fn nsteps(&mut self) -> usize
Get the number of steps (the number of frames) in a trajectory.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+
+println!("This trajectory contains {} steps", trajectory.nsteps());sourcepub fn memory_buffer(&self) -> Result<&str, Error>
pub fn memory_buffer(&self) -> Result<&str, Error>
Obtain the memory buffer written to by the trajectory.
+Errors
+This fails if the trajectory was not opened with
+Trajectory::memory_writer.
Example
+let mut trajectory_memory = Trajectory::memory_writer("SMI").unwrap();
+
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+frame.add_bond_with_order(0, 1, BondOrder::Single);
+
+trajectory_memory.write(&frame).unwrap();
+
+let result = trajectory_memory.memory_buffer();
+assert_eq!(result.unwrap(), "CC\n");Trait Implementations§
source§impl<'a> Deref for MemoryTrajectoryReader<'a>
impl<'a> Deref for MemoryTrajectoryReader<'a>
Auto Trait Implementations§
impl<'data> RefUnwindSafe for MemoryTrajectoryReader<'data>
impl<'data> !Send for MemoryTrajectoryReader<'data>
impl<'data> !Sync for MemoryTrajectoryReader<'data>
impl<'data> Unpin for MemoryTrajectoryReader<'data>
impl<'data> UnwindSafe for MemoryTrajectoryReader<'data>
Blanket Implementations§
Struct chemfiles::PropertiesIter
source · pub struct PropertiesIter<'a> { /* private fields */ }Expand description
An iterator over the properties in an atom/frame/residue
+Trait Implementations§
source§impl<'a> Iterator for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a>
source§fn next(&mut self) -> Option<Self::Item>
fn next(&mut self) -> Option<Self::Item>
Advances the iterator and returns the next value. Read more
source§fn size_hint(&self) -> (usize, Option<usize>)
fn size_hint(&self) -> (usize, Option<usize>)
Returns the bounds on the remaining length of the iterator. Read more
source§fn count(self) -> usize
fn count(self) -> usize
Consumes the iterator, counting the number of iterations and returning it. Read more
source§fn next_chunk<const N: usize>(
+ &mut self
+) -> Result<[Self::Item; N], IntoIter<Self::Item, N>>where
+ Self: Sized,
fn next_chunk<const N: usize>( + &mut self +) -> Result<[Self::Item; N], IntoIter<Self::Item, N>>where + Self: Sized,
🔬This is a nightly-only experimental API. (
iter_next_chunk)Advances the iterator and returns an array containing the next
N values. Read more1.0.0 · source§fn last(self) -> Option<Self::Item>where
+ Self: Sized,
fn last(self) -> Option<Self::Item>where + Self: Sized,
Consumes the iterator, returning the last element. Read more
source§fn advance_by(&mut self, n: usize) -> Result<(), usize>
fn advance_by(&mut self, n: usize) -> Result<(), usize>
🔬This is a nightly-only experimental API. (
iter_advance_by)Advances the iterator by
n elements. Read more1.0.0 · source§fn nth(&mut self, n: usize) -> Option<Self::Item>
fn nth(&mut self, n: usize) -> Option<Self::Item>
Returns the
nth element of the iterator. Read more1.28.0 · source§fn step_by(self, step: usize) -> StepBy<Self>where
+ Self: Sized,
fn step_by(self, step: usize) -> StepBy<Self>where + Self: Sized,
Creates an iterator starting at the same point, but stepping by
+the given amount at each iteration. Read more
1.0.0 · source§fn chain<U>(self, other: U) -> Chain<Self, <U as IntoIterator>::IntoIter>where
+ Self: Sized,
+ U: IntoIterator<Item = Self::Item>,
fn chain<U>(self, other: U) -> Chain<Self, <U as IntoIterator>::IntoIter>where + Self: Sized, + U: IntoIterator<Item = Self::Item>,
Takes two iterators and creates a new iterator over both in sequence. Read more
1.0.0 · source§fn zip<U>(self, other: U) -> Zip<Self, <U as IntoIterator>::IntoIter>where
+ Self: Sized,
+ U: IntoIterator,
fn zip<U>(self, other: U) -> Zip<Self, <U as IntoIterator>::IntoIter>where + Self: Sized, + U: IntoIterator,
‘Zips up’ two iterators into a single iterator of pairs. Read more
source§fn intersperse_with<G>(self, separator: G) -> IntersperseWith<Self, G>where
+ Self: Sized,
+ G: FnMut() -> Self::Item,
fn intersperse_with<G>(self, separator: G) -> IntersperseWith<Self, G>where + Self: Sized, + G: FnMut() -> Self::Item,
🔬This is a nightly-only experimental API. (
iter_intersperse)Creates a new iterator which places an item generated by
separator
+between adjacent items of the original iterator. Read more1.0.0 · source§fn map<B, F>(self, f: F) -> Map<Self, F>where
+ Self: Sized,
+ F: FnMut(Self::Item) -> B,
fn map<B, F>(self, f: F) -> Map<Self, F>where + Self: Sized, + F: FnMut(Self::Item) -> B,
Takes a closure and creates an iterator which calls that closure on each
+element. Read more
1.21.0 · source§fn for_each<F>(self, f: F)where
+ Self: Sized,
+ F: FnMut(Self::Item),
fn for_each<F>(self, f: F)where + Self: Sized, + F: FnMut(Self::Item),
Calls a closure on each element of an iterator. Read more
1.0.0 · source§fn filter<P>(self, predicate: P) -> Filter<Self, P>where
+ Self: Sized,
+ P: FnMut(&Self::Item) -> bool,
fn filter<P>(self, predicate: P) -> Filter<Self, P>where + Self: Sized, + P: FnMut(&Self::Item) -> bool,
Creates an iterator which uses a closure to determine if an element
+should be yielded. Read more
1.0.0 · source§fn filter_map<B, F>(self, f: F) -> FilterMap<Self, F>where
+ Self: Sized,
+ F: FnMut(Self::Item) -> Option<B>,
fn filter_map<B, F>(self, f: F) -> FilterMap<Self, F>where + Self: Sized, + F: FnMut(Self::Item) -> Option<B>,
Creates an iterator that both filters and maps. Read more
1.0.0 · source§fn enumerate(self) -> Enumerate<Self>where
+ Self: Sized,
fn enumerate(self) -> Enumerate<Self>where + Self: Sized,
Creates an iterator which gives the current iteration count as well as
+the next value. Read more
1.0.0 · source§fn skip_while<P>(self, predicate: P) -> SkipWhile<Self, P>where
+ Self: Sized,
+ P: FnMut(&Self::Item) -> bool,
fn skip_while<P>(self, predicate: P) -> SkipWhile<Self, P>where + Self: Sized, + P: FnMut(&Self::Item) -> bool,
1.0.0 · source§fn take_while<P>(self, predicate: P) -> TakeWhile<Self, P>where
+ Self: Sized,
+ P: FnMut(&Self::Item) -> bool,
fn take_while<P>(self, predicate: P) -> TakeWhile<Self, P>where + Self: Sized, + P: FnMut(&Self::Item) -> bool,
Creates an iterator that yields elements based on a predicate. Read more
1.57.0 · source§fn map_while<B, P>(self, predicate: P) -> MapWhile<Self, P>where
+ Self: Sized,
+ P: FnMut(Self::Item) -> Option<B>,
fn map_while<B, P>(self, predicate: P) -> MapWhile<Self, P>where + Self: Sized, + P: FnMut(Self::Item) -> Option<B>,
Creates an iterator that both yields elements based on a predicate and maps. Read more
1.0.0 · source§fn skip(self, n: usize) -> Skip<Self>where
+ Self: Sized,
fn skip(self, n: usize) -> Skip<Self>where + Self: Sized,
Creates an iterator that skips the first
n elements. Read more1.0.0 · source§fn take(self, n: usize) -> Take<Self>where
+ Self: Sized,
fn take(self, n: usize) -> Take<Self>where + Self: Sized,
Creates an iterator that yields the first
n elements, or fewer
+if the underlying iterator ends sooner. Read more1.0.0 · source§fn scan<St, B, F>(self, initial_state: St, f: F) -> Scan<Self, St, F>where
+ Self: Sized,
+ F: FnMut(&mut St, Self::Item) -> Option<B>,
fn scan<St, B, F>(self, initial_state: St, f: F) -> Scan<Self, St, F>where + Self: Sized, + F: FnMut(&mut St, Self::Item) -> Option<B>,
1.0.0 · source§fn flat_map<U, F>(self, f: F) -> FlatMap<Self, U, F>where
+ Self: Sized,
+ U: IntoIterator,
+ F: FnMut(Self::Item) -> U,
fn flat_map<U, F>(self, f: F) -> FlatMap<Self, U, F>where + Self: Sized, + U: IntoIterator, + F: FnMut(Self::Item) -> U,
Creates an iterator that works like map, but flattens nested structure. Read more
1.0.0 · source§fn inspect<F>(self, f: F) -> Inspect<Self, F>where
+ Self: Sized,
+ F: FnMut(&Self::Item),
fn inspect<F>(self, f: F) -> Inspect<Self, F>where + Self: Sized, + F: FnMut(&Self::Item),
Does something with each element of an iterator, passing the value on. Read more
1.0.0 · source§fn by_ref(&mut self) -> &mut Selfwhere
+ Self: Sized,
fn by_ref(&mut self) -> &mut Selfwhere + Self: Sized,
Borrows an iterator, rather than consuming it. Read more
1.0.0 · source§fn collect<B>(self) -> Bwhere
+ B: FromIterator<Self::Item>,
+ Self: Sized,
fn collect<B>(self) -> Bwhere + B: FromIterator<Self::Item>, + Self: Sized,
Transforms an iterator into a collection. Read more
source§fn collect_into<E>(self, collection: &mut E) -> &mut Ewhere
+ E: Extend<Self::Item>,
+ Self: Sized,
fn collect_into<E>(self, collection: &mut E) -> &mut Ewhere + E: Extend<Self::Item>, + Self: Sized,
🔬This is a nightly-only experimental API. (
iter_collect_into)Collects all the items from an iterator into a collection. Read more
1.0.0 · source§fn partition<B, F>(self, f: F) -> (B, B)where
+ Self: Sized,
+ B: Default + Extend<Self::Item>,
+ F: FnMut(&Self::Item) -> bool,
fn partition<B, F>(self, f: F) -> (B, B)where + Self: Sized, + B: Default + Extend<Self::Item>, + F: FnMut(&Self::Item) -> bool,
Consumes an iterator, creating two collections from it. Read more
source§fn is_partitioned<P>(self, predicate: P) -> boolwhere
+ Self: Sized,
+ P: FnMut(Self::Item) -> bool,
fn is_partitioned<P>(self, predicate: P) -> boolwhere + Self: Sized, + P: FnMut(Self::Item) -> bool,
🔬This is a nightly-only experimental API. (
iter_is_partitioned)Checks if the elements of this iterator are partitioned according to the given predicate,
+such that all those that return
true precede all those that return false. Read more1.27.0 · source§fn try_fold<B, F, R>(&mut self, init: B, f: F) -> Rwhere
+ Self: Sized,
+ F: FnMut(B, Self::Item) -> R,
+ R: Try<Output = B>,
fn try_fold<B, F, R>(&mut self, init: B, f: F) -> Rwhere + Self: Sized, + F: FnMut(B, Self::Item) -> R, + R: Try<Output = B>,
An iterator method that applies a function as long as it returns
+successfully, producing a single, final value. Read more
1.27.0 · source§fn try_for_each<F, R>(&mut self, f: F) -> Rwhere
+ Self: Sized,
+ F: FnMut(Self::Item) -> R,
+ R: Try<Output = ()>,
fn try_for_each<F, R>(&mut self, f: F) -> Rwhere + Self: Sized, + F: FnMut(Self::Item) -> R, + R: Try<Output = ()>,
An iterator method that applies a fallible function to each item in the
+iterator, stopping at the first error and returning that error. Read more
1.0.0 · source§fn fold<B, F>(self, init: B, f: F) -> Bwhere
+ Self: Sized,
+ F: FnMut(B, Self::Item) -> B,
fn fold<B, F>(self, init: B, f: F) -> Bwhere + Self: Sized, + F: FnMut(B, Self::Item) -> B,
Folds every element into an accumulator by applying an operation,
+returning the final result. Read more
1.51.0 · source§fn reduce<F>(self, f: F) -> Option<Self::Item>where
+ Self: Sized,
+ F: FnMut(Self::Item, Self::Item) -> Self::Item,
fn reduce<F>(self, f: F) -> Option<Self::Item>where + Self: Sized, + F: FnMut(Self::Item, Self::Item) -> Self::Item,
Reduces the elements to a single one, by repeatedly applying a reducing
+operation. Read more
source§fn try_reduce<F, R>(
+ &mut self,
+ f: F
+) -> <<R as Try>::Residual as Residual<Option<<R as Try>::Output>>>::TryTypewhere
+ Self: Sized,
+ F: FnMut(Self::Item, Self::Item) -> R,
+ R: Try<Output = Self::Item>,
+ <R as Try>::Residual: Residual<Option<Self::Item>>,
fn try_reduce<F, R>( + &mut self, + f: F +) -> <<R as Try>::Residual as Residual<Option<<R as Try>::Output>>>::TryTypewhere + Self: Sized, + F: FnMut(Self::Item, Self::Item) -> R, + R: Try<Output = Self::Item>, + <R as Try>::Residual: Residual<Option<Self::Item>>,
🔬This is a nightly-only experimental API. (
iterator_try_reduce)Reduces the elements to a single one by repeatedly applying a reducing operation. If the
+closure returns a failure, the failure is propagated back to the caller immediately. Read more
1.0.0 · source§fn all<F>(&mut self, f: F) -> boolwhere
+ Self: Sized,
+ F: FnMut(Self::Item) -> bool,
fn all<F>(&mut self, f: F) -> boolwhere + Self: Sized, + F: FnMut(Self::Item) -> bool,
Tests if every element of the iterator matches a predicate. Read more
1.0.0 · source§fn any<F>(&mut self, f: F) -> boolwhere
+ Self: Sized,
+ F: FnMut(Self::Item) -> bool,
fn any<F>(&mut self, f: F) -> boolwhere + Self: Sized, + F: FnMut(Self::Item) -> bool,
Tests if any element of the iterator matches a predicate. Read more
1.0.0 · source§fn find<P>(&mut self, predicate: P) -> Option<Self::Item>where
+ Self: Sized,
+ P: FnMut(&Self::Item) -> bool,
fn find<P>(&mut self, predicate: P) -> Option<Self::Item>where + Self: Sized, + P: FnMut(&Self::Item) -> bool,
Searches for an element of an iterator that satisfies a predicate. Read more
1.30.0 · source§fn find_map<B, F>(&mut self, f: F) -> Option<B>where
+ Self: Sized,
+ F: FnMut(Self::Item) -> Option<B>,
fn find_map<B, F>(&mut self, f: F) -> Option<B>where + Self: Sized, + F: FnMut(Self::Item) -> Option<B>,
Applies function to the elements of iterator and returns
+the first non-none result. Read more
source§fn try_find<F, R>(
+ &mut self,
+ f: F
+) -> <<R as Try>::Residual as Residual<Option<Self::Item>>>::TryTypewhere
+ Self: Sized,
+ F: FnMut(&Self::Item) -> R,
+ R: Try<Output = bool>,
+ <R as Try>::Residual: Residual<Option<Self::Item>>,
fn try_find<F, R>( + &mut self, + f: F +) -> <<R as Try>::Residual as Residual<Option<Self::Item>>>::TryTypewhere + Self: Sized, + F: FnMut(&Self::Item) -> R, + R: Try<Output = bool>, + <R as Try>::Residual: Residual<Option<Self::Item>>,
🔬This is a nightly-only experimental API. (
try_find)Applies function to the elements of iterator and returns
+the first true result or the first error. Read more
1.0.0 · source§fn position<P>(&mut self, predicate: P) -> Option<usize>where
+ Self: Sized,
+ P: FnMut(Self::Item) -> bool,
fn position<P>(&mut self, predicate: P) -> Option<usize>where + Self: Sized, + P: FnMut(Self::Item) -> bool,
Searches for an element in an iterator, returning its index. Read more
1.6.0 · source§fn max_by_key<B, F>(self, f: F) -> Option<Self::Item>where
+ B: Ord,
+ Self: Sized,
+ F: FnMut(&Self::Item) -> B,
fn max_by_key<B, F>(self, f: F) -> Option<Self::Item>where + B: Ord, + Self: Sized, + F: FnMut(&Self::Item) -> B,
Returns the element that gives the maximum value from the
+specified function. Read more
1.15.0 · source§fn max_by<F>(self, compare: F) -> Option<Self::Item>where
+ Self: Sized,
+ F: FnMut(&Self::Item, &Self::Item) -> Ordering,
fn max_by<F>(self, compare: F) -> Option<Self::Item>where + Self: Sized, + F: FnMut(&Self::Item, &Self::Item) -> Ordering,
Returns the element that gives the maximum value with respect to the
+specified comparison function. Read more
1.6.0 · source§fn min_by_key<B, F>(self, f: F) -> Option<Self::Item>where
+ B: Ord,
+ Self: Sized,
+ F: FnMut(&Self::Item) -> B,
fn min_by_key<B, F>(self, f: F) -> Option<Self::Item>where + B: Ord, + Self: Sized, + F: FnMut(&Self::Item) -> B,
Returns the element that gives the minimum value from the
+specified function. Read more
1.15.0 · source§fn min_by<F>(self, compare: F) -> Option<Self::Item>where
+ Self: Sized,
+ F: FnMut(&Self::Item, &Self::Item) -> Ordering,
fn min_by<F>(self, compare: F) -> Option<Self::Item>where + Self: Sized, + F: FnMut(&Self::Item, &Self::Item) -> Ordering,
Returns the element that gives the minimum value with respect to the
+specified comparison function. Read more
1.0.0 · source§fn unzip<A, B, FromA, FromB>(self) -> (FromA, FromB)where
+ FromA: Default + Extend<A>,
+ FromB: Default + Extend<B>,
+ Self: Sized + Iterator<Item = (A, B)>,
fn unzip<A, B, FromA, FromB>(self) -> (FromA, FromB)where + FromA: Default + Extend<A>, + FromB: Default + Extend<B>, + Self: Sized + Iterator<Item = (A, B)>,
Converts an iterator of pairs into a pair of containers. Read more
1.36.0 · source§fn copied<'a, T>(self) -> Copied<Self>where
+ T: 'a + Copy,
+ Self: Sized + Iterator<Item = &'a T>,
fn copied<'a, T>(self) -> Copied<Self>where + T: 'a + Copy, + Self: Sized + Iterator<Item = &'a T>,
Creates an iterator which copies all of its elements. Read more
1.0.0 · source§fn cloned<'a, T>(self) -> Cloned<Self>where
+ T: 'a + Clone,
+ Self: Sized + Iterator<Item = &'a T>,
fn cloned<'a, T>(self) -> Cloned<Self>where + T: 'a + Clone, + Self: Sized + Iterator<Item = &'a T>,
source§fn array_chunks<const N: usize>(self) -> ArrayChunks<Self, N>where
+ Self: Sized,
fn array_chunks<const N: usize>(self) -> ArrayChunks<Self, N>where + Self: Sized,
🔬This is a nightly-only experimental API. (
iter_array_chunks)Returns an iterator over
N elements of the iterator at a time. Read more1.11.0 · source§fn sum<S>(self) -> Swhere
+ Self: Sized,
+ S: Sum<Self::Item>,
fn sum<S>(self) -> Swhere + Self: Sized, + S: Sum<Self::Item>,
Sums the elements of an iterator. Read more
1.11.0 · source§fn product<P>(self) -> Pwhere
+ Self: Sized,
+ P: Product<Self::Item>,
fn product<P>(self) -> Pwhere + Self: Sized, + P: Product<Self::Item>,
Iterates over the entire iterator, multiplying all the elements Read more
source§fn cmp_by<I, F>(self, other: I, cmp: F) -> Orderingwhere
+ Self: Sized,
+ I: IntoIterator,
+ F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,
fn cmp_by<I, F>(self, other: I, cmp: F) -> Orderingwhere + Self: Sized, + I: IntoIterator, + F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,
🔬This is a nightly-only experimental API. (
iter_order_by)Lexicographically compares the elements of this
Iterator with those
+of another with respect to the specified comparison function. Read more1.5.0 · source§fn partial_cmp<I>(self, other: I) -> Option<Ordering>where
+ I: IntoIterator,
+ Self::Item: PartialOrd<<I as IntoIterator>::Item>,
+ Self: Sized,
fn partial_cmp<I>(self, other: I) -> Option<Ordering>where + I: IntoIterator, + Self::Item: PartialOrd<<I as IntoIterator>::Item>, + Self: Sized,
Lexicographically compares the
PartialOrd elements of
+this Iterator with those of another. The comparison works like short-circuit
+evaluation, returning a result without comparing the remaining elements.
+As soon as an order can be determined, the evaluation stops and a result is returned. Read moresource§fn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering>where
+ Self: Sized,
+ I: IntoIterator,
+ F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,
fn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering>where + Self: Sized, + I: IntoIterator, + F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,
🔬This is a nightly-only experimental API. (
iter_order_by)Lexicographically compares the elements of this
Iterator with those
+of another with respect to the specified comparison function. Read more1.5.0 · source§fn eq<I>(self, other: I) -> boolwhere
+ I: IntoIterator,
+ Self::Item: PartialEq<<I as IntoIterator>::Item>,
+ Self: Sized,
fn eq<I>(self, other: I) -> boolwhere + I: IntoIterator, + Self::Item: PartialEq<<I as IntoIterator>::Item>, + Self: Sized,
source§fn eq_by<I, F>(self, other: I, eq: F) -> boolwhere
+ Self: Sized,
+ I: IntoIterator,
+ F: FnMut(Self::Item, <I as IntoIterator>::Item) -> bool,
fn eq_by<I, F>(self, other: I, eq: F) -> boolwhere + Self: Sized, + I: IntoIterator, + F: FnMut(Self::Item, <I as IntoIterator>::Item) -> bool,
🔬This is a nightly-only experimental API. (
iter_order_by)1.5.0 · source§fn ne<I>(self, other: I) -> boolwhere
+ I: IntoIterator,
+ Self::Item: PartialEq<<I as IntoIterator>::Item>,
+ Self: Sized,
fn ne<I>(self, other: I) -> boolwhere + I: IntoIterator, + Self::Item: PartialEq<<I as IntoIterator>::Item>, + Self: Sized,
1.5.0 · source§fn lt<I>(self, other: I) -> boolwhere
+ I: IntoIterator,
+ Self::Item: PartialOrd<<I as IntoIterator>::Item>,
+ Self: Sized,
fn lt<I>(self, other: I) -> boolwhere + I: IntoIterator, + Self::Item: PartialOrd<<I as IntoIterator>::Item>, + Self: Sized,
Determines if the elements of this
Iterator are lexicographically
+less than those of another. Read more1.5.0 · source§fn le<I>(self, other: I) -> boolwhere
+ I: IntoIterator,
+ Self::Item: PartialOrd<<I as IntoIterator>::Item>,
+ Self: Sized,
fn le<I>(self, other: I) -> boolwhere + I: IntoIterator, + Self::Item: PartialOrd<<I as IntoIterator>::Item>, + Self: Sized,
Determines if the elements of this
Iterator are lexicographically
+less or equal to those of another. Read more1.5.0 · source§fn gt<I>(self, other: I) -> boolwhere
+ I: IntoIterator,
+ Self::Item: PartialOrd<<I as IntoIterator>::Item>,
+ Self: Sized,
fn gt<I>(self, other: I) -> boolwhere + I: IntoIterator, + Self::Item: PartialOrd<<I as IntoIterator>::Item>, + Self: Sized,
Determines if the elements of this
Iterator are lexicographically
+greater than those of another. Read more1.5.0 · source§fn ge<I>(self, other: I) -> boolwhere
+ I: IntoIterator,
+ Self::Item: PartialOrd<<I as IntoIterator>::Item>,
+ Self: Sized,
fn ge<I>(self, other: I) -> boolwhere + I: IntoIterator, + Self::Item: PartialOrd<<I as IntoIterator>::Item>, + Self: Sized,
Determines if the elements of this
Iterator are lexicographically
+greater than or equal to those of another. Read moresource§fn is_sorted_by<F>(self, compare: F) -> boolwhere
+ Self: Sized,
+ F: FnMut(&Self::Item, &Self::Item) -> Option<Ordering>,
fn is_sorted_by<F>(self, compare: F) -> boolwhere + Self: Sized, + F: FnMut(&Self::Item, &Self::Item) -> Option<Ordering>,
🔬This is a nightly-only experimental API. (
is_sorted)Checks if the elements of this iterator are sorted using the given comparator function. Read more
source§fn is_sorted_by_key<F, K>(self, f: F) -> boolwhere
+ Self: Sized,
+ F: FnMut(Self::Item) -> K,
+ K: PartialOrd<K>,
fn is_sorted_by_key<F, K>(self, f: F) -> boolwhere + Self: Sized, + F: FnMut(Self::Item) -> K, + K: PartialOrd<K>,
🔬This is a nightly-only experimental API. (
is_sorted)Checks if the elements of this iterator are sorted using the given key extraction
+function. Read more
Auto Trait Implementations§
impl<'a> !RefUnwindSafe for PropertiesIter<'a>
impl<'a> !Send for PropertiesIter<'a>
impl<'a> !Sync for PropertiesIter<'a>
impl<'a> Unpin for PropertiesIter<'a>
impl<'a> !UnwindSafe for PropertiesIter<'a>
Blanket Implementations§
source§impl<I> IntoIterator for Iwhere
+ I: Iterator,
impl<I> IntoIterator for Iwhere + I: Iterator,
pub struct Residue { /* private fields */ }Expand description
A Residue is a group of atoms belonging to the same logical unit. They
+can be small molecules, amino-acids in a protein, monomers in polymers,
+etc.
Implementations§
source§impl Residue
impl Residue
sourcepub fn new<'a>(name: impl Into<&'a str>) -> Residue
pub fn new<'a>(name: impl Into<&'a str>) -> Residue
Create a new residue with the given name
Example
+let residue = Residue::new("ALA");
+assert_eq!(residue.name(), "ALA");
+assert_eq!(residue.id(), None);sourcepub fn with_id<'a>(name: impl Into<&'a str>, id: i64) -> Residue
pub fn with_id<'a>(name: impl Into<&'a str>, id: i64) -> Residue
Create a new residue with the given name and id as identifier.
Example
+let residue = Residue::with_id("ALA", 67);
+assert_eq!(residue.name(), "ALA");
+assert_eq!(residue.id(), Some(67));sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the number of atoms in this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.size(), 0);
+
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+assert_eq!(residue.size(), 3);sourcepub fn id(&self) -> Option<i64>
pub fn id(&self) -> Option<i64>
Get the identifier of this residue in the initial topology file.
+Example
+let residue = Residue::with_id("", 42);
+assert_eq!(residue.id(), Some(42));sourcepub fn name(&self) -> String
pub fn name(&self) -> String
Get the name of this residue.
+Example
+let residue = Residue::new("water");
+assert_eq!(residue.name(), "water");sourcepub fn add_atom(&mut self, atom: usize)
pub fn add_atom(&mut self, atom: usize)
Add the atom at index atom in this residue.
This will fail if the atom is already in the residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.size(), 0);
+assert_eq!(residue.contains(56), false);
+
+residue.add_atom(56);
+assert_eq!(residue.size(), 1);
+assert_eq!(residue.contains(56), true);
+
+// Adding the same atom twice is fine
+residue.add_atom(56);
+assert_eq!(residue.size(), 1);sourcepub fn contains(&self, atom: usize) -> bool
pub fn contains(&self, atom: usize) -> bool
Check if the atom at index i is in this residue
Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.contains(56), false);
+
+residue.add_atom(56);
+assert_eq!(residue.contains(56), true);sourcepub fn atoms(&self) -> Vec<usize>
pub fn atoms(&self) -> Vec<usize>
Get the list of atoms of this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.atoms(), vec![]);
+
+residue.add_atom(56);
+assert_eq!(residue.atoms(), vec![56]);sourcepub fn set(&mut self, name: &str, property: impl Into<Property>)
pub fn set(&mut self, name: &str, property: impl Into<Property>)
Add a new property with the given name to this residue.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut residue = Residue::new("ALA");
+residue.set("a string", "hello");
+residue.set("a double", 3.2);
+
+assert_eq!(residue.get("a string"), Some(Property::String("hello".into())));
+assert_eq!(residue.get("a double"), Some(Property::Double(3.2)));sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this frame, if it exist.
Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+
+assert_eq!(residue.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(residue.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_> ⓘ
pub fn properties(&self) -> PropertiesIter<'_> ⓘ
Get an iterator over all (name, property) pairs for this frame
+Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+residue.set("bar", Property::Bool(false));
+
+for (name, property) in residue.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations§
Auto Trait Implementations§
impl RefUnwindSafe for Residue
impl !Send for Residue
impl !Sync for Residue
impl Unpin for Residue
impl UnwindSafe for Residue
Blanket Implementations§
Struct chemfiles::ResidueRef
source · pub struct ResidueRef<'a> { /* private fields */ }Expand description
An analog to a reference to a residue (&Residue)
Methods from Deref<Target = Residue>§
sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the number of atoms in this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.size(), 0);
+
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+assert_eq!(residue.size(), 3);sourcepub fn id(&self) -> Option<i64>
pub fn id(&self) -> Option<i64>
Get the identifier of this residue in the initial topology file.
+Example
+let residue = Residue::with_id("", 42);
+assert_eq!(residue.id(), Some(42));sourcepub fn name(&self) -> String
pub fn name(&self) -> String
Get the name of this residue.
+Example
+let residue = Residue::new("water");
+assert_eq!(residue.name(), "water");sourcepub fn contains(&self, atom: usize) -> bool
pub fn contains(&self, atom: usize) -> bool
Check if the atom at index i is in this residue
Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.contains(56), false);
+
+residue.add_atom(56);
+assert_eq!(residue.contains(56), true);sourcepub fn atoms(&self) -> Vec<usize>
pub fn atoms(&self) -> Vec<usize>
Get the list of atoms of this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.atoms(), vec![]);
+
+residue.add_atom(56);
+assert_eq!(residue.atoms(), vec![56]);sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this frame, if it exist.
Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+
+assert_eq!(residue.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(residue.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_> ⓘ
pub fn properties(&self) -> PropertiesIter<'_> ⓘ
Get an iterator over all (name, property) pairs for this frame
+Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+residue.set("bar", Property::Bool(false));
+
+for (name, property) in residue.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations§
source§impl<'a> Debug for ResidueRef<'a>
impl<'a> Debug for ResidueRef<'a>
Auto Trait Implementations§
impl<'a> RefUnwindSafe for ResidueRef<'a>
impl<'a> !Send for ResidueRef<'a>
impl<'a> !Sync for ResidueRef<'a>
impl<'a> Unpin for ResidueRef<'a>
impl<'a> UnwindSafe for ResidueRef<'a>
Blanket Implementations§
pub struct Selection { /* private fields */ }Expand description
A Selection allow to select atoms in a Frame, from a selection
+language. The selection language is built by combining basic operations.
+Each basic operation follows the <selector>[(<variable>)] <operator> <value> structure, where <operator> is a comparison operator in
+== != < <= > >=.
Implementations§
source§impl Selection
impl Selection
sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the size of the selection, i.e. the number of atoms we are selecting +together.
+This value is 1 for the ‘atom’ context, 2 for the ‘pair’ and ‘bond’ +context, 3 for the ‘three’ and ‘angles’ context and 4 for the ‘four’ +and ‘dihedral’ context.
+Example
+let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+assert_eq!(selection.size(), 2);sourcepub fn string(&self) -> String
pub fn string(&self) -> String
Get the selection string used to create this selection.
+Example
+let selection = Selection::new("name H").unwrap();
+assert_eq!(selection.string(), "name H");sourcepub fn evaluate(&mut self, frame: &Frame) -> Vec<Match>
pub fn evaluate(&mut self, frame: &Frame) -> Vec<Match>
Evaluate a selection for a given frame, and return the corresponding +matches.
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+
+let mut selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+let matches = selection.evaluate(&frame);
+
+assert_eq!(matches.len(), 2);
+
+assert_eq!(matches[0].len(), 2);
+assert_eq!(matches[0][0], 0);
+assert_eq!(matches[0][1], 1);
+
+assert_eq!(matches[1].len(), 2);
+assert_eq!(matches[1][0], 2);
+assert_eq!(matches[1][1], 1);sourcepub fn list(&mut self, frame: &Frame) -> Vec<usize>
pub fn list(&mut self, frame: &Frame) -> Vec<usize>
Evaluates a selection of size 1 on a given frame. This function
+returns the list of atomic indexes in the frame matching this selection.
Panics
+If the selection size is not 1
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+
+let mut selection = Selection::new("name H").unwrap();
+let matches = selection.list(&frame);
+
+assert_eq!(matches.len(), 2);
+assert_eq!(matches[0], 0);
+assert_eq!(matches[1], 2);Trait Implementations§
Auto Trait Implementations§
impl RefUnwindSafe for Selection
impl !Send for Selection
impl !Sync for Selection
impl Unpin for Selection
impl UnwindSafe for Selection
Blanket Implementations§
pub struct Topology { /* private fields */ }Expand description
A Topology contains the definition of all the atoms in the system, and
+the liaisons between the atoms (bonds, angles, dihedrals, …). It will
+also contain all the residues information if it is available.
Implementations§
source§impl Topology
impl Topology
sourcepub fn new() -> Topology
pub fn new() -> Topology
Create a new empty topology.
+Example
+let topology = Topology::new();
+assert_eq!(topology.size(), 0);sourcepub fn atom_mut(&mut self, index: usize) -> AtomMut<'_>
pub fn atom_mut(&mut self, index: usize) -> AtomMut<'_>
Get a mutable reference to the atom at the given index in this topology.
Panics
+If index is out of bounds.
Example
+let mut topology = Topology::new();
+topology.resize(6);
+
+assert_eq!(topology.atom(4).name(), "");
+
+topology.atom_mut(4).set_name("Fe");
+assert_eq!(topology.atom(4).name(), "Fe");sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the current number of atoms in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.size(), 0);
+
+topology.resize(6);
+assert_eq!(topology.size(), 6);sourcepub fn resize(&mut self, natoms: usize)
pub fn resize(&mut self, natoms: usize)
Resize this topology to hold natoms atoms, inserting dummy atoms if
+the new size if bigger than the old one.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.size(), 0);
+
+topology.resize(6);
+assert_eq!(topology.size(), 6);sourcepub fn add_atom(&mut self, atom: &Atom)
pub fn add_atom(&mut self, atom: &Atom)
Add an Atom at the end of this topology
Example
+let mut topology = Topology::new();
+topology.add_atom(&Atom::new("Mg"));
+
+let atom = topology.atom(0);
+assert_eq!(atom.name(), "Mg");sourcepub fn bonds_count(&self) -> usize
pub fn bonds_count(&self) -> usize
Get the number of bonds in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds_count(), 3);sourcepub fn angles_count(&self) -> usize
pub fn angles_count(&self) -> usize
Get the number of angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.angles_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles_count(), 2);sourcepub fn dihedrals_count(&self) -> usize
pub fn dihedrals_count(&self) -> usize
Get the number of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.dihedrals_count(), 1);sourcepub fn impropers_count(&self) -> usize
pub fn impropers_count(&self) -> usize
Get the number of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+assert_eq!(topology.impropers_count(), 1);sourcepub fn bonds(&self) -> Vec<[usize; 2]>
pub fn bonds(&self) -> Vec<[usize; 2]>
Get the list of bonds in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);sourcepub fn angles(&self) -> Vec<[usize; 3]>
pub fn angles(&self) -> Vec<[usize; 3]>
Get the list of angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);sourcepub fn dihedrals(&self) -> Vec<[usize; 4]>
pub fn dihedrals(&self) -> Vec<[usize; 4]>
Get the list of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+
+assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);sourcepub fn impropers(&self) -> Vec<[usize; 4]>
pub fn impropers(&self) -> Vec<[usize; 4]>
Get the list of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+
+assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);sourcepub fn clear_bonds(&mut self)
pub fn clear_bonds(&mut self)
Remove all existing bonds, angles, dihedral angles and improper +dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+assert_eq!(topology.bonds_count(), 2);
+assert_eq!(topology.angles().len(), 1);
+
+topology.clear_bonds();
+assert!(topology.bonds().is_empty());
+assert!(topology.angles().is_empty());sourcepub fn add_bond(&mut self, i: usize, j: usize)
pub fn add_bond(&mut self, i: usize, j: usize)
Add a bond between the atoms at indexes i and j in the topology.
The bond order is set to BondOrder::Unknown.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+assert_eq!(topology.bonds_count(), 2);
+
+assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);sourcepub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder)
pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder)
Add a bond between the atoms at indexes i and j in the topology
+with the given bond order.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(2);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(topology.bond_order(0, 1), BondOrder::Double);sourcepub fn bond_order(&self, i: usize, j: usize) -> BondOrder
pub fn bond_order(&self, i: usize, j: usize) -> BondOrder
Get the bond order for the bond between the atoms at indexes i and
+j.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(2);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(topology.bond_order(0, 1), BondOrder::Double);sourcepub fn bond_orders(&self) -> Vec<BondOrder>
pub fn bond_orders(&self) -> Vec<BondOrder>
Get the bond order for all the bonds in the topology
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(3);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+topology.add_bond_with_order(0, 2, BondOrder::Single);
+
+assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);sourcepub fn remove_bond(&mut self, i: usize, j: usize)
pub fn remove_bond(&mut self, i: usize, j: usize)
Remove any existing bond between the atoms at indexes i and j in
+this topology.
This function does nothing if there is no bond between i and j.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(1, 2);
+assert_eq!(topology.bonds_count(), 2);
+
+topology.remove_bond(0, 1);
+assert_eq!(topology.bonds_count(), 1);
+
+// Removing a bond that does not exists is fine
+topology.remove_bond(0, 2);
+assert_eq!(topology.bonds_count(), 1);sourcepub fn residue(&self, index: usize) -> Option<ResidueRef<'_>>
pub fn residue(&self, index: usize) -> Option<ResidueRef<'_>>
Get a reference to the residue at index index from this topology.
The residue index in the topology is not always the same as the residue
+id.
Example
+let mut topology = Topology::new();
+topology.add_residue(&Residue::new("water")).unwrap();
+
+let residue = topology.residue(0).unwrap();
+assert_eq!(residue.name(), "water");sourcepub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef<'_>>
pub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef<'_>>
Get a copy of the residue containing the atom at index index in this
+topology, if any.
Example
+let mut topology = Topology::new();
+topology.resize(8);
+
+let mut residue = Residue::new("water");
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+topology.add_residue(&residue).unwrap();
+
+let residue = topology.residue_for_atom(0).unwrap();
+assert_eq!(residue.name(), "water");
+
+assert!(topology.residue_for_atom(6).is_none());sourcepub fn residues_count(&self) -> u64
pub fn residues_count(&self) -> u64
Get the number of residues in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.residues_count(), 0);
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+assert_eq!(topology.residues_count(), 2);sourcepub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error>
pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error>
Add a residue to this topology.
+Errors
+This function fails is the residue id is not already in the topology,
+or if the residue contains atoms that are already in another residue.
Example
+let mut topology = Topology::new();
+topology.add_residue(&Residue::new("water")).unwrap();
+
+let residue = topology.residue(0).unwrap();
+assert_eq!(residue.name(), "water");sourcepub fn are_linked(&self, first: &Residue, second: &Residue) -> bool
pub fn are_linked(&self, first: &Residue, second: &Residue) -> bool
Check if the two residues first and second from the topology are
+linked together, i.e. if there is a bond between one atom in the
+first residue and one atom in the second one.
Example
+let mut topology = Topology::new();
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+
+let first = topology.residue(0).unwrap();
+let second = topology.residue(1).unwrap();
+assert_eq!(topology.are_linked(&first, &second), false);Trait Implementations§
Auto Trait Implementations§
impl RefUnwindSafe for Topology
impl !Send for Topology
impl !Sync for Topology
impl Unpin for Topology
impl UnwindSafe for Topology
Blanket Implementations§
Struct chemfiles::TopologyRef
source · pub struct TopologyRef<'a> { /* private fields */ }Expand description
An analog to a reference to a topology (&Topology)
Methods from Deref<Target = Topology>§
sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the current number of atoms in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.size(), 0);
+
+topology.resize(6);
+assert_eq!(topology.size(), 6);sourcepub fn bonds_count(&self) -> usize
pub fn bonds_count(&self) -> usize
Get the number of bonds in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds_count(), 3);sourcepub fn angles_count(&self) -> usize
pub fn angles_count(&self) -> usize
Get the number of angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.angles_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles_count(), 2);sourcepub fn dihedrals_count(&self) -> usize
pub fn dihedrals_count(&self) -> usize
Get the number of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.dihedrals_count(), 1);sourcepub fn impropers_count(&self) -> usize
pub fn impropers_count(&self) -> usize
Get the number of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+assert_eq!(topology.impropers_count(), 1);sourcepub fn bonds(&self) -> Vec<[usize; 2]>
pub fn bonds(&self) -> Vec<[usize; 2]>
Get the list of bonds in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);sourcepub fn angles(&self) -> Vec<[usize; 3]>
pub fn angles(&self) -> Vec<[usize; 3]>
Get the list of angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);sourcepub fn dihedrals(&self) -> Vec<[usize; 4]>
pub fn dihedrals(&self) -> Vec<[usize; 4]>
Get the list of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+
+assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);sourcepub fn impropers(&self) -> Vec<[usize; 4]>
pub fn impropers(&self) -> Vec<[usize; 4]>
Get the list of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+
+assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);sourcepub fn bond_order(&self, i: usize, j: usize) -> BondOrder
pub fn bond_order(&self, i: usize, j: usize) -> BondOrder
Get the bond order for the bond between the atoms at indexes i and
+j.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(2);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(topology.bond_order(0, 1), BondOrder::Double);sourcepub fn bond_orders(&self) -> Vec<BondOrder>
pub fn bond_orders(&self) -> Vec<BondOrder>
Get the bond order for all the bonds in the topology
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(3);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+topology.add_bond_with_order(0, 2, BondOrder::Single);
+
+assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);sourcepub fn residue(&self, index: usize) -> Option<ResidueRef<'_>>
pub fn residue(&self, index: usize) -> Option<ResidueRef<'_>>
Get a reference to the residue at index index from this topology.
The residue index in the topology is not always the same as the residue
+id.
Example
+let mut topology = Topology::new();
+topology.add_residue(&Residue::new("water")).unwrap();
+
+let residue = topology.residue(0).unwrap();
+assert_eq!(residue.name(), "water");sourcepub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef<'_>>
pub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef<'_>>
Get a copy of the residue containing the atom at index index in this
+topology, if any.
Example
+let mut topology = Topology::new();
+topology.resize(8);
+
+let mut residue = Residue::new("water");
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+topology.add_residue(&residue).unwrap();
+
+let residue = topology.residue_for_atom(0).unwrap();
+assert_eq!(residue.name(), "water");
+
+assert!(topology.residue_for_atom(6).is_none());sourcepub fn residues_count(&self) -> u64
pub fn residues_count(&self) -> u64
Get the number of residues in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.residues_count(), 0);
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+assert_eq!(topology.residues_count(), 2);sourcepub fn are_linked(&self, first: &Residue, second: &Residue) -> bool
pub fn are_linked(&self, first: &Residue, second: &Residue) -> bool
Check if the two residues first and second from the topology are
+linked together, i.e. if there is a bond between one atom in the
+first residue and one atom in the second one.
Example
+let mut topology = Topology::new();
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+
+let first = topology.residue(0).unwrap();
+let second = topology.residue(1).unwrap();
+assert_eq!(topology.are_linked(&first, &second), false);Trait Implementations§
source§impl<'a> Debug for TopologyRef<'a>
impl<'a> Debug for TopologyRef<'a>
Auto Trait Implementations§
impl<'a> RefUnwindSafe for TopologyRef<'a>
impl<'a> !Send for TopologyRef<'a>
impl<'a> !Sync for TopologyRef<'a>
impl<'a> Unpin for TopologyRef<'a>
impl<'a> UnwindSafe for TopologyRef<'a>
Blanket Implementations§
Struct chemfiles::Trajectory
source · pub struct Trajectory { /* private fields */ }Expand description
The Trajectory type is the main entry point when using chemfiles. A
+Trajectory behave a bit like a file, allowing to read and/or write
+Frame.
Implementations§
source§impl Trajectory
impl Trajectory
sourcepub fn open<P>(path: P, mode: char) -> Result<Trajectory, Error>where
+ P: AsRef<Path>,
pub fn open<P>(path: P, mode: char) -> Result<Trajectory, Error>where + P: AsRef<Path>,
Open the file at the given path in the given mode.
Valid modes are 'r' for read, 'w' for write and 'a' for append.
Errors
+This function fails if the file is not accessible for the given mode, if +it is incorrectly formatted for the corresponding format, or in case of +I/O errors from the OS.
+Example
+let trajectory = Trajectory::open("water.xyz", 'r').unwrap();sourcepub fn open_with_format<'a, P, S>(
+ filename: P,
+ mode: char,
+ format: S
+) -> Result<Trajectory, Error>where
+ P: AsRef<Path>,
+ S: Into<&'a str>,
pub fn open_with_format<'a, P, S>( + filename: P, + mode: char, + format: S +) -> Result<Trajectory, Error>where + P: AsRef<Path>, + S: Into<&'a str>,
Open the file at the given path using a specific file format and the
+given mode.
Valid modes are 'r' for read, 'w' for write and 'a' for append.
Specifying a format is needed when the file format does not match the
+extension, or when there is not standard extension for this format. If
+format is an empty string, the format will be guessed from the
+extension.
Errors
+This function fails if the file is not accessible for the given mode, if +it is incorrectly formatted for the corresponding format, or in case of +I/O errors from the OS.
+Example
+let trajectory = Trajectory::open_with_format("water.zeo", 'r', "XYZ").unwrap();sourcepub fn memory_writer<'a, S>(format: S) -> Result<Trajectory, Error>where
+ S: Into<&'a str>,
pub fn memory_writer<'a, S>(format: S) -> Result<Trajectory, Error>where + S: Into<&'a str>,
Write to a memory buffer as though it was a formatted file.
+The format parameter should follow the same rules as in the main
+Trajectory constructor, except that compression specification
+is not supported.
The memory_buffer function can be used to retrieve the data written
+to memory of the Trajectory.
Errors
+This function fails if the format do not support in-memory writers.
+Example
+let trajectory_memory = Trajectory::memory_writer("SMI");
+
+// Binary formats typically do not support this feature
+assert!(Trajectory::memory_writer("XTC").is_err());sourcepub fn read(&mut self, frame: &mut Frame) -> Result<(), Error>
pub fn read(&mut self, frame: &mut Frame) -> Result<(), Error>
Read the next step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of atom +in the next step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+let mut frame = Frame::new();
+
+trajectory.read(&mut frame).unwrap();sourcepub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error>
pub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error>
Read a specific step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of +atom at this step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+let mut frame = Frame::new();
+
+trajectory.read_step(10, &mut frame).unwrap();sourcepub fn set_topology(&mut self, topology: &Topology)
pub fn set_topology(&mut self, topology: &Topology)
Set the topology associated with this trajectory. This topology will
+be used when reading and writing the files, replacing any topology in
+the frames or files.
Example
+let mut topology = Topology::new();
+topology.add_atom(&Atom::new("H"));
+topology.add_atom(&Atom::new("O"));
+topology.add_atom(&Atom::new("H"));
+topology.add_bond(0, 1);
+topology.add_bond(1, 2);
+
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+trajectory.set_topology(&topology);sourcepub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error>where
+ P: AsRef<Path>,
pub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error>where + P: AsRef<Path>,
Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in format;
+and extracting the topology of this frame.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+trajectory.set_topology_file("topology.pdb").unwrap();sourcepub fn set_topology_with_format<'a, P, S>(
+ &mut self,
+ path: P,
+ format: S
+) -> Result<(), Error>where
+ P: AsRef<Path>,
+ S: Into<&'a str>,
pub fn set_topology_with_format<'a, P, S>( + &mut self, + path: P, + format: S +) -> Result<(), Error>where + P: AsRef<Path>, + S: Into<&'a str>,
Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in
+format; and extracting the topology of this frame.
If format is an empty string, the format will be guessed from the
+path extension.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+trajectory.set_topology_with_format("topology.mol", "PDB").unwrap();sourcepub fn set_cell(&mut self, cell: &UnitCell)
pub fn set_cell(&mut self, cell: &UnitCell)
Set the unit cell associated with a trajectory. This cell will be
+used when reading and writing the files, replacing any unit cell in the
+frames or files.
Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+trajectory.set_cell(&UnitCell::new([10.0, 11.0, 12.5]));sourcepub fn nsteps(&mut self) -> usize
pub fn nsteps(&mut self) -> usize
Get the number of steps (the number of frames) in a trajectory.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+
+println!("This trajectory contains {} steps", trajectory.nsteps());sourcepub fn memory_buffer(&self) -> Result<&str, Error>
pub fn memory_buffer(&self) -> Result<&str, Error>
Obtain the memory buffer written to by the trajectory.
+Errors
+This fails if the trajectory was not opened with
+Trajectory::memory_writer.
Example
+let mut trajectory_memory = Trajectory::memory_writer("SMI").unwrap();
+
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+frame.add_bond_with_order(0, 1, BondOrder::Single);
+
+trajectory_memory.write(&frame).unwrap();
+
+let result = trajectory_memory.memory_buffer();
+assert_eq!(result.unwrap(), "CC\n");Trait Implementations§
source§impl Debug for Trajectory
impl Debug for Trajectory
Auto Trait Implementations§
impl RefUnwindSafe for Trajectory
impl !Send for Trajectory
impl !Sync for Trajectory
impl Unpin for Trajectory
impl UnwindSafe for Trajectory
Blanket Implementations§
pub struct UnitCell { /* private fields */ }Expand description
An UnitCell represent the box containing the atoms, and its periodicity.
An unit cell is fully represented by three lengths (a, b, c); and three +angles (alpha, beta, gamma). The angles are stored in degrees, and the +lengths in Angstroms.
+A cell also has a matricial representation, by projecting the three base +vector into an orthonormal base. We choose to represent such matrix as an +upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |
+Implementations§
source§impl UnitCell
impl UnitCell
sourcepub fn new(lengths: [f64; 3]) -> UnitCell
pub fn new(lengths: [f64; 3]) -> UnitCell
Create an Orthorhombic UnitCell from the three lengths, in Angstroms.
Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);sourcepub fn infinite() -> UnitCell
pub fn infinite() -> UnitCell
Create an Infinite UnitCell.
Example
+let cell = UnitCell::infinite();
+
+assert_eq!(cell.lengths(), [0.0, 0.0, 0.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+assert_eq!(cell.shape(), CellShape::Infinite);sourcepub fn triclinic(lengths: [f64; 3], angles: [f64; 3]) -> UnitCell
pub fn triclinic(lengths: [f64; 3], angles: [f64; 3]) -> UnitCell
Create an Triclinic UnitCell from the three lengths (in Angstroms)
+and three angles (in degree). alpha is the angle between the vectors
+b and c; beta is the between the vectors a and c and gamma
+is the angle between the vectors a and b.
Example
+let cell = UnitCell::triclinic([10.0, 10.0, 10.0], [98.0, 99.0, 90.0]);
+
+assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);
+assert_eq!(cell.angles()[0], 98.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 99.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);
+assert_eq!(cell.shape(), CellShape::Triclinic);sourcepub fn from_matrix(matrix: [[f64; 3]; 3]) -> UnitCell
pub fn from_matrix(matrix: [[f64; 3]; 3]) -> UnitCell
Create an UnitCell from a cell matrix. If matrix contains only
+zeros, then an Infinite cell is created. If only the diagonal of the
+matrix is non-zero, then the cell is Orthorhombic. Else a
+Triclinic cell is created. The matrix entries should be in Angstroms.
Panics
+If the matrix has a negative determinant, or more generally is not +representing a unit cell.
+Example
+let cell = UnitCell::from_matrix([
+ [1.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]
+]);
+
+assert_eq!(cell.lengths(), [1.0, 2.0, 3.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);sourcepub fn lengths(&self) -> [f64; 3]
pub fn lengths(&self) -> [f64; 3]
Get the three lengths of the cell, in Angstroms.
+Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);sourcepub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error>
pub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error>
Set the three lengths of the cell, in Angstroms.
+Errors
+This function fails if the unit cell is infinite, or if one of the +lengths is negative.
+Example
+let mut cell = UnitCell::new([30.0, 30.0, 23.0]);
+
+cell.set_lengths([10.0, 30.0, 42.0]).unwrap();
+assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]);
+
+assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());sourcepub fn angles(&self) -> [f64; 3]
pub fn angles(&self) -> [f64; 3]
Get the three angles of the cell, in degrees.
+Example
+let cell = UnitCell::new([20.0, 20.0, 20.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+
+let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);sourcepub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error>
pub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error>
Set the three angles of the cell, in degrees.
+Errors
+This function fails if the unit cell is not Triclinic.
Example
+let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);
+
+cell.set_angles([90.0, 90.0, 90.0]).unwrap();
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);sourcepub fn matrix(&self) -> [[f64; 3]; 3]
pub fn matrix(&self) -> [[f64; 3]; 3]
Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+
+let matrix = cell.matrix();
+
+assert_eq!(matrix[0][0], 10.0);
+assert_eq!(matrix[1][1], 20.0);
+assert_eq!(matrix[2][2], 30.0);
+
+assert!(matrix[1][2].abs() < 1e-9);sourcepub fn shape(&self) -> CellShape
pub fn shape(&self) -> CellShape
Get the shape of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);sourcepub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error>
pub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error>
Set the shape of the unit cell to shape.
Errors
+This can fail if the cell length or angles are incompatible with the +new shape.
+Example
+let mut cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);
+
+cell.set_shape(CellShape::Triclinic).unwrap();
+assert_eq!(cell.shape(), CellShape::Triclinic);Trait Implementations§
Auto Trait Implementations§
impl RefUnwindSafe for UnitCell
impl !Send for UnitCell
impl !Sync for UnitCell
impl Unpin for UnitCell
impl UnwindSafe for UnitCell
Blanket Implementations§
Struct chemfiles::UnitCellMut
source · pub struct UnitCellMut<'a> { /* private fields */ }Expand description
An analog to a mutable reference to an unit cell (&mut UnitCell)
Methods from Deref<Target = UnitCell>§
sourcepub fn lengths(&self) -> [f64; 3]
pub fn lengths(&self) -> [f64; 3]
Get the three lengths of the cell, in Angstroms.
+Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);sourcepub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error>
pub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error>
Set the three lengths of the cell, in Angstroms.
+Errors
+This function fails if the unit cell is infinite, or if one of the +lengths is negative.
+Example
+let mut cell = UnitCell::new([30.0, 30.0, 23.0]);
+
+cell.set_lengths([10.0, 30.0, 42.0]).unwrap();
+assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]);
+
+assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());sourcepub fn angles(&self) -> [f64; 3]
pub fn angles(&self) -> [f64; 3]
Get the three angles of the cell, in degrees.
+Example
+let cell = UnitCell::new([20.0, 20.0, 20.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+
+let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);sourcepub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error>
pub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error>
Set the three angles of the cell, in degrees.
+Errors
+This function fails if the unit cell is not Triclinic.
Example
+let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);
+
+cell.set_angles([90.0, 90.0, 90.0]).unwrap();
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);sourcepub fn matrix(&self) -> [[f64; 3]; 3]
pub fn matrix(&self) -> [[f64; 3]; 3]
Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+
+let matrix = cell.matrix();
+
+assert_eq!(matrix[0][0], 10.0);
+assert_eq!(matrix[1][1], 20.0);
+assert_eq!(matrix[2][2], 30.0);
+
+assert!(matrix[1][2].abs() < 1e-9);sourcepub fn shape(&self) -> CellShape
pub fn shape(&self) -> CellShape
Get the shape of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);sourcepub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error>
pub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error>
Set the shape of the unit cell to shape.
Errors
+This can fail if the cell length or angles are incompatible with the +new shape.
+Example
+let mut cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);
+
+cell.set_shape(CellShape::Triclinic).unwrap();
+assert_eq!(cell.shape(), CellShape::Triclinic);Trait Implementations§
source§impl<'a> Debug for UnitCellMut<'a>
impl<'a> Debug for UnitCellMut<'a>
source§impl<'a> Deref for UnitCellMut<'a>
impl<'a> Deref for UnitCellMut<'a>
Auto Trait Implementations§
impl<'a> RefUnwindSafe for UnitCellMut<'a>
impl<'a> !Send for UnitCellMut<'a>
impl<'a> !Sync for UnitCellMut<'a>
impl<'a> Unpin for UnitCellMut<'a>
impl<'a> !UnwindSafe for UnitCellMut<'a>
Blanket Implementations§
Struct chemfiles::UnitCellRef
source · pub struct UnitCellRef<'a> { /* private fields */ }Expand description
An analog to a reference to an unit cell (&UnitCell)
Methods from Deref<Target = UnitCell>§
sourcepub fn lengths(&self) -> [f64; 3]
pub fn lengths(&self) -> [f64; 3]
Get the three lengths of the cell, in Angstroms.
+Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);sourcepub fn angles(&self) -> [f64; 3]
pub fn angles(&self) -> [f64; 3]
Get the three angles of the cell, in degrees.
+Example
+let cell = UnitCell::new([20.0, 20.0, 20.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+
+let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);sourcepub fn matrix(&self) -> [[f64; 3]; 3]
pub fn matrix(&self) -> [[f64; 3]; 3]
Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+
+let matrix = cell.matrix();
+
+assert_eq!(matrix[0][0], 10.0);
+assert_eq!(matrix[1][1], 20.0);
+assert_eq!(matrix[2][2], 30.0);
+
+assert!(matrix[1][2].abs() < 1e-9);sourcepub fn shape(&self) -> CellShape
pub fn shape(&self) -> CellShape
Get the shape of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);Trait Implementations§
source§impl<'a> Debug for UnitCellRef<'a>
impl<'a> Debug for UnitCellRef<'a>
Auto Trait Implementations§
impl<'a> RefUnwindSafe for UnitCellRef<'a>
impl<'a> !Send for UnitCellRef<'a>
impl<'a> !Sync for UnitCellRef<'a>
impl<'a> Unpin for UnitCellRef<'a>
impl<'a> UnwindSafe for UnitCellRef<'a>
Blanket Implementations§
Redirecting to ../../chemfiles/enum.BondOrder.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/topology/struct.Topology.html b/0.10.4/chemfiles/topology/struct.Topology.html new file mode 100644 index 000000000..1215dacfd --- /dev/null +++ b/0.10.4/chemfiles/topology/struct.Topology.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Topology.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/topology/struct.TopologyRef.html b/0.10.4/chemfiles/topology/struct.TopologyRef.html new file mode 100644 index 000000000..7cdec6164 --- /dev/null +++ b/0.10.4/chemfiles/topology/struct.TopologyRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.TopologyRef.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/trajectory/struct.MemoryTrajectoryReader.html b/0.10.4/chemfiles/trajectory/struct.MemoryTrajectoryReader.html new file mode 100644 index 000000000..2d8d0b029 --- /dev/null +++ b/0.10.4/chemfiles/trajectory/struct.MemoryTrajectoryReader.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.MemoryTrajectoryReader.html...
+ + + \ No newline at end of file diff --git a/0.10.4/chemfiles/trajectory/struct.Trajectory.html b/0.10.4/chemfiles/trajectory/struct.Trajectory.html new file mode 100644 index 000000000..bab83ffc9 --- /dev/null +++ b/0.10.4/chemfiles/trajectory/struct.Trajectory.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Trajectory.html...
+ + + \ No newline at end of file diff --git a/0.10.4/crates.js b/0.10.4/crates.js new file mode 100644 index 000000000..833ec8f70 --- /dev/null +++ b/0.10.4/crates.js @@ -0,0 +1 @@ +window.ALL_CRATES = ["chemfiles"]; \ No newline at end of file diff --git a/0.10.4/help.html b/0.10.4/help.html new file mode 100644 index 000000000..9c53f6f6c --- /dev/null +++ b/0.10.4/help.html @@ -0,0 +1 @@ +Rustdoc help
BackAtom is a particle in the current Frame. It stores the …","An analog to a mutable reference to an atom (&mut Atom)","An analog to a reference to an atom (&Atom)","Possible bond order associated with bonds","Boolean property","Available unit cell shapes.","Exception in the C++ chemfiles library","Error in configuration files syntax","Double bond","Floating point property","Error type for Chemfiles.","Error while reading or writing a file","Error in file formatting, i.e. the file is invalid","FormatMetadata contains metadata associated with one …","A Frame contains data from one simulation step: the …","Infinite cell, to use when there is no cell.","A Match is a set of atomic indexes matching a given …","Error in memory allocations","MemoryTrajectoryReader is a handle for a Trajectory in …","Orthorhombic cell, with the three angles equals to 90°.","Error for out of bounds indexing","An iterator over the properties in an atom/frame/residue","A Property is a piece of data that can be associated with …","Error related to properties","Quadruple bond (present in some metals)","Quintuplet bond (present in some metals)","A Residue is a group of atoms belonging to the same …","An analog to a reference to a residue (&Residue)","A Selection allow to select atoms in a Frame, from a …","Error in selection string syntax","Single bond","Possible causes of error in chemfiles","Exception in the C++ standard library","String property","No error","A Topology contains the definition of all the atoms in the …","An analog to a reference to a topology (&Topology)","The Trajectory type is the main entry point when using …","Triclinic cell, with any values for the angles.","Triple bond","The given path is not valid UTF8","An UnitCell represent the box containing the atoms, and …","An analog to a mutable reference to an unit cell (…","An analog to a reference to an unit cell (&UnitCell)","Unknown or unspecified bond order","3-dimensional vector property","Add the atom at index atom in this residue.","Add an Atom at the end of this topology","Add an Atom and the corresponding position and optionally …","Add a bond between the atoms at indexes i and j in the …","Add a bond between the atoms at indexes i and j in the …","Add a bond between the atoms at indexes i and j in the …","Add a bond between the atoms at indexes i and j in the …","Read configuration data from the file at path.","Add a residue to this topology.","Add a copy of residue to this frame.","Add velocity data to this frame. If the frame already have …","Get the angle formed by the atoms at indexes i, j and k in …","Get the three angles of the cell, in degrees.","Get the list of angles in the topology.","Get the number of angles in the topology.","Check if the two residues first and second from the …","Get a reference of the atom at the given index in this …","Get a reference to the atom at the given index in this …","Get a mutable reference to the atom at the given index in …","Get a mutable reference to the atom at the given index in …","Try to get the atomic number of the atom from the atomic …","Get the atom type.","Get the list of atoms of this residue.","Does this format support storing atom names or types?","Get the bond order for the bond between the atoms at …","Get the bond order for all the bonds in the topology","Get the list of bonds in the topology.","Does this format support storing bonds between atoms?","Get the number of bonds in the topology.","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","Get a reference to the UnitCell from this frame.","Get a mutable reference to the UnitCell from this frame.","Get the atom charge, in number of the electron charge e.","Clear any error from the C++ library","Remove all existing bonds, angles, dihedral angles and …","Remove all existing bonds, angles, dihedral angles and …","","","","","","","","","","","","","","","","","","","","","","","","","","","","Check if the atom at index i is in this residue","","Try to get the covalent radius of the atom from the atomic …","","","","","","","","","","","","Extended, user-facing description of the format.","Get the dihedral angle formed by the atoms at indexes i, j…","Get the list of dihedral angles in the topology.","Get the number of dihedral angles in the topology.","Get the distance between the atoms at indexes i and j in …","","","","","","","","","","","","","","","Evaluate a selection for a given frame, and return the …","Extension associated with the format.","","","","","","","","","","","","","","","","","","","","","","Get the list of formats known by chemfiles, as well as all …","Returns the argument unchanged.","Returns the argument unchanged.","","Returns the argument unchanged.","","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","","","","","Returns the argument unchanged.","","Returns the argument unchanged.","Create an UnitCell from a cell matrix. If matrix contains …","Try to get the full name of the atom from the atomic type. …","Get a property with the given name in this atom, if it …","Get a property with the given name in this frame, if it …","Get a property with the given name in this frame, if it …","Guess the bonds, angles and dihedrals in this frame.","Get the format that chemfiles would use to read a file at …","Check if this frame contains velocity data.","Get the identifier of this residue in the initial topology …","Get the list of improper dihedral angles in the topology.","Get the number of improper dihedral angles in the topology.","","Create an Infinite UnitCell.","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","","","Iterate over the atomic indexes in the match.","Gets an iterator over atoms","Get the last error message from the C++ library.","Get the length of the Match.","Get the three lengths of the cell, in Angstroms.","Evaluates a selection of size 1 on a given frame. This …","Get the atom mass, in atomic mass units.","Get the unit cell matricial representation.","Does this format support in-memory IO?","Obtain the memory buffer written to by the trajectory.","Write to a memory buffer as though it was a formatted file.","A message describing the error cause","Get the atom name.","Get the name of this residue.","Name of the format.","Read a memory buffer as though it was a formatted file.","Create an atom with the given name, and set the atom type …","Create an Orthorhombic UnitCell from the three lengths, in …","Create a new residue with the given name","Create a new empty topology.","Create an empty frame. It will be resized by the library …","Create a new match containing the atoms in the atoms slice.","Create a new selection from the given selection string.","","Get the number of steps (the number of frames) in a …","Open the file at the given path in the given mode.","Open the file at the given path using a specific file …","Get the out of plane distance formed by the atoms at …","","","Get file path for this trajectory.","Get a view into the positions of this frame.","Does this format support storing atomic positions?","Get a mutable view into the positions of this frame.","Get an iterator over all (name, property) pairs for this …","Get an iterator over all (name, property) pairs for this …","Get an iterator over all (name, property) pairs for this …","","Read the next step of this trajectory into a frame.","Is reading files in this format implemented?","Read a specific step of this trajectory into a frame.","URL pointing to the format definition/reference.","Remove an Atom from this topology by index. This modify …","Remove the atom at index i in this frame.","Remove any existing bond between the atoms at indexes i …","Remove any existing bond between the atoms at indexes i …","Get a reference to the residue at index index from this …","Get a copy of the residue containing the atom at index …","Does this format support storing residues?","Get the number of residues in this topology.","Resize this topology to hold natoms atoms, inserting dummy …","Resize the positions and the velocities in this frame, to …","Add a new property with the given name to this atom.","Add a new property with the given name to this residue.","Add a new property with the given name to this frame.","Set the three angles of the cell, in degrees.","Set the atom type to atomic_type.","Set the UnitCell of this frame to cell.","Set the unit cell associated with a trajectory. This cell …","Set the atom charge to charge, in number of the electron …","Set the three lengths of the cell, in Angstroms.","Set the atom mass to mass, in atomic mass units.","Set the atom name to name.","Set the shape of the unit cell to shape.","Set this frame step to step.","Set the Topology of this frame to topology.","Set the topology associated with this trajectory. This …","Set the topology associated with this trajectory by …","Set the topology associated with this trajectory by …","Use callback for every chemfiles warning. The callback …","Get the shape of the unit cell.","Get the number of atoms in this residue.","Get the current number of atoms in this topology.","Get the current number of atoms in this frame.","Get the size of the selection, i.e. the number of atoms we …","","The error status code","Get this frame step, i.e. the frame number in the …","Get the selection string used to create this selection.","","","","","","","","","","","","","","","Get a reference to the Topology of this frame.","Create an Triclinic UnitCell from the three lengths (in …","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","Does this format support storing unit cell information?","Try to get the Van der Waals radius of the atom from the …","Get a view into the velocities of this frame.","Does this format support storing atomic velocities?","Get a mutable view into the velocities of this frame.","Get the version of the chemfiles library.","Get the volume of the unit cell.","Create a new residue with the given name and id as …","Wrap a vector in this unit cell.","Write a frame to this trajectory.","Is writing files in this format 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+}');
+if (typeof window !== 'undefined' && window.initSearch) {window.initSearch(searchIndex)};
+if (typeof exports !== 'undefined') {exports.searchIndex = searchIndex};
diff --git a/0.10.4/settings.html b/0.10.4/settings.html
new file mode 100644
index 000000000..9135508e6
--- /dev/null
+++ b/0.10.4/settings.html
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+Rustdoc settings
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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::marker::PhantomData;
+
+use chemfiles_sys::*;
+
+use crate::errors::{check_not_null, check_success};
+use crate::property::{PropertiesIter, Property, RawProperty};
+use crate::strings;
+
+/// An `Atom` is a particle in the current `Frame`. It stores the following
+/// atomic properties:
+///
+/// - atom name;
+/// - atom type;
+/// - atom mass;
+/// - atom charge.
+///
+/// The atom name is usually an unique identifier (`H1`, `C_a`) while the
+/// atom type will be shared between all particles of the same type: `H`,
+/// `Ow`, `CH3`.
+#[derive(Debug)]
+pub struct Atom {
+ handle: *mut CHFL_ATOM,
+}
+
+/// An analog to a reference to an atom (`&Atom`)
+#[derive(Debug)]
+pub struct AtomRef<'a> {
+ inner: Atom,
+ marker: PhantomData<&'a Atom>,
+}
+
+impl<'a> std::ops::Deref for AtomRef<'a> {
+ type Target = Atom;
+ fn deref(&self) -> &Atom {
+ &self.inner
+ }
+}
+
+/// An analog to a mutable reference to an atom (`&mut Atom`)
+#[derive(Debug)]
+pub struct AtomMut<'a> {
+ inner: Atom,
+ marker: PhantomData<&'a mut Atom>,
+}
+
+impl<'a> std::ops::Deref for AtomMut<'a> {
+ type Target = Atom;
+ fn deref(&self) -> &Atom {
+ &self.inner
+ }
+}
+
+impl<'a> std::ops::DerefMut for AtomMut<'a> {
+ fn deref_mut(&mut self) -> &mut Atom {
+ &mut self.inner
+ }
+}
+
+impl Clone for Atom {
+ fn clone(&self) -> Atom {
+ unsafe {
+ let new_handle = chfl_atom_copy(self.as_ptr());
+ Atom::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Atom {
+ /// Create an owned `Atom` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_ATOM) -> Atom {
+ check_not_null(ptr);
+ Atom { handle: ptr }
+ }
+
+ /// Create a borrowed `Atom` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, and the caller is responsible for setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_ATOM) -> AtomRef<'a> {
+ AtomRef {
+ inner: Atom::from_ptr(ptr as *mut CHFL_ATOM),
+ marker: PhantomData,
+ }
+ }
+
+ /// Create a mutably borrowed `Atom` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, and the caller is responsible for setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_mut_from_ptr<'a>(ptr: *mut CHFL_ATOM) -> AtomMut<'a> {
+ AtomMut {
+ inner: Atom::from_ptr(ptr),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_ATOM {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_ATOM {
+ self.handle
+ }
+
+ /// Create an atom with the given `name`, and set the atom type to `name`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.name(), "He");
+ /// ```
+ pub fn new<'a>(name: impl Into<&'a str>) -> Atom {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ let handle = chfl_atom(buffer.as_ptr());
+ Atom::from_ptr(handle)
+ }
+ }
+
+ /// Get the atom mass, in atomic mass units.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.mass(), 4.002602);
+ /// ```
+ pub fn mass(&self) -> f64 {
+ let mut mass = 0.0;
+ unsafe {
+ check_success(chfl_atom_mass(self.as_ptr(), &mut mass));
+ }
+ return mass;
+ }
+
+ /// Set the atom mass to `mass`, in atomic mass units.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_mass(34.9);
+ /// assert_eq!(atom.mass(), 34.9);
+ /// ```
+ pub fn set_mass(&mut self, mass: f64) {
+ unsafe {
+ check_success(chfl_atom_set_mass(self.as_mut_ptr(), mass));
+ }
+ }
+
+ /// Get the atom charge, in number of the electron charge *e*.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.charge(), 0.0);
+ /// ```
+ pub fn charge(&self) -> f64 {
+ let mut charge = 0.0;
+ unsafe {
+ check_success(chfl_atom_charge(self.as_ptr(), &mut charge));
+ }
+ return charge;
+ }
+
+ /// Set the atom charge to `charge`, in number of the electron charge *e*.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_charge(-2.0);
+ /// assert_eq!(atom.charge(), -2.0);
+ /// ```
+ pub fn set_charge(&mut self, charge: f64) {
+ unsafe {
+ check_success(chfl_atom_set_charge(self.as_mut_ptr(), charge));
+ }
+ }
+
+ /// Get the atom name.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.name(), "He");
+ /// ```
+ pub fn name(&self) -> String {
+ let get_name = |ptr, len| unsafe { chfl_atom_name(self.as_ptr(), ptr, len) };
+ let name = strings::call_autogrow_buffer(10, get_name).expect("getting name failed");
+ return strings::from_c(name.as_ptr());
+ }
+
+ /// Get the atom type.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.atomic_type(), "He");
+ /// ```
+ pub fn atomic_type(&self) -> String {
+ let get_type = |ptr, len| unsafe { chfl_atom_type(self.as_ptr(), ptr, len) };
+ let buffer = strings::call_autogrow_buffer(10, get_type).expect("getting type failed");
+ return strings::from_c(buffer.as_ptr());
+ }
+
+ /// Set the atom name to `name`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_name("Zn3");
+ /// assert_eq!(atom.name(), "Zn3");
+ /// ```
+ pub fn set_name<'a>(&mut self, name: impl Into<&'a str>) {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ check_success(chfl_atom_set_name(self.as_mut_ptr(), buffer.as_ptr()));
+ }
+ }
+
+ /// Set the atom type to `atomic_type`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_atomic_type("F");
+ /// assert_eq!(atom.atomic_type(), "F");
+ /// ```
+ pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>) {
+ let buffer = strings::to_c(atomic_type.into());
+ unsafe {
+ check_success(chfl_atom_set_type(self.as_mut_ptr(), buffer.as_ptr()));
+ }
+ }
+
+ /// Try to get the full name of the atom from the atomic type. For example,
+ /// the full name of "He" is "Helium", and so on. If the name can not be
+ /// found, this function returns the empty string.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("Zn");
+ /// assert_eq!(atom.full_name(), "Zinc");
+ /// ```
+ pub fn full_name(&self) -> String {
+ let get_full_name = |ptr, len| unsafe { chfl_atom_full_name(self.as_ptr(), ptr, len) };
+ let name = strings::call_autogrow_buffer(10, get_full_name).expect("getting full name failed");
+ return strings::from_c(name.as_ptr());
+ }
+
+ /// Try to get the Van der Waals radius of the atom from the atomic type.
+ /// If the radius can not be found, returns 0.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+ /// assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);
+ /// ```
+ pub fn vdw_radius(&self) -> f64 {
+ let mut radius: f64 = 0.0;
+ unsafe {
+ check_success(chfl_atom_vdw_radius(self.as_ptr(), &mut radius));
+ }
+ return radius;
+ }
+
+ /// Try to get the covalent radius of the atom from the atomic type. If the
+ /// radius can not be found, returns 0.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+ /// assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);
+ /// ```
+ pub fn covalent_radius(&self) -> f64 {
+ let mut radius: f64 = 0.0;
+ unsafe {
+ check_success(chfl_atom_covalent_radius(self.as_ptr(), &mut radius));
+ }
+ return radius;
+ }
+
+ /// Try to get the atomic number of the atom from the atomic type. If the
+ /// number can not be found, returns 0.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// assert_eq!(Atom::new("He").atomic_number(), 2);
+ /// assert_eq!(Atom::new("Xxx").atomic_number(), 0);
+ /// ```
+ pub fn atomic_number(&self) -> u64 {
+ let mut number = 0;
+ unsafe {
+ check_success(chfl_atom_atomic_number(self.as_ptr(), &mut number));
+ }
+ return number;
+ }
+
+ /// Add a new `property` with the given `name` to this atom.
+ ///
+ /// If a property with the same name already exists, this function override
+ /// the existing property with the new one.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Atom, Property};
+ /// let mut atom = Atom::new("He");
+ /// atom.set("a bool", true);
+ /// atom.set("a string", "test");
+ ///
+ /// assert_eq!(atom.get("a bool"), Some(Property::Bool(true)));
+ /// assert_eq!(atom.get("a string"), Some(Property::String("test".into())));
+ /// ```
+ pub fn set(&mut self, name: &str, property: impl Into<Property>) {
+ let buffer = strings::to_c(name);
+ let property = property.into().as_raw();
+ unsafe {
+ check_success(chfl_atom_set_property(
+ self.as_mut_ptr(),
+ buffer.as_ptr(),
+ property.as_ptr(),
+ ));
+ }
+ }
+
+ /// Get a property with the given `name` in this atom, if it exist.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Atom, Property};
+ /// let mut atom = Atom::new("He");
+ /// atom.set("foo", Property::Double(22.2));
+ ///
+ /// assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+ /// assert_eq!(atom.get("Bar"), None);
+ /// ```
+ pub fn get(&self, name: &str) -> Option<Property> {
+ let buffer = strings::to_c(name);
+ unsafe {
+ let handle = chfl_atom_get_property(self.as_ptr(), buffer.as_ptr());
+ if handle.is_null() {
+ None
+ } else {
+ let raw = RawProperty::from_ptr(handle);
+ let property = Property::from_raw(raw);
+ Some(property)
+ }
+ }
+ }
+
+ /// Get an iterator over all (name, property) pairs for this atom
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Atom, Property};
+ /// let mut atom = Atom::new("He");
+ /// atom.set("foo", Property::Double(22.2));
+ /// atom.set("bar", Property::Bool(false));
+ ///
+ /// for (name, property) in atom.properties() {
+ /// if name == "foo" {
+ /// assert_eq!(property, Property::Double(22.2));
+ /// } else if name == "bar" {
+ /// assert_eq!(property, Property::Bool(false));
+ /// }
+ /// }
+ /// ```
+ pub fn properties(&self) -> PropertiesIter {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_atom_properties_count(self.as_ptr(), &mut count));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = count as usize;
+ let mut c_names = vec![std::ptr::null_mut(); size];
+ unsafe {
+ check_success(chfl_atom_list_properties(self.as_ptr(), c_names.as_mut_ptr(), count));
+ }
+
+ let mut names = Vec::new();
+ for ptr in c_names {
+ names.push(strings::from_c(ptr));
+ }
+
+ PropertiesIter {
+ names: names.into_iter(),
+ getter: Box::new(move |name| self.get(name).expect("failed to get property")),
+ }
+ }
+}
+
+impl Drop for Atom {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.name(), "He");
+
+ let copy = atom.clone();
+ assert_eq!(copy.name(), "He");
+
+ atom.set_name("Na");
+ assert_eq!(atom.name(), "Na");
+ assert_eq!(copy.name(), "He");
+ }
+
+ #[test]
+ fn mass() {
+ let mut atom = Atom::new("He");
+ approx::assert_ulps_eq!(atom.mass(), 4.002602);
+ atom.set_mass(15.0);
+ assert_eq!(atom.mass(), 15.0);
+ }
+
+ #[test]
+ fn charge() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.charge(), 0.0);
+ atom.set_charge(-1.5);
+ assert_eq!(atom.charge(), -1.5);
+ }
+
+ #[test]
+ fn name() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.name(), "He");
+ atom.set_name("Zn-12");
+ assert_eq!(atom.name(), "Zn-12");
+ }
+
+ #[test]
+ fn atomic_type() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.atomic_type(), "He");
+ atom.set_atomic_type("Zn");
+ assert_eq!(atom.atomic_type(), "Zn");
+ }
+
+ #[test]
+ fn full_name() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.full_name(), "Helium");
+
+ atom.set_atomic_type("Zn");
+ assert_eq!(atom.full_name(), "Zinc");
+
+ let atom = Atom::new("Unknown");
+ assert_eq!(atom.full_name(), "");
+ }
+
+ #[test]
+ fn radii() {
+ let atom = Atom::new("He");
+ approx::assert_ulps_eq!(atom.vdw_radius(), 1.4);
+ approx::assert_ulps_eq!(atom.covalent_radius(), 0.32);
+
+ let atom = Atom::new("Unknown");
+ assert_eq!(atom.vdw_radius(), 0.0);
+ assert_eq!(atom.covalent_radius(), 0.0);
+ }
+
+ #[test]
+ fn atomic_number() {
+ let atom = Atom::new("He");
+ assert_eq!(atom.atomic_number(), 2);
+
+ let atom = Atom::new("Unknown");
+ assert_eq!(atom.atomic_number(), 0);
+ }
+
+ #[test]
+ fn property() {
+ let mut atom = Atom::new("F");
+
+ atom.set("foo", -22.0);
+ assert_eq!(atom.get("foo"), Some(Property::Double(-22.0)));
+ assert_eq!(atom.get("bar"), None);
+
+ atom.set("bar", Property::String("here".into()));
+ for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(-22.0));
+ } else if name == "bar" {
+ assert_eq!(property, Property::String("here".into()));
+ }
+ }
+ }
+}
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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::marker::PhantomData;
+
+use chemfiles_sys::*;
+
+use crate::errors::{check, check_not_null, check_success, Error};
+
+/// Available unit cell shapes.
+#[derive(Clone, Debug, PartialEq, Eq)]
+pub enum CellShape {
+ /// Orthorhombic cell, with the three angles equals to 90°.
+ Orthorhombic,
+ /// Triclinic cell, with any values for the angles.
+ Triclinic,
+ /// Infinite cell, to use when there is no cell.
+ Infinite,
+}
+
+impl From<chfl_cellshape> for CellShape {
+ fn from(celltype: chfl_cellshape) -> CellShape {
+ match celltype {
+ chfl_cellshape::CHFL_CELL_ORTHORHOMBIC => CellShape::Orthorhombic,
+ chfl_cellshape::CHFL_CELL_TRICLINIC => CellShape::Triclinic,
+ chfl_cellshape::CHFL_CELL_INFINITE => CellShape::Infinite,
+ }
+ }
+}
+
+impl From<CellShape> for chfl_cellshape {
+ fn from(celltype: CellShape) -> chfl_cellshape {
+ match celltype {
+ CellShape::Orthorhombic => chfl_cellshape::CHFL_CELL_ORTHORHOMBIC,
+ CellShape::Triclinic => chfl_cellshape::CHFL_CELL_TRICLINIC,
+ CellShape::Infinite => chfl_cellshape::CHFL_CELL_INFINITE,
+ }
+ }
+}
+
+/// An `UnitCell` represent the box containing the atoms, and its periodicity.
+///
+/// An unit cell is fully represented by three lengths (a, b, c); and three
+/// angles (alpha, beta, gamma). The angles are stored in degrees, and the
+/// lengths in Angstroms.
+///
+/// A cell also has a matricial representation, by projecting the three base
+/// vector into an orthonormal base. We choose to represent such matrix as an
+/// upper triangular matrix:
+///
+/// ```text
+/// | a_x b_x c_x |
+/// | 0 b_y c_y |
+/// | 0 0 c_z |
+/// ```
+#[derive(Debug)]
+pub struct UnitCell {
+ handle: *mut CHFL_CELL,
+}
+
+/// An analog to a reference to an unit cell (`&UnitCell`)
+#[derive(Debug)]
+pub struct UnitCellRef<'a> {
+ inner: UnitCell,
+ marker: PhantomData<&'a UnitCell>,
+}
+
+impl<'a> std::ops::Deref for UnitCellRef<'a> {
+ type Target = UnitCell;
+ fn deref(&self) -> &UnitCell {
+ &self.inner
+ }
+}
+
+/// An analog to a mutable reference to an unit cell (`&mut UnitCell`)
+#[derive(Debug)]
+pub struct UnitCellMut<'a> {
+ inner: UnitCell,
+ marker: PhantomData<&'a mut UnitCell>,
+}
+
+impl<'a> std::ops::Deref for UnitCellMut<'a> {
+ type Target = UnitCell;
+ fn deref(&self) -> &UnitCell {
+ &self.inner
+ }
+}
+
+impl<'a> std::ops::DerefMut for UnitCellMut<'a> {
+ fn deref_mut(&mut self) -> &mut UnitCell {
+ &mut self.inner
+ }
+}
+
+impl Clone for UnitCell {
+ fn clone(&self) -> UnitCell {
+ unsafe {
+ let new_handle = chfl_cell_copy(self.as_ptr());
+ UnitCell::from_ptr(new_handle)
+ }
+ }
+}
+
+impl UnitCell {
+ /// Create an owned `UnitCell` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_CELL) -> UnitCell {
+ check_not_null(ptr);
+ UnitCell { handle: ptr }
+ }
+
+ /// Create a borrowed `UnitCell` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, and the caller is responsible for setting the right lifetime.
+ #[inline]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_CELL) -> UnitCellRef<'a> {
+ UnitCellRef {
+ inner: UnitCell::from_ptr(ptr as *mut CHFL_CELL),
+ marker: PhantomData,
+ }
+ }
+
+ /// Create a borrowed `UnitCell` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, except for it being non-null, and the caller is responsible for
+ /// setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_mut_from_ptr<'a>(ptr: *mut CHFL_CELL) -> UnitCellMut<'a> {
+ UnitCellMut {
+ inner: UnitCell::from_ptr(ptr),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_CELL {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_CELL {
+ self.handle
+ }
+
+ /// Create an `Orthorhombic` `UnitCell` from the three lengths, in Angstroms.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::new([30.0, 30.0, 23.0]);
+ ///
+ /// assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// ```
+ pub fn new(lengths: [f64; 3]) -> UnitCell {
+ unsafe {
+ let handle = chfl_cell(lengths.as_ptr(), std::ptr::null());
+ UnitCell::from_ptr(handle)
+ }
+ }
+
+ /// Create an `Infinite` `UnitCell`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::infinite();
+ ///
+ /// assert_eq!(cell.lengths(), [0.0, 0.0, 0.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// assert_eq!(cell.shape(), CellShape::Infinite);
+ /// ```
+ pub fn infinite() -> UnitCell {
+ let mut cell = UnitCell::new([0.0, 0.0, 0.0]);
+ cell.set_shape(CellShape::Infinite).expect("could not set cell shape");
+ return cell;
+ }
+
+ /// Create an `Triclinic` `UnitCell` from the three lengths (in Angstroms)
+ /// and three angles (in degree). `alpha` is the angle between the vectors
+ /// `b` and `c`; `beta` is the between the vectors `a` and `c` and `gamma`
+ /// is the angle between the vectors `a` and `b`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::triclinic([10.0, 10.0, 10.0], [98.0, 99.0, 90.0]);
+ ///
+ /// assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);
+ /// assert_eq!(cell.angles()[0], 98.0);
+ /// // Rounding errors might occur due to internal representation
+ /// assert!((cell.angles()[1] - 99.0).abs() < 1e-12);
+ /// assert_eq!(cell.angles()[2], 90.0);
+ /// assert_eq!(cell.shape(), CellShape::Triclinic);
+ /// ```
+ pub fn triclinic(lengths: [f64; 3], angles: [f64; 3]) -> UnitCell {
+ unsafe {
+ let handle = chfl_cell(lengths.as_ptr(), angles.as_ptr());
+ UnitCell::from_ptr(handle)
+ }
+ }
+
+ /// Create an `UnitCell` from a cell matrix. If `matrix` contains only
+ /// zeros, then an `Infinite` cell is created. If only the diagonal of the
+ /// matrix is non-zero, then the cell is `Orthorhombic`. Else a
+ /// `Triclinic` cell is created. The matrix entries should be in Angstroms.
+ ///
+ /// # Panics
+ ///
+ /// If the matrix has a negative determinant, or more generally is not
+ /// representing a unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::from_matrix([
+ /// [1.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]
+ /// ]);
+ ///
+ /// assert_eq!(cell.lengths(), [1.0, 2.0, 3.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// ```
+ pub fn from_matrix(mut matrix: [[f64; 3]; 3]) -> UnitCell {
+ unsafe {
+ let handle = chfl_cell_from_matrix(matrix.as_mut_ptr());
+ UnitCell::from_ptr(handle)
+ }
+ }
+
+ /// Get the three lengths of the cell, in Angstroms.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([30.0, 30.0, 23.0]);
+ /// assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
+ /// ```
+ pub fn lengths(&self) -> [f64; 3] {
+ let mut lengths = [0.0; 3];
+ unsafe {
+ check_success(chfl_cell_lengths(self.as_ptr(), lengths.as_mut_ptr()));
+ }
+ return lengths;
+ }
+
+ /// Set the three lengths of the cell, in Angstroms.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the unit cell is infinite, or if one of the
+ /// lengths is negative.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let mut cell = UnitCell::new([30.0, 30.0, 23.0]);
+ ///
+ /// cell.set_lengths([10.0, 30.0, 42.0]).unwrap();
+ /// assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]);
+ ///
+ /// assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());
+ /// ```
+ pub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error> {
+ unsafe { check(chfl_cell_set_lengths(self.as_mut_ptr(), lengths.as_ptr())) }
+ }
+
+ /// Get the three angles of the cell, in degrees.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([20.0, 20.0, 20.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ ///
+ /// let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+ /// assert_eq!(cell.angles()[0], 100.0);
+ /// // Rounding errors might occur due to internal representation
+ /// assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+ /// assert_eq!(cell.angles()[2], 90.0);
+ /// ```
+ pub fn angles(&self) -> [f64; 3] {
+ let mut angles = [0.0; 3];
+ unsafe {
+ check_success(chfl_cell_angles(self.as_ptr(), angles.as_mut_ptr()));
+ }
+ return angles;
+ }
+
+ /// Set the three angles of the cell, in degrees.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the unit cell is not `Triclinic`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+ /// assert_eq!(cell.angles()[0], 100.0);
+ /// // Rounding errors might occur due to internal representation
+ /// assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+ /// assert_eq!(cell.angles()[2], 90.0);
+ ///
+ /// cell.set_angles([90.0, 90.0, 90.0]).unwrap();
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// ```
+ pub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error> {
+ unsafe { check(chfl_cell_set_angles(self.as_mut_ptr(), angles.as_ptr())) }
+ }
+
+ /// Get the unit cell matricial representation.
+ ///
+ /// The unit cell representation is obtained by aligning the a vector along
+ /// the *x* axis and putting the b vector in the *xy* plane. This make the
+ /// matrix an upper triangular matrix:
+ ///
+ /// ```text
+ /// | a_x b_x c_x |
+ /// | 0 b_y c_y |
+ /// | 0 0 c_z |
+ /// ```
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ ///
+ /// let matrix = cell.matrix();
+ ///
+ /// assert_eq!(matrix[0][0], 10.0);
+ /// assert_eq!(matrix[1][1], 20.0);
+ /// assert_eq!(matrix[2][2], 30.0);
+ ///
+ /// assert!(matrix[1][2].abs() < 1e-9);
+ /// ```
+ pub fn matrix(&self) -> [[f64; 3]; 3] {
+ let mut matrix = [[0.0; 3]; 3];
+ unsafe {
+ check_success(chfl_cell_matrix(self.as_ptr(), matrix.as_mut_ptr()));
+ }
+ return matrix;
+ }
+
+ /// Get the shape of the unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// ```
+ pub fn shape(&self) -> CellShape {
+ let mut shape = chfl_cellshape::CHFL_CELL_INFINITE;
+ unsafe {
+ check_success(chfl_cell_shape(self.as_ptr(), &mut shape));
+ }
+ return CellShape::from(shape);
+ }
+
+ /// Set the shape of the unit cell to `shape`.
+ ///
+ /// # Errors
+ ///
+ /// This can fail if the cell length or angles are incompatible with the
+ /// new shape.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let mut cell = UnitCell::new([10.0, 20.0, 30.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ ///
+ /// cell.set_shape(CellShape::Triclinic).unwrap();
+ /// assert_eq!(cell.shape(), CellShape::Triclinic);
+ /// ```
+ pub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error> {
+ unsafe { check(chfl_cell_set_shape(self.as_mut_ptr(), shape.into())) }
+ }
+
+ /// Get the volume of the unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ /// assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0);
+ /// ```
+ pub fn volume(&self) -> f64 {
+ let mut volume = 0.0;
+ unsafe {
+ check_success(chfl_cell_volume(self.as_ptr(), &mut volume));
+ }
+ return volume;
+ }
+
+ /// Wrap a `vector` in this unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ ///
+ /// let mut vector = [12.0, 5.2, -45.3];
+ /// cell.wrap(&mut vector);
+ /// assert_eq!(vector, [2.0, 5.2, 14.700000000000003]);
+ /// ```
+ pub fn wrap(&self, vector: &mut [f64; 3]) {
+ unsafe {
+ check_success(chfl_cell_wrap(self.as_ptr(), vector.as_mut_ptr()));
+ }
+ }
+}
+
+impl Drop for UnitCell {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.lengths(), [2.0, 3.0, 4.0]);
+
+ let copy = cell.clone();
+ assert_eq!(copy.lengths(), [2.0, 3.0, 4.0]);
+
+ cell.set_lengths([10.0, 12.0, 11.0]).unwrap();
+ assert_eq!(cell.lengths(), [10.0, 12.0, 11.0]);
+ assert_eq!(copy.lengths(), [2.0, 3.0, 4.0]);
+ }
+
+ #[test]
+ fn lengths() {
+ let mut cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.lengths(), [2.0, 3.0, 4.0]);
+ cell.set_lengths([10.0, 12.0, 11.0]).unwrap();
+ assert_eq!(cell.lengths(), [10.0, 12.0, 11.0]);
+ }
+
+ #[test]
+ fn angles() {
+ let mut cell = UnitCell::new([2.0, 3.0, 4.0]);
+ crate::assert_vector3d_eq(&cell.angles(), &[90.0, 90.0, 90.0], 1e-6);
+
+ cell.set_shape(CellShape::Triclinic).unwrap();
+ cell.set_angles([80.0, 89.0, 100.0]).unwrap();
+
+ crate::assert_vector3d_eq(&cell.angles(), &[80.0, 89.0, 100.0], 1e-6);
+
+ let cell = UnitCell::triclinic([1., 2., 3.], [80., 90., 100.]);
+ crate::assert_vector3d_eq(&cell.angles(), &[80.0, 90.0, 100.0], 1e-6);
+ }
+
+ #[test]
+ fn volume() {
+ let cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.volume(), 2.0 * 3.0 * 4.0);
+ }
+
+ #[test]
+ fn wrap() {
+ let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ let mut vector = [12.0, 5.2, -45.3];
+ cell.wrap(&mut vector);
+ crate::assert_vector3d_eq(&vector, &[2.0, 5.2, 14.7], 1e-6);
+ }
+
+ #[test]
+ fn matrix() {
+ let cell = UnitCell::new([2.0, 3.0, 4.0]);
+
+ let matrix = cell.matrix();
+ let result = [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]];
+
+ for i in 0..3 {
+ for j in 0..3 {
+ approx::assert_ulps_eq!(matrix[i][j], result[i][j], epsilon = 1e-12);
+ }
+ }
+ }
+
+ #[test]
+ fn from_matrix() {
+ let cell = UnitCell::from_matrix([[10.0, 0.0, 0.0], [0.0, 21.0, 0.0], [0.0, 0.0, 32.0]]);
+ assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ assert_eq!(cell.lengths(), [10.0, 21.0, 32.0]);
+
+ let result_matrix = [[123.0, 4.08386, 71.7295], [0.0, 233.964, 133.571], [0.0, 0.0, 309.901]];
+ let cell = UnitCell::from_matrix(result_matrix);
+
+ assert_eq!(cell.shape(), CellShape::Triclinic);
+ for i in 0..3 {
+ approx::assert_ulps_eq!(cell.lengths()[i], [123.0, 234.0, 345.0][i], epsilon = 1e-3);
+ approx::assert_ulps_eq!(cell.angles()[i], [67.0, 78.0, 89.0][i], epsilon = 1e-3);
+ }
+
+ let matrix = cell.matrix();
+ for i in 0..3 {
+ for j in 0..3 {
+ approx::assert_ulps_eq!(matrix[i][j], result_matrix[i][j], epsilon = 1e-12);
+ }
+ }
+ }
+
+ #[test]
+ fn shape() {
+ let cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.shape(), CellShape::Orthorhombic);
+
+ let cell = UnitCell::infinite();
+ assert_eq!(cell.shape(), CellShape::Infinite);
+
+ let cell = UnitCell::triclinic([1.0, 2.0, 3.0], [80.0, 90.0, 100.0]);
+ assert_eq!(cell.shape(), CellShape::Triclinic);
+
+ let mut cell = UnitCell::new([10.0, 10.0, 10.0]);
+ assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ cell.set_shape(CellShape::Triclinic).unwrap();
+ assert_eq!(cell.shape(), CellShape::Triclinic);
+ }
+}
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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::os::raw::c_char;
+use std::panic::{self, RefUnwindSafe};
+use std::path::Path;
+
+use chemfiles_sys::*;
+
+use crate::strings;
+
+#[derive(Clone, Debug, PartialEq, Eq)]
+/// Error type for Chemfiles.
+pub struct Error {
+ /// The error status code
+ pub status: Status,
+ /// A message describing the error cause
+ pub message: String,
+}
+
+#[repr(C)]
+#[non_exhaustive]
+#[derive(Clone, Debug, PartialEq, Eq)]
+/// Possible causes of error in chemfiles
+pub enum Status {
+ /// No error
+ Success = chfl_status::CHFL_SUCCESS as isize,
+ /// Error in memory allocations
+ MemoryError = chfl_status::CHFL_MEMORY_ERROR as isize,
+ /// Error while reading or writing a file
+ FileError = chfl_status::CHFL_FILE_ERROR as isize,
+ /// Error in file formatting, *i.e.* the file is invalid
+ FormatError = chfl_status::CHFL_FORMAT_ERROR as isize,
+ /// Error in selection string syntax
+ SelectionError = chfl_status::CHFL_SELECTION_ERROR as isize,
+ /// Error in configuration files syntax
+ ConfigurationError = chfl_status::CHFL_CONFIGURATION_ERROR as isize,
+ /// Error for out of bounds indexing
+ OutOfBounds = chfl_status::CHFL_OUT_OF_BOUNDS as isize,
+ /// Error related to properties
+ PropertyError = chfl_status::CHFL_PROPERTY_ERROR as isize,
+ /// Exception in the C++ chemfiles library
+ ChemfilesError = chfl_status::CHFL_GENERIC_ERROR as isize,
+ /// Exception in the C++ standard library
+ StdCppError = chfl_status::CHFL_CXX_ERROR as isize,
+ /// The given path is not valid UTF8
+ // TODO: rename this to UTF8Error in the next breaking release
+ UTF8PathError,
+}
+
+impl From<chfl_status> for Error {
+ fn from(status: chfl_status) -> Error {
+ let status = match status {
+ chfl_status::CHFL_SUCCESS => Status::Success,
+ chfl_status::CHFL_CXX_ERROR => Status::StdCppError,
+ chfl_status::CHFL_GENERIC_ERROR => Status::ChemfilesError,
+ chfl_status::CHFL_MEMORY_ERROR => Status::MemoryError,
+ chfl_status::CHFL_FILE_ERROR => Status::FileError,
+ chfl_status::CHFL_FORMAT_ERROR => Status::FormatError,
+ chfl_status::CHFL_SELECTION_ERROR => Status::SelectionError,
+ chfl_status::CHFL_CONFIGURATION_ERROR => Status::ConfigurationError,
+ chfl_status::CHFL_OUT_OF_BOUNDS => Status::OutOfBounds,
+ chfl_status::CHFL_PROPERTY_ERROR => Status::PropertyError,
+ };
+
+ let message = Error::last_error();
+ Error { status, message }
+ }
+}
+
+impl From<std::str::Utf8Error> for Error {
+ fn from(_: std::str::Utf8Error) -> Self {
+ Error {
+ status: Status::UTF8PathError,
+ message: "failed to convert data to UTF8 string".into(),
+ }
+ }
+}
+
+impl Error {
+ /// Create a new error because the given `path` is invalid UTF-8 data
+ pub(crate) fn utf8_path_error(path: &Path) -> Error {
+ Error {
+ status: Status::UTF8PathError,
+ message: format!("Could not convert '{}' to UTF8", path.display()),
+ }
+ }
+
+ /// Get the last error message from the C++ library.
+ pub fn last_error() -> String {
+ unsafe { strings::from_c(chfl_last_error()) }
+ }
+
+ /// Clear any error from the C++ library
+ pub fn cleanup() {
+ unsafe {
+ check(chfl_clear_errors()).expect("error in chfl_clear_errors. Things went very bad");
+ }
+ }
+}
+
+/// Check return value of a C function, and get the error if needed.
+pub(crate) fn check(status: chfl_status) -> Result<(), Error> {
+ if status == chfl_status::CHFL_SUCCESS {
+ Ok(())
+ } else {
+ Err(Error::from(status))
+ }
+}
+
+/// Check return value of a C function, panic if it failed.
+pub(crate) fn check_success(status: chfl_status) {
+ assert!(
+ status == chfl_status::CHFL_SUCCESS,
+ "unexpected failure: {}",
+ Error::last_error()
+ );
+}
+
+/// Check a pointer for null.
+pub(crate) fn check_not_null<T>(ptr: *const T) {
+ assert!(!ptr.is_null(), "unexpected null pointer: {}", Error::last_error());
+}
+
+pub trait WarningCallback: RefUnwindSafe + Fn(&str) {}
+impl<T> WarningCallback for T where T: RefUnwindSafe + Fn(&str) {}
+
+static mut LOGGING_CALLBACK: Option<*mut dyn WarningCallback<Output = ()>> = None;
+
+extern "C" fn warning_callback(message: *const c_char) {
+ unsafe {
+ let callback = &*LOGGING_CALLBACK.expect("No callback provided, this is an internal bug");
+ // ignore result. If a panic happened, everything is going badly anyway
+ let _result = panic::catch_unwind(|| {
+ callback(&strings::from_c(message));
+ });
+ }
+}
+
+/// Use `callback` for every chemfiles warning. The callback will be passed
+/// the warning message. This will drop any previous warning callback.
+pub fn set_warning_callback<F>(callback: F)
+where
+ F: WarningCallback + 'static,
+{
+ // box callback to ensure it stays accessible
+ let callback = Box::into_raw(Box::new(callback));
+ unsafe {
+ if let Some(previous) = LOGGING_CALLBACK {
+ // drop the previous callback
+ let previous = Box::from_raw(previous);
+ std::mem::drop(previous);
+ // set the LOGGING_CALLBACK to the new one
+ LOGGING_CALLBACK = Some(callback);
+ } else {
+ // set the LOGGING_CALLBACK
+ LOGGING_CALLBACK = Some(callback);
+ // Tell C code to use Rust-provided callback
+ check_success(chfl_set_warning_callback(warning_callback));
+ }
+ }
+}
+
+impl std::fmt::Display for Error {
+ fn fmt(&self, fmt: &mut std::fmt::Formatter) -> Result<(), std::fmt::Error> {
+ write!(fmt, "{}", self.message)
+ }
+}
+
+impl std::error::Error for Error {
+ fn description(&self) -> &str {
+ match self.status {
+ Status::Success => "Success",
+ Status::StdCppError => "Exception from the C++ standard library",
+ Status::ChemfilesError => "Exception from the chemfiles library",
+ Status::MemoryError => "Error in memory allocations",
+ Status::FileError => "Error while reading or writing a file",
+ Status::FormatError => "Error in file formatting, i.e. the file is invalid",
+ Status::SelectionError => "Error in selection string syntax",
+ Status::UTF8PathError => "A string is not valid UTF8",
+ Status::ConfigurationError => "Error in configuration files",
+ Status::OutOfBounds => "Out of bounds indexing",
+ Status::PropertyError => "Error in property",
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+ use crate::Trajectory;
+
+ #[test]
+ fn errors() {
+ Error::cleanup();
+ assert_eq!(Error::last_error(), "");
+ assert!(Trajectory::open("nope", 'r').is_err());
+ assert_eq!(
+ Error::last_error(),
+ "file at \'nope\' does not have an extension, provide a format name to read it"
+ );
+ Error::cleanup();
+ assert_eq!(Error::last_error(), "");
+ }
+
+ #[test]
+ fn codes() {
+ assert_eq!(Error::from(chfl_status::CHFL_SUCCESS).status, Status::Success);
+ assert_eq!(Error::from(chfl_status::CHFL_CXX_ERROR).status, Status::StdCppError);
+ assert_eq!(
+ Error::from(chfl_status::CHFL_GENERIC_ERROR).status,
+ Status::ChemfilesError
+ );
+ assert_eq!(Error::from(chfl_status::CHFL_MEMORY_ERROR).status, Status::MemoryError);
+ assert_eq!(Error::from(chfl_status::CHFL_FILE_ERROR).status, Status::FileError);
+ assert_eq!(Error::from(chfl_status::CHFL_FORMAT_ERROR).status, Status::FormatError);
+ assert_eq!(
+ Error::from(chfl_status::CHFL_SELECTION_ERROR).status,
+ Status::SelectionError
+ );
+ assert_eq!(Error::from(chfl_status::CHFL_OUT_OF_BOUNDS).status, Status::OutOfBounds);
+ assert_eq!(
+ Error::from(chfl_status::CHFL_PROPERTY_ERROR).status,
+ Status::PropertyError
+ );
+ }
+}
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+1184 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use chemfiles_sys::*;
+
+use crate::{Atom, AtomMut, AtomRef};
+use crate::{BondOrder, Residue, Topology, TopologyRef};
+use crate::{UnitCell, UnitCellMut, UnitCellRef};
+
+use crate::errors::{check, check_not_null, check_success, Error};
+use crate::property::{PropertiesIter, Property, RawProperty};
+use crate::strings;
+
+/// A `Frame` contains data from one simulation step: the current unit
+/// cell, the topology, the positions, and the velocities of the particles in
+/// the system. If some information is missing (topology or velocity or unit
+/// cell), the corresponding data is filled with a default value.
+#[derive(Debug)]
+pub struct Frame {
+ handle: *mut CHFL_FRAME,
+}
+
+impl Clone for Frame {
+ fn clone(&self) -> Frame {
+ unsafe {
+ let new_handle = chfl_frame_copy(self.as_ptr());
+ Frame::from_ptr(new_handle)
+ }
+ }
+}
+
+#[derive(Debug)]
+pub struct AtomIter<'a> {
+ frame: &'a Frame,
+ index: usize,
+ size: usize,
+}
+
+impl Frame {
+ /// Create a `Frame` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer,
+ /// except for it being non-null.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_FRAME) -> Frame {
+ check_not_null(ptr);
+ Frame { handle: ptr }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_FRAME {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_FRAME {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer FROM A SHARED REFERENCE.
+ ///
+ /// For uses with functions of the C API using mut pointers for both read
+ /// and write access. Users should check that this does not lead to multiple
+ /// mutable borrows
+ #[inline]
+ #[allow(non_snake_case)]
+ pub(crate) fn as_mut_ptr_MANUALLY_CHECKING_BORROW(&self) -> *mut CHFL_FRAME {
+ self.handle
+ }
+
+ /// Create an empty frame. It will be resized by the library as needed.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let frame = Frame::new();
+ ///
+ /// assert_eq!(frame.size(), 0);
+ /// ```
+ pub fn new() -> Frame {
+ unsafe { Frame::from_ptr(chfl_frame()) }
+ }
+
+ /// Get a reference to the atom at the given `index` in this frame.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+ ///
+ /// let atom = frame.atom(0);
+ /// assert_eq!(atom.name(), "Zn");
+ /// ```
+ pub fn atom(&self, index: usize) -> AtomRef {
+ unsafe {
+ let handle = chfl_atom_from_frame(self.as_mut_ptr_MANUALLY_CHECKING_BORROW(), index as u64);
+ Atom::ref_from_ptr(handle)
+ }
+ }
+
+ /// Get a mutable reference to the atom at the given `index` in this frame.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+ ///
+ /// assert_eq!(frame.atom(0).name(), "Zn");
+ ///
+ /// frame.atom_mut(0).set_name("Fe");
+ /// assert_eq!(frame.atom(0).name(), "Fe");
+ /// ```
+ pub fn atom_mut(&mut self, index: usize) -> AtomMut {
+ unsafe {
+ let handle = chfl_atom_from_frame(self.as_mut_ptr(), index as u64);
+ Atom::ref_mut_from_ptr(handle)
+ }
+ }
+
+ /// Get the current number of atoms in this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.size(), 0);
+ ///
+ /// frame.resize(67);
+ /// assert_eq!(frame.size(), 67);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(chfl_frame_atoms_count(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Resize the positions and the velocities in this frame, to make space for
+ /// `natoms` atoms. Previous data is conserved, as well as the presence of
+ /// absence of velocities.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// assert_eq!(frame.size(), 67);
+ /// ```
+ pub fn resize(&mut self, natoms: usize) {
+ unsafe {
+ check_success(chfl_frame_resize(self.as_mut_ptr(), natoms as u64));
+ }
+ }
+
+ /// Add an `Atom` and the corresponding position and optionally velocity
+ /// data to this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [1.0, 1.0, 2.0], None);
+ ///
+ /// frame.add_velocities();
+ /// frame.add_atom(&Atom::new("Zn"), [-1.0, 1.0, 2.0], [0.2, 0.1, 0.0]);
+ /// ```
+ pub fn add_atom(&mut self, atom: &Atom, position: [f64; 3], velocity: impl Into<Option<[f64; 3]>>) {
+ let velocity = velocity.into();
+ let velocity_ptr = match velocity {
+ Some(ref data) => data.as_ptr(),
+ None => std::ptr::null(),
+ };
+
+ unsafe {
+ check_success(chfl_frame_add_atom(
+ self.as_mut_ptr(),
+ atom.as_ptr(),
+ position.as_ptr(),
+ velocity_ptr,
+ ));
+ }
+ }
+
+ /// Remove the atom at index `i` in this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+ /// frame.add_atom(&Atom::new("Fe"), [0.0; 3], None);
+ /// frame.add_atom(&Atom::new("Sn"), [0.0; 3], None);
+ /// assert_eq!(frame.size(), 3);
+ ///
+ /// frame.remove(1);
+ /// assert_eq!(frame.size(), 2);
+ /// assert_eq!(frame.atom(1).name(), "Sn");
+ /// ```
+ pub fn remove(&mut self, i: usize) {
+ unsafe {
+ check_success(chfl_frame_remove(self.as_mut_ptr(), i as u64));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the frame.
+ ///
+ /// The bond order is set to `BondOrder::Unknown`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, BondOrder};
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.topology().bonds_count(), 0);
+ /// frame.resize(5);
+ ///
+ /// frame.add_bond(0, 1);
+ /// frame.add_bond(3, 1);
+ /// frame.add_bond(2, 4);
+ /// assert_eq!(frame.topology().bonds_count(), 3);
+ ///
+ /// assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown);
+ /// assert_eq!(frame.topology().bonds(), vec![[0, 1], [1, 3], [2, 4]]);
+ /// ```
+ pub fn add_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(chfl_frame_add_bond(self.as_mut_ptr(), i as u64, j as u64));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the frame
+ /// with the given bond `order`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, BondOrder};
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.topology().bonds_count(), 0);
+ /// frame.resize(2);
+ ///
+ /// frame.add_bond_with_order(0, 1, BondOrder::Double);
+ /// assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Double);
+ /// ```
+ pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder) {
+ unsafe {
+ check_success(chfl_frame_bond_with_order(
+ self.as_mut_ptr(),
+ i as u64,
+ j as u64,
+ order.as_raw(),
+ ));
+ }
+ }
+
+ /// Remove any existing bond between the atoms at indexes `i` and `j` in
+ /// the frame.
+ ///
+ /// This function does nothing if there is no bond between `i` and `j`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(5);
+ ///
+ /// frame.add_bond(0, 1);
+ /// frame.add_bond(3, 1);
+ /// frame.add_bond(2, 4);
+ ///
+ /// let bonds = frame.topology().bonds();
+ /// assert_eq!(bonds, vec![[0, 1], [1, 3], [2, 4]]);
+ ///
+ /// frame.remove_bond(2, 4);
+ /// let bonds = frame.topology().bonds();
+ /// assert_eq!(bonds, vec![[0, 1], [1, 3]]);
+ /// ```
+ pub fn remove_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(chfl_frame_remove_bond(self.as_mut_ptr(), i as u64, j as u64));
+ }
+ }
+
+ /// Add a copy of `residue` to this frame.
+ ///
+ /// # Errors
+ ///
+ /// This function fails is the residue id is already in this frame's
+ /// topology, or if the residue contain atoms that are already in another
+ /// residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Residue};
+ /// let mut frame = Frame::new();
+ ///
+ /// let residue = Residue::new("foo");
+ /// frame.add_residue(&residue).unwrap();
+ ///
+ /// let topology = frame.topology();
+ /// assert_eq!(topology.residues_count(), 1);
+ /// assert_eq!(topology.residue(0).unwrap().name(), "foo");
+ /// ```
+ pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error> {
+ unsafe { check(chfl_frame_add_residue(self.as_mut_ptr(), residue.as_ptr())) }
+ }
+
+ /// Get the distance between the atoms at indexes `i` and `j` in this frame,
+ /// accounting for periodic boundary conditions. The result is expressed in
+ /// Angstroms.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [1.0, 2.0, 3.0], None);
+ ///
+ /// assert_eq!(frame.distance(0, 1), f64::sqrt(14.0));
+ /// ```
+ pub fn distance(&self, i: usize, j: usize) -> f64 {
+ let mut distance = 0.0;
+ unsafe {
+ check_success(chfl_frame_distance(self.as_ptr(), i as u64, j as u64, &mut distance));
+ }
+ return distance;
+ }
+
+ /// Get the angle formed by the atoms at indexes `i`, `j` and `k` in this
+ /// frame, accounting for periodic boundary conditions. The result is
+ /// expressed in radians.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// # use std::f64;
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+ ///
+ /// assert_eq!(frame.angle(0, 1, 2), f64::consts::PI / 2.0);
+ /// ```
+ pub fn angle(&self, i: usize, j: usize, k: usize) -> f64 {
+ let mut angle = 0.0;
+ unsafe {
+ check_success(chfl_frame_angle(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ k as u64,
+ &mut angle,
+ ));
+ }
+ return angle;
+ }
+
+ /// Get the dihedral angle formed by the atoms at indexes `i`, `j`, `k` and
+ /// `m` in this frame, accounting for periodic boundary conditions. The
+ /// result is expressed in radians.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// # use std::f64;
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("D"), [0.0, 1.0, 1.0], None);
+ ///
+ /// assert_eq!(frame.dihedral(0, 1, 2, 3), f64::consts::PI / 2.0);
+ /// ```
+ pub fn dihedral(&self, i: usize, j: usize, k: usize, m: usize) -> f64 {
+ let mut dihedral = 0.0;
+ unsafe {
+ check_success(chfl_frame_dihedral(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ k as u64,
+ m as u64,
+ &mut dihedral,
+ ));
+ }
+ return dihedral;
+ }
+
+ /// Get the out of plane distance formed by the atoms at indexes `i`, `j`,
+ /// `k` and `m` in this frame, accounting for periodic boundary conditions.
+ /// The result is expressed in angstroms.
+ ///
+ /// This is the distance between the atom j and the ikm plane. The j atom
+ /// is the center of the improper dihedral angle formed by i, j, k and m.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 2.0], None);
+ /// frame.add_atom(&Atom::new("C"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("D"), [0.0, 1.0, 0.0], None);
+ ///
+ /// assert_eq!(frame.out_of_plane(0, 1, 2, 3), 2.0);
+ /// ```
+ pub fn out_of_plane(&self, i: usize, j: usize, k: usize, m: usize) -> f64 {
+ let mut distance = 0.0;
+ unsafe {
+ check_success(chfl_frame_out_of_plane(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ k as u64,
+ m as u64,
+ &mut distance,
+ ));
+ }
+ return distance;
+ }
+
+ /// Get a view into the positions of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ ///
+ /// let positions = frame.positions();
+ /// assert_eq!(positions.len(), 67);
+ /// assert_eq!(positions[0], [0.0, 0.0, 0.0]);
+ /// ```
+ pub fn positions(&self) -> &[[f64; 3]] {
+ let mut ptr = std::ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(chfl_frame_positions(
+ self.as_mut_ptr_MANUALLY_CHECKING_BORROW(),
+ &mut ptr,
+ &mut natoms,
+ ));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return std::slice::from_raw_parts(ptr, size);
+ }
+ }
+
+ /// Get a mutable view into the positions of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// {
+ /// let positions = frame.positions_mut();
+ /// assert_eq!(positions[0], [0.0, 0.0, 0.0]);
+ /// positions[0] = [1.0, 2.0, 3.0];
+ /// }
+ ///
+ /// let positions = frame.positions();
+ /// assert_eq!(positions[0], [1.0, 2.0, 3.0]);
+ /// ```
+ pub fn positions_mut(&mut self) -> &mut [[f64; 3]] {
+ let mut ptr = std::ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(chfl_frame_positions(self.as_mut_ptr(), &mut ptr, &mut natoms));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return std::slice::from_raw_parts_mut(ptr, size);
+ }
+ }
+
+ /// Get a view into the velocities of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// frame.add_velocities();
+ ///
+ /// let velocities = frame.velocities().expect("missing velocities");
+ /// assert_eq!(velocities.len(), 67);
+ /// assert_eq!(velocities[0], [0.0, 0.0, 0.0]);
+ /// ```
+ pub fn velocities(&self) -> Option<&[[f64; 3]]> {
+ if !self.has_velocities() {
+ return None;
+ }
+
+ let mut ptr = std::ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(chfl_frame_velocities(
+ self.as_mut_ptr_MANUALLY_CHECKING_BORROW(),
+ &mut ptr,
+ &mut natoms,
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return Some(std::slice::from_raw_parts(ptr, size));
+ }
+ }
+
+ /// Get a mutable view into the velocities of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// frame.add_velocities();
+ /// {
+ /// let velocities = frame.velocities_mut().expect("missing velocities");
+ /// assert_eq!(velocities[0], [0.0, 0.0, 0.0]);
+ /// velocities[0] = [1.0, 2.0, 3.0];
+ /// }
+ ///
+ /// let velocities = frame.velocities().expect("missing velocities");
+ /// assert_eq!(velocities[0], [1.0, 2.0, 3.0]);
+ /// ```
+ pub fn velocities_mut(&mut self) -> Option<&mut [[f64; 3]]> {
+ if !self.has_velocities() {
+ return None;
+ }
+
+ let mut ptr = std::ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(chfl_frame_velocities(self.as_mut_ptr(), &mut ptr, &mut natoms));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return Some(std::slice::from_raw_parts_mut(ptr, size));
+ }
+ }
+
+ /// Check if this frame contains velocity data.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.has_velocities(), false);
+ ///
+ /// frame.add_velocities();
+ /// assert_eq!(frame.has_velocities(), true);
+ /// ```
+ pub fn has_velocities(&self) -> bool {
+ let mut res = 0;
+ unsafe {
+ check_success(chfl_frame_has_velocities(self.as_ptr(), &mut res));
+ }
+ return res != 0;
+ }
+
+ /// Add velocity data to this frame. If the frame already have velocities,
+ /// this does nothing.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.has_velocities(), false);
+ ///
+ /// frame.add_velocities();
+ /// assert_eq!(frame.has_velocities(), true);
+ /// ```
+ pub fn add_velocities(&mut self) {
+ unsafe {
+ check_success(chfl_frame_add_velocities(self.as_mut_ptr()));
+ }
+ }
+
+ /// Get a reference to the `UnitCell` from this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, CellShape};
+ /// let frame = Frame::new();
+ ///
+ /// let cell = frame.cell();
+ /// assert_eq!(cell.shape(), CellShape::Infinite);
+ /// ```
+ pub fn cell(&self) -> UnitCellRef {
+ unsafe {
+ let handle = chfl_cell_from_frame(self.as_mut_ptr_MANUALLY_CHECKING_BORROW());
+ UnitCell::ref_from_ptr(handle)
+ }
+ }
+
+ /// Get a mutable reference to the `UnitCell` from this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, CellShape};
+ /// let mut frame = Frame::new();
+ ///
+ /// assert_eq!(frame.cell().shape(), CellShape::Infinite);
+ ///
+ /// frame.cell_mut().set_shape(CellShape::Triclinic).unwrap();
+ /// assert_eq!(frame.cell().shape(), CellShape::Triclinic);
+ /// ```
+ pub fn cell_mut(&mut self) -> UnitCellMut {
+ unsafe {
+ let handle = chfl_cell_from_frame(self.as_mut_ptr());
+ UnitCell::ref_mut_from_ptr(handle)
+ }
+ }
+
+ /// Set the `UnitCell` of this frame to `cell`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, UnitCell, CellShape};
+ /// let mut frame = Frame::new();
+ ///
+ /// frame.set_cell(&UnitCell::new([10.0, 10.0, 10.0]));
+ ///
+ /// let cell = frame.cell();
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);
+ /// ```
+ pub fn set_cell(&mut self, cell: &UnitCell) {
+ unsafe {
+ check_success(chfl_frame_set_cell(self.as_mut_ptr(), cell.as_ptr()));
+ }
+ }
+
+ /// Get a reference to the `Topology` of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(42);
+ ///
+ /// let topology = frame.topology();
+ /// assert_eq!(topology.size(), 42);
+ /// ```
+ pub fn topology(&self) -> TopologyRef {
+ unsafe {
+ let handle = chfl_topology_from_frame(self.as_ptr());
+ Topology::ref_from_ptr(handle)
+ }
+ }
+
+ /// Set the `Topology` of this frame to `topology`.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the topology contains a different number of atoms
+ /// than this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Topology, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.resize(2);
+ ///
+ /// let mut topology = Topology::new();
+ /// topology.add_atom(&Atom::new("Cl"));
+ /// topology.add_atom(&Atom::new("Cl"));
+ /// topology.add_bond(0, 1);
+ ///
+ /// frame.set_topology(&topology).unwrap();
+ /// assert_eq!(frame.atom(0).name(), "Cl");
+ /// ```
+ pub fn set_topology(&mut self, topology: &Topology) -> Result<(), Error> {
+ unsafe { check(chfl_frame_set_topology(self.as_mut_ptr(), topology.as_ptr())) }
+ }
+
+ /// Get this frame step, i.e. the frame number in the trajectory
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let frame = Frame::new();
+ /// assert_eq!(frame.step(), 0);
+ /// ```
+ pub fn step(&self) -> usize {
+ let mut step = 0;
+ unsafe {
+ check_success(chfl_frame_step(self.as_ptr(), &mut step));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return step as usize;
+ }
+
+ /// Set this frame step to `step`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.step(), 0);
+ ///
+ /// frame.set_step(10);
+ /// assert_eq!(frame.step(), 10);
+ /// ```
+ pub fn set_step(&mut self, step: usize) {
+ unsafe {
+ check_success(chfl_frame_set_step(self.as_mut_ptr(), step as u64));
+ }
+ }
+
+ /// Guess the bonds, angles and dihedrals in this `frame`.
+ ///
+ /// The bonds are guessed using a distance-based algorithm, and then angles
+ /// and dihedrals are guessed from the bonds.
+ ///
+ /// # Errors
+ ////
+ /// This function can fail if the covalent radius is unknown for some atoms
+ /// in the frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ ///
+ /// frame.add_atom(&Atom::new("Cl"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("Cl"), [1.5, 0.0, 0.0], None);
+ /// assert_eq!(frame.topology().bonds_count(), 0);
+ ///
+ /// frame.guess_bonds().unwrap();
+ /// assert_eq!(frame.topology().bonds_count(), 1);
+ /// ```
+ pub fn guess_bonds(&mut self) -> Result<(), Error> {
+ unsafe { check(chfl_frame_guess_bonds(self.as_mut_ptr())) }
+ }
+
+ /// Remove all existing bonds, angles, dihedral angles and improper
+ /// dihedral angles in the topology of the frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Atom, Frame};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [0.0, 1.0, 0.0], None);
+ ///
+ /// frame.add_bond(0, 1);
+ /// frame.add_bond(1, 2);
+ ///
+ /// assert_eq!(frame.topology().bonds().len(), 2);
+ /// assert_eq!(frame.topology().angles().len(), 1);
+ ///
+ /// frame.clear_bonds();
+ /// assert!(frame.topology().bonds().is_empty());
+ /// assert!(frame.topology().angles().is_empty());
+ /// ```
+ pub fn clear_bonds(&mut self) {
+ unsafe {
+ check_success(chfl_frame_clear_bonds(self.as_mut_ptr()));
+ }
+ }
+
+ /// Add a new `property` with the given `name` to this frame.
+ ///
+ /// If a property with the same name already exists, this function override
+ /// the existing property with the new one.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Frame, Property};
+ /// let mut frame = Frame::new();
+ /// frame.set("a string", "hello");
+ /// frame.set("a double", 4.3);
+ ///
+ /// assert_eq!(frame.get("a string"), Some(Property::String("hello".into())));
+ /// assert_eq!(frame.get("a double"), Some(Property::Double(4.3)));
+ /// ```
+ pub fn set(&mut self, name: &str, property: impl Into<Property>) {
+ let buffer = strings::to_c(name);
+ let property = property.into().as_raw();
+ unsafe {
+ check_success(chfl_frame_set_property(
+ self.as_mut_ptr(),
+ buffer.as_ptr(),
+ property.as_ptr(),
+ ));
+ }
+ }
+
+ /// Get a property with the given `name` in this frame, if it exist.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Frame, Property};
+ /// let mut frame = Frame::new();
+ /// frame.set("foo", Property::Double(22.2));
+ ///
+ /// assert_eq!(frame.get("foo"), Some(Property::Double(22.2)));
+ /// assert_eq!(frame.get("Bar"), None);
+ /// ```
+ pub fn get(&self, name: &str) -> Option<Property> {
+ let buffer = strings::to_c(name);
+ unsafe {
+ let handle = chfl_frame_get_property(self.as_ptr(), buffer.as_ptr());
+ if handle.is_null() {
+ None
+ } else {
+ let raw = RawProperty::from_ptr(handle);
+ Some(Property::from_raw(raw))
+ }
+ }
+ }
+
+ /// Get an iterator over all (name, property) pairs for this frame
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Frame, Property};
+ /// let mut frame = Frame::new();
+ /// frame.set("foo", Property::Double(22.2));
+ /// frame.set("bar", Property::Bool(false));
+ ///
+ /// for (name, property) in frame.properties() {
+ /// if name == "foo" {
+ /// assert_eq!(property, Property::Double(22.2));
+ /// } else if name == "bar" {
+ /// assert_eq!(property, Property::Bool(false));
+ /// }
+ /// }
+ /// ```
+ pub fn properties(&self) -> PropertiesIter {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_frame_properties_count(self.as_ptr(), &mut count));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = count as usize;
+ let mut c_names = vec![std::ptr::null_mut(); size];
+ unsafe {
+ check_success(chfl_frame_list_properties(self.as_ptr(), c_names.as_mut_ptr(), count));
+ }
+
+ let mut names = Vec::new();
+ for ptr in c_names {
+ names.push(strings::from_c(ptr));
+ }
+
+ PropertiesIter {
+ names: names.into_iter(),
+ getter: Box::new(move |name| self.get(name).expect("failed to get property")),
+ }
+ }
+
+ /// Gets an iterator over atoms
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Atom, AtomRef, Frame};
+ /// let mut frame = Frame::new();
+ ///
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ ///
+ /// let mut atoms: Vec<AtomRef> = Vec::new();
+ ///
+ /// for atom in frame.iter_atoms() {
+ /// atoms.push(atom);
+ /// }
+ ///
+ /// assert_eq!(atoms.len(), 2);
+ /// ```
+ pub fn iter_atoms(&self) -> AtomIter<'_> {
+ AtomIter {
+ frame: self,
+ index: 0,
+ size: self.size(),
+ }
+ }
+}
+
+impl Drop for Frame {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+impl<'a> Iterator for AtomIter<'a> {
+ type Item = AtomRef<'a>;
+
+ fn next(&mut self) -> Option<Self::Item> {
+ if self.size <= self.index {
+ return None;
+ }
+ let atom = self.frame.atom(self.index);
+ self.index += 1;
+ Some(atom)
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.size(), 0);
+ let copy = frame.clone();
+ assert_eq!(copy.size(), 0);
+
+ frame.resize(42);
+ assert_eq!(frame.size(), 42);
+ assert_eq!(copy.size(), 0);
+ }
+
+ #[test]
+ fn size() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.size(), 0);
+
+ frame.resize(12);
+ assert_eq!(frame.size(), 12);
+ }
+
+ #[test]
+ fn add_atom() {
+ let mut frame = Frame::new();
+
+ frame.add_atom(&Atom::new("U"), [1.0, 1.0, 2.0], None);
+ assert_eq!(frame.size(), 1);
+ assert_eq!(frame.atom(0).name(), "U");
+
+ let positions = &[[1.0, 1.0, 2.0]];
+ assert_eq!(frame.positions(), positions);
+
+ frame.add_velocities();
+ frame.add_atom(&Atom::new("F"), [1.0, 1.0, 2.0], [4.0, 3.0, 2.0]);
+ assert_eq!(frame.size(), 2);
+ assert_eq!(frame.atom(0).name(), "U");
+ assert_eq!(frame.atom(1).name(), "F");
+
+ let positions = &[[1.0, 1.0, 2.0], [1.0, 1.0, 2.0]];
+ assert_eq!(frame.positions(), positions);
+
+ let velocities = &[[0.0, 0.0, 0.0], [4.0, 3.0, 2.0]];
+ assert_eq!(frame.velocities().unwrap(), velocities);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_atom() {
+ let mut frame = Frame::new();
+ frame.resize(22);
+ let _atom = frame.atom(23);
+ }
+
+ #[test]
+ fn remove_atom() {
+ let mut frame = Frame::new();
+ frame.add_atom(&Atom::new("U"), [1.0, 1.0, 2.0], None);
+ frame.add_atom(&Atom::new("F"), [1.0, 1.0, 2.0], None);
+
+ assert_eq!(frame.size(), 2);
+ assert_eq!(frame.atom(0).name(), "U");
+
+ frame.remove(0);
+ assert_eq!(frame.size(), 1);
+ assert_eq!(frame.atom(0).name(), "F");
+ }
+
+ #[test]
+ #[should_panic]
+ fn remove_out_of_bounds() {
+ let mut frame = Frame::new();
+ frame.resize(32);
+
+ frame.remove(100);
+ }
+
+ #[test]
+ fn positions() {
+ let mut frame = Frame::new();
+ frame.resize(4);
+ let expected = &[[1.0, 2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0], [10.0, 11.0, 12.0]];
+
+ frame.positions_mut().clone_from_slice(expected);
+ assert_eq!(frame.positions(), expected);
+ }
+
+ #[test]
+ fn velocities() {
+ let mut frame = Frame::new();
+ frame.resize(4);
+ assert!(!frame.has_velocities());
+ frame.add_velocities();
+ assert!(frame.has_velocities());
+
+ let expected = &[[1.0, 2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0], [10.0, 11.0, 12.0]];
+
+ frame.velocities_mut().unwrap().clone_from_slice(expected);
+ assert_eq!(frame.velocities().unwrap(), expected);
+ }
+
+ #[test]
+ fn cell() {
+ let mut frame = Frame::new();
+ frame.set_cell(&UnitCell::new([3.0, 4.0, 5.0]));
+ let cell = frame.cell();
+ assert_eq!(cell.lengths(), [3.0, 4.0, 5.0]);
+ }
+
+ #[test]
+ fn topology() {
+ let mut frame = Frame::new();
+ frame.resize(2);
+ let mut topology = Topology::new();
+
+ topology.add_atom(&Atom::new("Zn"));
+ topology.add_atom(&Atom::new("Ar"));
+
+ assert!(frame.set_topology(&topology).is_ok());
+
+ let topology = frame.topology();
+
+ assert_eq!(topology.atom(0).name(), "Zn");
+ assert_eq!(topology.atom(1).name(), "Ar");
+
+ assert_eq!(frame.atom(0).name(), "Zn");
+ assert_eq!(frame.atom(1).name(), "Ar");
+ }
+
+ #[test]
+ fn bonds() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ assert_eq!(frame.topology().bonds_count(), 0);
+
+ frame.add_bond(0, 1);
+ frame.add_bond(9, 2);
+ frame.add_bond_with_order(3, 7, BondOrder::Aromatic);
+ assert_eq!(frame.topology().bonds_count(), 3);
+
+ assert_eq!(frame.topology().bonds(), vec![[0, 1], [2, 9], [3, 7]]);
+ let expected = vec![BondOrder::Unknown, BondOrder::Unknown, BondOrder::Aromatic];
+ assert_eq!(frame.topology().bond_orders(), expected);
+
+ assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown);
+ assert_eq!(frame.topology().bond_order(3, 7), BondOrder::Aromatic);
+
+ frame.remove_bond(3, 7);
+ // Removing unexisting bond is OK if both indexes are in bounds
+ frame.remove_bond(8, 7);
+ assert_eq!(frame.topology().bonds_count(), 2);
+
+ frame.clear_bonds();
+ assert_eq!(frame.topology().bonds_count(), 0);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ frame.add_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_remove_bond() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ frame.remove_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds_with_order() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ frame.add_bond_with_order(300, 7, BondOrder::Unknown);
+ }
+
+ #[test]
+ fn residues() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.topology().residues_count(), 0);
+
+ let residue = &Residue::new("foobar");
+ frame.add_residue(residue).unwrap();
+ frame.add_residue(residue).unwrap();
+ frame.add_residue(residue).unwrap();
+
+ assert_eq!(frame.topology().residues_count(), 3);
+ assert_eq!(frame.topology().residue(0).unwrap().name(), "foobar");
+ }
+
+ #[test]
+ fn step() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.step(), 0);
+ frame.set_step(42);
+ assert_eq!(frame.step(), 42);
+ }
+
+ #[test]
+ fn property() {
+ let mut frame = Frame::new();
+ frame.set("foo", -22.0);
+ assert_eq!(frame.get("foo"), Some(Property::Double(-22.0)));
+ assert_eq!(frame.get("bar"), None);
+
+ frame.set("bar", Property::String("here".into()));
+ for (name, property) in frame.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(-22.0));
+ } else if name == "bar" {
+ assert_eq!(property, Property::String("here".into()));
+ }
+ }
+ }
+
+ #[test]
+ fn pbc_geometry() {
+ use std::f64::consts::PI;
+
+ let mut frame = Frame::new();
+ let atom = &Atom::new("");
+
+ frame.add_atom(atom, [1.0, 0.0, 0.0], None);
+ frame.add_atom(atom, [0.0, 0.0, 0.0], None);
+ frame.add_atom(atom, [0.0, 1.0, 0.0], None);
+ frame.add_atom(atom, [0.0, 1.0, 1.0], None);
+ frame.add_atom(atom, [0.0, 0.0, 2.0], None);
+
+ assert_eq!(frame.distance(0, 2), f64::sqrt(2.0));
+ assert_eq!(frame.angle(0, 1, 2), PI / 2.0);
+ assert_eq!(frame.dihedral(0, 1, 2, 3), PI / 2.0);
+ assert_eq!(frame.out_of_plane(1, 4, 0, 2), 2.0);
+ }
+
+ #[test]
+ fn atom_iterator() {
+ let mut frame = Frame::new();
+
+ frame.add_atom(&Atom::new("H1"), [1.0, 0.0, 0.0], None);
+ frame.add_atom(&Atom::new("H2"), [0.0, 1.0, 0.0], None);
+ frame.add_atom(&Atom::new("H3"), [0.0, 0.0, 1.0], None);
+ frame.add_atom(&Atom::new("H4"), [1.0, 1.0, 1.0], None);
+
+ let mut items: Vec<(AtomRef, &[f64; 3])> = Vec::new();
+
+ for item in frame.iter_atoms().zip(frame.positions()) {
+ items.push(item);
+ }
+
+ assert_eq!(items[0].0.name(), "H1");
+ assert_eq!(items[2].0.name(), "H3");
+
+ assert_eq!(items[1].1, &[0.0_f64, 1.0_f64, 0.0_f64]);
+ assert_eq!(items[3].1, &[1.0_f64, 1.0_f64, 1.0_f64]);
+ }
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+
+//! Chemfiles is a multi-language library written in modern C++ for reading and
+//! writing from and to molecular trajectory files. These files are created by
+//! your favorite theoretical chemistry program, and contains information about
+//! atomic or residues names and positions. Some format also have additional
+//! information, such as velocities, forces, energy, …
+//!
+//! This crate expose the C API of chemfiles to Rust, and make all the
+//! functionalities accessible. For more information on the C++ library,
+//! please see its [documentation][cxx_doc]. Specifically, the following pages
+//! are worth reading:
+//!
+//! - The [overview][overview] of the classes organization;
+//! - The list of [supported formats][formats];
+//! - The documentation for the [selection language][selections];
+//!
+//! [cxx_doc]: https://chemfiles.org/chemfiles
+//! [overview]: https://chemfiles.org/chemfiles/latest/overview.html
+//! [formats]: https://chemfiles.org/chemfiles/latest/formats.html
+//! [selections]: https://chemfiles.org/chemfiles/latest/selections.html
+
+#![deny(missing_docs)]
+#![warn(trivial_casts, unused_import_braces, variant_size_differences)]
+#![warn(unused_results)]
+// Configuration for clippy lints
+#![warn(clippy::all, clippy::pedantic)]
+#![allow(clippy::needless_return, clippy::module_name_repetitions)]
+#![allow(clippy::must_use_candidate, clippy::wildcard_imports)]
+#![allow(clippy::let_underscore_untyped, clippy::bool_to_int_with_if)]
+// Allow a few more clippy lints in test mode
+#![cfg_attr(test, allow(clippy::float_cmp, clippy::unreadable_literal, clippy::shadow_unrelated))]
+// deny(warnings) in doc tests
+#![doc(test(attr(deny(warnings))))]
+#![doc(test(attr(allow(unused_variables))))]
+
+use chemfiles_sys::{chfl_add_configuration, chfl_version};
+
+mod strings;
+
+mod errors;
+pub use self::errors::set_warning_callback;
+pub use self::errors::{Error, Status};
+
+mod atom;
+pub use self::atom::Atom;
+pub use self::atom::AtomMut;
+pub use self::atom::AtomRef;
+
+mod cell;
+pub use self::cell::CellShape;
+pub use self::cell::UnitCell;
+pub use self::cell::UnitCellMut;
+pub use self::cell::UnitCellRef;
+
+mod residue;
+pub use self::residue::Residue;
+pub use self::residue::ResidueRef;
+
+mod topology;
+pub use self::topology::BondOrder;
+pub use self::topology::Topology;
+pub use self::topology::TopologyRef;
+
+mod frame;
+pub use self::frame::Frame;
+
+mod trajectory;
+pub use self::trajectory::MemoryTrajectoryReader;
+pub use self::trajectory::Trajectory;
+
+mod selection;
+pub use self::selection::{Match, Selection};
+
+mod property;
+pub use self::property::PropertiesIter;
+pub use self::property::Property;
+
+mod misc;
+pub use self::misc::{formats_list, guess_format, FormatMetadata};
+
+/// Get the version of the chemfiles library.
+///
+/// # Example
+/// ```
+/// let version = chemfiles::version();
+/// assert!(version.starts_with("0.10"));
+/// ```
+pub fn version() -> String {
+ unsafe { strings::from_c(chfl_version()) }
+}
+
+/// Read configuration data from the file at `path`.
+///
+/// By default, chemfiles reads configuration from any file named
+/// `.chemfiles.toml` in the current directory or any parent directory. This
+/// function can be used to add data from another configuration file. Data from
+/// the new configuration file will overwrite any existing data.
+///
+/// # Errors
+///
+/// This function will fail if there is no file at `path`, or if the file is
+/// incorrectly formatted.
+///
+/// # Example
+/// ```no_run
+/// chemfiles::add_configuration("local-config.toml").unwrap();
+/// // from now on, the data from "local-config.toml" will be used
+/// ```
+pub fn add_configuration<S>(path: S) -> Result<(), Error>
+where
+ S: AsRef<str>,
+{
+ let buffer = strings::to_c(path.as_ref());
+ unsafe { errors::check(chfl_add_configuration(buffer.as_ptr())) }
+}
+
+#[cfg(test)]
+mod tests {
+ #[test]
+ fn version() {
+ assert!(!crate::version().is_empty());
+ assert!(crate::version().starts_with("0.10"));
+ }
+}
+
+#[cfg(test)]
+fn assert_vector3d_eq(lhs: &[f64; 3], rhs: &[f64; 3], eps: f64) {
+ lhs.iter()
+ .zip(rhs)
+ .for_each(|(l, r)| approx::assert_ulps_eq!(l, r, epsilon = eps));
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2020 Guillaume Fraux -- BSD licensed
+use std::convert::TryInto;
+use std::ffi::CStr;
+use std::path::Path;
+
+use chemfiles_sys::{chfl_format_metadata, chfl_formats_list, chfl_free, chfl_guess_format};
+
+use crate::errors::check_success;
+
+use crate::{errors::check, Error};
+
+/// `FormatMetadata` contains metadata associated with one format.
+#[allow(clippy::struct_excessive_bools)]
+#[derive(Debug, Clone, PartialEq, Eq)]
+pub struct FormatMetadata {
+ /// Name of the format.
+ pub name: &'static str,
+ /// Extension associated with the format.
+ pub extension: Option<&'static str>,
+ /// Extended, user-facing description of the format.
+ pub description: &'static str,
+ /// URL pointing to the format definition/reference.
+ pub reference: &'static str,
+ /// Is reading files in this format implemented?
+ pub read: bool,
+ /// Is writing files in this format implemented?
+ pub write: bool,
+ /// Does this format support in-memory IO?
+ pub memory: bool,
+ /// Does this format support storing atomic positions?
+ pub positions: bool,
+ /// Does this format support storing atomic velocities?
+ pub velocities: bool,
+ /// Does this format support storing unit cell information?
+ pub unit_cell: bool,
+ /// Does this format support storing atom names or types?
+ pub atoms: bool,
+ /// Does this format support storing bonds between atoms?
+ pub bonds: bool,
+ /// Does this format support storing residues?
+ pub residues: bool,
+}
+
+impl FormatMetadata {
+ pub(crate) fn from_raw(raw: &chfl_format_metadata) -> Self {
+ let str_from_ptr = |ptr| unsafe { CStr::from_ptr(ptr).to_str().expect("Invalid Rust str from C") };
+ let extension = if raw.extension.is_null() {
+ None
+ } else {
+ Some(str_from_ptr(raw.extension))
+ };
+ Self {
+ name: str_from_ptr(raw.name),
+ extension,
+ description: str_from_ptr(raw.description),
+ reference: str_from_ptr(raw.reference),
+ read: raw.read,
+ write: raw.write,
+ memory: raw.memory,
+ positions: raw.positions,
+ velocities: raw.velocities,
+ unit_cell: raw.unit_cell,
+ atoms: raw.atoms,
+ bonds: raw.bonds,
+ residues: raw.residues,
+ }
+ }
+}
+
+/// Get the list of formats known by chemfiles, as well as all associated metadata.
+///
+/// # Example
+/// ```
+/// let formats = chemfiles::formats_list();
+/// println!("chemfiles supports {} formats:", formats.len());
+/// for format in &formats {
+/// println!(
+/// " {:<15} {}",
+/// format.name,
+/// format.extension.as_deref().unwrap_or("")
+/// );
+/// }
+/// ```
+#[must_use]
+pub fn formats_list() -> Vec<FormatMetadata> {
+ let mut formats = std::ptr::null_mut();
+ let mut count: u64 = 0;
+ let formats_slice = unsafe {
+ check_success(chfl_formats_list(&mut formats, &mut count));
+ std::slice::from_raw_parts(formats, count.try_into().expect("failed to convert u64 to usize"))
+ };
+ let formats_vec = formats_slice.iter().map(FormatMetadata::from_raw).collect();
+ unsafe {
+ let _ = chfl_free(formats as *const _);
+ }
+ return formats_vec;
+}
+
+#[allow(clippy::doc_markdown)]
+/// Get the format that chemfiles would use to read a file at the given
+/// ``path``.
+///
+/// The format is mostly guessed from the path extension, chemfiles only tries
+/// to read the file to distinguish between CIF and mmCIF files. Opening the
+/// file using the returned format string might still fail. For example, it will
+/// fail if the file is not actually formatted according to the guessed format;
+/// or the format/compression combination is not supported (e.g. `XTC / GZ` will
+/// not work since the XTC reader does not support compressed files).
+///
+/// The returned format is represented in a way compatible with the various
+/// `Trajectory` constructors, i.e. `"<format name> [/ <compression>]"`, where
+/// compression is optional.
+///
+/// # Errors
+///
+/// This function returns an error if the file format couldn't be guessed.
+///
+/// # Panics
+///
+/// This function panics if the path can't be converted to a Unicode string.
+///
+/// # Examples
+/// ```
+/// let format = chemfiles::guess_format("trajectory.xyz.xz").unwrap();
+/// assert_eq!(format, "XYZ / XZ");
+///
+/// let format = chemfiles::guess_format("trajectory.nc").unwrap();
+/// assert_eq!(format, "Amber NetCDF");
+///
+/// let format = chemfiles::guess_format("trajectory.unknown.format");
+/// assert!(format.is_err());
+/// ```
+pub fn guess_format<P>(path: P) -> Result<String, Error>
+where
+ P: AsRef<Path>,
+{
+ let path = path.as_ref().to_str().expect("couldn't convert path to Unicode");
+ let path = crate::strings::to_c(path);
+ let mut buffer = vec![0; 128];
+ unsafe {
+ check(chfl_guess_format(
+ path.as_ptr(),
+ buffer.as_mut_ptr(),
+ buffer.len() as u64,
+ ))?;
+ }
+ Ok(crate::strings::from_c(buffer.as_ptr()))
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use chemfiles_sys::*;
+
+use crate::errors::{check, check_not_null, check_success, Error};
+use crate::strings;
+
+/// A thin wrapper around `CHFL_PROPERTY`
+#[derive(Debug)]
+pub(crate) struct RawProperty {
+ handle: *mut CHFL_PROPERTY,
+}
+
+impl RawProperty {
+ /// Create a `RawProperty` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ pub unsafe fn from_ptr(ptr: *mut CHFL_PROPERTY) -> RawProperty {
+ check_not_null(ptr);
+ RawProperty { handle: ptr }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ pub fn as_ptr(&self) -> *const CHFL_PROPERTY {
+ self.handle
+ }
+
+ fn double(value: f64) -> RawProperty {
+ unsafe {
+ let handle = chfl_property_double(value);
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn bool(value: bool) -> RawProperty {
+ let value = if value { 1 } else { 0 };
+ unsafe {
+ let handle = chfl_property_bool(value);
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn vector3d(value: [f64; 3]) -> RawProperty {
+ unsafe {
+ let handle = chfl_property_vector3d(value.as_ptr());
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn string(value: &str) -> RawProperty {
+ let buffer = strings::to_c(value);
+ unsafe {
+ let handle = chfl_property_string(buffer.as_ptr());
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn get_kind(&self) -> chfl_property_kind {
+ let mut kind = chfl_property_kind::CHFL_PROPERTY_BOOL;
+ unsafe {
+ check_success(chfl_property_get_kind(self.as_ptr(), &mut kind));
+ }
+ return kind;
+ }
+
+ fn get_bool(&self) -> Result<bool, Error> {
+ let mut value = 0;
+ unsafe {
+ check(chfl_property_get_bool(self.as_ptr(), &mut value))?;
+ }
+ return Ok(value != 0);
+ }
+
+ fn get_double(&self) -> Result<f64, Error> {
+ let mut value = 0.0;
+ unsafe {
+ check(chfl_property_get_double(self.as_ptr(), &mut value))?;
+ }
+ return Ok(value);
+ }
+
+ fn get_string(&self) -> Result<String, Error> {
+ let get_string = |ptr, len| unsafe { chfl_property_get_string(self.as_ptr(), ptr, len) };
+ let value = strings::call_autogrow_buffer(64, get_string)?;
+ return Ok(strings::from_c(value.as_ptr()));
+ }
+
+ fn get_vector3d(&self) -> Result<[f64; 3], Error> {
+ let mut value = [0.0; 3];
+ unsafe {
+ check(chfl_property_get_vector3d(self.as_ptr(), value.as_mut_ptr()))?;
+ }
+ return Ok(value);
+ }
+}
+
+impl Drop for RawProperty {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+/// A `Property` is a piece of data that can be associated with an `Atom` or a
+/// `Frame`.
+#[derive(Debug, Clone, PartialEq, PartialOrd)]
+pub enum Property {
+ /// Boolean property
+ Bool(bool),
+ /// Floating point property
+ Double(f64),
+ /// String property
+ String(String),
+ /// 3-dimensional vector property
+ Vector3D([f64; 3]),
+}
+
+impl From<bool> for Property {
+ fn from(value: bool) -> Self {
+ Property::Bool(value)
+ }
+}
+
+impl From<f64> for Property {
+ fn from(value: f64) -> Self {
+ Property::Double(value)
+ }
+}
+
+impl From<String> for Property {
+ fn from(value: String) -> Self {
+ Property::String(value)
+ }
+}
+
+impl<'a> From<&'a str> for Property {
+ fn from(value: &'a str) -> Self {
+ Property::String(value.into())
+ }
+}
+
+impl From<[f64; 3]> for Property {
+ fn from(value: [f64; 3]) -> Self {
+ Property::Vector3D(value)
+ }
+}
+
+impl Property {
+ pub(crate) fn as_raw(&self) -> RawProperty {
+ match *self {
+ Property::Bool(value) => RawProperty::bool(value),
+ Property::Double(value) => RawProperty::double(value),
+ Property::String(ref value) => RawProperty::string(value),
+ Property::Vector3D(value) => RawProperty::vector3d(value),
+ }
+ }
+
+ #[allow(clippy::needless_pass_by_value)] // raw property
+ pub(crate) fn from_raw(raw: RawProperty) -> Property {
+ match raw.get_kind() {
+ chfl_property_kind::CHFL_PROPERTY_BOOL => Self::Bool(raw.get_bool().expect("should be a bool")),
+ chfl_property_kind::CHFL_PROPERTY_DOUBLE => Self::Double(raw.get_double().expect("should be a double")),
+ chfl_property_kind::CHFL_PROPERTY_STRING => Self::String(raw.get_string().expect("should be a string")),
+ chfl_property_kind::CHFL_PROPERTY_VECTOR3D => {
+ Property::Vector3D(raw.get_vector3d().expect("should be a vector3d"))
+ }
+ }
+ }
+}
+
+/// An iterator over the properties in an atom/frame/residue
+pub struct PropertiesIter<'a> {
+ pub(crate) names: std::vec::IntoIter<String>,
+ pub(crate) getter: Box<dyn Fn(&str) -> Property + 'a>,
+}
+
+impl<'a> Iterator for PropertiesIter<'a> {
+ type Item = (String, Property);
+ fn next(&mut self) -> Option<Self::Item> {
+ self.names.next().map(|name| {
+ let property = (self.getter)(&name);
+ (name, property)
+ })
+ }
+
+ fn size_hint(&self) -> (usize, Option<usize>) {
+ self.names.size_hint()
+ }
+
+ fn count(self) -> usize {
+ self.names.count()
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ mod raw {
+ use super::super::*;
+
+ #[test]
+ fn bool() {
+ let property = RawProperty::bool(false);
+ assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_BOOL);
+ assert_eq!(property.get_bool(), Ok(false));
+ }
+
+ #[test]
+ fn double() {
+ let property = RawProperty::double(45.0);
+ assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_DOUBLE);
+ assert_eq!(property.get_double(), Ok(45.0));
+ }
+
+ #[test]
+ fn string() {
+ let property = RawProperty::string("test");
+ assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_STRING);
+ assert_eq!(property.get_string(), Ok("test".into()));
+ }
+
+ #[test]
+ fn vector3d() {
+ let property = RawProperty::vector3d([1.2, 3.4, 5.6]);
+ assert_eq!(property.get_kind(), chfl_property_kind::CHFL_PROPERTY_VECTOR3D);
+ assert_eq!(property.get_vector3d(), Ok([1.2, 3.4, 5.6]));
+ }
+ }
+
+ mod rust {
+ use super::super::*;
+
+ #[test]
+ fn bool() {
+ let property = Property::Bool(false);
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_BOOL);
+ assert_eq!(raw.get_bool(), Ok(false));
+
+ assert_eq!(Property::from_raw(raw), property);
+ }
+
+ #[test]
+ fn double() {
+ let property = Property::Double(45.0);
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_DOUBLE);
+ assert_eq!(raw.get_double(), Ok(45.0));
+
+ assert_eq!(Property::from_raw(raw), property);
+ }
+
+ #[test]
+ fn string() {
+ let property = Property::String("test".into());
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_STRING);
+ assert_eq!(raw.get_string(), Ok("test".into()));
+
+ assert_eq!(Property::from_raw(raw), property);
+
+ let property = Property::String("long string ".repeat(128));
+ let raw = property.as_raw();
+ assert_eq!(raw.get_string(), Ok("long string ".repeat(128)));
+ }
+
+ #[test]
+ fn vector3d() {
+ let property = Property::Vector3D([1.2, 3.4, 5.6]);
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), chfl_property_kind::CHFL_PROPERTY_VECTOR3D);
+ assert_eq!(raw.get_vector3d(), Ok([1.2, 3.4, 5.6]));
+
+ assert_eq!(Property::from_raw(raw), property);
+ }
+ }
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371 +372 +373 +374 +375 +376 +377 +378 +379 +380 +381 +382 +383 +384 +385 +386 +387 +388 +389 +390 +391 +392 +393 +394 +395 +396 +397 +398 +399 +400 +401 +402 +403 +404 +405 +406 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::marker::PhantomData;
+
+use chemfiles_sys::*;
+
+use crate::errors::{check_not_null, check_success};
+use crate::property::{PropertiesIter, Property, RawProperty};
+use crate::strings;
+
+/// A `Residue` is a group of atoms belonging to the same logical unit. They
+/// can be small molecules, amino-acids in a protein, monomers in polymers,
+/// *etc.*
+#[derive(Debug)]
+pub struct Residue {
+ handle: *mut CHFL_RESIDUE,
+}
+
+/// An analog to a reference to a residue (`&Residue`)
+#[derive(Debug)]
+pub struct ResidueRef<'a> {
+ inner: Residue,
+ marker: PhantomData<&'a Residue>,
+}
+
+impl<'a> std::ops::Deref for ResidueRef<'a> {
+ type Target = Residue;
+ fn deref(&self) -> &Residue {
+ &self.inner
+ }
+}
+
+impl Clone for Residue {
+ fn clone(&self) -> Residue {
+ unsafe {
+ let new_handle = chfl_residue_copy(self.as_ptr());
+ Residue::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Residue {
+ /// Create a `Residue` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_RESIDUE) -> Residue {
+ check_not_null(ptr);
+ Residue { handle: ptr }
+ }
+
+ /// Create a borrowed `Residue` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, except for it being non-null, and the caller is responsible
+ /// for setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_RESIDUE) -> ResidueRef<'a> {
+ ResidueRef {
+ inner: Residue::from_ptr(ptr as *mut CHFL_RESIDUE),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_RESIDUE {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_RESIDUE {
+ self.handle
+ }
+
+ /// Create a new residue with the given `name`
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::new("ALA");
+ /// assert_eq!(residue.name(), "ALA");
+ /// assert_eq!(residue.id(), None);
+ /// ```
+ pub fn new<'a>(name: impl Into<&'a str>) -> Residue {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ let handle = chfl_residue(buffer.as_ptr());
+ Residue::from_ptr(handle)
+ }
+ }
+
+ /// Create a new residue with the given `name` and `id` as identifier.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::with_id("ALA", 67);
+ /// assert_eq!(residue.name(), "ALA");
+ /// assert_eq!(residue.id(), Some(67));
+ /// ```
+ pub fn with_id<'a>(name: impl Into<&'a str>, id: i64) -> Residue {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ let handle = chfl_residue_with_id(buffer.as_ptr(), id);
+ Residue::from_ptr(handle)
+ }
+ }
+
+ /// Get the number of atoms in this residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.size(), 0);
+ ///
+ /// residue.add_atom(0);
+ /// residue.add_atom(1);
+ /// residue.add_atom(2);
+ /// assert_eq!(residue.size(), 3);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(chfl_residue_atoms_count(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Get the identifier of this residue in the initial topology file.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::with_id("", 42);
+ /// assert_eq!(residue.id(), Some(42));
+ /// ```
+ pub fn id(&self) -> Option<i64> {
+ let mut resid = 0;
+ let status = unsafe { chfl_residue_id(self.as_ptr(), &mut resid) };
+
+ if status == chfl_status::CHFL_SUCCESS {
+ return Some(resid);
+ } else if status == chfl_status::CHFL_GENERIC_ERROR {
+ return None;
+ }
+
+ // call check_success to panic in case of error
+ check_success(status);
+ unreachable!();
+ }
+
+ /// Get the name of this residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::new("water");
+ /// assert_eq!(residue.name(), "water");
+ /// ```
+ pub fn name(&self) -> String {
+ let get_name = |ptr, len| unsafe { chfl_residue_name(self.as_ptr(), ptr, len) };
+ let name = strings::call_autogrow_buffer(64, get_name).expect("getting residue name failed");
+ return strings::from_c(name.as_ptr());
+ }
+
+ /// Add the atom at index `atom` in this residue.
+ ///
+ /// This will fail if the atom is already in the residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.size(), 0);
+ /// assert_eq!(residue.contains(56), false);
+ ///
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.size(), 1);
+ /// assert_eq!(residue.contains(56), true);
+ ///
+ /// // Adding the same atom twice is fine
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.size(), 1);
+ /// ```
+ pub fn add_atom(&mut self, atom: usize) {
+ unsafe {
+ check_success(chfl_residue_add_atom(self.as_mut_ptr(), atom as u64));
+ }
+ }
+
+ /// Check if the atom at index `i` is in this residue
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.contains(56), false);
+ ///
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.contains(56), true);
+ /// ```
+ pub fn contains(&self, atom: usize) -> bool {
+ let mut inside = 0;
+ unsafe {
+ check_success(chfl_residue_contains(self.as_ptr(), atom as u64, &mut inside));
+ }
+ return inside != 0;
+ }
+
+ /// Get the list of atoms of this residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.atoms(), vec![]);
+ ///
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.atoms(), vec![56]);
+ /// ```
+ pub fn atoms(&self) -> Vec<usize> {
+ let size = self.size();
+ let count = size as u64;
+ let mut indices = vec![u64::max_value(); size];
+ unsafe {
+ check_success(chfl_residue_atoms(self.as_ptr(), indices.as_mut_ptr(), count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return indices.into_iter().map(|idx| idx as usize).collect();
+ }
+
+ /// Add a new `property` with the given `name` to this residue.
+ ///
+ /// If a property with the same name already exists, this function override
+ /// the existing property with the new one.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Residue, Property};
+ /// let mut residue = Residue::new("ALA");
+ /// residue.set("a string", "hello");
+ /// residue.set("a double", 3.2);
+ ///
+ /// assert_eq!(residue.get("a string"), Some(Property::String("hello".into())));
+ /// assert_eq!(residue.get("a double"), Some(Property::Double(3.2)));
+ /// ```
+ pub fn set(&mut self, name: &str, property: impl Into<Property>) {
+ let buffer = strings::to_c(name);
+ let property = property.into().as_raw();
+ unsafe {
+ check_success(chfl_residue_set_property(
+ self.as_mut_ptr(),
+ buffer.as_ptr(),
+ property.as_ptr(),
+ ));
+ }
+ }
+
+ /// Get a property with the given `name` in this frame, if it exist.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Residue, Property};
+ /// let mut residue = Residue::new("ALA");
+ /// residue.set("foo", Property::Double(22.2));
+ ///
+ /// assert_eq!(residue.get("foo"), Some(Property::Double(22.2)));
+ /// assert_eq!(residue.get("Bar"), None);
+ /// ```
+ pub fn get(&self, name: &str) -> Option<Property> {
+ let buffer = strings::to_c(name);
+ unsafe {
+ let handle = chfl_residue_get_property(self.as_ptr(), buffer.as_ptr());
+ if handle.is_null() {
+ None
+ } else {
+ let raw = RawProperty::from_ptr(handle);
+ Some(Property::from_raw(raw))
+ }
+ }
+ }
+
+ /// Get an iterator over all (name, property) pairs for this frame
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Residue, Property};
+ /// let mut residue = Residue::new("ALA");
+ /// residue.set("foo", Property::Double(22.2));
+ /// residue.set("bar", Property::Bool(false));
+ ///
+ /// for (name, property) in residue.properties() {
+ /// if name == "foo" {
+ /// assert_eq!(property, Property::Double(22.2));
+ /// } else if name == "bar" {
+ /// assert_eq!(property, Property::Bool(false));
+ /// }
+ /// }
+ /// ```
+ pub fn properties(&self) -> PropertiesIter {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_residue_properties_count(self.as_ptr(), &mut count));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = count as usize;
+ let mut c_names = vec![std::ptr::null_mut(); size];
+ unsafe {
+ check_success(chfl_residue_list_properties(self.as_ptr(), c_names.as_mut_ptr(), count));
+ }
+
+ let mut names = Vec::new();
+ for ptr in c_names {
+ names.push(strings::from_c(ptr));
+ }
+
+ PropertiesIter {
+ names: names.into_iter(),
+ getter: Box::new(move |name| self.get(name).expect("failed to get property")),
+ }
+ }
+}
+
+impl Drop for Residue {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut residue = Residue::new("A");
+ assert_eq!(residue.size(), 0);
+
+ let copy = residue.clone();
+ assert_eq!(copy.size(), 0);
+
+ residue.add_atom(3);
+ residue.add_atom(7);
+ assert_eq!(residue.size(), 2);
+ assert_eq!(copy.size(), 0);
+ }
+
+ #[test]
+ fn name() {
+ let residue = Residue::new("A");
+ assert_eq!(residue.name(), "A");
+ }
+
+ #[test]
+ fn id() {
+ let residue = Residue::new("A");
+ assert_eq!(residue.id(), None);
+
+ let residue = Residue::with_id("A", 42);
+ assert_eq!(residue.id(), Some(42));
+
+ let residue = Residue::with_id("A", -3);
+ assert_eq!(residue.id(), Some(-3));
+ }
+
+ #[test]
+ fn atoms() {
+ let mut residue = Residue::new("A");
+ assert_eq!(residue.size(), 0);
+
+ residue.add_atom(0);
+ residue.add_atom(3);
+ residue.add_atom(45);
+ assert_eq!(residue.size(), 3);
+
+ assert!(residue.contains(3));
+ assert!(!residue.contains(5));
+
+ assert_eq!(residue.atoms(), vec![0, 3, 45]);
+ }
+
+ #[test]
+ fn property() {
+ let mut residue = Residue::new("ALA");
+
+ residue.set("foo", -22.0);
+ assert_eq!(residue.get("foo"), Some(Property::Double(-22.0)));
+ assert_eq!(residue.get("bar"), None);
+
+ residue.set("bar", Property::String("here".into()));
+ for (name, property) in residue.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(-22.0));
+ } else if name == "bar" {
+ assert_eq!(property, Property::String("here".into()));
+ }
+ }
+ }
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371 +372 +373 +374 +375 +376 +377 +378 +379 +380 +381 +382 +383 +384 +385 +386 +387 +388 +389 +390 +391 +392 +393 +394 +395 +396 +397 +398 +399 +400 +401 +402 +403 +404 +405 +406 +407 +408 +409 +410 +411 +412 +413 +414 +415 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use chemfiles_sys::*;
+
+use crate::errors::{check, check_not_null, check_success, Error, Status};
+use crate::frame::Frame;
+use crate::strings;
+
+#[derive(Debug, Clone, PartialEq, Eq)]
+/// A `Match` is a set of atomic indexes matching a given selection. It can
+/// mostly be used like a `&[usize]`.
+pub struct Match {
+ size: usize,
+ atoms: [usize; 4],
+}
+
+#[allow(clippy::len_without_is_empty)]
+impl Match {
+ /// Get the length of the Match.
+ ///
+ /// # Example
+ ///
+ /// ```
+ /// # use chemfiles::Match;
+ /// let atomic_match = Match::new(&[3, 4, 5]);
+ /// assert_eq!(atomic_match.len(), 3);
+ /// ```
+ pub fn len(&self) -> usize {
+ self.size
+ }
+
+ /// Create a new match containing the atoms in the `atoms` slice.
+ ///
+ /// # Panics
+ ///
+ /// If the slice contains more than 4 elements, which is the maximal size
+ /// of a match.
+ ///
+ /// # Example
+ ///
+ /// ```
+ /// # use chemfiles::Match;
+ /// let atomic_match = Match::new(&[3, 4, 5]);
+ /// assert_eq!(atomic_match.len(), 3);
+ /// assert_eq!(atomic_match[0], 3);
+ /// assert_eq!(atomic_match[1], 4);
+ /// assert_eq!(atomic_match[2], 5);
+ /// ```
+ pub fn new(atoms: &[usize]) -> Match {
+ assert!(atoms.len() <= 4);
+ let size = atoms.len();
+ let mut matches = [usize::max_value(); 4];
+ for (i, atom) in atoms.iter().enumerate() {
+ matches[i] = *atom;
+ }
+ Match { size, atoms: matches }
+ }
+
+ /// Iterate over the atomic indexes in the match.
+ ///
+ /// # Example
+ ///
+ /// ```
+ /// # use chemfiles::Match;
+ /// let atomic_match = Match::new(&[3, 4, 5]);
+ /// let mut iter = atomic_match.iter();
+ ///
+ /// assert_eq!(iter.next(), Some(&3));
+ /// assert_eq!(iter.next(), Some(&4));
+ /// assert_eq!(iter.next(), Some(&5));
+ /// assert_eq!(iter.next(), None);
+ /// ```
+ pub fn iter(&self) -> std::slice::Iter<usize> {
+ self.atoms[..self.len()].iter()
+ }
+}
+
+impl std::ops::Index<usize> for Match {
+ type Output = usize;
+ fn index(&self, i: usize) -> &Self::Output {
+ assert!(i < self.len());
+ &self.atoms[i]
+ }
+}
+
+impl<'a> IntoIterator for &'a Match {
+ type Item = &'a usize;
+ type IntoIter = std::slice::Iter<'a, usize>;
+
+ fn into_iter(self) -> Self::IntoIter {
+ self.atoms[..self.len()].iter()
+ }
+}
+
+/// A `Selection` allow to select atoms in a `Frame`, from a selection
+/// language. The selection language is built by combining basic operations.
+/// Each basic operation follows the `<selector>[(<variable>)] <operator>
+/// <value>` structure, where `<operator>` is a comparison operator in
+/// `== != < <= > >=`.
+#[derive(Debug)]
+pub struct Selection {
+ handle: *mut CHFL_SELECTION,
+}
+
+impl Clone for Selection {
+ fn clone(&self) -> Selection {
+ unsafe {
+ let new_handle = chfl_selection_copy(self.as_ptr());
+ Selection::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Drop for Selection {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+impl Selection {
+ /// Create a `Selection` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_SELECTION) -> Selection {
+ check_not_null(ptr);
+ Selection { handle: ptr }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_SELECTION {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_SELECTION {
+ self.handle
+ }
+
+ /// Create a new selection from the given selection string.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the selection string is invalid.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Selection;
+ /// let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+ /// ```
+ pub fn new<'a, S: Into<&'a str>>(selection: S) -> Result<Selection, Error> {
+ let buffer = strings::to_c(selection.into());
+ unsafe {
+ let handle = chfl_selection(buffer.as_ptr());
+ if handle.is_null() {
+ Err(Error {
+ status: Status::SelectionError,
+ message: Error::last_error(),
+ })
+ } else {
+ Ok(Selection::from_ptr(handle))
+ }
+ }
+ }
+
+ /// Get the size of the selection, i.e. the number of atoms we are selecting
+ /// together.
+ ///
+ /// This value is 1 for the 'atom' context, 2 for the 'pair' and 'bond'
+ /// context, 3 for the 'three' and 'angles' context and 4 for the 'four'
+ /// and 'dihedral' context.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Selection;
+ /// let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+ /// assert_eq!(selection.size(), 2);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(chfl_selection_size(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Get the selection string used to create this selection.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Selection;
+ /// let selection = Selection::new("name H").unwrap();
+ /// assert_eq!(selection.string(), "name H");
+ /// ```
+ pub fn string(&self) -> String {
+ let get_string = |ptr, len| unsafe { chfl_selection_string(self.as_ptr(), ptr, len) };
+ let selection = strings::call_autogrow_buffer(1024, get_string).expect("failed to get selection string");
+ return strings::from_c(selection.as_ptr());
+ }
+
+ /// Evaluate a selection for a given frame, and return the corresponding
+ /// matches.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Selection, Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+ ///
+ /// let mut selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+ /// let matches = selection.evaluate(&frame);
+ ///
+ /// assert_eq!(matches.len(), 2);
+ ///
+ /// assert_eq!(matches[0].len(), 2);
+ /// assert_eq!(matches[0][0], 0);
+ /// assert_eq!(matches[0][1], 1);
+ ///
+ /// assert_eq!(matches[1].len(), 2);
+ /// assert_eq!(matches[1][0], 2);
+ /// assert_eq!(matches[1][1], 1);
+ /// ```
+ pub fn evaluate(&mut self, frame: &Frame) -> Vec<Match> {
+ #![allow(clippy::cast_possible_truncation)]
+ let mut count = 0;
+ unsafe {
+ check(chfl_selection_evaluate(self.as_mut_ptr(), frame.as_ptr(), &mut count))
+ .expect("failed to evaluate selection");
+ }
+
+ let size = count as usize;
+ let mut chfl_matches = vec![chfl_match { size: 0, atoms: [0; 4] }; size];
+ unsafe {
+ check(chfl_selection_matches(self.handle, chfl_matches.as_mut_ptr(), count))
+ .expect("failed to extract matches");
+ }
+
+ return chfl_matches
+ .into_iter()
+ .map(|chfl_match| Match {
+ size: chfl_match.size as usize,
+ atoms: [
+ chfl_match.atoms[0] as usize,
+ chfl_match.atoms[1] as usize,
+ chfl_match.atoms[2] as usize,
+ chfl_match.atoms[3] as usize,
+ ],
+ })
+ .collect();
+ }
+
+ /// Evaluates a selection of size 1 on a given `frame`. This function
+ /// returns the list of atomic indexes in the frame matching this selection.
+ ///
+ /// # Panics
+ ///
+ /// If the selection size is not 1
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Selection, Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+ ///
+ /// let mut selection = Selection::new("name H").unwrap();
+ /// let matches = selection.list(&frame);
+ ///
+ /// assert_eq!(matches.len(), 2);
+ /// assert_eq!(matches[0], 0);
+ /// assert_eq!(matches[1], 2);
+ /// ```
+ pub fn list(&mut self, frame: &Frame) -> Vec<usize> {
+ assert!(
+ self.size() == 1,
+ "can not call `Selection::list` on a multiple selection"
+ );
+ return self.evaluate(frame).into_iter().map(|m| m[0]).collect();
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ use super::*;
+ use crate::{Atom, Topology};
+
+ #[test]
+ fn clone() {
+ let selection = Selection::new("name H").unwrap();
+
+ let copy = selection.clone();
+ assert_eq!(selection.size(), 1);
+ assert_eq!(copy.size(), 1);
+ }
+
+ fn testing_frame() -> Frame {
+ let mut topology = Topology::new();
+
+ topology.add_atom(&Atom::new("H"));
+ topology.add_atom(&Atom::new("O"));
+ topology.add_atom(&Atom::new("O"));
+ topology.add_atom(&Atom::new("H"));
+
+ topology.add_bond(0, 1);
+ topology.add_bond(1, 2);
+ topology.add_bond(2, 3);
+
+ let mut frame = Frame::new();
+ frame.resize(4);
+ frame.set_topology(&topology).unwrap();
+ return frame;
+ }
+
+ mod matches {
+ use super::*;
+
+ #[test]
+ fn index() {
+ let m = Match::new(&[1, 2, 3, 4]);
+ assert_eq!(m[0], 1);
+ assert_eq!(m[1], 2);
+ assert_eq!(m[2], 3);
+ assert_eq!(m[3], 4);
+
+ let m = Match::new(&[1, 2]);
+ assert_eq!(m[0], 1);
+ assert_eq!(m[1], 2);
+ }
+
+ #[test]
+ fn iter() {
+ let match_ = Match::new(&[1, 2, 3, 4]);
+ assert_eq!(match_.iter().copied().collect::<Vec<usize>>(), vec![1, 2, 3, 4]);
+
+ let v = vec![1, 2, 3, 4];
+ for (i, &m) in match_.iter().enumerate() {
+ assert_eq!(v[i], m);
+ }
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bound() {
+ let m = Match::new(&[1, 2]);
+ let _ = m[2];
+ }
+
+ #[test]
+ #[should_panic]
+ fn too_big() {
+ let _ = Match::new(&[1, 2, 3, 5, 4]);
+ }
+ }
+
+ #[test]
+ fn size() {
+ let selection = Selection::new("name H").unwrap();
+ assert_eq!(selection.size(), 1);
+
+ let selection = Selection::new("angles: name(#1) H").unwrap();
+ assert_eq!(selection.size(), 3);
+
+ let selection = Selection::new("four: name(#1) H").unwrap();
+ assert_eq!(selection.size(), 4);
+ }
+
+ #[test]
+ fn string() {
+ let selection = Selection::new("name H").unwrap();
+ assert_eq!(selection.string(), "name H");
+
+ let selection = Selection::new("angles: name(#1) H").unwrap();
+ assert_eq!(selection.string(), "angles: name(#1) H");
+ }
+
+ #[test]
+ fn evaluate() {
+ let frame = testing_frame();
+
+ let mut selection = Selection::new("name H").unwrap();
+ let res = selection.evaluate(&frame);
+ assert_eq!(res, &[Match::new(&[0]), Match::new(&[3])]);
+
+ let mut selection = Selection::new("angles: all").unwrap();
+ let res = selection.evaluate(&frame);
+ for m in &[Match::new(&[0, 1, 2]), Match::new(&[1, 2, 3])] {
+ assert!(res.iter().any(|r| r == m));
+ }
+ }
+
+ #[test]
+ fn list() {
+ let frame = testing_frame();
+
+ let mut selection = Selection::new("name H").unwrap();
+ let res = selection.list(&frame);
+ assert_eq!(res, vec![0, 3]);
+ }
+
+ #[test]
+ #[should_panic = "can not call `Selection::list` on a multiple selection"]
+ fn list_on_size_1_selection() {
+ let frame = testing_frame();
+ let mut selection = Selection::new("pairs: name(#1) H").unwrap();
+ let _list = selection.list(&frame);
+ }
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+
+//! String conversions between C and Rust
+use std::ffi::{CStr, CString};
+use std::os::raw::c_char;
+
+use crate::errors::{check, Error};
+
+use chemfiles_sys::chfl_status;
+
+/// Create a Rust string from a C string. Clones all characters in `buffer`.
+pub fn from_c(buffer: *const c_char) -> String {
+ unsafe {
+ let rust_str = CStr::from_ptr(buffer).to_str().expect("Invalid Rust string from C");
+ return String::from(rust_str);
+ }
+}
+
+/// Create a C string from a Rust string.
+pub fn to_c<S>(string: S) -> CString
+where
+ S: Into<Vec<u8>>,
+{
+ CString::new(string).expect("Invalid C string from Rust")
+}
+
+/// Check if a string buffer was big enough when passed to a C function
+fn buffer_was_big_enough(buffer: &[c_char]) -> bool {
+ let len = buffer.len();
+ if len < 2 {
+ false
+ } else {
+ // The C code should always set the last element to 0
+ debug_assert_eq!(buffer[len - 1], 0);
+ buffer[len - 2] == 0
+ }
+}
+
+/// Call `callback` C function with a string buffer and it length, using
+/// `initial` as the buffer initial size. If the buffer was filled and the
+/// result truncated by the C library, grow the buffer and try again until we
+/// get all the data. Then return the filled buffer to the caller.
+pub fn call_autogrow_buffer<F>(initial: usize, callback: F) -> Result<Vec<c_char>, Error>
+where
+ F: Fn(*mut c_char, u64) -> chfl_status,
+{
+ let mut size = initial;
+ let mut buffer = vec![0; size];
+ check(callback(buffer.as_mut_ptr(), buffer.len() as u64))?;
+
+ while !buffer_was_big_enough(&buffer) {
+ // Grow the buffer and retry
+ size *= 2;
+ buffer.resize(size, 0);
+ check(callback(buffer.as_mut_ptr(), buffer.len() as u64))?;
+ }
+
+ Ok(buffer)
+}
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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::marker::PhantomData;
+use std::ops::{Deref, Drop};
+
+use chemfiles_sys::*;
+
+use crate::errors::{check, check_not_null, check_success, Error};
+use crate::{Atom, AtomMut, AtomRef};
+use crate::{Residue, ResidueRef};
+
+/// Possible bond order associated with bonds
+#[repr(C)]
+#[non_exhaustive]
+#[derive(Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord)]
+pub enum BondOrder {
+ /// Unknown or unspecified bond order
+ Unknown = chfl_bond_order::CHFL_BOND_UNKNOWN as isize,
+ /// Single bond
+ Single = chfl_bond_order::CHFL_BOND_SINGLE as isize,
+ /// Double bond
+ Double = chfl_bond_order::CHFL_BOND_DOUBLE as isize,
+ /// Triple bond
+ Triple = chfl_bond_order::CHFL_BOND_TRIPLE as isize,
+ /// Quadruple bond (present in some metals)
+ Quadruple = chfl_bond_order::CHFL_BOND_QUADRUPLE as isize,
+ /// Quintuplet bond (present in some metals)
+ Quintuplet = chfl_bond_order::CHFL_BOND_QUINTUPLET as isize,
+ /// Amide bond (required by some file formats)
+ Amide = chfl_bond_order::CHFL_BOND_AMIDE as isize,
+ /// Aromatic bond (required by some file formats)
+ Aromatic = chfl_bond_order::CHFL_BOND_AROMATIC as isize,
+}
+
+impl BondOrder {
+ pub(crate) fn as_raw(self) -> chfl_bond_order {
+ match self {
+ BondOrder::Unknown => chfl_bond_order::CHFL_BOND_UNKNOWN,
+ BondOrder::Single => chfl_bond_order::CHFL_BOND_SINGLE,
+ BondOrder::Double => chfl_bond_order::CHFL_BOND_DOUBLE,
+ BondOrder::Triple => chfl_bond_order::CHFL_BOND_TRIPLE,
+ BondOrder::Quadruple => chfl_bond_order::CHFL_BOND_QUADRUPLE,
+ BondOrder::Quintuplet => chfl_bond_order::CHFL_BOND_QUINTUPLET,
+ BondOrder::Amide => chfl_bond_order::CHFL_BOND_AMIDE,
+ BondOrder::Aromatic => chfl_bond_order::CHFL_BOND_AROMATIC,
+ }
+ }
+}
+
+impl From<chfl_bond_order> for BondOrder {
+ fn from(order: chfl_bond_order) -> BondOrder {
+ match order {
+ chfl_bond_order::CHFL_BOND_UNKNOWN => BondOrder::Unknown,
+ chfl_bond_order::CHFL_BOND_SINGLE => BondOrder::Single,
+ chfl_bond_order::CHFL_BOND_DOUBLE => BondOrder::Double,
+ chfl_bond_order::CHFL_BOND_TRIPLE => BondOrder::Triple,
+ chfl_bond_order::CHFL_BOND_QUADRUPLE => BondOrder::Quadruple,
+ chfl_bond_order::CHFL_BOND_QUINTUPLET => BondOrder::Quintuplet,
+ chfl_bond_order::CHFL_BOND_AMIDE => BondOrder::Amide,
+ chfl_bond_order::CHFL_BOND_AROMATIC => BondOrder::Aromatic,
+ }
+ }
+}
+
+/// A `Topology` contains the definition of all the atoms in the system, and
+/// the liaisons between the atoms (bonds, angles, dihedrals, ...). It will
+/// also contain all the residues information if it is available.
+#[derive(Debug)]
+pub struct Topology {
+ handle: *mut CHFL_TOPOLOGY,
+}
+
+/// An analog to a reference to a topology (`&Topology`)
+#[derive(Debug)]
+pub struct TopologyRef<'a> {
+ inner: Topology,
+ marker: PhantomData<&'a Topology>,
+}
+
+impl<'a> Deref for TopologyRef<'a> {
+ type Target = Topology;
+ fn deref(&self) -> &Topology {
+ &self.inner
+ }
+}
+
+impl Clone for Topology {
+ fn clone(&self) -> Topology {
+ unsafe {
+ let new_handle = chfl_topology_copy(self.as_ptr());
+ Topology::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Topology {
+ /// Create a `Topology` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer,
+ /// except for it being non-null.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_TOPOLOGY) -> Topology {
+ check_not_null(ptr);
+ Topology { handle: ptr }
+ }
+
+ /// Create a borrowed `Topology` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, except for it being non-null, and the caller is responsible
+ /// for setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const CHFL_TOPOLOGY) -> TopologyRef<'a> {
+ TopologyRef {
+ inner: Topology::from_ptr(ptr as *mut CHFL_TOPOLOGY),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_TOPOLOGY {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_TOPOLOGY {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer FROM A SHARED REFERENCE.
+ ///
+ /// For uses with functions of the C API using mut pointers for both read
+ /// and write access. Users should check that this does not lead to multiple
+ /// mutable borrows
+ #[inline]
+ #[allow(non_snake_case)]
+ pub(crate) fn as_mut_ptr_MANUALLY_CHECKING_BORROW(&self) -> *mut CHFL_TOPOLOGY {
+ self.handle
+ }
+
+ /// Create a new empty topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let topology = Topology::new();
+ /// assert_eq!(topology.size(), 0);
+ /// ```
+ pub fn new() -> Topology {
+ unsafe { Topology::from_ptr(chfl_topology()) }
+ }
+
+ /// Get a reference of the atom at the given `index` in this topology.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(6);
+ ///
+ /// let atom = topology.atom(4);
+ /// assert_eq!(atom.name(), "");
+ /// ```
+ pub fn atom(&self, index: usize) -> AtomRef {
+ unsafe {
+ let handle = chfl_atom_from_topology(self.as_mut_ptr_MANUALLY_CHECKING_BORROW(), index as u64);
+ Atom::ref_from_ptr(handle)
+ }
+ }
+
+ /// Get a mutable reference to the atom at the given `index` in this topology.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(6);
+ ///
+ /// assert_eq!(topology.atom(4).name(), "");
+ ///
+ /// topology.atom_mut(4).set_name("Fe");
+ /// assert_eq!(topology.atom(4).name(), "Fe");
+ /// ```
+ pub fn atom_mut(&mut self, index: usize) -> AtomMut {
+ unsafe {
+ let handle = chfl_atom_from_topology(self.as_mut_ptr(), index as u64);
+ Atom::ref_mut_from_ptr(handle)
+ }
+ }
+
+ /// Get the current number of atoms in this topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.size(), 0);
+ ///
+ /// topology.resize(6);
+ /// assert_eq!(topology.size(), 6);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(chfl_topology_atoms_count(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Resize this topology to hold `natoms` atoms, inserting dummy atoms if
+ /// the new size if bigger than the old one.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.size(), 0);
+ ///
+ /// topology.resize(6);
+ /// assert_eq!(topology.size(), 6);
+ /// ```
+ pub fn resize(&mut self, natoms: usize) {
+ unsafe {
+ check_success(chfl_topology_resize(self.as_mut_ptr(), natoms as u64));
+ }
+ }
+
+ /// Add an `Atom` at the end of this topology
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Atom};
+ /// let mut topology = Topology::new();
+ /// topology.add_atom(&Atom::new("Mg"));
+ ///
+ /// let atom = topology.atom(0);
+ /// assert_eq!(atom.name(), "Mg");
+ /// ```
+ pub fn add_atom(&mut self, atom: &Atom) {
+ unsafe {
+ check_success(chfl_topology_add_atom(self.as_mut_ptr(), atom.as_ptr()));
+ }
+ }
+
+ /// Remove an `Atom` from this topology by `index`. This modify all the
+ /// other atoms indexes.
+ ///
+ /// # Panics
+ ///
+ /// If the `index` is out of bounds
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(9);
+ /// assert_eq!(topology.size(), 9);
+ ///
+ /// topology.remove(7);
+ /// assert_eq!(topology.size(), 8);
+ /// ```
+ pub fn remove(&mut self, index: usize) {
+ unsafe {
+ check_success(chfl_topology_remove(self.as_mut_ptr(), index as u64));
+ }
+ }
+
+ /// Get the number of bonds in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.bonds_count(), 3);
+ /// ```
+ pub fn bonds_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_bonds_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the number of angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.angles_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.angles_count(), 2);
+ /// ```
+ pub fn angles_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_angles_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the number of dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.dihedrals_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.dihedrals_count(), 1);
+ /// ```
+ pub fn dihedrals_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_dihedrals_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the number of improper dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.dihedrals_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// topology.add_bond(0, 3);
+ /// assert_eq!(topology.impropers_count(), 1);
+ /// ```
+ pub fn impropers_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_impropers_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the list of bonds in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);
+ /// ```
+ pub fn bonds(&self) -> Vec<[usize; 2]> {
+ let size = self.bonds_count();
+ let count = size as u64;
+ let mut bonds = vec![[u64::max_value(); 2]; size];
+ unsafe {
+ check_success(chfl_topology_bonds(self.as_ptr(), bonds.as_mut_ptr(), count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return bonds
+ .into_iter()
+ .map(|bond| [bond[0] as usize, bond[1] as usize])
+ .collect();
+ }
+
+ /// Get the list of angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);
+ /// ```
+ pub fn angles(&self) -> Vec<[usize; 3]> {
+ let size = self.angles_count();
+ let count = size as u64;
+ let mut angles = vec![[u64::max_value(); 3]; size];
+ unsafe {
+ check_success(chfl_topology_angles(self.as_ptr(), angles.as_mut_ptr(), count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return angles
+ .into_iter()
+ .map(|angle| [angle[0] as usize, angle[1] as usize, angle[2] as usize])
+ .collect();
+ }
+
+ /// Get the list of dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ ///
+ /// assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);
+ /// ```
+ pub fn dihedrals(&self) -> Vec<[usize; 4]> {
+ let size = self.dihedrals_count();
+ let count = size as u64;
+ let mut dihedrals = vec![[u64::max_value(); 4]; size];
+ unsafe {
+ check_success(chfl_topology_dihedrals(self.as_ptr(), dihedrals.as_mut_ptr(), count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return dihedrals
+ .into_iter()
+ .map(|dihedral| {
+ [
+ dihedral[0] as usize,
+ dihedral[1] as usize,
+ dihedral[2] as usize,
+ dihedral[3] as usize,
+ ]
+ })
+ .collect();
+ }
+
+ /// Get the list of improper dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// topology.add_bond(0, 3);
+ ///
+ /// assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);
+ /// ```
+ pub fn impropers(&self) -> Vec<[usize; 4]> {
+ let size = self.impropers_count();
+ let count = size as u64;
+ let mut impropers = vec![[u64::max_value(); 4]; size];
+ unsafe {
+ check_success(chfl_topology_impropers(self.as_ptr(), impropers.as_mut_ptr(), count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return impropers
+ .into_iter()
+ .map(|improper| {
+ [
+ improper[0] as usize,
+ improper[1] as usize,
+ improper[2] as usize,
+ improper[3] as usize,
+ ]
+ })
+ .collect();
+ }
+
+ /// Remove all existing bonds, angles, dihedral angles and improper
+ /// dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// assert_eq!(topology.bonds_count(), 2);
+ /// assert_eq!(topology.angles().len(), 1);
+ ///
+ /// topology.clear_bonds();
+ /// assert!(topology.bonds().is_empty());
+ /// assert!(topology.angles().is_empty());
+ /// ```
+ pub fn clear_bonds(&mut self) {
+ unsafe {
+ check_success(chfl_topology_clear_bonds(self.as_mut_ptr()));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the topology.
+ ///
+ /// The bond order is set to `BondOrder::Unknown`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// assert_eq!(topology.bonds_count(), 2);
+ ///
+ /// assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);
+ /// ```
+ pub fn add_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(chfl_topology_add_bond(self.as_mut_ptr(), i as u64, j as u64));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the topology
+ /// with the given bond `order`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(2);
+ ///
+ /// topology.add_bond_with_order(0, 1, BondOrder::Double);
+ /// assert_eq!(topology.bond_order(0, 1), BondOrder::Double);
+ /// ```
+ pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder) {
+ unsafe {
+ check_success(chfl_topology_bond_with_order(
+ self.as_mut_ptr(),
+ i as u64,
+ j as u64,
+ order.as_raw(),
+ ));
+ }
+ }
+
+ /// Get the bond order for the bond between the atoms at indexes `i` and
+ /// `j`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(2);
+ ///
+ /// topology.add_bond_with_order(0, 1, BondOrder::Double);
+ /// assert_eq!(topology.bond_order(0, 1), BondOrder::Double);
+ /// ```
+ pub fn bond_order(&self, i: usize, j: usize) -> BondOrder {
+ let mut order = chfl_bond_order::CHFL_BOND_UNKNOWN;
+ unsafe {
+ check_success(chfl_topology_bond_order(self.as_ptr(), i as u64, j as u64, &mut order));
+ }
+ return order.into();
+ }
+
+ /// Get the bond order for all the bonds in the topology
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(3);
+ ///
+ /// topology.add_bond_with_order(0, 1, BondOrder::Double);
+ /// topology.add_bond_with_order(0, 2, BondOrder::Single);
+ ///
+ /// assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);
+ /// ```
+ pub fn bond_orders(&self) -> Vec<BondOrder> {
+ let size = self.bonds_count();
+ let count = size as u64;
+ let mut bonds = vec![BondOrder::Unknown; size];
+ unsafe {
+ check_success(chfl_topology_bond_orders(
+ self.as_ptr(),
+ // Casting BondOrder to chfl_bond_order is safe, as they are
+ // both `repr(C)` enums with the same values.
+ bonds.as_mut_ptr().cast(),
+ count,
+ ));
+ }
+ return bonds;
+ }
+
+ /// Remove any existing bond between the atoms at indexes `i` and `j` in
+ /// this topology.
+ ///
+ /// This function does nothing if there is no bond between `i` and `j`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(1, 2);
+ /// assert_eq!(topology.bonds_count(), 2);
+ ///
+ /// topology.remove_bond(0, 1);
+ /// assert_eq!(topology.bonds_count(), 1);
+ ///
+ /// // Removing a bond that does not exists is fine
+ /// topology.remove_bond(0, 2);
+ /// assert_eq!(topology.bonds_count(), 1);
+ /// ```
+ pub fn remove_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(chfl_topology_remove_bond(self.as_mut_ptr(), i as u64, j as u64));
+ }
+ }
+
+ /// Get a reference to the residue at index `index` from this topology.
+ ///
+ /// The residue index in the topology is not always the same as the residue
+ /// `id`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// topology.add_residue(&Residue::new("water")).unwrap();
+ ///
+ /// let residue = topology.residue(0).unwrap();
+ /// assert_eq!(residue.name(), "water");
+ /// ```
+ pub fn residue(&self, index: usize) -> Option<ResidueRef> {
+ unsafe {
+ let handle = chfl_residue_from_topology(self.as_ptr(), index as u64);
+ if handle.is_null() {
+ None
+ } else {
+ Some(Residue::ref_from_ptr(handle))
+ }
+ }
+ }
+
+ /// Get a copy of the residue containing the atom at index `index` in this
+ /// topology, if any.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// topology.resize(8);
+ ///
+ /// let mut residue = Residue::new("water");
+ /// residue.add_atom(0);
+ /// residue.add_atom(1);
+ /// residue.add_atom(2);
+ /// topology.add_residue(&residue).unwrap();
+ ///
+ /// let residue = topology.residue_for_atom(0).unwrap();
+ /// assert_eq!(residue.name(), "water");
+ ///
+ /// assert!(topology.residue_for_atom(6).is_none());
+ /// ```
+ pub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef> {
+ let handle = unsafe { chfl_residue_for_atom(self.as_ptr(), index as u64) };
+ if handle.is_null() {
+ None
+ } else {
+ unsafe { Some(Residue::ref_from_ptr(handle)) }
+ }
+ }
+
+ /// Get the number of residues in this topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.residues_count(), 0);
+ ///
+ /// topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+ /// topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+ /// assert_eq!(topology.residues_count(), 2);
+ /// ```
+ pub fn residues_count(&self) -> u64 {
+ let mut count = 0;
+ unsafe {
+ check_success(chfl_topology_residues_count(self.as_ptr(), &mut count));
+ }
+ return count;
+ }
+
+ /// Add a residue to this topology.
+ ///
+ /// # Errors
+ ///
+ /// This function fails is the residue `id` is not already in the topology,
+ /// or if the residue contains atoms that are already in another residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// topology.add_residue(&Residue::new("water")).unwrap();
+ ///
+ /// let residue = topology.residue(0).unwrap();
+ /// assert_eq!(residue.name(), "water");
+ /// ```
+ pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error> {
+ unsafe { check(chfl_topology_add_residue(self.as_mut_ptr(), residue.as_ptr())) }
+ }
+
+ /// Check if the two residues `first` and `second` from the `topology` are
+ /// linked together, *i.e.* if there is a bond between one atom in the
+ /// first residue and one atom in the second one.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ ///
+ /// topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+ /// topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+ ///
+ /// let first = topology.residue(0).unwrap();
+ /// let second = topology.residue(1).unwrap();
+ /// assert_eq!(topology.are_linked(&first, &second), false);
+ /// ```
+ pub fn are_linked(&self, first: &Residue, second: &Residue) -> bool {
+ let mut linked = 0;
+ unsafe {
+ check_success(chfl_topology_residues_linked(
+ self.as_ptr(),
+ first.as_ptr(),
+ second.as_ptr(),
+ &mut linked,
+ ));
+ }
+ return linked != 0;
+ }
+}
+
+impl Drop for Topology {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut topology = Topology::new();
+ assert_eq!(topology.size(), 0);
+
+ let copy = topology.clone();
+ assert_eq!(copy.size(), 0);
+
+ topology.resize(10);
+ assert_eq!(topology.size(), 10);
+ assert_eq!(copy.size(), 0);
+ }
+
+ #[test]
+ fn size() {
+ let mut topology = Topology::new();
+ assert_eq!(topology.size(), 0);
+
+ topology.resize(10);
+ assert_eq!(topology.size(), 10);
+
+ topology.remove(7);
+ assert_eq!(topology.size(), 9);
+
+ topology.add_atom(&Atom::new("Hg"));
+ assert_eq!(topology.size(), 10);
+ }
+
+ #[test]
+ fn atoms() {
+ let mut topology = Topology::new();
+
+ topology.add_atom(&Atom::new("Hg"));
+ topology.add_atom(&Atom::new("Mn"));
+ topology.add_atom(&Atom::new("W"));
+ topology.add_atom(&Atom::new("Fe"));
+
+ assert_eq!(topology.atom(0).name(), "Hg");
+ assert_eq!(topology.atom(3).name(), "Fe");
+ }
+
+ #[test]
+ fn remove() {
+ let mut topology = Topology::new();
+ topology.add_atom(&Atom::new("Hg"));
+ topology.add_atom(&Atom::new("Mn"));
+ topology.add_atom(&Atom::new("W"));
+ topology.add_atom(&Atom::new("Fe"));
+
+ assert_eq!(topology.atom(0).name(), "Hg");
+ assert_eq!(topology.atom(2).name(), "W");
+
+ topology.remove(1);
+ assert_eq!(topology.atom(0).name(), "Hg");
+ assert_eq!(topology.atom(2).name(), "Fe");
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_remove() {
+ let mut topology = Topology::new();
+ topology.resize(18);
+ topology.remove(33);
+ }
+
+ #[test]
+ fn bonds() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.bonds_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(9, 2);
+ topology.add_bond_with_order(3, 7, BondOrder::Aromatic);
+ assert_eq!(topology.bonds_count(), 3);
+
+ assert_eq!(topology.bonds(), vec![[0, 1], [2, 9], [3, 7]]);
+ let expected = vec![BondOrder::Unknown, BondOrder::Unknown, BondOrder::Aromatic];
+ assert_eq!(topology.bond_orders(), expected);
+
+ assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);
+ assert_eq!(topology.bond_order(3, 7), BondOrder::Aromatic);
+
+ topology.remove_bond(3, 7);
+ // Removing unexisting bond is OK if both indexes are in bounds
+ topology.remove_bond(8, 7);
+ assert_eq!(topology.bonds_count(), 2);
+
+ topology.clear_bonds();
+ assert_eq!(topology.bonds_count(), 0);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ topology.add_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_remove_bond() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ topology.remove_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds_with_order() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ topology.add_bond_with_order(300, 7, BondOrder::Unknown);
+ }
+
+ #[test]
+ fn angles() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.angles_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(1, 2);
+ topology.add_bond(3, 7);
+ topology.add_bond(3, 5);
+ assert_eq!(topology.angles_count(), 2);
+
+ assert_eq!(topology.angles(), vec![[0, 1, 2], [5, 3, 7]]);
+
+ topology.clear_bonds();
+ assert_eq!(topology.angles_count(), 0);
+ }
+
+ #[test]
+ fn dihedrals() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.dihedrals_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(1, 2);
+ topology.add_bond(3, 2);
+ topology.add_bond(4, 7);
+ topology.add_bond(4, 5);
+ topology.add_bond(7, 10);
+ assert_eq!(topology.dihedrals_count(), 2);
+
+ assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3], [5, 4, 7, 10]]);
+
+ topology.clear_bonds();
+ assert_eq!(topology.dihedrals_count(), 0);
+ }
+
+ #[test]
+ fn impropers() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.impropers_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(0, 2);
+ topology.add_bond(0, 3);
+ topology.add_bond(4, 7);
+ topology.add_bond(4, 5);
+ topology.add_bond(4, 8);
+ assert_eq!(topology.impropers_count(), 2);
+
+ assert_eq!(topology.impropers(), vec![[1, 0, 2, 3], [5, 4, 7, 8]]);
+
+ topology.clear_bonds();
+ assert_eq!(topology.impropers_count(), 0);
+ }
+
+ #[test]
+ fn residues() {
+ let mut topology = Topology::new();
+ topology.resize(4);
+ assert_eq!(topology.residues_count(), 0);
+
+ let mut residue = Residue::new("Foo");
+ residue.add_atom(0);
+ residue.add_atom(2);
+
+ topology.add_residue(&residue).unwrap();
+ assert_eq!(topology.residues_count(), 1);
+
+ assert_eq!(topology.residue(0).unwrap().name(), "Foo");
+ {
+ let residue = topology.residue_for_atom(2).unwrap();
+ assert_eq!(residue.name(), "Foo");
+ }
+
+ let mut residue = Residue::new("Bar");
+ residue.add_atom(3);
+ topology.add_residue(&residue).unwrap();
+ assert_eq!(topology.residues_count(), 2);
+
+ let first = topology.residue(0).unwrap();
+ let second = topology.residue(0).unwrap();
+ assert!(topology.are_linked(&first, &second));
+
+ // missing residue
+ assert!(topology.residue_for_atom(1).is_none());
+ // out of bounds
+ assert!(topology.residue_for_atom(67).is_none());
+ }
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371 +372 +373 +374 +375 +376 +377 +378 +379 +380 +381 +382 +383 +384 +385 +386 +387 +388 +389 +390 +391 +392 +393 +394 +395 +396 +397 +398 +399 +400 +401 +402 +403 +404 +405 +406 +407 +408 +409 +410 +411 +412 +413 +414 +415 +416 +417 +418 +419 +420 +421 +422 +423 +424 +425 +426 +427 +428 +429 +430 +431 +432 +433 +434 +435 +436 +437 +438 +439 +440 +441 +442 +443 +444 +445 +446 +447 +448 +449 +450 +451 +452 +453 +454 +455 +456 +457 +458 +459 +460 +461 +462 +463 +464 +465 +466 +467 +468 +469 +470 +471 +472 +473 +474 +475 +476 +477 +478 +479 +480 +481 +482 +483 +484 +485 +486 +487 +488 +489 +490 +491 +492 +493 +494 +495 +496 +497 +498 +499 +500 +501 +502 +503 +504 +505 +506 +507 +508 +509 +510 +511 +512 +513 +514 +515 +516 +517 +518 +519 +520 +521 +522 +523 +524 +525 +526 +527 +528 +529 +530 +531 +532 +533 +534 +535 +536 +537 +538 +539 +540 +541 +542 +543 +544 +545 +546 +547 +548 +549 +550 +551 +552 +553 +554 +555 +556 +557 +558 +559 +560 +561 +562 +563 +564 +565 +566 +567 +568 +569 +570 +571 +572 +573 +574 +575 +576 +577 +578 +579 +580 +581 +582 +583 +584 +585 +586 +587 +588 +589 +590 +591 +592 +593 +594 +595 +596 +597 +598 +599 +600 +601 +602 +603 +604 +605 +606 +607 +608 +609 +610 +611 +612 +613 +614 +615 +616 +617 +618 +619 +620 +621 +622 +623 +624 +625 +626 +627 +628 +629 +630 +631 +632 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::convert::TryInto;
+use std::os::raw::c_char;
+use std::path::Path;
+
+use chemfiles_sys::*;
+
+use crate::errors::{check, check_success, Error, Status};
+use crate::strings;
+use crate::{Frame, Topology, UnitCell};
+
+/// The `Trajectory` type is the main entry point when using chemfiles. A
+/// `Trajectory` behave a bit like a file, allowing to read and/or write
+/// `Frame`.
+#[derive(Debug)]
+pub struct Trajectory {
+ handle: *mut CHFL_TRAJECTORY,
+}
+
+impl Drop for Trajectory {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = chfl_trajectory_close(self.as_ptr());
+ }
+ }
+}
+
+impl Trajectory {
+ /// Create a `Trajectory` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut CHFL_TRAJECTORY) -> Result<Trajectory, Error> {
+ if ptr.is_null() {
+ Err(Error {
+ status: Status::FileError,
+ message: Error::last_error(),
+ })
+ } else {
+ Ok(Trajectory { handle: ptr })
+ }
+ }
+
+ /// Get the underlying C pointer as a pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const CHFL_TRAJECTORY {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut CHFL_TRAJECTORY {
+ self.handle
+ }
+
+ /// Open the file at the given `path` in the given `mode`.
+ ///
+ /// Valid modes are `'r'` for read, `'w'` for write and `'a'` for append.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the file is not accessible for the given mode, if
+ /// it is incorrectly formatted for the corresponding format, or in case of
+ /// I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// ```
+ pub fn open<P>(path: P, mode: char) -> Result<Trajectory, Error>
+ where
+ P: AsRef<Path>,
+ {
+ let path = path
+ .as_ref()
+ .to_str()
+ .ok_or_else(|| Error::utf8_path_error(path.as_ref()))?;
+
+ let path = strings::to_c(path);
+ unsafe {
+ #[allow(clippy::cast_possible_wrap)]
+ let handle = chfl_trajectory_open(path.as_ptr(), mode as c_char);
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Open the file at the given `path` using a specific file `format` and the
+ /// given `mode`.
+ ///
+ /// Valid modes are `'r'` for read, `'w'` for write and `'a'` for append.
+ ///
+ /// Specifying a format is needed when the file format does not match the
+ /// extension, or when there is not standard extension for this format. If
+ /// `format` is an empty string, the format will be guessed from the
+ /// extension.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the file is not accessible for the given mode, if
+ /// it is incorrectly formatted for the corresponding format, or in case of
+ /// I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let trajectory = Trajectory::open_with_format("water.zeo", 'r', "XYZ").unwrap();
+ /// ```
+ pub fn open_with_format<'a, P, S>(filename: P, mode: char, format: S) -> Result<Trajectory, Error>
+ where
+ P: AsRef<Path>,
+ S: Into<&'a str>,
+ {
+ let filename = filename
+ .as_ref()
+ .to_str()
+ .ok_or_else(|| Error::utf8_path_error(filename.as_ref()))?;
+
+ let filename = strings::to_c(filename);
+ let format = strings::to_c(format.into());
+ unsafe {
+ #[allow(clippy::cast_possible_wrap)]
+ let handle = chfl_trajectory_with_format(filename.as_ptr(), mode as c_char, format.as_ptr());
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Write to a memory buffer as though it was a formatted file.
+ ///
+ /// The `format` parameter should follow the same rules as in the main
+ /// `Trajectory` constructor, except that compression specification
+ /// is not supported.
+ ///
+ /// The `memory_buffer` function can be used to retrieve the data written
+ /// to memory of the `Trajectory`.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the format do not support in-memory writers.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Trajectory;
+ /// let trajectory_memory = Trajectory::memory_writer("SMI");
+ ///
+ /// // Binary formats typically do not support this feature
+ /// assert!(Trajectory::memory_writer("XTC").is_err());
+ /// ```
+ pub fn memory_writer<'a, S>(format: S) -> Result<Trajectory, Error>
+ where
+ S: Into<&'a str>,
+ {
+ let format = strings::to_c(format.into());
+ unsafe {
+ let handle = chfl_trajectory_memory_writer(format.as_ptr());
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Read the next step of this trajectory into a `frame`.
+ ///
+ /// If the number of atoms in frame does not correspond to the number of atom
+ /// in the next step, the frame is resized.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format, or in case of I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// let mut frame = Frame::new();
+ ///
+ /// trajectory.read(&mut frame).unwrap();
+ /// ```
+ pub fn read(&mut self, frame: &mut Frame) -> Result<(), Error> {
+ unsafe { check(chfl_trajectory_read(self.as_mut_ptr(), frame.as_mut_ptr())) }
+ }
+
+ /// Read a specific `step` of this trajectory into a `frame`.
+ ///
+ /// If the number of atoms in frame does not correspond to the number of
+ /// atom at this step, the frame is resized.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// let mut frame = Frame::new();
+ ///
+ /// trajectory.read_step(10, &mut frame).unwrap();
+ /// ```
+ pub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error> {
+ unsafe {
+ check(chfl_trajectory_read_step(
+ self.as_mut_ptr(),
+ step as u64,
+ frame.as_mut_ptr(),
+ ))
+ }
+ }
+
+ /// Write a `frame` to this trajectory.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let mut trajectory = Trajectory::open("water.pdb", 'w').unwrap();
+ /// let mut frame = Frame::new();
+ ///
+ /// trajectory.write(&mut frame).unwrap();
+ /// ```
+ pub fn write(&mut self, frame: &Frame) -> Result<(), Error> {
+ unsafe { check(chfl_trajectory_write(self.as_mut_ptr(), frame.as_ptr())) }
+ }
+
+ /// Set the `topology` associated with this trajectory. This topology will
+ /// be used when reading and writing the files, replacing any topology in
+ /// the frames or files.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Atom, Topology};
+ /// let mut topology = Topology::new();
+ /// topology.add_atom(&Atom::new("H"));
+ /// topology.add_atom(&Atom::new("O"));
+ /// topology.add_atom(&Atom::new("H"));
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(1, 2);
+ ///
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// trajectory.set_topology(&topology);
+ /// ```
+ pub fn set_topology(&mut self, topology: &Topology) {
+ unsafe {
+ check_success(chfl_trajectory_set_topology(self.as_mut_ptr(), topology.as_ptr()));
+ }
+ }
+
+ /// Set the topology associated with this trajectory by reading the first
+ /// frame of the file at the given `path` using the file format in `format`;
+ /// and extracting the topology of this frame.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the topology file is incorrectly formatted for
+ /// the corresponding format, or in case of I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+ /// trajectory.set_topology_file("topology.pdb").unwrap();
+ /// ```
+ pub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error>
+ where
+ P: AsRef<Path>,
+ {
+ let path = path
+ .as_ref()
+ .to_str()
+ .ok_or_else(|| Error::utf8_path_error(path.as_ref()))?;
+
+ let path = strings::to_c(path);
+ unsafe {
+ check(chfl_trajectory_topology_file(
+ self.as_mut_ptr(),
+ path.as_ptr(),
+ std::ptr::null(),
+ ))
+ }
+ }
+
+ /// Set the topology associated with this trajectory by reading the first
+ /// frame of the file at the given `path` using the file format in
+ /// `format`; and extracting the topology of this frame.
+ ///
+ /// If `format` is an empty string, the format will be guessed from the
+ /// `path` extension.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the topology file is incorrectly formatted for
+ /// the corresponding format, or in case of I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+ /// trajectory.set_topology_with_format("topology.mol", "PDB").unwrap();
+ /// ```
+ pub fn set_topology_with_format<'a, P, S>(&mut self, path: P, format: S) -> Result<(), Error>
+ where
+ P: AsRef<Path>,
+ S: Into<&'a str>,
+ {
+ let path = path
+ .as_ref()
+ .to_str()
+ .ok_or_else(|| Error::utf8_path_error(path.as_ref()))?;
+
+ let format = strings::to_c(format.into());
+ let path = strings::to_c(path);
+ unsafe {
+ check(chfl_trajectory_topology_file(
+ self.as_mut_ptr(),
+ path.as_ptr(),
+ format.as_ptr(),
+ ))
+ }
+ }
+
+ /// Set the unit `cell` associated with a trajectory. This cell will be
+ /// used when reading and writing the files, replacing any unit cell in the
+ /// frames or files.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, UnitCell};
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// trajectory.set_cell(&UnitCell::new([10.0, 11.0, 12.5]));
+ /// ```
+ pub fn set_cell(&mut self, cell: &UnitCell) {
+ unsafe {
+ check_success(chfl_trajectory_set_cell(self.as_mut_ptr(), cell.as_ptr()));
+ }
+ }
+
+ /// Get the number of steps (the number of frames) in a trajectory.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ ///
+ /// println!("This trajectory contains {} steps", trajectory.nsteps());
+ /// ```
+ // FIXME should this take &self instead? The file can be modified by this
+ // function, but the format should reset the state.
+ pub fn nsteps(&mut self) -> usize {
+ let mut res = 0;
+ unsafe {
+ check(chfl_trajectory_nsteps(self.as_mut_ptr(), &mut res))
+ .expect("failed to get the number of steps in this trajectory");
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return res as usize;
+ }
+
+ /// Obtain the memory buffer written to by the trajectory.
+ ///
+ /// # Errors
+ ///
+ /// This fails if the trajectory was not opened with
+ /// `Trajectory::memory_writer`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Atom, BondOrder, Frame, Trajectory};
+ /// let mut trajectory_memory = Trajectory::memory_writer("SMI").unwrap();
+ ///
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+ /// frame.add_bond_with_order(0, 1, BondOrder::Single);
+ ///
+ /// trajectory_memory.write(&frame).unwrap();
+ ///
+ /// let result = trajectory_memory.memory_buffer();
+ /// assert_eq!(result.unwrap(), "CC\n");
+ /// ```
+ #[allow(clippy::cast_possible_truncation)]
+ pub fn memory_buffer(&self) -> Result<&str, Error> {
+ let mut ptr: *const c_char = std::ptr::null();
+ let mut count: u64 = 0;
+ let buffer = unsafe {
+ check(chfl_trajectory_memory_buffer(self.as_ptr(), &mut ptr, &mut count))?;
+ std::slice::from_raw_parts(ptr.cast(), count.try_into().expect("failed to convert u64 to usize"))
+ };
+
+ let string = std::str::from_utf8(buffer)?;
+ Ok(string)
+ }
+
+ /// Get file path for this trajectory.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ ///
+ /// assert_eq!(trajectory.path(), "water.xyz");
+ /// ```
+ pub fn path(&self) -> String {
+ let get_string = |ptr, len| unsafe { chfl_trajectory_path(self.as_ptr(), ptr, len) };
+ let path = strings::call_autogrow_buffer(1024, get_string).expect("failed to get path string");
+ return strings::from_c(path.as_ptr());
+ }
+}
+
+/// `MemoryTrajectoryReader` is a handle for a `Trajectory` in memory.
+pub struct MemoryTrajectoryReader<'data> {
+ inner: Trajectory,
+ phantom: std::marker::PhantomData<&'data [u8]>,
+}
+
+impl<'data> MemoryTrajectoryReader<'data> {
+ /// Read a memory buffer as though it was a formatted file.
+ ///
+ /// The memory buffer used to store the file is given using the `data`
+ /// argument. The `format` parameter is required and should follow the same
+ /// rules as in the main `Trajectory` constructor.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format, or if the format do not support in-memory readers.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{MemoryTrajectoryReader, Frame};
+ /// let aromatics = "c1ccccc1\nc1ccco1\nc1ccccn1\n";
+ /// let mut trajectory = MemoryTrajectoryReader::new(aromatics.as_bytes(), "SMI").unwrap();
+ /// let mut frame = Frame::new();
+ /// trajectory.read(&mut frame).unwrap();
+ /// assert_eq!(frame.size(), 6);
+ /// ```
+ pub fn new<Data, Format>(data: Data, format: Format) -> Result<MemoryTrajectoryReader<'data>, Error>
+ where
+ Data: Into<&'data [u8]>,
+ Format: AsRef<str>,
+ {
+ let data = data.into();
+ let format = strings::to_c(format.as_ref());
+ let trajectory = unsafe {
+ let handle = chfl_trajectory_memory_reader(data.as_ptr().cast(), data.len() as u64, format.as_ptr());
+ Trajectory::from_ptr(handle)
+ };
+ Ok(MemoryTrajectoryReader {
+ inner: trajectory?,
+ phantom: std::marker::PhantomData,
+ })
+ }
+}
+
+impl<'a> std::ops::Deref for MemoryTrajectoryReader<'a> {
+ type Target = Trajectory;
+
+ #[inline]
+ fn deref(&self) -> &Self::Target {
+ &self.inner
+ }
+}
+
+impl<'a> std::ops::DerefMut for MemoryTrajectoryReader<'a> {
+ #[inline]
+ fn deref_mut(&mut self) -> &mut Self::Target {
+ &mut self.inner
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ use std::io::Read;
+ use std::path::Path;
+
+ use approx::assert_ulps_eq;
+
+ use crate::{Atom, CellShape, Frame, Topology, UnitCell};
+
+ #[test]
+ fn read() {
+ let root = Path::new(file!()).parent().unwrap().join("..");
+ let filename = root.join("data").join("water.xyz");
+ let mut file = Trajectory::open(filename.to_str().unwrap(), 'r').unwrap();
+
+ if cfg!(target_family = "unix") {
+ assert_eq!(file.path(), "src/../data/water.xyz");
+ } else if cfg!(target_family = "windows") {
+ assert_eq!(file.path(), "src\\..\\data\\water.xyz");
+ } else {
+ panic!("please add test for this OS!");
+ }
+
+ assert_eq!(file.nsteps(), 100);
+
+ let mut frame = Frame::new();
+ assert!(file.read(&mut frame).is_ok());
+
+ assert_eq!(frame.size(), 297);
+ assert_ulps_eq!(frame.positions()[0][0], 0.417219);
+ assert_ulps_eq!(frame.positions()[0][1], 8.303366);
+ assert_ulps_eq!(frame.positions()[0][2], 11.737172);
+ assert_ulps_eq!(frame.positions()[124][0], 5.099554);
+ assert_ulps_eq!(frame.positions()[124][1], -0.045104);
+ assert_ulps_eq!(frame.positions()[124][2], 14.153846);
+
+ assert_eq!(frame.atom(0).name(), "O");
+
+ file.set_cell(&UnitCell::new([30.0, 30.0, 30.0]));
+ assert!(file.read_step(41, &mut frame).is_ok());
+ let cell = frame.cell().clone();
+ assert_eq!(cell.lengths(), [30.0, 30.0, 30.0]);
+
+ assert_ulps_eq!(frame.positions()[0][0], 0.761277);
+ assert_ulps_eq!(frame.positions()[0][1], 8.106125);
+ assert_ulps_eq!(frame.positions()[0][2], 10.622949);
+ assert_ulps_eq!(frame.positions()[124][0], 5.13242);
+ assert_ulps_eq!(frame.positions()[124][1], 0.079862);
+ assert_ulps_eq!(frame.positions()[124][2], 14.194161);
+
+ {
+ let topology = frame.topology();
+ assert_eq!(topology.size(), 297);
+ assert_eq!(topology.bonds_count(), 0);
+ }
+
+ assert!(frame.guess_bonds().is_ok());
+ {
+ let topology = frame.topology();
+ assert_eq!(topology.size(), 297);
+ assert_eq!(topology.bonds_count(), 180);
+ assert_eq!(topology.angles_count(), 84);
+ }
+
+ let mut topology = Topology::new();
+ let atom = Atom::new("Cs");
+ for _ in 0..297 {
+ topology.add_atom(&atom);
+ }
+
+ file.set_topology(&topology);
+ assert!(file.read_step(10, &mut frame).is_ok());
+ assert_eq!(frame.atom(42).name(), "Cs");
+
+ let filename = root.join("data").join("topology.xyz");
+ assert!(file.set_topology_file(filename.to_str().unwrap()).is_ok());
+ assert!(file.read(&mut frame).is_ok());
+ assert_eq!(frame.atom(100).name(), "Rd");
+
+ let filename = root.join("data").join("helium.xyz.but.not.really");
+ let filename = filename.to_str().unwrap();
+ let mut file = Trajectory::open_with_format(filename, 'r', "XYZ").unwrap();
+ assert!(file.read(&mut frame).is_ok());
+ assert_eq!(frame.size(), 125);
+ }
+
+ fn write_file<P>(path: P)
+ where
+ P: AsRef<Path>,
+ {
+ let mut file = Trajectory::open(path, 'w').unwrap();
+ let mut frame = Frame::new();
+ frame.resize(4);
+
+ for position in frame.positions_mut() {
+ *position = [1.0, 2.0, 3.0];
+ }
+
+ let mut topology = Topology::new();
+ let atom = Atom::new("X");
+ for _ in 0..4 {
+ topology.add_atom(&atom);
+ }
+ frame.set_topology(&topology).unwrap();
+ assert!(file.write(&frame).is_ok());
+ }
+
+ #[test]
+ fn write() {
+ let filename = "test-tmp.xyz";
+ write_file(filename);
+
+ let expected_content = "4
+Properties=species:S:1:pos:R:3
+X 1 2 3
+X 1 2 3
+X 1 2 3
+X 1 2 3"
+ .lines()
+ .collect::<Vec<_>>();
+
+ let mut file = std::fs::File::open(filename).unwrap();
+ let mut content = String::new();
+ let _ = file.read_to_string(&mut content).unwrap();
+
+ assert_eq!(expected_content, content.lines().collect::<Vec<_>>());
+ std::fs::remove_file(filename).unwrap();
+ }
+
+ #[test]
+ fn memory() {
+ // formats in decreasing order of their memory buffer length to check null termination
+ for format in &["CSSR", "GRO", "XYZ"] {
+ let mut frame_write = Frame::new();
+ frame_write.add_atom(&Atom::new("H"), [1.5, 3.0, -10.0], None);
+ frame_write.add_atom(&Atom::new("O"), [2.3, -1.4, 50.0], None);
+ frame_write.add_atom(&Atom::new("H"), [-1.5, 10.0, 0.0], None);
+ let cell = UnitCell::new([10.0, 11.0, 12.5]);
+
+ let mut trajectory_write = Trajectory::memory_writer(*format).unwrap();
+ trajectory_write.set_cell(&cell);
+ trajectory_write.write(&frame_write).unwrap();
+
+ let buffer = trajectory_write.memory_buffer().unwrap();
+ let mut trajectory_read = MemoryTrajectoryReader::new(buffer.as_bytes(), *format).unwrap();
+ let mut frame_read = Frame::new();
+ trajectory_read.read(&mut frame_read).unwrap();
+
+ assert_eq!(trajectory_read.nsteps(), 1);
+ assert_eq!(frame_read.cell().shape(), CellShape::Orthorhombic);
+ assert_eq!(frame_read.size(), 3);
+ assert_eq!(frame_read.atom(1).name(), "O");
+ crate::assert_vector3d_eq(&frame_read.positions()[2], &[-1.5, 10.0, 0.0], 1e-4);
+ }
+ }
+}
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"+"Or try looking in one of these:
- The Rust Reference "+" for technical details about the language.
- Rust By "+"Example for expository code examples.
- The Rust Book for "+"introductions to language features and the language itself.
- Docs.rs for documentation of crates released on"+" crates.io.
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+
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+${setting_name}
+ `;onEach(setting["options"],option=>{const checked=option===setting["default"]?" checked":"";const full=`${js_data_name}-${option.replace(/ /g,"-")}`;output+=`\
+ `});output+=`\
+
+\
+ \
+
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new file mode 100644
index 000000000..73a9fcd43
--- /dev/null
+++ b/0.10.4/static.files/source-script-1b95b7cca98b26e5.js
@@ -0,0 +1 @@
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+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/atom/struct.AtomMut.html b/0.10.40/chemfiles/atom/struct.AtomMut.html new file mode 100644 index 000000000..2843d6f36 --- /dev/null +++ b/0.10.40/chemfiles/atom/struct.AtomMut.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.AtomMut.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/atom/struct.AtomRef.html b/0.10.40/chemfiles/atom/struct.AtomRef.html new file mode 100644 index 000000000..fc21ff8b9 --- /dev/null +++ b/0.10.40/chemfiles/atom/struct.AtomRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.AtomRef.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/cell/enum.CellShape.html b/0.10.40/chemfiles/cell/enum.CellShape.html new file mode 100644 index 000000000..9d3d95dbc --- /dev/null +++ b/0.10.40/chemfiles/cell/enum.CellShape.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/enum.CellShape.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/cell/struct.UnitCell.html b/0.10.40/chemfiles/cell/struct.UnitCell.html new file mode 100644 index 000000000..c199c7635 --- /dev/null +++ b/0.10.40/chemfiles/cell/struct.UnitCell.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.UnitCell.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/cell/struct.UnitCellMut.html b/0.10.40/chemfiles/cell/struct.UnitCellMut.html new file mode 100644 index 000000000..a07e76605 --- /dev/null +++ b/0.10.40/chemfiles/cell/struct.UnitCellMut.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.UnitCellMut.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/cell/struct.UnitCellRef.html b/0.10.40/chemfiles/cell/struct.UnitCellRef.html new file mode 100644 index 000000000..7455c76ac --- /dev/null +++ b/0.10.40/chemfiles/cell/struct.UnitCellRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.UnitCellRef.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/enum.BondOrder.html b/0.10.40/chemfiles/enum.BondOrder.html new file mode 100644 index 000000000..855f77d9c --- /dev/null +++ b/0.10.40/chemfiles/enum.BondOrder.html @@ -0,0 +1,37 @@ +#[repr(C)]#[non_exhaustive]pub enum BondOrder {
+ Unknown,
+ Single,
+ Double,
+ Triple,
+ Quadruple,
+ Quintuplet,
+ Amide,
+ Aromatic,
+}Expand description
Possible bond order associated with bonds
+Variants (Non-exhaustive)§
This enum is marked as non-exhaustive
Non-exhaustive enums could have additional variants added in future. Therefore, when matching against variants of non-exhaustive enums, an extra wildcard arm must be added to account for any future variants.
Unknown
Unknown or unspecified bond order
+Single
Single bond
+Double
Double bond
+Triple
Triple bond
+Quadruple
Quadruple bond (present in some metals)
+Quintuplet
Quintuplet bond (present in some metals)
+Amide
Amide bond (required by some file formats)
+Aromatic
Aromatic bond (required by some file formats)
+Trait Implementations§
source§impl Ord for BondOrder
impl Ord for BondOrder
1.21.0 · source§fn max(self, other: Self) -> Selfwhere
+ Self: Sized,
fn max(self, other: Self) -> Selfwhere + Self: Sized,
Compares and returns the maximum of two values. Read more
source§impl PartialEq<BondOrder> for BondOrder
impl PartialEq<BondOrder> for BondOrder
source§impl PartialOrd<BondOrder> for BondOrder
impl PartialOrd<BondOrder> for BondOrder
1.0.0 · source§fn le(&self, other: &Rhs) -> bool
fn le(&self, other: &Rhs) -> bool
This method tests less than or equal to (for
self and other) and is used by the <=
+operator. Read moreimpl Copy for BondOrder
impl Eq for BondOrder
impl StructuralEq for BondOrder
impl StructuralPartialEq for BondOrder
Auto Trait Implementations§
impl RefUnwindSafe for BondOrder
impl Send for BondOrder
impl Sync for BondOrder
impl Unpin for BondOrder
impl UnwindSafe for BondOrder
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
pub enum CellShape {
+ Orthorhombic,
+ Triclinic,
+ Infinite,
+}Expand description
Available unit cell shapes.
+Variants§
Orthorhombic
Orthorhombic cell, with the three angles equals to 90°.
+Triclinic
Triclinic cell, with any values for the angles.
+Infinite
Infinite cell, to use when there is no cell.
+Trait Implementations§
source§impl PartialEq<CellShape> for CellShape
impl PartialEq<CellShape> for CellShape
impl Eq for CellShape
impl StructuralEq for CellShape
impl StructuralPartialEq for CellShape
Auto Trait Implementations§
impl RefUnwindSafe for CellShape
impl Send for CellShape
impl Sync for CellShape
impl Unpin for CellShape
impl UnwindSafe for CellShape
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
pub enum Property {
+ Bool(bool),
+ Double(f64),
+ String(String),
+ Vector3D([f64; 3]),
+}Expand description
A Property is a piece of data that can be associated with an Atom or a
+Frame.
Variants§
Bool(bool)
Boolean property
+Double(f64)
Floating point property
+String(String)
String property
+Vector3D([f64; 3])
3-dimensional vector property
+Trait Implementations§
source§impl PartialEq<Property> for Property
impl PartialEq<Property> for Property
source§impl PartialOrd<Property> for Property
impl PartialOrd<Property> for Property
1.0.0 · source§fn le(&self, other: &Rhs) -> bool
fn le(&self, other: &Rhs) -> bool
This method tests less than or equal to (for
self and other) and is used by the <=
+operator. Read moreimpl StructuralPartialEq for Property
Auto Trait Implementations§
impl RefUnwindSafe for Property
impl Send for Property
impl Sync for Property
impl Unpin for Property
impl UnwindSafe for Property
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
#[repr(C)]#[non_exhaustive]pub enum Status {
+ Success,
+ MemoryError,
+ FileError,
+ FormatError,
+ SelectionError,
+ ConfigurationError,
+ OutOfBounds,
+ PropertyError,
+ ChemfilesError,
+ StdCppError,
+ UTF8PathError,
+}Expand description
Possible causes of error in chemfiles
+Variants (Non-exhaustive)§
This enum is marked as non-exhaustive
Non-exhaustive enums could have additional variants added in future. Therefore, when matching against variants of non-exhaustive enums, an extra wildcard arm must be added to account for any future variants.
Success
No error
+MemoryError
Error in memory allocations
+FileError
Error while reading or writing a file
+FormatError
Error in file formatting, i.e. the file is invalid
+SelectionError
Error in selection string syntax
+ConfigurationError
Error in configuration files syntax
+OutOfBounds
Error for out of bounds indexing
+PropertyError
Error related to properties
+ChemfilesError
Exception in the C++ chemfiles library
+StdCppError
Exception in the C++ standard library
+UTF8PathError
The given path is not valid UTF8
+Trait Implementations§
source§impl PartialEq<Status> for Status
impl PartialEq<Status> for Status
impl Eq for Status
impl StructuralEq for Status
impl StructuralPartialEq for Status
Auto Trait Implementations§
impl RefUnwindSafe for Status
impl Send for Status
impl Sync for Status
impl Unpin for Status
impl UnwindSafe for Status
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
Redirecting to ../../chemfiles/enum.Status.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/errors/fn.set_warning_callback.html b/0.10.40/chemfiles/errors/fn.set_warning_callback.html new file mode 100644 index 000000000..97bc2a1ba --- /dev/null +++ b/0.10.40/chemfiles/errors/fn.set_warning_callback.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/fn.set_warning_callback.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/errors/struct.Error.html b/0.10.40/chemfiles/errors/struct.Error.html new file mode 100644 index 000000000..34339c749 --- /dev/null +++ b/0.10.40/chemfiles/errors/struct.Error.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Error.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/fn.add_configuration.html b/0.10.40/chemfiles/fn.add_configuration.html new file mode 100644 index 000000000..25eb931db --- /dev/null +++ b/0.10.40/chemfiles/fn.add_configuration.html @@ -0,0 +1,13 @@ +Function chemfiles::add_configuration
source · pub fn add_configuration<S>(path: S) -> Result<(), Error>where
+ S: AsRef<str>,Expand description
Read configuration data from the file at path.
By default, chemfiles reads configuration from any file named
+.chemfiles.toml in the current directory or any parent directory. This
+function can be used to add data from another configuration file. Data from
+the new configuration file will overwrite any existing data.
Errors
+This function will fail if there is no file at path, or if the file is
+incorrectly formatted.
Example
+chemfiles::add_configuration("local-config.toml").unwrap();
+// from now on, the data from "local-config.toml" will be usedFunction chemfiles::formats_list
source · pub fn formats_list() -> Vec<FormatMetadata>Expand description
Get the list of formats known by chemfiles, as well as all associated metadata.
+Example
+let formats = chemfiles::formats_list();
+println!("chemfiles supports {} formats:", formats.len());
+for format in &formats {
+ println!(
+ " {:<15} {}",
+ format.name,
+ format.extension.as_deref().unwrap_or("")
+ );
+}Function chemfiles::guess_format
source · pub fn guess_format<P>(path: P) -> Result<String, Error>where
+ P: AsRef<Path>,Expand description
Get the format that chemfiles would use to read a file at the given
+path.
The format is mostly guessed from the path extension, chemfiles only tries
+to read the file to distinguish between CIF and mmCIF files. Opening the
+file using the returned format string might still fail. For example, it will
+fail if the file is not actually formatted according to the guessed format;
+or the format/compression combination is not supported (e.g. XTC / GZ will
+not work since the XTC reader does not support compressed files).
The returned format is represented in a way compatible with the various
+Trajectory constructors, i.e. "<format name> [/ <compression>]", where
+compression is optional.
Errors
+This function returns an error if the file format couldn’t be guessed.
+Panics
+This function panics if the path can’t be converted to a Unicode string.
+Examples
+let format = chemfiles::guess_format("trajectory.xyz.xz").unwrap();
+assert_eq!(format, "XYZ / XZ");
+
+let format = chemfiles::guess_format("trajectory.nc").unwrap();
+assert_eq!(format, "Amber NetCDF");
+
+let format = chemfiles::guess_format("trajectory.unknown.format");
+assert!(format.is_err());Function chemfiles::set_warning_callback
source · pub fn set_warning_callback<F>(callback: F)where
+ F: WarningCallback + 'static,Expand description
Use callback for every chemfiles warning. The callback will be passed
+the warning message. This will drop any previous warning callback.
Redirecting to ../../chemfiles/struct.Frame.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/index.html b/0.10.40/chemfiles/index.html new file mode 100644 index 000000000..6631a2144 --- /dev/null +++ b/0.10.40/chemfiles/index.html @@ -0,0 +1,32 @@ +Expand description
Chemfiles is a multi-language library written in modern C++ for reading and +writing from and to molecular trajectory files. These files are created by +your favorite theoretical chemistry program, and contains information about +atomic or residues names and positions. Some format also have additional +information, such as velocities, forces, energy, …
+This crate expose the C API of chemfiles to Rust, and make all the +functionalities accessible. For more information on the C++ library, +please see its documentation. Specifically, the following pages +are worth reading:
+-
+
- The overview of the classes organization; +
- The list of supported formats; +
- The documentation for the selection language; +
Structs
- An
Atomis a particle in the currentFrame. It stores the following +atomic properties: - An analog to a mutable reference to an atom (
&mut Atom) - An analog to a reference to an atom (
&Atom) - Error type for Chemfiles.
FormatMetadatacontains metadata associated with one format.- A
Framecontains data from one simulation step: the current unit +cell, the topology, the positions, and the velocities of the particles in +the system. If some information is missing (topology or velocity or unit +cell), the corresponding data is filled with a default value. - A
Matchis a set of atomic indexes matching a given selection. It can +mostly be used like a&[usize]. MemoryTrajectoryReaderis a handle for aTrajectoryin memory.- An iterator over the properties in an atom/frame/residue
- A
Residueis a group of atoms belonging to the same logical unit. They +can be small molecules, amino-acids in a protein, monomers in polymers, +etc. - An analog to a reference to a residue (
&Residue) - A
Selectionallow to select atoms in aFrame, from a selection +language. The selection language is built by combining basic operations. +Each basic operation follows the<selector>[(<variable>)] <operator> <value>structure, where<operator>is a comparison operator in +== != < <= > >=. - A
Topologycontains the definition of all the atoms in the system, and +the liaisons between the atoms (bonds, angles, dihedrals, …). It will +also contain all the residues information if it is available. - An analog to a reference to a topology (
&Topology) - The
Trajectorytype is the main entry point when using chemfiles. A +Trajectorybehave a bit like a file, allowing to read and/or write +Frame. - An
UnitCellrepresent the box containing the atoms, and its periodicity. - An analog to a mutable reference to an unit cell (
&mut UnitCell) - An analog to a reference to an unit cell (
&UnitCell)
Enums
- Possible bond order associated with bonds
- Available unit cell shapes.
- A
Propertyis a piece of data that can be associated with anAtomor a +Frame. - Possible causes of error in chemfiles
Functions
- Read configuration data from the file at
path. - Get the list of formats known by chemfiles, as well as all associated metadata.
- Get the format that chemfiles would use to read a file at the given +
path. - Use
callbackfor every chemfiles warning. The callback will be passed +the warning message. This will drop any previous warning callback. - Get the version of the chemfiles library.
Redirecting to ../../chemfiles/fn.formats_list.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/misc/fn.guess_format.html b/0.10.40/chemfiles/misc/fn.guess_format.html new file mode 100644 index 000000000..681a66ce5 --- /dev/null +++ b/0.10.40/chemfiles/misc/fn.guess_format.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/fn.guess_format.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/misc/struct.FormatMetadata.html b/0.10.40/chemfiles/misc/struct.FormatMetadata.html new file mode 100644 index 000000000..10fda814b --- /dev/null +++ b/0.10.40/chemfiles/misc/struct.FormatMetadata.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.FormatMetadata.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/property/enum.Property.html b/0.10.40/chemfiles/property/enum.Property.html new file mode 100644 index 000000000..87bfc97da --- /dev/null +++ b/0.10.40/chemfiles/property/enum.Property.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/enum.Property.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/property/struct.PropertiesIter.html b/0.10.40/chemfiles/property/struct.PropertiesIter.html new file mode 100644 index 000000000..2faef8a54 --- /dev/null +++ b/0.10.40/chemfiles/property/struct.PropertiesIter.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.PropertiesIter.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/residue/struct.Residue.html b/0.10.40/chemfiles/residue/struct.Residue.html new file mode 100644 index 000000000..e8f25ad8a --- /dev/null +++ b/0.10.40/chemfiles/residue/struct.Residue.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Residue.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/residue/struct.ResidueRef.html b/0.10.40/chemfiles/residue/struct.ResidueRef.html new file mode 100644 index 000000000..9d26d5daa --- /dev/null +++ b/0.10.40/chemfiles/residue/struct.ResidueRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.ResidueRef.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/selection/struct.Match.html b/0.10.40/chemfiles/selection/struct.Match.html new file mode 100644 index 000000000..3c7b0b709 --- /dev/null +++ b/0.10.40/chemfiles/selection/struct.Match.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Match.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/selection/struct.Selection.html b/0.10.40/chemfiles/selection/struct.Selection.html new file mode 100644 index 000000000..8ed2b5d77 --- /dev/null +++ b/0.10.40/chemfiles/selection/struct.Selection.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Selection.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/sidebar-items.js b/0.10.40/chemfiles/sidebar-items.js new file mode 100644 index 000000000..99ded65b4 --- /dev/null +++ b/0.10.40/chemfiles/sidebar-items.js @@ -0,0 +1 @@ +window.SIDEBAR_ITEMS = {"enum":["BondOrder","CellShape","Property","Status"],"fn":["add_configuration","formats_list","guess_format","set_warning_callback","version"],"struct":["Atom","AtomMut","AtomRef","Error","FormatMetadata","Frame","Match","MemoryTrajectoryReader","PropertiesIter","Residue","ResidueRef","Selection","Topology","TopologyRef","Trajectory","UnitCell","UnitCellMut","UnitCellRef"]}; \ No newline at end of file diff --git a/0.10.40/chemfiles/struct.Atom.html b/0.10.40/chemfiles/struct.Atom.html new file mode 100644 index 000000000..158223a93 --- /dev/null +++ b/0.10.40/chemfiles/struct.Atom.html @@ -0,0 +1,118 @@ +pub struct Atom { /* private fields */ }Expand description
An Atom is a particle in the current Frame. It stores the following
+atomic properties:
-
+
- atom name; +
- atom type; +
- atom mass; +
- atom charge. +
The atom name is usually an unique identifier (H1, C_a) while the
+atom type will be shared between all particles of the same type: H,
+Ow, CH3.
Implementations§
source§impl Atom
impl Atom
sourcepub fn new<'a>(name: impl Into<&'a str>) -> Atom
pub fn new<'a>(name: impl Into<&'a str>) -> Atom
Create an atom with the given name, and set the atom type to name.
Example
+let atom = Atom::new("He");
+assert_eq!(atom.name(), "He");sourcepub fn mass(&self) -> f64
pub fn mass(&self) -> f64
Get the atom mass, in atomic mass units.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.mass(), 4.002602);sourcepub fn set_mass(&mut self, mass: f64)
pub fn set_mass(&mut self, mass: f64)
Set the atom mass to mass, in atomic mass units.
Example
+let mut atom = Atom::new("He");
+
+atom.set_mass(34.9);
+assert_eq!(atom.mass(), 34.9);sourcepub fn charge(&self) -> f64
pub fn charge(&self) -> f64
Get the atom charge, in number of the electron charge e.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.charge(), 0.0);sourcepub fn set_charge(&mut self, charge: f64)
pub fn set_charge(&mut self, charge: f64)
Set the atom charge to charge, in number of the electron charge e.
Example
+let mut atom = Atom::new("He");
+
+atom.set_charge(-2.0);
+assert_eq!(atom.charge(), -2.0);sourcepub fn atomic_type(&self) -> String
pub fn atomic_type(&self) -> String
sourcepub fn set_name<'a>(&mut self, name: impl Into<&'a str>)
pub fn set_name<'a>(&mut self, name: impl Into<&'a str>)
Set the atom name to name.
Example
+let mut atom = Atom::new("He");
+
+atom.set_name("Zn3");
+assert_eq!(atom.name(), "Zn3");sourcepub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>)
pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>)
Set the atom type to atomic_type.
Example
+let mut atom = Atom::new("He");
+
+atom.set_atomic_type("F");
+assert_eq!(atom.atomic_type(), "F");sourcepub fn full_name(&self) -> String
pub fn full_name(&self) -> String
Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
+let atom = Atom::new("Zn");
+assert_eq!(atom.full_name(), "Zinc");sourcepub fn vdw_radius(&self) -> f64
pub fn vdw_radius(&self) -> f64
Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);sourcepub fn covalent_radius(&self) -> f64
pub fn covalent_radius(&self) -> f64
Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);sourcepub fn atomic_number(&self) -> u64
pub fn atomic_number(&self) -> u64
Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").atomic_number(), 2);
+assert_eq!(Atom::new("Xxx").atomic_number(), 0);sourcepub fn set(&mut self, name: &str, property: impl Into<Property>)
pub fn set(&mut self, name: &str, property: impl Into<Property>)
Add a new property with the given name to this atom.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut atom = Atom::new("He");
+atom.set("a bool", true);
+atom.set("a string", "test");
+
+assert_eq!(atom.get("a bool"), Some(Property::Bool(true)));
+assert_eq!(atom.get("a string"), Some(Property::String("test".into())));sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this atom, if it exist.
Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+
+assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(atom.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_> ⓘ
pub fn properties(&self) -> PropertiesIter<'_> ⓘ
Get an iterator over all (name, property) pairs for this atom
+Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+atom.set("bar", Property::Bool(false));
+
+for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations§
Auto Trait Implementations§
impl RefUnwindSafe for Atom
impl !Send for Atom
impl !Sync for Atom
impl Unpin for Atom
impl UnwindSafe for Atom
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
pub struct AtomMut<'a> { /* private fields */ }Expand description
An analog to a mutable reference to an atom (&mut Atom)
Methods from Deref<Target = Atom>§
sourcepub fn mass(&self) -> f64
pub fn mass(&self) -> f64
Get the atom mass, in atomic mass units.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.mass(), 4.002602);sourcepub fn set_mass(&mut self, mass: f64)
pub fn set_mass(&mut self, mass: f64)
Set the atom mass to mass, in atomic mass units.
Example
+let mut atom = Atom::new("He");
+
+atom.set_mass(34.9);
+assert_eq!(atom.mass(), 34.9);sourcepub fn charge(&self) -> f64
pub fn charge(&self) -> f64
Get the atom charge, in number of the electron charge e.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.charge(), 0.0);sourcepub fn set_charge(&mut self, charge: f64)
pub fn set_charge(&mut self, charge: f64)
Set the atom charge to charge, in number of the electron charge e.
Example
+let mut atom = Atom::new("He");
+
+atom.set_charge(-2.0);
+assert_eq!(atom.charge(), -2.0);sourcepub fn atomic_type(&self) -> String
pub fn atomic_type(&self) -> String
sourcepub fn set_name<'a>(&mut self, name: impl Into<&'a str>)
pub fn set_name<'a>(&mut self, name: impl Into<&'a str>)
Set the atom name to name.
Example
+let mut atom = Atom::new("He");
+
+atom.set_name("Zn3");
+assert_eq!(atom.name(), "Zn3");sourcepub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>)
pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>)
Set the atom type to atomic_type.
Example
+let mut atom = Atom::new("He");
+
+atom.set_atomic_type("F");
+assert_eq!(atom.atomic_type(), "F");sourcepub fn full_name(&self) -> String
pub fn full_name(&self) -> String
Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
+let atom = Atom::new("Zn");
+assert_eq!(atom.full_name(), "Zinc");sourcepub fn vdw_radius(&self) -> f64
pub fn vdw_radius(&self) -> f64
Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);sourcepub fn covalent_radius(&self) -> f64
pub fn covalent_radius(&self) -> f64
Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);sourcepub fn atomic_number(&self) -> u64
pub fn atomic_number(&self) -> u64
Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").atomic_number(), 2);
+assert_eq!(Atom::new("Xxx").atomic_number(), 0);sourcepub fn set(&mut self, name: &str, property: impl Into<Property>)
pub fn set(&mut self, name: &str, property: impl Into<Property>)
Add a new property with the given name to this atom.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut atom = Atom::new("He");
+atom.set("a bool", true);
+atom.set("a string", "test");
+
+assert_eq!(atom.get("a bool"), Some(Property::Bool(true)));
+assert_eq!(atom.get("a string"), Some(Property::String("test".into())));sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this atom, if it exist.
Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+
+assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(atom.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_> ⓘ
pub fn properties(&self) -> PropertiesIter<'_> ⓘ
Get an iterator over all (name, property) pairs for this atom
+Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+atom.set("bar", Property::Bool(false));
+
+for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations§
Auto Trait Implementations§
impl<'a> RefUnwindSafe for AtomMut<'a>
impl<'a> !Send for AtomMut<'a>
impl<'a> !Sync for AtomMut<'a>
impl<'a> Unpin for AtomMut<'a>
impl<'a> !UnwindSafe for AtomMut<'a>
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
pub struct AtomRef<'a> { /* private fields */ }Expand description
An analog to a reference to an atom (&Atom)
Methods from Deref<Target = Atom>§
sourcepub fn mass(&self) -> f64
pub fn mass(&self) -> f64
Get the atom mass, in atomic mass units.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.mass(), 4.002602);sourcepub fn charge(&self) -> f64
pub fn charge(&self) -> f64
Get the atom charge, in number of the electron charge e.
+Example
+let atom = Atom::new("He");
+assert_eq!(atom.charge(), 0.0);sourcepub fn atomic_type(&self) -> String
pub fn atomic_type(&self) -> String
sourcepub fn full_name(&self) -> String
pub fn full_name(&self) -> String
Try to get the full name of the atom from the atomic type. For example, +the full name of “He” is “Helium”, and so on. If the name can not be +found, this function returns the empty string.
+Example
+let atom = Atom::new("Zn");
+assert_eq!(atom.full_name(), "Zinc");sourcepub fn vdw_radius(&self) -> f64
pub fn vdw_radius(&self) -> f64
Try to get the Van der Waals radius of the atom from the atomic type. +If the radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);sourcepub fn covalent_radius(&self) -> f64
pub fn covalent_radius(&self) -> f64
Try to get the covalent radius of the atom from the atomic type. If the +radius can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);sourcepub fn atomic_number(&self) -> u64
pub fn atomic_number(&self) -> u64
Try to get the atomic number of the atom from the atomic type. If the +number can not be found, returns 0.
+Example
+assert_eq!(Atom::new("He").atomic_number(), 2);
+assert_eq!(Atom::new("Xxx").atomic_number(), 0);sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this atom, if it exist.
Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+
+assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(atom.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_> ⓘ
pub fn properties(&self) -> PropertiesIter<'_> ⓘ
Get an iterator over all (name, property) pairs for this atom
+Examples
+let mut atom = Atom::new("He");
+atom.set("foo", Property::Double(22.2));
+atom.set("bar", Property::Bool(false));
+
+for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations§
Auto Trait Implementations§
impl<'a> RefUnwindSafe for AtomRef<'a>
impl<'a> !Send for AtomRef<'a>
impl<'a> !Sync for AtomRef<'a>
impl<'a> Unpin for AtomRef<'a>
impl<'a> UnwindSafe for AtomRef<'a>
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
pub struct Error {
+ pub status: Status,
+ pub message: String,
+}Expand description
Error type for Chemfiles.
+Fields§
§status: StatusThe error status code
+message: StringA message describing the error cause
+Implementations§
Trait Implementations§
source§impl Error for Error
impl Error for Error
source§fn description(&self) -> &str
fn description(&self) -> &str
👎Deprecated since 1.42.0: use the Display impl or to_string()
1.30.0 · source§fn source(&self) -> Option<&(dyn Error + 'static)>
fn source(&self) -> Option<&(dyn Error + 'static)>
The lower-level source of this error, if any. Read more
source§impl PartialEq<Error> for Error
impl PartialEq<Error> for Error
impl Eq for Error
impl StructuralEq for Error
impl StructuralPartialEq for Error
Auto Trait Implementations§
impl RefUnwindSafe for Error
impl Send for Error
impl Sync for Error
impl Unpin for Error
impl UnwindSafe for Error
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
Struct chemfiles::FormatMetadata
source · pub struct FormatMetadata {Show 13 fields
+ pub name: &'static str,
+ pub extension: Option<&'static str>,
+ pub description: &'static str,
+ pub reference: &'static str,
+ pub read: bool,
+ pub write: bool,
+ pub memory: bool,
+ pub positions: bool,
+ pub velocities: bool,
+ pub unit_cell: bool,
+ pub atoms: bool,
+ pub bonds: bool,
+ pub residues: bool,
+}Expand description
FormatMetadata contains metadata associated with one format.
Fields§
§name: &'static strName of the format.
+extension: Option<&'static str>Extension associated with the format.
+description: &'static strExtended, user-facing description of the format.
+reference: &'static strURL pointing to the format definition/reference.
+read: boolIs reading files in this format implemented?
+write: boolIs writing files in this format implemented?
+memory: boolDoes this format support in-memory IO?
+positions: boolDoes this format support storing atomic positions?
+velocities: boolDoes this format support storing atomic velocities?
+unit_cell: boolDoes this format support storing unit cell information?
+atoms: boolDoes this format support storing atom names or types?
+bonds: boolDoes this format support storing bonds between atoms?
+residues: boolDoes this format support storing residues?
+Trait Implementations§
source§impl Clone for FormatMetadata
impl Clone for FormatMetadata
source§fn clone(&self) -> FormatMetadata
fn clone(&self) -> FormatMetadata
Returns a copy of the value. Read more
1.0.0 · source§fn clone_from(&mut self, source: &Self)
fn clone_from(&mut self, source: &Self)
Performs copy-assignment from
source. Read moresource§impl Debug for FormatMetadata
impl Debug for FormatMetadata
source§impl PartialEq<FormatMetadata> for FormatMetadata
impl PartialEq<FormatMetadata> for FormatMetadata
source§fn eq(&self, other: &FormatMetadata) -> bool
fn eq(&self, other: &FormatMetadata) -> bool
This method tests for
self and other values to be equal, and is used
+by ==.impl Eq for FormatMetadata
impl StructuralEq for FormatMetadata
impl StructuralPartialEq for FormatMetadata
Auto Trait Implementations§
impl RefUnwindSafe for FormatMetadata
impl Send for FormatMetadata
impl Sync for FormatMetadata
impl Unpin for FormatMetadata
impl UnwindSafe for FormatMetadata
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
pub struct Frame { /* private fields */ }Expand description
A Frame contains data from one simulation step: the current unit
+cell, the topology, the positions, and the velocities of the particles in
+the system. If some information is missing (topology or velocity or unit
+cell), the corresponding data is filled with a default value.
Implementations§
source§impl Frame
impl Frame
sourcepub fn new() -> Frame
pub fn new() -> Frame
Create an empty frame. It will be resized by the library as needed.
+Example
+let frame = Frame::new();
+
+assert_eq!(frame.size(), 0);sourcepub fn atom_mut(&mut self, index: usize) -> AtomMut<'_>
pub fn atom_mut(&mut self, index: usize) -> AtomMut<'_>
Get a mutable reference to the atom at the given index in this frame.
Panics
+If index is out of bounds.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+
+assert_eq!(frame.atom(0).name(), "Zn");
+
+frame.atom_mut(0).set_name("Fe");
+assert_eq!(frame.atom(0).name(), "Fe");sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the current number of atoms in this frame.
+Example
+let mut frame = Frame::new();
+assert_eq!(frame.size(), 0);
+
+frame.resize(67);
+assert_eq!(frame.size(), 67);sourcepub fn resize(&mut self, natoms: usize)
pub fn resize(&mut self, natoms: usize)
Resize the positions and the velocities in this frame, to make space for
+natoms atoms. Previous data is conserved, as well as the presence of
+absence of velocities.
Example
+let mut frame = Frame::new();
+frame.resize(67);
+assert_eq!(frame.size(), 67);sourcepub fn add_atom(
+ &mut self,
+ atom: &Atom,
+ position: [f64; 3],
+ velocity: impl Into<Option<[f64; 3]>>
+)
pub fn add_atom( + &mut self, + atom: &Atom, + position: [f64; 3], + velocity: impl Into<Option<[f64; 3]>> +)
Add an Atom and the corresponding position and optionally velocity
+data to this frame.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("Zn"), [1.0, 1.0, 2.0], None);
+
+frame.add_velocities();
+frame.add_atom(&Atom::new("Zn"), [-1.0, 1.0, 2.0], [0.2, 0.1, 0.0]);sourcepub fn remove(&mut self, i: usize)
pub fn remove(&mut self, i: usize)
Remove the atom at index i in this frame.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+frame.add_atom(&Atom::new("Fe"), [0.0; 3], None);
+frame.add_atom(&Atom::new("Sn"), [0.0; 3], None);
+assert_eq!(frame.size(), 3);
+
+frame.remove(1);
+assert_eq!(frame.size(), 2);
+assert_eq!(frame.atom(1).name(), "Sn");sourcepub fn add_bond(&mut self, i: usize, j: usize)
pub fn add_bond(&mut self, i: usize, j: usize)
Add a bond between the atoms at indexes i and j in the frame.
The bond order is set to BondOrder::Unknown.
Example
+let mut frame = Frame::new();
+assert_eq!(frame.topology().bonds_count(), 0);
+frame.resize(5);
+
+frame.add_bond(0, 1);
+frame.add_bond(3, 1);
+frame.add_bond(2, 4);
+assert_eq!(frame.topology().bonds_count(), 3);
+
+assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown);
+assert_eq!(frame.topology().bonds(), vec![[0, 1], [1, 3], [2, 4]]);sourcepub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder)
pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder)
Add a bond between the atoms at indexes i and j in the frame
+with the given bond order.
Example
+let mut frame = Frame::new();
+assert_eq!(frame.topology().bonds_count(), 0);
+frame.resize(2);
+
+frame.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Double);sourcepub fn remove_bond(&mut self, i: usize, j: usize)
pub fn remove_bond(&mut self, i: usize, j: usize)
Remove any existing bond between the atoms at indexes i and j in
+the frame.
This function does nothing if there is no bond between i and j.
Example
+let mut frame = Frame::new();
+frame.resize(5);
+
+frame.add_bond(0, 1);
+frame.add_bond(3, 1);
+frame.add_bond(2, 4);
+
+let bonds = frame.topology().bonds();
+assert_eq!(bonds, vec![[0, 1], [1, 3], [2, 4]]);
+
+frame.remove_bond(2, 4);
+let bonds = frame.topology().bonds();
+assert_eq!(bonds, vec![[0, 1], [1, 3]]);sourcepub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error>
pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error>
Add a copy of residue to this frame.
Errors
+This function fails is the residue id is already in this frame’s +topology, or if the residue contain atoms that are already in another +residue.
+Example
+let mut frame = Frame::new();
+
+let residue = Residue::new("foo");
+frame.add_residue(&residue).unwrap();
+
+let topology = frame.topology();
+assert_eq!(topology.residues_count(), 1);
+assert_eq!(topology.residue(0).unwrap().name(), "foo");sourcepub fn distance(&self, i: usize, j: usize) -> f64
pub fn distance(&self, i: usize, j: usize) -> f64
Get the distance between the atoms at indexes i and j in this frame,
+accounting for periodic boundary conditions. The result is expressed in
+Angstroms.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [1.0, 2.0, 3.0], None);
+
+assert_eq!(frame.distance(0, 1), f64::sqrt(14.0));sourcepub fn angle(&self, i: usize, j: usize, k: usize) -> f64
pub fn angle(&self, i: usize, j: usize, k: usize) -> f64
Get the angle formed by the atoms at indexes i, j and k in this
+frame, accounting for periodic boundary conditions. The result is
+expressed in radians.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+
+assert_eq!(frame.angle(0, 1, 2), f64::consts::PI / 2.0);sourcepub fn dihedral(&self, i: usize, j: usize, k: usize, m: usize) -> f64
pub fn dihedral(&self, i: usize, j: usize, k: usize, m: usize) -> f64
Get the dihedral angle formed by the atoms at indexes i, j, k and
+m in this frame, accounting for periodic boundary conditions. The
+result is expressed in radians.
Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+frame.add_atom(&Atom::new("D"), [0.0, 1.0, 1.0], None);
+
+assert_eq!(frame.dihedral(0, 1, 2, 3), f64::consts::PI / 2.0);sourcepub fn out_of_plane(&self, i: usize, j: usize, k: usize, m: usize) -> f64
pub fn out_of_plane(&self, i: usize, j: usize, k: usize, m: usize) -> f64
Get the out of plane distance formed by the atoms at indexes i, j,
+k and m in this frame, accounting for periodic boundary conditions.
+The result is expressed in angstroms.
This is the distance between the atom j and the ikm plane. The j atom +is the center of the improper dihedral angle formed by i, j, k and m.
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("B"), [0.0, 0.0, 2.0], None);
+frame.add_atom(&Atom::new("C"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("D"), [0.0, 1.0, 0.0], None);
+
+assert_eq!(frame.out_of_plane(0, 1, 2, 3), 2.0);sourcepub fn positions(&self) -> &[[f64; 3]]
pub fn positions(&self) -> &[[f64; 3]]
Get a view into the positions of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+
+let positions = frame.positions();
+assert_eq!(positions.len(), 67);
+assert_eq!(positions[0], [0.0, 0.0, 0.0]);sourcepub fn positions_mut(&mut self) -> &mut [[f64; 3]]
pub fn positions_mut(&mut self) -> &mut [[f64; 3]]
Get a mutable view into the positions of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+{
+ let positions = frame.positions_mut();
+ assert_eq!(positions[0], [0.0, 0.0, 0.0]);
+ positions[0] = [1.0, 2.0, 3.0];
+}
+
+let positions = frame.positions();
+assert_eq!(positions[0], [1.0, 2.0, 3.0]);sourcepub fn velocities(&self) -> Option<&[[f64; 3]]>
pub fn velocities(&self) -> Option<&[[f64; 3]]>
Get a view into the velocities of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+frame.add_velocities();
+
+let velocities = frame.velocities().expect("missing velocities");
+assert_eq!(velocities.len(), 67);
+assert_eq!(velocities[0], [0.0, 0.0, 0.0]);sourcepub fn velocities_mut(&mut self) -> Option<&mut [[f64; 3]]>
pub fn velocities_mut(&mut self) -> Option<&mut [[f64; 3]]>
Get a mutable view into the velocities of this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(67);
+frame.add_velocities();
+{
+ let velocities = frame.velocities_mut().expect("missing velocities");
+ assert_eq!(velocities[0], [0.0, 0.0, 0.0]);
+ velocities[0] = [1.0, 2.0, 3.0];
+}
+
+let velocities = frame.velocities().expect("missing velocities");
+assert_eq!(velocities[0], [1.0, 2.0, 3.0]);sourcepub fn has_velocities(&self) -> bool
pub fn has_velocities(&self) -> bool
Check if this frame contains velocity data.
+Example
+let mut frame = Frame::new();
+assert_eq!(frame.has_velocities(), false);
+
+frame.add_velocities();
+assert_eq!(frame.has_velocities(), true);sourcepub fn add_velocities(&mut self)
pub fn add_velocities(&mut self)
Add velocity data to this frame. If the frame already have velocities, +this does nothing.
+Example
+let mut frame = Frame::new();
+assert_eq!(frame.has_velocities(), false);
+
+frame.add_velocities();
+assert_eq!(frame.has_velocities(), true);sourcepub fn cell(&self) -> UnitCellRef<'_>
pub fn cell(&self) -> UnitCellRef<'_>
Get a reference to the UnitCell from this frame.
Example
+let frame = Frame::new();
+
+let cell = frame.cell();
+assert_eq!(cell.shape(), CellShape::Infinite);sourcepub fn cell_mut(&mut self) -> UnitCellMut<'_>
pub fn cell_mut(&mut self) -> UnitCellMut<'_>
Get a mutable reference to the UnitCell from this frame.
Example
+let mut frame = Frame::new();
+
+assert_eq!(frame.cell().shape(), CellShape::Infinite);
+
+frame.cell_mut().set_shape(CellShape::Triclinic).unwrap();
+assert_eq!(frame.cell().shape(), CellShape::Triclinic);sourcepub fn set_cell(&mut self, cell: &UnitCell)
pub fn set_cell(&mut self, cell: &UnitCell)
Set the UnitCell of this frame to cell.
Example
+let mut frame = Frame::new();
+
+frame.set_cell(&UnitCell::new([10.0, 10.0, 10.0]));
+
+let cell = frame.cell();
+assert_eq!(cell.shape(), CellShape::Orthorhombic);
+assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);sourcepub fn topology(&self) -> TopologyRef<'_>
pub fn topology(&self) -> TopologyRef<'_>
Get a reference to the Topology of this frame.
Example
+let mut frame = Frame::new();
+frame.resize(42);
+
+let topology = frame.topology();
+assert_eq!(topology.size(), 42);sourcepub fn set_topology(&mut self, topology: &Topology) -> Result<(), Error>
pub fn set_topology(&mut self, topology: &Topology) -> Result<(), Error>
Set the Topology of this frame to topology.
Errors
+This function fails if the topology contains a different number of atoms +than this frame.
+Example
+let mut frame = Frame::new();
+frame.resize(2);
+
+let mut topology = Topology::new();
+topology.add_atom(&Atom::new("Cl"));
+topology.add_atom(&Atom::new("Cl"));
+topology.add_bond(0, 1);
+
+frame.set_topology(&topology).unwrap();
+assert_eq!(frame.atom(0).name(), "Cl");sourcepub fn step(&self) -> usize
pub fn step(&self) -> usize
Get this frame step, i.e. the frame number in the trajectory
+Example
+let frame = Frame::new();
+assert_eq!(frame.step(), 0);sourcepub fn set_step(&mut self, step: usize)
pub fn set_step(&mut self, step: usize)
Set this frame step to step.
Example
+let mut frame = Frame::new();
+assert_eq!(frame.step(), 0);
+
+frame.set_step(10);
+assert_eq!(frame.step(), 10);sourcepub fn guess_bonds(&mut self) -> Result<(), Error>
pub fn guess_bonds(&mut self) -> Result<(), Error>
Guess the bonds, angles and dihedrals in this frame.
The bonds are guessed using a distance-based algorithm, and then angles +and dihedrals are guessed from the bonds.
+Errors
+This function can fail if the covalent radius is unknown for some atoms +in the frame.
+Example
+let mut frame = Frame::new();
+
+frame.add_atom(&Atom::new("Cl"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("Cl"), [1.5, 0.0, 0.0], None);
+assert_eq!(frame.topology().bonds_count(), 0);
+
+frame.guess_bonds().unwrap();
+assert_eq!(frame.topology().bonds_count(), 1);sourcepub fn clear_bonds(&mut self)
pub fn clear_bonds(&mut self)
Remove all existing bonds, angles, dihedral angles and improper +dihedral angles in the topology of the frame.
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [0.0, 1.0, 0.0], None);
+
+frame.add_bond(0, 1);
+frame.add_bond(1, 2);
+
+assert_eq!(frame.topology().bonds().len(), 2);
+assert_eq!(frame.topology().angles().len(), 1);
+
+frame.clear_bonds();
+assert!(frame.topology().bonds().is_empty());
+assert!(frame.topology().angles().is_empty());sourcepub fn set(&mut self, name: &str, property: impl Into<Property>)
pub fn set(&mut self, name: &str, property: impl Into<Property>)
Add a new property with the given name to this frame.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut frame = Frame::new();
+frame.set("a string", "hello");
+frame.set("a double", 4.3);
+
+assert_eq!(frame.get("a string"), Some(Property::String("hello".into())));
+assert_eq!(frame.get("a double"), Some(Property::Double(4.3)));sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this frame, if it exist.
Examples
+let mut frame = Frame::new();
+frame.set("foo", Property::Double(22.2));
+
+assert_eq!(frame.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(frame.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_> ⓘ
pub fn properties(&self) -> PropertiesIter<'_> ⓘ
Get an iterator over all (name, property) pairs for this frame
+Examples
+let mut frame = Frame::new();
+frame.set("foo", Property::Double(22.2));
+frame.set("bar", Property::Bool(false));
+
+for (name, property) in frame.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}sourcepub fn iter_atoms(&self) -> AtomIter<'_>
pub fn iter_atoms(&self) -> AtomIter<'_>
Gets an iterator over atoms
+Example
+let mut frame = Frame::new();
+
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+
+let mut atoms: Vec<AtomRef> = Vec::new();
+
+for atom in frame.iter_atoms() {
+ atoms.push(atom);
+}
+
+assert_eq!(atoms.len(), 2);Trait Implementations§
Auto Trait Implementations§
impl RefUnwindSafe for Frame
impl !Send for Frame
impl !Sync for Frame
impl Unpin for Frame
impl UnwindSafe for Frame
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
pub struct Match { /* private fields */ }Expand description
A Match is a set of atomic indexes matching a given selection. It can
+mostly be used like a &[usize].
Implementations§
source§impl Match
impl Match
sourcepub fn len(&self) -> usize
pub fn len(&self) -> usize
Get the length of the Match.
+Example
+let atomic_match = Match::new(&[3, 4, 5]);
+assert_eq!(atomic_match.len(), 3);sourcepub fn new(atoms: &[usize]) -> Match
pub fn new(atoms: &[usize]) -> Match
Create a new match containing the atoms in the atoms slice.
Panics
+If the slice contains more than 4 elements, which is the maximal size +of a match.
+Example
+let atomic_match = Match::new(&[3, 4, 5]);
+assert_eq!(atomic_match.len(), 3);
+assert_eq!(atomic_match[0], 3);
+assert_eq!(atomic_match[1], 4);
+assert_eq!(atomic_match[2], 5);sourcepub fn iter(&self) -> Iter<'_, usize>
pub fn iter(&self) -> Iter<'_, usize>
Iterate over the atomic indexes in the match.
+Example
+let atomic_match = Match::new(&[3, 4, 5]);
+let mut iter = atomic_match.iter();
+
+assert_eq!(iter.next(), Some(&3));
+assert_eq!(iter.next(), Some(&4));
+assert_eq!(iter.next(), Some(&5));
+assert_eq!(iter.next(), None);Trait Implementations§
source§impl<'a> IntoIterator for &'a Match
impl<'a> IntoIterator for &'a Match
source§impl PartialEq<Match> for Match
impl PartialEq<Match> for Match
impl Eq for Match
impl StructuralEq for Match
impl StructuralPartialEq for Match
Auto Trait Implementations§
impl RefUnwindSafe for Match
impl Send for Match
impl Sync for Match
impl Unpin for Match
impl UnwindSafe for Match
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
Struct chemfiles::MemoryTrajectoryReader
source · pub struct MemoryTrajectoryReader<'data> { /* private fields */ }Expand description
MemoryTrajectoryReader is a handle for a Trajectory in memory.
Implementations§
source§impl<'data> MemoryTrajectoryReader<'data>
impl<'data> MemoryTrajectoryReader<'data>
sourcepub fn new<Data, Format>(
+ data: Data,
+ format: Format
+) -> Result<MemoryTrajectoryReader<'data>, Error>where
+ Data: Into<&'data [u8]>,
+ Format: AsRef<str>,
pub fn new<Data, Format>( + data: Data, + format: Format +) -> Result<MemoryTrajectoryReader<'data>, Error>where + Data: Into<&'data [u8]>, + Format: AsRef<str>,
Read a memory buffer as though it was a formatted file.
+The memory buffer used to store the file is given using the data
+argument. The format parameter is required and should follow the same
+rules as in the main Trajectory constructor.
Errors
+This function fails if the data is incorrectly formatted for the +corresponding format, or if the format do not support in-memory readers.
+Example
+let aromatics = "c1ccccc1\nc1ccco1\nc1ccccn1\n";
+let mut trajectory = MemoryTrajectoryReader::new(aromatics.as_bytes(), "SMI").unwrap();
+let mut frame = Frame::new();
+trajectory.read(&mut frame).unwrap();
+assert_eq!(frame.size(), 6);Methods from Deref<Target = Trajectory>§
sourcepub fn read(&mut self, frame: &mut Frame) -> Result<(), Error>
pub fn read(&mut self, frame: &mut Frame) -> Result<(), Error>
Read the next step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of atom +in the next step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+let mut frame = Frame::new();
+
+trajectory.read(&mut frame).unwrap();sourcepub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error>
pub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error>
Read a specific step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of +atom at this step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+let mut frame = Frame::new();
+
+trajectory.read_step(10, &mut frame).unwrap();sourcepub fn set_topology(&mut self, topology: &Topology)
pub fn set_topology(&mut self, topology: &Topology)
Set the topology associated with this trajectory. This topology will
+be used when reading and writing the files, replacing any topology in
+the frames or files.
Example
+let mut topology = Topology::new();
+topology.add_atom(&Atom::new("H"));
+topology.add_atom(&Atom::new("O"));
+topology.add_atom(&Atom::new("H"));
+topology.add_bond(0, 1);
+topology.add_bond(1, 2);
+
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+trajectory.set_topology(&topology);sourcepub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error>where
+ P: AsRef<Path>,
pub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error>where + P: AsRef<Path>,
Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in format;
+and extracting the topology of this frame.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+trajectory.set_topology_file("topology.pdb").unwrap();sourcepub fn set_topology_with_format<'a, P, S>(
+ &mut self,
+ path: P,
+ format: S
+) -> Result<(), Error>where
+ P: AsRef<Path>,
+ S: Into<&'a str>,
pub fn set_topology_with_format<'a, P, S>( + &mut self, + path: P, + format: S +) -> Result<(), Error>where + P: AsRef<Path>, + S: Into<&'a str>,
Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in
+format; and extracting the topology of this frame.
If format is an empty string, the format will be guessed from the
+path extension.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+trajectory.set_topology_with_format("topology.mol", "PDB").unwrap();sourcepub fn set_cell(&mut self, cell: &UnitCell)
pub fn set_cell(&mut self, cell: &UnitCell)
Set the unit cell associated with a trajectory. This cell will be
+used when reading and writing the files, replacing any unit cell in the
+frames or files.
Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+trajectory.set_cell(&UnitCell::new([10.0, 11.0, 12.5]));sourcepub fn nsteps(&mut self) -> usize
pub fn nsteps(&mut self) -> usize
Get the number of steps (the number of frames) in a trajectory.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+
+println!("This trajectory contains {} steps", trajectory.nsteps());sourcepub fn memory_buffer(&self) -> Result<&str, Error>
pub fn memory_buffer(&self) -> Result<&str, Error>
Obtain the memory buffer written to by the trajectory.
+Errors
+This fails if the trajectory was not opened with
+Trajectory::memory_writer.
Example
+let mut trajectory_memory = Trajectory::memory_writer("SMI").unwrap();
+
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+frame.add_bond_with_order(0, 1, BondOrder::Single);
+
+trajectory_memory.write(&frame).unwrap();
+
+let result = trajectory_memory.memory_buffer();
+assert_eq!(result.unwrap(), "CC\n");Trait Implementations§
source§impl<'a> Deref for MemoryTrajectoryReader<'a>
impl<'a> Deref for MemoryTrajectoryReader<'a>
Auto Trait Implementations§
impl<'data> RefUnwindSafe for MemoryTrajectoryReader<'data>
impl<'data> !Send for MemoryTrajectoryReader<'data>
impl<'data> !Sync for MemoryTrajectoryReader<'data>
impl<'data> Unpin for MemoryTrajectoryReader<'data>
impl<'data> UnwindSafe for MemoryTrajectoryReader<'data>
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
Struct chemfiles::PropertiesIter
source · pub struct PropertiesIter<'a> { /* private fields */ }Expand description
An iterator over the properties in an atom/frame/residue
+Trait Implementations§
source§impl<'a> Iterator for PropertiesIter<'a>
impl<'a> Iterator for PropertiesIter<'a>
source§fn next(&mut self) -> Option<Self::Item>
fn next(&mut self) -> Option<Self::Item>
Advances the iterator and returns the next value. Read more
source§fn size_hint(&self) -> (usize, Option<usize>)
fn size_hint(&self) -> (usize, Option<usize>)
Returns the bounds on the remaining length of the iterator. Read more
source§fn count(self) -> usize
fn count(self) -> usize
Consumes the iterator, counting the number of iterations and returning it. Read more
source§fn next_chunk<const N: usize>(
+ &mut self
+) -> Result<[Self::Item; N], IntoIter<Self::Item, N>>where
+ Self: Sized,
fn next_chunk<const N: usize>( + &mut self +) -> Result<[Self::Item; N], IntoIter<Self::Item, N>>where + Self: Sized,
🔬This is a nightly-only experimental API. (
iter_next_chunk)Advances the iterator and returns an array containing the next
N values. Read more1.0.0 · source§fn last(self) -> Option<Self::Item>where
+ Self: Sized,
fn last(self) -> Option<Self::Item>where + Self: Sized,
Consumes the iterator, returning the last element. Read more
source§fn advance_by(&mut self, n: usize) -> Result<(), NonZeroUsize>
fn advance_by(&mut self, n: usize) -> Result<(), NonZeroUsize>
🔬This is a nightly-only experimental API. (
iter_advance_by)Advances the iterator by
n elements. Read more1.0.0 · source§fn nth(&mut self, n: usize) -> Option<Self::Item>
fn nth(&mut self, n: usize) -> Option<Self::Item>
Returns the
nth element of the iterator. Read more1.28.0 · source§fn step_by(self, step: usize) -> StepBy<Self>where
+ Self: Sized,
fn step_by(self, step: usize) -> StepBy<Self>where + Self: Sized,
Creates an iterator starting at the same point, but stepping by
+the given amount at each iteration. Read more
1.0.0 · source§fn chain<U>(self, other: U) -> Chain<Self, <U as IntoIterator>::IntoIter>where
+ Self: Sized,
+ U: IntoIterator<Item = Self::Item>,
fn chain<U>(self, other: U) -> Chain<Self, <U as IntoIterator>::IntoIter>where + Self: Sized, + U: IntoIterator<Item = Self::Item>,
Takes two iterators and creates a new iterator over both in sequence. Read more
1.0.0 · source§fn zip<U>(self, other: U) -> Zip<Self, <U as IntoIterator>::IntoIter>where
+ Self: Sized,
+ U: IntoIterator,
fn zip<U>(self, other: U) -> Zip<Self, <U as IntoIterator>::IntoIter>where + Self: Sized, + U: IntoIterator,
‘Zips up’ two iterators into a single iterator of pairs. Read more
source§fn intersperse_with<G>(self, separator: G) -> IntersperseWith<Self, G>where
+ Self: Sized,
+ G: FnMut() -> Self::Item,
fn intersperse_with<G>(self, separator: G) -> IntersperseWith<Self, G>where + Self: Sized, + G: FnMut() -> Self::Item,
🔬This is a nightly-only experimental API. (
iter_intersperse)Creates a new iterator which places an item generated by
separator
+between adjacent items of the original iterator. Read more1.0.0 · source§fn map<B, F>(self, f: F) -> Map<Self, F>where
+ Self: Sized,
+ F: FnMut(Self::Item) -> B,
fn map<B, F>(self, f: F) -> Map<Self, F>where + Self: Sized, + F: FnMut(Self::Item) -> B,
Takes a closure and creates an iterator which calls that closure on each
+element. Read more
1.21.0 · source§fn for_each<F>(self, f: F)where
+ Self: Sized,
+ F: FnMut(Self::Item),
fn for_each<F>(self, f: F)where + Self: Sized, + F: FnMut(Self::Item),
Calls a closure on each element of an iterator. Read more
1.0.0 · source§fn filter<P>(self, predicate: P) -> Filter<Self, P>where
+ Self: Sized,
+ P: FnMut(&Self::Item) -> bool,
fn filter<P>(self, predicate: P) -> Filter<Self, P>where + Self: Sized, + P: FnMut(&Self::Item) -> bool,
Creates an iterator which uses a closure to determine if an element
+should be yielded. Read more
1.0.0 · source§fn filter_map<B, F>(self, f: F) -> FilterMap<Self, F>where
+ Self: Sized,
+ F: FnMut(Self::Item) -> Option<B>,
fn filter_map<B, F>(self, f: F) -> FilterMap<Self, F>where + Self: Sized, + F: FnMut(Self::Item) -> Option<B>,
Creates an iterator that both filters and maps. Read more
1.0.0 · source§fn enumerate(self) -> Enumerate<Self>where
+ Self: Sized,
fn enumerate(self) -> Enumerate<Self>where + Self: Sized,
Creates an iterator which gives the current iteration count as well as
+the next value. Read more
1.0.0 · source§fn skip_while<P>(self, predicate: P) -> SkipWhile<Self, P>where
+ Self: Sized,
+ P: FnMut(&Self::Item) -> bool,
fn skip_while<P>(self, predicate: P) -> SkipWhile<Self, P>where + Self: Sized, + P: FnMut(&Self::Item) -> bool,
1.0.0 · source§fn take_while<P>(self, predicate: P) -> TakeWhile<Self, P>where
+ Self: Sized,
+ P: FnMut(&Self::Item) -> bool,
fn take_while<P>(self, predicate: P) -> TakeWhile<Self, P>where + Self: Sized, + P: FnMut(&Self::Item) -> bool,
Creates an iterator that yields elements based on a predicate. Read more
1.57.0 · source§fn map_while<B, P>(self, predicate: P) -> MapWhile<Self, P>where
+ Self: Sized,
+ P: FnMut(Self::Item) -> Option<B>,
fn map_while<B, P>(self, predicate: P) -> MapWhile<Self, P>where + Self: Sized, + P: FnMut(Self::Item) -> Option<B>,
Creates an iterator that both yields elements based on a predicate and maps. Read more
1.0.0 · source§fn skip(self, n: usize) -> Skip<Self>where
+ Self: Sized,
fn skip(self, n: usize) -> Skip<Self>where + Self: Sized,
Creates an iterator that skips the first
n elements. Read more1.0.0 · source§fn take(self, n: usize) -> Take<Self>where
+ Self: Sized,
fn take(self, n: usize) -> Take<Self>where + Self: Sized,
Creates an iterator that yields the first
n elements, or fewer
+if the underlying iterator ends sooner. Read more1.0.0 · source§fn scan<St, B, F>(self, initial_state: St, f: F) -> Scan<Self, St, F>where
+ Self: Sized,
+ F: FnMut(&mut St, Self::Item) -> Option<B>,
fn scan<St, B, F>(self, initial_state: St, f: F) -> Scan<Self, St, F>where + Self: Sized, + F: FnMut(&mut St, Self::Item) -> Option<B>,
1.0.0 · source§fn flat_map<U, F>(self, f: F) -> FlatMap<Self, U, F>where
+ Self: Sized,
+ U: IntoIterator,
+ F: FnMut(Self::Item) -> U,
fn flat_map<U, F>(self, f: F) -> FlatMap<Self, U, F>where + Self: Sized, + U: IntoIterator, + F: FnMut(Self::Item) -> U,
Creates an iterator that works like map, but flattens nested structure. Read more
1.0.0 · source§fn inspect<F>(self, f: F) -> Inspect<Self, F>where
+ Self: Sized,
+ F: FnMut(&Self::Item),
fn inspect<F>(self, f: F) -> Inspect<Self, F>where + Self: Sized, + F: FnMut(&Self::Item),
Does something with each element of an iterator, passing the value on. Read more
1.0.0 · source§fn by_ref(&mut self) -> &mut Selfwhere
+ Self: Sized,
fn by_ref(&mut self) -> &mut Selfwhere + Self: Sized,
Borrows an iterator, rather than consuming it. Read more
1.0.0 · source§fn collect<B>(self) -> Bwhere
+ B: FromIterator<Self::Item>,
+ Self: Sized,
fn collect<B>(self) -> Bwhere + B: FromIterator<Self::Item>, + Self: Sized,
Transforms an iterator into a collection. Read more
source§fn collect_into<E>(self, collection: &mut E) -> &mut Ewhere
+ E: Extend<Self::Item>,
+ Self: Sized,
fn collect_into<E>(self, collection: &mut E) -> &mut Ewhere + E: Extend<Self::Item>, + Self: Sized,
🔬This is a nightly-only experimental API. (
iter_collect_into)Collects all the items from an iterator into a collection. Read more
1.0.0 · source§fn partition<B, F>(self, f: F) -> (B, B)where
+ Self: Sized,
+ B: Default + Extend<Self::Item>,
+ F: FnMut(&Self::Item) -> bool,
fn partition<B, F>(self, f: F) -> (B, B)where + Self: Sized, + B: Default + Extend<Self::Item>, + F: FnMut(&Self::Item) -> bool,
Consumes an iterator, creating two collections from it. Read more
source§fn is_partitioned<P>(self, predicate: P) -> boolwhere
+ Self: Sized,
+ P: FnMut(Self::Item) -> bool,
fn is_partitioned<P>(self, predicate: P) -> boolwhere + Self: Sized, + P: FnMut(Self::Item) -> bool,
🔬This is a nightly-only experimental API. (
iter_is_partitioned)Checks if the elements of this iterator are partitioned according to the given predicate,
+such that all those that return
true precede all those that return false. Read more1.27.0 · source§fn try_fold<B, F, R>(&mut self, init: B, f: F) -> Rwhere
+ Self: Sized,
+ F: FnMut(B, Self::Item) -> R,
+ R: Try<Output = B>,
fn try_fold<B, F, R>(&mut self, init: B, f: F) -> Rwhere + Self: Sized, + F: FnMut(B, Self::Item) -> R, + R: Try<Output = B>,
An iterator method that applies a function as long as it returns
+successfully, producing a single, final value. Read more
1.27.0 · source§fn try_for_each<F, R>(&mut self, f: F) -> Rwhere
+ Self: Sized,
+ F: FnMut(Self::Item) -> R,
+ R: Try<Output = ()>,
fn try_for_each<F, R>(&mut self, f: F) -> Rwhere + Self: Sized, + F: FnMut(Self::Item) -> R, + R: Try<Output = ()>,
An iterator method that applies a fallible function to each item in the
+iterator, stopping at the first error and returning that error. Read more
1.0.0 · source§fn fold<B, F>(self, init: B, f: F) -> Bwhere
+ Self: Sized,
+ F: FnMut(B, Self::Item) -> B,
fn fold<B, F>(self, init: B, f: F) -> Bwhere + Self: Sized, + F: FnMut(B, Self::Item) -> B,
Folds every element into an accumulator by applying an operation,
+returning the final result. Read more
1.51.0 · source§fn reduce<F>(self, f: F) -> Option<Self::Item>where
+ Self: Sized,
+ F: FnMut(Self::Item, Self::Item) -> Self::Item,
fn reduce<F>(self, f: F) -> Option<Self::Item>where + Self: Sized, + F: FnMut(Self::Item, Self::Item) -> Self::Item,
Reduces the elements to a single one, by repeatedly applying a reducing
+operation. Read more
source§fn try_reduce<F, R>(
+ &mut self,
+ f: F
+) -> <<R as Try>::Residual as Residual<Option<<R as Try>::Output>>>::TryTypewhere
+ Self: Sized,
+ F: FnMut(Self::Item, Self::Item) -> R,
+ R: Try<Output = Self::Item>,
+ <R as Try>::Residual: Residual<Option<Self::Item>>,
fn try_reduce<F, R>( + &mut self, + f: F +) -> <<R as Try>::Residual as Residual<Option<<R as Try>::Output>>>::TryTypewhere + Self: Sized, + F: FnMut(Self::Item, Self::Item) -> R, + R: Try<Output = Self::Item>, + <R as Try>::Residual: Residual<Option<Self::Item>>,
🔬This is a nightly-only experimental API. (
iterator_try_reduce)Reduces the elements to a single one by repeatedly applying a reducing operation. If the
+closure returns a failure, the failure is propagated back to the caller immediately. Read more
1.0.0 · source§fn all<F>(&mut self, f: F) -> boolwhere
+ Self: Sized,
+ F: FnMut(Self::Item) -> bool,
fn all<F>(&mut self, f: F) -> boolwhere + Self: Sized, + F: FnMut(Self::Item) -> bool,
Tests if every element of the iterator matches a predicate. Read more
1.0.0 · source§fn any<F>(&mut self, f: F) -> boolwhere
+ Self: Sized,
+ F: FnMut(Self::Item) -> bool,
fn any<F>(&mut self, f: F) -> boolwhere + Self: Sized, + F: FnMut(Self::Item) -> bool,
Tests if any element of the iterator matches a predicate. Read more
1.0.0 · source§fn find<P>(&mut self, predicate: P) -> Option<Self::Item>where
+ Self: Sized,
+ P: FnMut(&Self::Item) -> bool,
fn find<P>(&mut self, predicate: P) -> Option<Self::Item>where + Self: Sized, + P: FnMut(&Self::Item) -> bool,
Searches for an element of an iterator that satisfies a predicate. Read more
1.30.0 · source§fn find_map<B, F>(&mut self, f: F) -> Option<B>where
+ Self: Sized,
+ F: FnMut(Self::Item) -> Option<B>,
fn find_map<B, F>(&mut self, f: F) -> Option<B>where + Self: Sized, + F: FnMut(Self::Item) -> Option<B>,
Applies function to the elements of iterator and returns
+the first non-none result. Read more
source§fn try_find<F, R>(
+ &mut self,
+ f: F
+) -> <<R as Try>::Residual as Residual<Option<Self::Item>>>::TryTypewhere
+ Self: Sized,
+ F: FnMut(&Self::Item) -> R,
+ R: Try<Output = bool>,
+ <R as Try>::Residual: Residual<Option<Self::Item>>,
fn try_find<F, R>( + &mut self, + f: F +) -> <<R as Try>::Residual as Residual<Option<Self::Item>>>::TryTypewhere + Self: Sized, + F: FnMut(&Self::Item) -> R, + R: Try<Output = bool>, + <R as Try>::Residual: Residual<Option<Self::Item>>,
🔬This is a nightly-only experimental API. (
try_find)Applies function to the elements of iterator and returns
+the first true result or the first error. Read more
1.0.0 · source§fn position<P>(&mut self, predicate: P) -> Option<usize>where
+ Self: Sized,
+ P: FnMut(Self::Item) -> bool,
fn position<P>(&mut self, predicate: P) -> Option<usize>where + Self: Sized, + P: FnMut(Self::Item) -> bool,
Searches for an element in an iterator, returning its index. Read more
1.6.0 · source§fn max_by_key<B, F>(self, f: F) -> Option<Self::Item>where
+ B: Ord,
+ Self: Sized,
+ F: FnMut(&Self::Item) -> B,
fn max_by_key<B, F>(self, f: F) -> Option<Self::Item>where + B: Ord, + Self: Sized, + F: FnMut(&Self::Item) -> B,
Returns the element that gives the maximum value from the
+specified function. Read more
1.15.0 · source§fn max_by<F>(self, compare: F) -> Option<Self::Item>where
+ Self: Sized,
+ F: FnMut(&Self::Item, &Self::Item) -> Ordering,
fn max_by<F>(self, compare: F) -> Option<Self::Item>where + Self: Sized, + F: FnMut(&Self::Item, &Self::Item) -> Ordering,
Returns the element that gives the maximum value with respect to the
+specified comparison function. Read more
1.6.0 · source§fn min_by_key<B, F>(self, f: F) -> Option<Self::Item>where
+ B: Ord,
+ Self: Sized,
+ F: FnMut(&Self::Item) -> B,
fn min_by_key<B, F>(self, f: F) -> Option<Self::Item>where + B: Ord, + Self: Sized, + F: FnMut(&Self::Item) -> B,
Returns the element that gives the minimum value from the
+specified function. Read more
1.15.0 · source§fn min_by<F>(self, compare: F) -> Option<Self::Item>where
+ Self: Sized,
+ F: FnMut(&Self::Item, &Self::Item) -> Ordering,
fn min_by<F>(self, compare: F) -> Option<Self::Item>where + Self: Sized, + F: FnMut(&Self::Item, &Self::Item) -> Ordering,
Returns the element that gives the minimum value with respect to the
+specified comparison function. Read more
1.0.0 · source§fn unzip<A, B, FromA, FromB>(self) -> (FromA, FromB)where
+ FromA: Default + Extend<A>,
+ FromB: Default + Extend<B>,
+ Self: Sized + Iterator<Item = (A, B)>,
fn unzip<A, B, FromA, FromB>(self) -> (FromA, FromB)where + FromA: Default + Extend<A>, + FromB: Default + Extend<B>, + Self: Sized + Iterator<Item = (A, B)>,
Converts an iterator of pairs into a pair of containers. Read more
1.36.0 · source§fn copied<'a, T>(self) -> Copied<Self>where
+ T: 'a + Copy,
+ Self: Sized + Iterator<Item = &'a T>,
fn copied<'a, T>(self) -> Copied<Self>where + T: 'a + Copy, + Self: Sized + Iterator<Item = &'a T>,
Creates an iterator which copies all of its elements. Read more
1.0.0 · source§fn cloned<'a, T>(self) -> Cloned<Self>where
+ T: 'a + Clone,
+ Self: Sized + Iterator<Item = &'a T>,
fn cloned<'a, T>(self) -> Cloned<Self>where + T: 'a + Clone, + Self: Sized + Iterator<Item = &'a T>,
source§fn array_chunks<const N: usize>(self) -> ArrayChunks<Self, N>where
+ Self: Sized,
fn array_chunks<const N: usize>(self) -> ArrayChunks<Self, N>where + Self: Sized,
🔬This is a nightly-only experimental API. (
iter_array_chunks)Returns an iterator over
N elements of the iterator at a time. Read more1.11.0 · source§fn sum<S>(self) -> Swhere
+ Self: Sized,
+ S: Sum<Self::Item>,
fn sum<S>(self) -> Swhere + Self: Sized, + S: Sum<Self::Item>,
Sums the elements of an iterator. Read more
1.11.0 · source§fn product<P>(self) -> Pwhere
+ Self: Sized,
+ P: Product<Self::Item>,
fn product<P>(self) -> Pwhere + Self: Sized, + P: Product<Self::Item>,
Iterates over the entire iterator, multiplying all the elements Read more
source§fn cmp_by<I, F>(self, other: I, cmp: F) -> Orderingwhere
+ Self: Sized,
+ I: IntoIterator,
+ F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,
fn cmp_by<I, F>(self, other: I, cmp: F) -> Orderingwhere + Self: Sized, + I: IntoIterator, + F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,
🔬This is a nightly-only experimental API. (
iter_order_by)Lexicographically compares the elements of this
Iterator with those
+of another with respect to the specified comparison function. Read more1.5.0 · source§fn partial_cmp<I>(self, other: I) -> Option<Ordering>where
+ I: IntoIterator,
+ Self::Item: PartialOrd<<I as IntoIterator>::Item>,
+ Self: Sized,
fn partial_cmp<I>(self, other: I) -> Option<Ordering>where + I: IntoIterator, + Self::Item: PartialOrd<<I as IntoIterator>::Item>, + Self: Sized,
Lexicographically compares the
PartialOrd elements of
+this Iterator with those of another. The comparison works like short-circuit
+evaluation, returning a result without comparing the remaining elements.
+As soon as an order can be determined, the evaluation stops and a result is returned. Read moresource§fn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering>where
+ Self: Sized,
+ I: IntoIterator,
+ F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,
fn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering>where + Self: Sized, + I: IntoIterator, + F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,
🔬This is a nightly-only experimental API. (
iter_order_by)Lexicographically compares the elements of this
Iterator with those
+of another with respect to the specified comparison function. Read more1.5.0 · source§fn eq<I>(self, other: I) -> boolwhere
+ I: IntoIterator,
+ Self::Item: PartialEq<<I as IntoIterator>::Item>,
+ Self: Sized,
fn eq<I>(self, other: I) -> boolwhere + I: IntoIterator, + Self::Item: PartialEq<<I as IntoIterator>::Item>, + Self: Sized,
source§fn eq_by<I, F>(self, other: I, eq: F) -> boolwhere
+ Self: Sized,
+ I: IntoIterator,
+ F: FnMut(Self::Item, <I as IntoIterator>::Item) -> bool,
fn eq_by<I, F>(self, other: I, eq: F) -> boolwhere + Self: Sized, + I: IntoIterator, + F: FnMut(Self::Item, <I as IntoIterator>::Item) -> bool,
🔬This is a nightly-only experimental API. (
iter_order_by)1.5.0 · source§fn ne<I>(self, other: I) -> boolwhere
+ I: IntoIterator,
+ Self::Item: PartialEq<<I as IntoIterator>::Item>,
+ Self: Sized,
fn ne<I>(self, other: I) -> boolwhere + I: IntoIterator, + Self::Item: PartialEq<<I as IntoIterator>::Item>, + Self: Sized,
1.5.0 · source§fn lt<I>(self, other: I) -> boolwhere
+ I: IntoIterator,
+ Self::Item: PartialOrd<<I as IntoIterator>::Item>,
+ Self: Sized,
fn lt<I>(self, other: I) -> boolwhere + I: IntoIterator, + Self::Item: PartialOrd<<I as IntoIterator>::Item>, + Self: Sized,
Determines if the elements of this
Iterator are lexicographically
+less than those of another. Read more1.5.0 · source§fn le<I>(self, other: I) -> boolwhere
+ I: IntoIterator,
+ Self::Item: PartialOrd<<I as IntoIterator>::Item>,
+ Self: Sized,
fn le<I>(self, other: I) -> boolwhere + I: IntoIterator, + Self::Item: PartialOrd<<I as IntoIterator>::Item>, + Self: Sized,
Determines if the elements of this
Iterator are lexicographically
+less or equal to those of another. Read more1.5.0 · source§fn gt<I>(self, other: I) -> boolwhere
+ I: IntoIterator,
+ Self::Item: PartialOrd<<I as IntoIterator>::Item>,
+ Self: Sized,
fn gt<I>(self, other: I) -> boolwhere + I: IntoIterator, + Self::Item: PartialOrd<<I as IntoIterator>::Item>, + Self: Sized,
Determines if the elements of this
Iterator are lexicographically
+greater than those of another. Read more1.5.0 · source§fn ge<I>(self, other: I) -> boolwhere
+ I: IntoIterator,
+ Self::Item: PartialOrd<<I as IntoIterator>::Item>,
+ Self: Sized,
fn ge<I>(self, other: I) -> boolwhere + I: IntoIterator, + Self::Item: PartialOrd<<I as IntoIterator>::Item>, + Self: Sized,
Determines if the elements of this
Iterator are lexicographically
+greater than or equal to those of another. Read moresource§fn is_sorted_by<F>(self, compare: F) -> boolwhere
+ Self: Sized,
+ F: FnMut(&Self::Item, &Self::Item) -> Option<Ordering>,
fn is_sorted_by<F>(self, compare: F) -> boolwhere + Self: Sized, + F: FnMut(&Self::Item, &Self::Item) -> Option<Ordering>,
🔬This is a nightly-only experimental API. (
is_sorted)Checks if the elements of this iterator are sorted using the given comparator function. Read more
source§fn is_sorted_by_key<F, K>(self, f: F) -> boolwhere
+ Self: Sized,
+ F: FnMut(Self::Item) -> K,
+ K: PartialOrd<K>,
fn is_sorted_by_key<F, K>(self, f: F) -> boolwhere + Self: Sized, + F: FnMut(Self::Item) -> K, + K: PartialOrd<K>,
🔬This is a nightly-only experimental API. (
is_sorted)Checks if the elements of this iterator are sorted using the given key extraction
+function. Read more
Auto Trait Implementations§
impl<'a> !RefUnwindSafe for PropertiesIter<'a>
impl<'a> !Send for PropertiesIter<'a>
impl<'a> !Sync for PropertiesIter<'a>
impl<'a> Unpin for PropertiesIter<'a>
impl<'a> !UnwindSafe for PropertiesIter<'a>
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
source§impl<I> IntoIterator for Iwhere
+ I: Iterator,
impl<I> IntoIterator for Iwhere + I: Iterator,
pub struct Residue { /* private fields */ }Expand description
A Residue is a group of atoms belonging to the same logical unit. They
+can be small molecules, amino-acids in a protein, monomers in polymers,
+etc.
Implementations§
source§impl Residue
impl Residue
sourcepub fn new<'a>(name: impl Into<&'a str>) -> Residue
pub fn new<'a>(name: impl Into<&'a str>) -> Residue
Create a new residue with the given name
Example
+let residue = Residue::new("ALA");
+assert_eq!(residue.name(), "ALA");
+assert_eq!(residue.id(), None);sourcepub fn with_id<'a>(name: impl Into<&'a str>, id: i64) -> Residue
pub fn with_id<'a>(name: impl Into<&'a str>, id: i64) -> Residue
Create a new residue with the given name and id as identifier.
Example
+let residue = Residue::with_id("ALA", 67);
+assert_eq!(residue.name(), "ALA");
+assert_eq!(residue.id(), Some(67));sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the number of atoms in this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.size(), 0);
+
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+assert_eq!(residue.size(), 3);sourcepub fn id(&self) -> Option<i64>
pub fn id(&self) -> Option<i64>
Get the identifier of this residue in the initial topology file.
+Example
+let residue = Residue::with_id("", 42);
+assert_eq!(residue.id(), Some(42));sourcepub fn name(&self) -> String
pub fn name(&self) -> String
Get the name of this residue.
+Example
+let residue = Residue::new("water");
+assert_eq!(residue.name(), "water");sourcepub fn add_atom(&mut self, atom: usize)
pub fn add_atom(&mut self, atom: usize)
Add the atom at index atom in this residue.
This will fail if the atom is already in the residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.size(), 0);
+assert_eq!(residue.contains(56), false);
+
+residue.add_atom(56);
+assert_eq!(residue.size(), 1);
+assert_eq!(residue.contains(56), true);
+
+// Adding the same atom twice is fine
+residue.add_atom(56);
+assert_eq!(residue.size(), 1);sourcepub fn contains(&self, atom: usize) -> bool
pub fn contains(&self, atom: usize) -> bool
Check if the atom at index i is in this residue
Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.contains(56), false);
+
+residue.add_atom(56);
+assert_eq!(residue.contains(56), true);sourcepub fn atoms(&self) -> Vec<usize>
pub fn atoms(&self) -> Vec<usize>
Get the list of atoms of this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.atoms(), vec![]);
+
+residue.add_atom(56);
+assert_eq!(residue.atoms(), vec![56]);sourcepub fn set(&mut self, name: &str, property: impl Into<Property>)
pub fn set(&mut self, name: &str, property: impl Into<Property>)
Add a new property with the given name to this residue.
If a property with the same name already exists, this function override +the existing property with the new one.
+Examples
+let mut residue = Residue::new("ALA");
+residue.set("a string", "hello");
+residue.set("a double", 3.2);
+
+assert_eq!(residue.get("a string"), Some(Property::String("hello".into())));
+assert_eq!(residue.get("a double"), Some(Property::Double(3.2)));sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this frame, if it exist.
Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+
+assert_eq!(residue.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(residue.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_> ⓘ
pub fn properties(&self) -> PropertiesIter<'_> ⓘ
Get an iterator over all (name, property) pairs for this frame
+Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+residue.set("bar", Property::Bool(false));
+
+for (name, property) in residue.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations§
Auto Trait Implementations§
impl RefUnwindSafe for Residue
impl !Send for Residue
impl !Sync for Residue
impl Unpin for Residue
impl UnwindSafe for Residue
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
Struct chemfiles::ResidueRef
source · pub struct ResidueRef<'a> { /* private fields */ }Expand description
An analog to a reference to a residue (&Residue)
Methods from Deref<Target = Residue>§
sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the number of atoms in this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.size(), 0);
+
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+assert_eq!(residue.size(), 3);sourcepub fn id(&self) -> Option<i64>
pub fn id(&self) -> Option<i64>
Get the identifier of this residue in the initial topology file.
+Example
+let residue = Residue::with_id("", 42);
+assert_eq!(residue.id(), Some(42));sourcepub fn name(&self) -> String
pub fn name(&self) -> String
Get the name of this residue.
+Example
+let residue = Residue::new("water");
+assert_eq!(residue.name(), "water");sourcepub fn contains(&self, atom: usize) -> bool
pub fn contains(&self, atom: usize) -> bool
Check if the atom at index i is in this residue
Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.contains(56), false);
+
+residue.add_atom(56);
+assert_eq!(residue.contains(56), true);sourcepub fn atoms(&self) -> Vec<usize>
pub fn atoms(&self) -> Vec<usize>
Get the list of atoms of this residue.
+Example
+let mut residue = Residue::new("water");
+assert_eq!(residue.atoms(), vec![]);
+
+residue.add_atom(56);
+assert_eq!(residue.atoms(), vec![56]);sourcepub fn get(&self, name: &str) -> Option<Property>
pub fn get(&self, name: &str) -> Option<Property>
Get a property with the given name in this frame, if it exist.
Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+
+assert_eq!(residue.get("foo"), Some(Property::Double(22.2)));
+assert_eq!(residue.get("Bar"), None);sourcepub fn properties(&self) -> PropertiesIter<'_> ⓘ
pub fn properties(&self) -> PropertiesIter<'_> ⓘ
Get an iterator over all (name, property) pairs for this frame
+Examples
+let mut residue = Residue::new("ALA");
+residue.set("foo", Property::Double(22.2));
+residue.set("bar", Property::Bool(false));
+
+for (name, property) in residue.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(22.2));
+ } else if name == "bar" {
+ assert_eq!(property, Property::Bool(false));
+ }
+}Trait Implementations§
source§impl<'a> Debug for ResidueRef<'a>
impl<'a> Debug for ResidueRef<'a>
Auto Trait Implementations§
impl<'a> RefUnwindSafe for ResidueRef<'a>
impl<'a> !Send for ResidueRef<'a>
impl<'a> !Sync for ResidueRef<'a>
impl<'a> Unpin for ResidueRef<'a>
impl<'a> UnwindSafe for ResidueRef<'a>
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
pub struct Selection { /* private fields */ }Expand description
A Selection allow to select atoms in a Frame, from a selection
+language. The selection language is built by combining basic operations.
+Each basic operation follows the <selector>[(<variable>)] <operator> <value> structure, where <operator> is a comparison operator in
+== != < <= > >=.
Implementations§
source§impl Selection
impl Selection
sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the size of the selection, i.e. the number of atoms we are selecting +together.
+This value is 1 for the ‘atom’ context, 2 for the ‘pair’ and ‘bond’ +context, 3 for the ‘three’ and ‘angles’ context and 4 for the ‘four’ +and ‘dihedral’ context.
+Example
+let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+assert_eq!(selection.size(), 2);sourcepub fn string(&self) -> String
pub fn string(&self) -> String
Get the selection string used to create this selection.
+Example
+let selection = Selection::new("name H").unwrap();
+assert_eq!(selection.string(), "name H");sourcepub fn evaluate(&mut self, frame: &Frame) -> Vec<Match>
pub fn evaluate(&mut self, frame: &Frame) -> Vec<Match>
Evaluate a selection for a given frame, and return the corresponding +matches.
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+
+let mut selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+let matches = selection.evaluate(&frame);
+
+assert_eq!(matches.len(), 2);
+
+assert_eq!(matches[0].len(), 2);
+assert_eq!(matches[0][0], 0);
+assert_eq!(matches[0][1], 1);
+
+assert_eq!(matches[1].len(), 2);
+assert_eq!(matches[1][0], 2);
+assert_eq!(matches[1][1], 1);sourcepub fn list(&mut self, frame: &Frame) -> Vec<usize>
pub fn list(&mut self, frame: &Frame) -> Vec<usize>
Evaluates a selection of size 1 on a given frame. This function
+returns the list of atomic indexes in the frame matching this selection.
Panics
+If the selection size is not 1
+Example
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+
+let mut selection = Selection::new("name H").unwrap();
+let matches = selection.list(&frame);
+
+assert_eq!(matches.len(), 2);
+assert_eq!(matches[0], 0);
+assert_eq!(matches[1], 2);Trait Implementations§
Auto Trait Implementations§
impl RefUnwindSafe for Selection
impl !Send for Selection
impl !Sync for Selection
impl Unpin for Selection
impl UnwindSafe for Selection
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
pub struct Topology { /* private fields */ }Expand description
A Topology contains the definition of all the atoms in the system, and
+the liaisons between the atoms (bonds, angles, dihedrals, …). It will
+also contain all the residues information if it is available.
Implementations§
source§impl Topology
impl Topology
sourcepub fn new() -> Topology
pub fn new() -> Topology
Create a new empty topology.
+Example
+let topology = Topology::new();
+assert_eq!(topology.size(), 0);sourcepub fn atom_mut(&mut self, index: usize) -> AtomMut<'_>
pub fn atom_mut(&mut self, index: usize) -> AtomMut<'_>
Get a mutable reference to the atom at the given index in this topology.
Panics
+If index is out of bounds.
Example
+let mut topology = Topology::new();
+topology.resize(6);
+
+assert_eq!(topology.atom(4).name(), "");
+
+topology.atom_mut(4).set_name("Fe");
+assert_eq!(topology.atom(4).name(), "Fe");sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the current number of atoms in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.size(), 0);
+
+topology.resize(6);
+assert_eq!(topology.size(), 6);sourcepub fn resize(&mut self, natoms: usize)
pub fn resize(&mut self, natoms: usize)
Resize this topology to hold natoms atoms, inserting dummy atoms if
+the new size if bigger than the old one.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.size(), 0);
+
+topology.resize(6);
+assert_eq!(topology.size(), 6);sourcepub fn add_atom(&mut self, atom: &Atom)
pub fn add_atom(&mut self, atom: &Atom)
Add an Atom at the end of this topology
Example
+let mut topology = Topology::new();
+topology.add_atom(&Atom::new("Mg"));
+
+let atom = topology.atom(0);
+assert_eq!(atom.name(), "Mg");sourcepub fn bonds_count(&self) -> usize
pub fn bonds_count(&self) -> usize
Get the number of bonds in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds_count(), 3);sourcepub fn angles_count(&self) -> usize
pub fn angles_count(&self) -> usize
Get the number of angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.angles_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles_count(), 2);sourcepub fn dihedrals_count(&self) -> usize
pub fn dihedrals_count(&self) -> usize
Get the number of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.dihedrals_count(), 1);sourcepub fn impropers_count(&self) -> usize
pub fn impropers_count(&self) -> usize
Get the number of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+assert_eq!(topology.impropers_count(), 1);sourcepub fn bonds(&self) -> Vec<[usize; 2]>
pub fn bonds(&self) -> Vec<[usize; 2]>
Get the list of bonds in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);sourcepub fn angles(&self) -> Vec<[usize; 3]>
pub fn angles(&self) -> Vec<[usize; 3]>
Get the list of angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);sourcepub fn dihedrals(&self) -> Vec<[usize; 4]>
pub fn dihedrals(&self) -> Vec<[usize; 4]>
Get the list of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+
+assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);sourcepub fn impropers(&self) -> Vec<[usize; 4]>
pub fn impropers(&self) -> Vec<[usize; 4]>
Get the list of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+
+assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);sourcepub fn clear_bonds(&mut self)
pub fn clear_bonds(&mut self)
Remove all existing bonds, angles, dihedral angles and improper +dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+assert_eq!(topology.bonds_count(), 2);
+assert_eq!(topology.angles().len(), 1);
+
+topology.clear_bonds();
+assert!(topology.bonds().is_empty());
+assert!(topology.angles().is_empty());sourcepub fn add_bond(&mut self, i: usize, j: usize)
pub fn add_bond(&mut self, i: usize, j: usize)
Add a bond between the atoms at indexes i and j in the topology.
The bond order is set to BondOrder::Unknown.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+assert_eq!(topology.bonds_count(), 2);
+
+assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);sourcepub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder)
pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder)
Add a bond between the atoms at indexes i and j in the topology
+with the given bond order.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(2);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(topology.bond_order(0, 1), BondOrder::Double);sourcepub fn bond_order(&self, i: usize, j: usize) -> BondOrder
pub fn bond_order(&self, i: usize, j: usize) -> BondOrder
Get the bond order for the bond between the atoms at indexes i and
+j.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(2);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(topology.bond_order(0, 1), BondOrder::Double);sourcepub fn bond_orders(&self) -> Vec<BondOrder>
pub fn bond_orders(&self) -> Vec<BondOrder>
Get the bond order for all the bonds in the topology
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(3);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+topology.add_bond_with_order(0, 2, BondOrder::Single);
+
+assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);sourcepub fn remove_bond(&mut self, i: usize, j: usize)
pub fn remove_bond(&mut self, i: usize, j: usize)
Remove any existing bond between the atoms at indexes i and j in
+this topology.
This function does nothing if there is no bond between i and j.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(1, 2);
+assert_eq!(topology.bonds_count(), 2);
+
+topology.remove_bond(0, 1);
+assert_eq!(topology.bonds_count(), 1);
+
+// Removing a bond that does not exists is fine
+topology.remove_bond(0, 2);
+assert_eq!(topology.bonds_count(), 1);sourcepub fn residue(&self, index: usize) -> Option<ResidueRef<'_>>
pub fn residue(&self, index: usize) -> Option<ResidueRef<'_>>
Get a reference to the residue at index index from this topology.
The residue index in the topology is not always the same as the residue
+id.
Example
+let mut topology = Topology::new();
+topology.add_residue(&Residue::new("water")).unwrap();
+
+let residue = topology.residue(0).unwrap();
+assert_eq!(residue.name(), "water");sourcepub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef<'_>>
pub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef<'_>>
Get a copy of the residue containing the atom at index index in this
+topology, if any.
Example
+let mut topology = Topology::new();
+topology.resize(8);
+
+let mut residue = Residue::new("water");
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+topology.add_residue(&residue).unwrap();
+
+let residue = topology.residue_for_atom(0).unwrap();
+assert_eq!(residue.name(), "water");
+
+assert!(topology.residue_for_atom(6).is_none());sourcepub fn residues_count(&self) -> u64
pub fn residues_count(&self) -> u64
Get the number of residues in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.residues_count(), 0);
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+assert_eq!(topology.residues_count(), 2);sourcepub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error>
pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error>
Add a residue to this topology.
+Errors
+This function fails is the residue id is not already in the topology,
+or if the residue contains atoms that are already in another residue.
Example
+let mut topology = Topology::new();
+topology.add_residue(&Residue::new("water")).unwrap();
+
+let residue = topology.residue(0).unwrap();
+assert_eq!(residue.name(), "water");sourcepub fn are_linked(&self, first: &Residue, second: &Residue) -> bool
pub fn are_linked(&self, first: &Residue, second: &Residue) -> bool
Check if the two residues first and second from the topology are
+linked together, i.e. if there is a bond between one atom in the
+first residue and one atom in the second one.
Example
+let mut topology = Topology::new();
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+
+let first = topology.residue(0).unwrap();
+let second = topology.residue(1).unwrap();
+assert_eq!(topology.are_linked(&first, &second), false);Trait Implementations§
Auto Trait Implementations§
impl RefUnwindSafe for Topology
impl !Send for Topology
impl !Sync for Topology
impl Unpin for Topology
impl UnwindSafe for Topology
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
Struct chemfiles::TopologyRef
source · pub struct TopologyRef<'a> { /* private fields */ }Expand description
An analog to a reference to a topology (&Topology)
Methods from Deref<Target = Topology>§
sourcepub fn size(&self) -> usize
pub fn size(&self) -> usize
Get the current number of atoms in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.size(), 0);
+
+topology.resize(6);
+assert_eq!(topology.size(), 6);sourcepub fn bonds_count(&self) -> usize
pub fn bonds_count(&self) -> usize
Get the number of bonds in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds_count(), 3);sourcepub fn angles_count(&self) -> usize
pub fn angles_count(&self) -> usize
Get the number of angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.angles_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles_count(), 2);sourcepub fn dihedrals_count(&self) -> usize
pub fn dihedrals_count(&self) -> usize
Get the number of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.dihedrals_count(), 1);sourcepub fn impropers_count(&self) -> usize
pub fn impropers_count(&self) -> usize
Get the number of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.dihedrals_count(), 0);
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+assert_eq!(topology.impropers_count(), 1);sourcepub fn bonds(&self) -> Vec<[usize; 2]>
pub fn bonds(&self) -> Vec<[usize; 2]>
Get the list of bonds in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);sourcepub fn angles(&self) -> Vec<[usize; 3]>
pub fn angles(&self) -> Vec<[usize; 3]>
Get the list of angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);sourcepub fn dihedrals(&self) -> Vec<[usize; 4]>
pub fn dihedrals(&self) -> Vec<[usize; 4]>
Get the list of dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(2, 1);
+topology.add_bond(2, 3);
+
+assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);sourcepub fn impropers(&self) -> Vec<[usize; 4]>
pub fn impropers(&self) -> Vec<[usize; 4]>
Get the list of improper dihedral angles in the topology.
+Example
+let mut topology = Topology::new();
+topology.resize(4);
+
+topology.add_bond(0, 1);
+topology.add_bond(0, 2);
+topology.add_bond(0, 3);
+
+assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);sourcepub fn bond_order(&self, i: usize, j: usize) -> BondOrder
pub fn bond_order(&self, i: usize, j: usize) -> BondOrder
Get the bond order for the bond between the atoms at indexes i and
+j.
Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(2);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+assert_eq!(topology.bond_order(0, 1), BondOrder::Double);sourcepub fn bond_orders(&self) -> Vec<BondOrder>
pub fn bond_orders(&self) -> Vec<BondOrder>
Get the bond order for all the bonds in the topology
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.bonds_count(), 0);
+topology.resize(3);
+
+topology.add_bond_with_order(0, 1, BondOrder::Double);
+topology.add_bond_with_order(0, 2, BondOrder::Single);
+
+assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);sourcepub fn residue(&self, index: usize) -> Option<ResidueRef<'_>>
pub fn residue(&self, index: usize) -> Option<ResidueRef<'_>>
Get a reference to the residue at index index from this topology.
The residue index in the topology is not always the same as the residue
+id.
Example
+let mut topology = Topology::new();
+topology.add_residue(&Residue::new("water")).unwrap();
+
+let residue = topology.residue(0).unwrap();
+assert_eq!(residue.name(), "water");sourcepub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef<'_>>
pub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef<'_>>
Get a copy of the residue containing the atom at index index in this
+topology, if any.
Example
+let mut topology = Topology::new();
+topology.resize(8);
+
+let mut residue = Residue::new("water");
+residue.add_atom(0);
+residue.add_atom(1);
+residue.add_atom(2);
+topology.add_residue(&residue).unwrap();
+
+let residue = topology.residue_for_atom(0).unwrap();
+assert_eq!(residue.name(), "water");
+
+assert!(topology.residue_for_atom(6).is_none());sourcepub fn residues_count(&self) -> u64
pub fn residues_count(&self) -> u64
Get the number of residues in this topology.
+Example
+let mut topology = Topology::new();
+assert_eq!(topology.residues_count(), 0);
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+assert_eq!(topology.residues_count(), 2);sourcepub fn are_linked(&self, first: &Residue, second: &Residue) -> bool
pub fn are_linked(&self, first: &Residue, second: &Residue) -> bool
Check if the two residues first and second from the topology are
+linked together, i.e. if there is a bond between one atom in the
+first residue and one atom in the second one.
Example
+let mut topology = Topology::new();
+
+topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+
+let first = topology.residue(0).unwrap();
+let second = topology.residue(1).unwrap();
+assert_eq!(topology.are_linked(&first, &second), false);Trait Implementations§
source§impl<'a> Debug for TopologyRef<'a>
impl<'a> Debug for TopologyRef<'a>
Auto Trait Implementations§
impl<'a> RefUnwindSafe for TopologyRef<'a>
impl<'a> !Send for TopologyRef<'a>
impl<'a> !Sync for TopologyRef<'a>
impl<'a> Unpin for TopologyRef<'a>
impl<'a> UnwindSafe for TopologyRef<'a>
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
Struct chemfiles::Trajectory
source · pub struct Trajectory { /* private fields */ }Expand description
The Trajectory type is the main entry point when using chemfiles. A
+Trajectory behave a bit like a file, allowing to read and/or write
+Frame.
Implementations§
source§impl Trajectory
impl Trajectory
sourcepub fn open<P>(path: P, mode: char) -> Result<Trajectory, Error>where
+ P: AsRef<Path>,
pub fn open<P>(path: P, mode: char) -> Result<Trajectory, Error>where + P: AsRef<Path>,
Open the file at the given path in the given mode.
Valid modes are 'r' for read, 'w' for write and 'a' for append.
Errors
+This function fails if the file is not accessible for the given mode, if +it is incorrectly formatted for the corresponding format, or in case of +I/O errors from the OS.
+Example
+let trajectory = Trajectory::open("water.xyz", 'r').unwrap();sourcepub fn open_with_format<'a, P, S>(
+ filename: P,
+ mode: char,
+ format: S
+) -> Result<Trajectory, Error>where
+ P: AsRef<Path>,
+ S: Into<&'a str>,
pub fn open_with_format<'a, P, S>( + filename: P, + mode: char, + format: S +) -> Result<Trajectory, Error>where + P: AsRef<Path>, + S: Into<&'a str>,
Open the file at the given path using a specific file format and the
+given mode.
Valid modes are 'r' for read, 'w' for write and 'a' for append.
Specifying a format is needed when the file format does not match the
+extension, or when there is not standard extension for this format. If
+format is an empty string, the format will be guessed from the
+extension.
Errors
+This function fails if the file is not accessible for the given mode, if +it is incorrectly formatted for the corresponding format, or in case of +I/O errors from the OS.
+Example
+let trajectory = Trajectory::open_with_format("water.zeo", 'r', "XYZ").unwrap();sourcepub fn memory_writer<'a, S>(format: S) -> Result<Trajectory, Error>where
+ S: Into<&'a str>,
pub fn memory_writer<'a, S>(format: S) -> Result<Trajectory, Error>where + S: Into<&'a str>,
Write to a memory buffer as though it was a formatted file.
+The format parameter should follow the same rules as in the main
+Trajectory constructor, except that compression specification
+is not supported.
The memory_buffer function can be used to retrieve the data written
+to memory of the Trajectory.
Errors
+This function fails if the format do not support in-memory writers.
+Example
+let trajectory_memory = Trajectory::memory_writer("SMI");
+
+// Binary formats typically do not support this feature
+assert!(Trajectory::memory_writer("XTC").is_err());sourcepub fn read(&mut self, frame: &mut Frame) -> Result<(), Error>
pub fn read(&mut self, frame: &mut Frame) -> Result<(), Error>
Read the next step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of atom +in the next step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+let mut frame = Frame::new();
+
+trajectory.read(&mut frame).unwrap();sourcepub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error>
pub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error>
Read a specific step of this trajectory into a frame.
If the number of atoms in frame does not correspond to the number of +atom at this step, the frame is resized.
+Errors
+This function fails if the data is incorrectly formatted for the +corresponding format.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+let mut frame = Frame::new();
+
+trajectory.read_step(10, &mut frame).unwrap();sourcepub fn set_topology(&mut self, topology: &Topology)
pub fn set_topology(&mut self, topology: &Topology)
Set the topology associated with this trajectory. This topology will
+be used when reading and writing the files, replacing any topology in
+the frames or files.
Example
+let mut topology = Topology::new();
+topology.add_atom(&Atom::new("H"));
+topology.add_atom(&Atom::new("O"));
+topology.add_atom(&Atom::new("H"));
+topology.add_bond(0, 1);
+topology.add_bond(1, 2);
+
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+trajectory.set_topology(&topology);sourcepub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error>where
+ P: AsRef<Path>,
pub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error>where + P: AsRef<Path>,
Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in format;
+and extracting the topology of this frame.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+trajectory.set_topology_file("topology.pdb").unwrap();sourcepub fn set_topology_with_format<'a, P, S>(
+ &mut self,
+ path: P,
+ format: S
+) -> Result<(), Error>where
+ P: AsRef<Path>,
+ S: Into<&'a str>,
pub fn set_topology_with_format<'a, P, S>( + &mut self, + path: P, + format: S +) -> Result<(), Error>where + P: AsRef<Path>, + S: Into<&'a str>,
Set the topology associated with this trajectory by reading the first
+frame of the file at the given path using the file format in
+format; and extracting the topology of this frame.
If format is an empty string, the format will be guessed from the
+path extension.
Errors
+This function fails if the topology file is incorrectly formatted for +the corresponding format, or in case of I/O errors from the OS.
+Example
+let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+trajectory.set_topology_with_format("topology.mol", "PDB").unwrap();sourcepub fn set_cell(&mut self, cell: &UnitCell)
pub fn set_cell(&mut self, cell: &UnitCell)
Set the unit cell associated with a trajectory. This cell will be
+used when reading and writing the files, replacing any unit cell in the
+frames or files.
Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+trajectory.set_cell(&UnitCell::new([10.0, 11.0, 12.5]));sourcepub fn nsteps(&mut self) -> usize
pub fn nsteps(&mut self) -> usize
Get the number of steps (the number of frames) in a trajectory.
+Example
+let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+
+println!("This trajectory contains {} steps", trajectory.nsteps());sourcepub fn memory_buffer(&self) -> Result<&str, Error>
pub fn memory_buffer(&self) -> Result<&str, Error>
Obtain the memory buffer written to by the trajectory.
+Errors
+This fails if the trajectory was not opened with
+Trajectory::memory_writer.
Example
+let mut trajectory_memory = Trajectory::memory_writer("SMI").unwrap();
+
+let mut frame = Frame::new();
+frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+frame.add_bond_with_order(0, 1, BondOrder::Single);
+
+trajectory_memory.write(&frame).unwrap();
+
+let result = trajectory_memory.memory_buffer();
+assert_eq!(result.unwrap(), "CC\n");Trait Implementations§
source§impl Debug for Trajectory
impl Debug for Trajectory
Auto Trait Implementations§
impl RefUnwindSafe for Trajectory
impl !Send for Trajectory
impl !Sync for Trajectory
impl Unpin for Trajectory
impl UnwindSafe for Trajectory
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
pub struct UnitCell { /* private fields */ }Expand description
An UnitCell represent the box containing the atoms, and its periodicity.
An unit cell is fully represented by three lengths (a, b, c); and three +angles (alpha, beta, gamma). The angles are stored in degrees, and the +lengths in Angstroms.
+A cell also has a matricial representation, by projecting the three base +vector into an orthonormal base. We choose to represent such matrix as an +upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |
+Implementations§
source§impl UnitCell
impl UnitCell
sourcepub fn new(lengths: [f64; 3]) -> UnitCell
pub fn new(lengths: [f64; 3]) -> UnitCell
Create an Orthorhombic UnitCell from the three lengths, in Angstroms.
Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);sourcepub fn infinite() -> UnitCell
pub fn infinite() -> UnitCell
Create an Infinite UnitCell.
Example
+let cell = UnitCell::infinite();
+
+assert_eq!(cell.lengths(), [0.0, 0.0, 0.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+assert_eq!(cell.shape(), CellShape::Infinite);sourcepub fn triclinic(lengths: [f64; 3], angles: [f64; 3]) -> UnitCell
pub fn triclinic(lengths: [f64; 3], angles: [f64; 3]) -> UnitCell
Create an Triclinic UnitCell from the three lengths (in Angstroms)
+and three angles (in degree). alpha is the angle between the vectors
+b and c; beta is the between the vectors a and c and gamma
+is the angle between the vectors a and b.
Example
+let cell = UnitCell::triclinic([10.0, 10.0, 10.0], [98.0, 99.0, 90.0]);
+
+assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);
+assert_eq!(cell.angles()[0], 98.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 99.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);
+assert_eq!(cell.shape(), CellShape::Triclinic);sourcepub fn from_matrix(matrix: [[f64; 3]; 3]) -> UnitCell
pub fn from_matrix(matrix: [[f64; 3]; 3]) -> UnitCell
Create an UnitCell from a cell matrix. If matrix contains only
+zeros, then an Infinite cell is created. If only the diagonal of the
+matrix is non-zero, then the cell is Orthorhombic. Else a
+Triclinic cell is created. The matrix entries should be in Angstroms.
Panics
+If the matrix has a negative determinant, or more generally is not +representing a unit cell.
+Example
+let cell = UnitCell::from_matrix([
+ [1.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]
+]);
+
+assert_eq!(cell.lengths(), [1.0, 2.0, 3.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);sourcepub fn lengths(&self) -> [f64; 3]
pub fn lengths(&self) -> [f64; 3]
Get the three lengths of the cell, in Angstroms.
+Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);sourcepub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error>
pub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error>
Set the three lengths of the cell, in Angstroms.
+Errors
+This function fails if the unit cell is infinite, or if one of the +lengths is negative.
+Example
+let mut cell = UnitCell::new([30.0, 30.0, 23.0]);
+
+cell.set_lengths([10.0, 30.0, 42.0]).unwrap();
+assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]);
+
+assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());sourcepub fn angles(&self) -> [f64; 3]
pub fn angles(&self) -> [f64; 3]
Get the three angles of the cell, in degrees.
+Example
+let cell = UnitCell::new([20.0, 20.0, 20.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+
+let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);sourcepub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error>
pub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error>
Set the three angles of the cell, in degrees.
+Errors
+This function fails if the unit cell is not Triclinic.
Example
+let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);
+
+cell.set_angles([90.0, 90.0, 90.0]).unwrap();
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);sourcepub fn matrix(&self) -> [[f64; 3]; 3]
pub fn matrix(&self) -> [[f64; 3]; 3]
Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+
+let matrix = cell.matrix();
+
+assert_eq!(matrix[0][0], 10.0);
+assert_eq!(matrix[1][1], 20.0);
+assert_eq!(matrix[2][2], 30.0);
+
+assert!(matrix[1][2].abs() < 1e-9);sourcepub fn shape(&self) -> CellShape
pub fn shape(&self) -> CellShape
Get the shape of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);sourcepub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error>
pub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error>
Set the shape of the unit cell to shape.
Errors
+This can fail if the cell length or angles are incompatible with the +new shape.
+Example
+let mut cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);
+
+cell.set_shape(CellShape::Triclinic).unwrap();
+assert_eq!(cell.shape(), CellShape::Triclinic);Trait Implementations§
Auto Trait Implementations§
impl RefUnwindSafe for UnitCell
impl !Send for UnitCell
impl !Sync for UnitCell
impl Unpin for UnitCell
impl UnwindSafe for UnitCell
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
Struct chemfiles::UnitCellMut
source · pub struct UnitCellMut<'a> { /* private fields */ }Expand description
An analog to a mutable reference to an unit cell (&mut UnitCell)
Methods from Deref<Target = UnitCell>§
sourcepub fn lengths(&self) -> [f64; 3]
pub fn lengths(&self) -> [f64; 3]
Get the three lengths of the cell, in Angstroms.
+Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);sourcepub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error>
pub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error>
Set the three lengths of the cell, in Angstroms.
+Errors
+This function fails if the unit cell is infinite, or if one of the +lengths is negative.
+Example
+let mut cell = UnitCell::new([30.0, 30.0, 23.0]);
+
+cell.set_lengths([10.0, 30.0, 42.0]).unwrap();
+assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]);
+
+assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());sourcepub fn angles(&self) -> [f64; 3]
pub fn angles(&self) -> [f64; 3]
Get the three angles of the cell, in degrees.
+Example
+let cell = UnitCell::new([20.0, 20.0, 20.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+
+let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);sourcepub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error>
pub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error>
Set the three angles of the cell, in degrees.
+Errors
+This function fails if the unit cell is not Triclinic.
Example
+let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);
+
+cell.set_angles([90.0, 90.0, 90.0]).unwrap();
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);sourcepub fn matrix(&self) -> [[f64; 3]; 3]
pub fn matrix(&self) -> [[f64; 3]; 3]
Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+
+let matrix = cell.matrix();
+
+assert_eq!(matrix[0][0], 10.0);
+assert_eq!(matrix[1][1], 20.0);
+assert_eq!(matrix[2][2], 30.0);
+
+assert!(matrix[1][2].abs() < 1e-9);sourcepub fn shape(&self) -> CellShape
pub fn shape(&self) -> CellShape
Get the shape of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);sourcepub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error>
pub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error>
Set the shape of the unit cell to shape.
Errors
+This can fail if the cell length or angles are incompatible with the +new shape.
+Example
+let mut cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);
+
+cell.set_shape(CellShape::Triclinic).unwrap();
+assert_eq!(cell.shape(), CellShape::Triclinic);Trait Implementations§
source§impl<'a> Debug for UnitCellMut<'a>
impl<'a> Debug for UnitCellMut<'a>
source§impl<'a> Deref for UnitCellMut<'a>
impl<'a> Deref for UnitCellMut<'a>
Auto Trait Implementations§
impl<'a> RefUnwindSafe for UnitCellMut<'a>
impl<'a> !Send for UnitCellMut<'a>
impl<'a> !Sync for UnitCellMut<'a>
impl<'a> Unpin for UnitCellMut<'a>
impl<'a> !UnwindSafe for UnitCellMut<'a>
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
Struct chemfiles::UnitCellRef
source · pub struct UnitCellRef<'a> { /* private fields */ }Expand description
An analog to a reference to an unit cell (&UnitCell)
Methods from Deref<Target = UnitCell>§
sourcepub fn lengths(&self) -> [f64; 3]
pub fn lengths(&self) -> [f64; 3]
Get the three lengths of the cell, in Angstroms.
+Example
+let cell = UnitCell::new([30.0, 30.0, 23.0]);
+assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);sourcepub fn angles(&self) -> [f64; 3]
pub fn angles(&self) -> [f64; 3]
Get the three angles of the cell, in degrees.
+Example
+let cell = UnitCell::new([20.0, 20.0, 20.0]);
+assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+
+let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+assert_eq!(cell.angles()[0], 100.0);
+// Rounding errors might occur due to internal representation
+assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+assert_eq!(cell.angles()[2], 90.0);sourcepub fn matrix(&self) -> [[f64; 3]; 3]
pub fn matrix(&self) -> [[f64; 3]; 3]
Get the unit cell matricial representation.
+The unit cell representation is obtained by aligning the a vector along +the x axis and putting the b vector in the xy plane. This make the +matrix an upper triangular matrix:
+| a_x b_x c_x |
+| 0 b_y c_y |
+| 0 0 c_z |
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+
+let matrix = cell.matrix();
+
+assert_eq!(matrix[0][0], 10.0);
+assert_eq!(matrix[1][1], 20.0);
+assert_eq!(matrix[2][2], 30.0);
+
+assert!(matrix[1][2].abs() < 1e-9);sourcepub fn shape(&self) -> CellShape
pub fn shape(&self) -> CellShape
Get the shape of the unit cell.
+Example
+let cell = UnitCell::new([10.0, 20.0, 30.0]);
+assert_eq!(cell.shape(), CellShape::Orthorhombic);Trait Implementations§
source§impl<'a> Debug for UnitCellRef<'a>
impl<'a> Debug for UnitCellRef<'a>
Auto Trait Implementations§
impl<'a> RefUnwindSafe for UnitCellRef<'a>
impl<'a> !Send for UnitCellRef<'a>
impl<'a> !Sync for UnitCellRef<'a>
impl<'a> Unpin for UnitCellRef<'a>
impl<'a> UnwindSafe for UnitCellRef<'a>
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
+ T: ?Sized,
impl<T> BorrowMut<T> for Twhere + T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
Redirecting to ../../chemfiles/enum.BondOrder.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/topology/struct.Topology.html b/0.10.40/chemfiles/topology/struct.Topology.html new file mode 100644 index 000000000..1215dacfd --- /dev/null +++ b/0.10.40/chemfiles/topology/struct.Topology.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Topology.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/topology/struct.TopologyRef.html b/0.10.40/chemfiles/topology/struct.TopologyRef.html new file mode 100644 index 000000000..7cdec6164 --- /dev/null +++ b/0.10.40/chemfiles/topology/struct.TopologyRef.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.TopologyRef.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/trajectory/struct.MemoryTrajectoryReader.html b/0.10.40/chemfiles/trajectory/struct.MemoryTrajectoryReader.html new file mode 100644 index 000000000..2d8d0b029 --- /dev/null +++ b/0.10.40/chemfiles/trajectory/struct.MemoryTrajectoryReader.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.MemoryTrajectoryReader.html...
+ + + \ No newline at end of file diff --git a/0.10.40/chemfiles/trajectory/struct.Trajectory.html b/0.10.40/chemfiles/trajectory/struct.Trajectory.html new file mode 100644 index 000000000..bab83ffc9 --- /dev/null +++ b/0.10.40/chemfiles/trajectory/struct.Trajectory.html @@ -0,0 +1,11 @@ + + + + +Redirecting to ../../chemfiles/struct.Trajectory.html...
+ + + \ No newline at end of file diff --git a/0.10.40/crates.js b/0.10.40/crates.js new file mode 100644 index 000000000..833ec8f70 --- /dev/null +++ b/0.10.40/crates.js @@ -0,0 +1 @@ +window.ALL_CRATES = ["chemfiles"]; \ No newline at end of file diff --git a/0.10.40/help.html b/0.10.40/help.html new file mode 100644 index 000000000..b73ce6d22 --- /dev/null +++ b/0.10.40/help.html @@ -0,0 +1 @@ +Rustdoc help
BackAtom is a particle in the current Frame. It stores the …","An analog to a mutable reference to an atom (&mut Atom)","An analog to a reference to an atom (&Atom)","Possible bond order associated with bonds","Boolean property","Available unit cell shapes.","Exception in the C++ chemfiles library","Error in configuration files syntax","Double bond","Floating point property","Error type for Chemfiles.","Error while reading or writing a file","Error in file formatting, i.e. the file is invalid","FormatMetadata contains metadata associated with one …","A Frame contains data from one simulation step: the …","Infinite cell, to use when there is no cell.","A Match is a set of atomic indexes matching a given …","Error in memory allocations","MemoryTrajectoryReader is a handle for a Trajectory in …","Orthorhombic cell, with the three angles equals to 90°.","Error for out of bounds indexing","An iterator over the properties in an atom/frame/residue","A Property is a piece of data that can be associated with …","Error related to properties","Quadruple bond (present in some metals)","Quintuplet bond (present in some metals)","A Residue is a group of atoms belonging to the same …","An analog to a reference to a residue (&Residue)","A Selection allow to select atoms in a Frame, from a …","Error in selection string syntax","Single bond","Possible causes of error in chemfiles","Exception in the C++ standard library","String property","No error","A Topology contains the definition of all the atoms in the …","An analog to a reference to a topology (&Topology)","The Trajectory type is the main entry point when using …","Triclinic cell, with any values for the angles.","Triple bond","The given path is not valid UTF8","An UnitCell represent the box containing the atoms, and …","An analog to a mutable reference to an unit cell (…","An analog to a reference to an unit cell (&UnitCell)","Unknown or unspecified bond order","3-dimensional vector property","Add the atom at index atom in this residue.","Add an Atom at the end of this topology","Add an Atom and the corresponding position and optionally …","Add a bond between the atoms at indexes i and j in the …","Add a bond between the atoms at indexes i and j in the …","Add a bond between the atoms at indexes i and j in the …","Add a bond between the atoms at indexes i and j in the …","Read configuration data from the file at path.","Add a residue to this topology.","Add a copy of residue to this frame.","Add velocity data to this frame. If the frame already have …","Get the angle formed by the atoms at indexes i, j and k in …","Get the three angles of the cell, in degrees.","Get the list of angles in the topology.","Get the number of angles in the topology.","Check if the two residues first and second from the …","Get a reference of the atom at the given index in this …","Get a reference to the atom at the given index in this …","Get a mutable reference to the atom at the given index in …","Get a mutable reference to the atom at the given index in …","Try to get the atomic number of the atom from the atomic …","Get the atom type.","Get the list of atoms of this residue.","Does this format support storing atom names or types?","Get the bond order for the bond between the atoms at …","Get the bond order for all the bonds in the topology","Get the list of bonds in the topology.","Does this format support storing bonds between atoms?","Get the number of bonds in the topology.","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","Get a reference to the UnitCell from this frame.","Get a mutable reference to the UnitCell from this frame.","Get the atom charge, in number of the electron charge e.","Clear any error from the C++ library","Remove all existing bonds, angles, dihedral angles and …","Remove all existing bonds, angles, dihedral angles and …","","","","","","","","","","","","","","","","","","","","","","","","","","","","Check if the atom at index i is in this residue","","Try to get the covalent radius of the atom from the atomic …","","","","","","","","","","","","Extended, user-facing description of the format.","Get the dihedral angle formed by the atoms at indexes i, j…","Get the list of dihedral angles in the topology.","Get the number of dihedral angles in the topology.","Get the distance between the atoms at indexes i and j in …","","","","","","","","","","","","","","","","","","","","","Evaluate a selection for a given frame, and return the …","Extension associated with the format.","","","","","","","","","","","","","","","","","","","","","","Get the list of formats known by chemfiles, as well as all …","Returns the argument unchanged.","Returns the argument unchanged.","","","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","Returns the argument unchanged.","","","Returns the argument unchanged.","","","","Returns the argument unchanged.","Create an UnitCell from a cell matrix. If matrix contains …","Try to get the full name of the atom from the atomic type. …","Get a property with the given name in this atom, if it …","Get a property with the given name in this frame, if it …","Get a property with the given name in this frame, if it …","Guess the bonds, angles and dihedrals in this frame.","Get the format that chemfiles would use to read a file at …","Check if this frame contains velocity data.","Get the identifier of this residue in the initial topology …","Get the list of improper dihedral angles in the topology.","Get the number of improper dihedral angles in the topology.","","Create an Infinite UnitCell.","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","Calls U::from(self).","","","Iterate over the atomic indexes in the match.","Gets an iterator over atoms","Get the last error message from the C++ library.","Get the length of the Match.","Get the three lengths of the cell, in Angstroms.","Evaluates a selection of size 1 on a given frame. This …","Get the atom mass, in atomic mass units.","Get the unit cell matricial representation.","Does this format support in-memory IO?","Obtain the memory buffer written to by the trajectory.","Write to a memory buffer as though it was a formatted file.","A message describing the error cause","Get the atom name.","Get the name of this residue.","Name of the format.","Read a memory buffer as though it was a formatted file.","Create an atom with the given name, and set the atom type …","Create an Orthorhombic UnitCell from the three lengths, in …","Create a new residue with the given name","Create a new empty topology.","Create an empty frame. It will be resized by the library …","Create a new match containing the atoms in the atoms slice.","Create a new selection from the given selection string.","","Get the number of steps (the number of frames) in a …","Open the file at the given path in the given mode.","Open the file at the given path using a specific file …","Get the out of plane distance formed by the atoms at …","","","Get file path for this trajectory.","Get a view into the positions of this frame.","Does this format support storing atomic positions?","Get a mutable view into the positions of this frame.","Get an iterator over all (name, property) pairs for this …","Get an iterator over all (name, property) pairs for this …","Get an iterator over all (name, property) pairs for this …","","Read the next step of this trajectory into a frame.","Is reading files in this format implemented?","Read a specific step of this trajectory into a frame.","URL pointing to the format definition/reference.","Remove an Atom from this topology by index. This modify …","Remove the atom at index i in this frame.","Remove any existing bond between the atoms at indexes i …","Remove any existing bond between the atoms at indexes i …","Get a reference to the residue at index index from this …","Get a copy of the residue containing the atom at index …","Does this format support storing residues?","Get the number of residues in this topology.","Resize this topology to hold natoms atoms, inserting dummy …","Resize the positions and the velocities in this frame, to …","Add a new property with the given name to this atom.","Add a new property with the given name to this residue.","Add a new property with the given name to this frame.","Set the three angles of the cell, in degrees.","Set the atom type to atomic_type.","Set the UnitCell of this frame to cell.","Set the unit cell associated with a trajectory. This cell …","Set the atom charge to charge, in number of the electron …","Set the three lengths of the cell, in Angstroms.","Set the atom mass to mass, in atomic mass units.","Set the atom name to name.","Set the shape of the unit cell to shape.","Set this frame step to step.","Set the Topology of this frame to topology.","Set the topology associated with this trajectory. This …","Set the topology associated with this trajectory by …","Set the topology associated with this trajectory by …","Use callback for every chemfiles warning. The callback …","Get the shape of the unit cell.","Get the number of atoms in this residue.","Get the current number of atoms in this topology.","Get the current number of atoms in this frame.","Get the size of the selection, i.e. the number of atoms we …","","The error status code","Get this frame step, i.e. the frame number in the …","Get the selection string used to create this selection.","","","","","","","","","","","","","","","Get a reference to the Topology of this frame.","Create an Triclinic UnitCell from the three lengths (in …","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","Does this format support storing unit cell information?","Try to get the Van der Waals radius of the atom from the …","Get a view into the velocities of this frame.","Does this format support storing atomic velocities?","Get a mutable view into the velocities of this frame.","Get the version of the chemfiles library.","Get the volume of the unit cell.","Create a new residue with the given name and id as …","Wrap a vector in this unit cell.","Write a frame to this trajectory.","Is writing files in this format 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+}');
+if (typeof window !== 'undefined' && window.initSearch) {window.initSearch(searchIndex)};
+if (typeof exports !== 'undefined') {exports.searchIndex = searchIndex};
diff --git a/0.10.40/settings.html b/0.10.40/settings.html
new file mode 100644
index 000000000..2e13b17b2
--- /dev/null
+++ b/0.10.40/settings.html
@@ -0,0 +1 @@
+Rustdoc settings
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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::marker::PhantomData;
+
+use chemfiles_sys as ffi;
+
+use crate::errors::{check_not_null, check_success};
+use crate::property::{PropertiesIter, Property, RawProperty};
+use crate::strings;
+
+/// An `Atom` is a particle in the current `Frame`. It stores the following
+/// atomic properties:
+///
+/// - atom name;
+/// - atom type;
+/// - atom mass;
+/// - atom charge.
+///
+/// The atom name is usually an unique identifier (`H1`, `C_a`) while the
+/// atom type will be shared between all particles of the same type: `H`,
+/// `Ow`, `CH3`.
+#[derive(Debug)]
+pub struct Atom {
+ handle: *mut ffi::CHFL_ATOM,
+}
+
+/// An analog to a reference to an atom (`&Atom`)
+#[derive(Debug)]
+pub struct AtomRef<'a> {
+ inner: Atom,
+ marker: PhantomData<&'a Atom>,
+}
+
+impl<'a> std::ops::Deref for AtomRef<'a> {
+ type Target = Atom;
+ fn deref(&self) -> &Atom {
+ &self.inner
+ }
+}
+
+/// An analog to a mutable reference to an atom (`&mut Atom`)
+#[derive(Debug)]
+pub struct AtomMut<'a> {
+ inner: Atom,
+ marker: PhantomData<&'a mut Atom>,
+}
+
+impl<'a> std::ops::Deref for AtomMut<'a> {
+ type Target = Atom;
+ fn deref(&self) -> &Atom {
+ &self.inner
+ }
+}
+
+impl<'a> std::ops::DerefMut for AtomMut<'a> {
+ fn deref_mut(&mut self) -> &mut Atom {
+ &mut self.inner
+ }
+}
+
+impl Clone for Atom {
+ fn clone(&self) -> Atom {
+ unsafe {
+ let new_handle = ffi::chfl_atom_copy(self.as_ptr());
+ Atom::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Atom {
+ /// Create an owned `Atom` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut ffi::CHFL_ATOM) -> Atom {
+ check_not_null(ptr);
+ Atom { handle: ptr }
+ }
+
+ /// Create a borrowed `Atom` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, and the caller is responsible for setting the right lifetime
+ #[inline]
+ #[allow(clippy::ptr_cast_constness)]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const ffi::CHFL_ATOM) -> AtomRef<'a> {
+ AtomRef {
+ inner: Atom::from_ptr(ptr as *mut ffi::CHFL_ATOM),
+ marker: PhantomData,
+ }
+ }
+
+ /// Create a mutably borrowed `Atom` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, and the caller is responsible for setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_mut_from_ptr<'a>(ptr: *mut ffi::CHFL_ATOM) -> AtomMut<'a> {
+ AtomMut {
+ inner: Atom::from_ptr(ptr),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const ffi::CHFL_ATOM {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut ffi::CHFL_ATOM {
+ self.handle
+ }
+
+ /// Create an atom with the given `name`, and set the atom type to `name`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.name(), "He");
+ /// ```
+ pub fn new<'a>(name: impl Into<&'a str>) -> Atom {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ let handle = ffi::chfl_atom(buffer.as_ptr());
+ Atom::from_ptr(handle)
+ }
+ }
+
+ /// Get the atom mass, in atomic mass units.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.mass(), 4.002602);
+ /// ```
+ pub fn mass(&self) -> f64 {
+ let mut mass = 0.0;
+ unsafe {
+ check_success(ffi::chfl_atom_mass(self.as_ptr(), &mut mass));
+ }
+ return mass;
+ }
+
+ /// Set the atom mass to `mass`, in atomic mass units.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_mass(34.9);
+ /// assert_eq!(atom.mass(), 34.9);
+ /// ```
+ pub fn set_mass(&mut self, mass: f64) {
+ unsafe {
+ check_success(ffi::chfl_atom_set_mass(self.as_mut_ptr(), mass));
+ }
+ }
+
+ /// Get the atom charge, in number of the electron charge *e*.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.charge(), 0.0);
+ /// ```
+ pub fn charge(&self) -> f64 {
+ let mut charge = 0.0;
+ unsafe {
+ check_success(ffi::chfl_atom_charge(self.as_ptr(), &mut charge));
+ }
+ return charge;
+ }
+
+ /// Set the atom charge to `charge`, in number of the electron charge *e*.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_charge(-2.0);
+ /// assert_eq!(atom.charge(), -2.0);
+ /// ```
+ pub fn set_charge(&mut self, charge: f64) {
+ unsafe {
+ check_success(ffi::chfl_atom_set_charge(self.as_mut_ptr(), charge));
+ }
+ }
+
+ /// Get the atom name.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.name(), "He");
+ /// ```
+ pub fn name(&self) -> String {
+ let get_name = |ptr, len| unsafe { ffi::chfl_atom_name(self.as_ptr(), ptr, len) };
+ let name = strings::call_autogrow_buffer(10, get_name).expect("getting name failed");
+ return strings::from_c(name.as_ptr());
+ }
+
+ /// Get the atom type.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("He");
+ /// assert_eq!(atom.atomic_type(), "He");
+ /// ```
+ pub fn atomic_type(&self) -> String {
+ let get_type = |ptr, len| unsafe { ffi::chfl_atom_type(self.as_ptr(), ptr, len) };
+ let buffer = strings::call_autogrow_buffer(10, get_type).expect("getting type failed");
+ return strings::from_c(buffer.as_ptr());
+ }
+
+ /// Set the atom name to `name`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_name("Zn3");
+ /// assert_eq!(atom.name(), "Zn3");
+ /// ```
+ pub fn set_name<'a>(&mut self, name: impl Into<&'a str>) {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ check_success(ffi::chfl_atom_set_name(self.as_mut_ptr(), buffer.as_ptr()));
+ }
+ }
+
+ /// Set the atom type to `atomic_type`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let mut atom = Atom::new("He");
+ ///
+ /// atom.set_atomic_type("F");
+ /// assert_eq!(atom.atomic_type(), "F");
+ /// ```
+ pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>) {
+ let buffer = strings::to_c(atomic_type.into());
+ unsafe {
+ check_success(ffi::chfl_atom_set_type(self.as_mut_ptr(), buffer.as_ptr()));
+ }
+ }
+
+ /// Try to get the full name of the atom from the atomic type. For example,
+ /// the full name of "He" is "Helium", and so on. If the name can not be
+ /// found, this function returns the empty string.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// let atom = Atom::new("Zn");
+ /// assert_eq!(atom.full_name(), "Zinc");
+ /// ```
+ pub fn full_name(&self) -> String {
+ let get_full_name = |ptr, len| unsafe { ffi::chfl_atom_full_name(self.as_ptr(), ptr, len) };
+ let name = strings::call_autogrow_buffer(10, get_full_name).expect("getting full name failed");
+ return strings::from_c(name.as_ptr());
+ }
+
+ /// Try to get the Van der Waals radius of the atom from the atomic type.
+ /// If the radius can not be found, returns 0.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// assert_eq!(Atom::new("He").vdw_radius(), 1.4);
+ /// assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);
+ /// ```
+ pub fn vdw_radius(&self) -> f64 {
+ let mut radius: f64 = 0.0;
+ unsafe {
+ check_success(ffi::chfl_atom_vdw_radius(self.as_ptr(), &mut radius));
+ }
+ return radius;
+ }
+
+ /// Try to get the covalent radius of the atom from the atomic type. If the
+ /// radius can not be found, returns 0.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// assert_eq!(Atom::new("He").covalent_radius(), 0.32);
+ /// assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);
+ /// ```
+ pub fn covalent_radius(&self) -> f64 {
+ let mut radius: f64 = 0.0;
+ unsafe {
+ check_success(ffi::chfl_atom_covalent_radius(self.as_ptr(), &mut radius));
+ }
+ return radius;
+ }
+
+ /// Try to get the atomic number of the atom from the atomic type. If the
+ /// number can not be found, returns 0.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Atom;
+ /// assert_eq!(Atom::new("He").atomic_number(), 2);
+ /// assert_eq!(Atom::new("Xxx").atomic_number(), 0);
+ /// ```
+ pub fn atomic_number(&self) -> u64 {
+ let mut number = 0;
+ unsafe {
+ check_success(ffi::chfl_atom_atomic_number(self.as_ptr(), &mut number));
+ }
+ return number;
+ }
+
+ /// Add a new `property` with the given `name` to this atom.
+ ///
+ /// If a property with the same name already exists, this function override
+ /// the existing property with the new one.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Atom, Property};
+ /// let mut atom = Atom::new("He");
+ /// atom.set("a bool", true);
+ /// atom.set("a string", "test");
+ ///
+ /// assert_eq!(atom.get("a bool"), Some(Property::Bool(true)));
+ /// assert_eq!(atom.get("a string"), Some(Property::String("test".into())));
+ /// ```
+ pub fn set(&mut self, name: &str, property: impl Into<Property>) {
+ let buffer = strings::to_c(name);
+ let property = property.into().as_raw();
+ unsafe {
+ check_success(ffi::chfl_atom_set_property(
+ self.as_mut_ptr(),
+ buffer.as_ptr(),
+ property.as_ptr(),
+ ));
+ }
+ }
+
+ /// Get a property with the given `name` in this atom, if it exist.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Atom, Property};
+ /// let mut atom = Atom::new("He");
+ /// atom.set("foo", Property::Double(22.2));
+ ///
+ /// assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
+ /// assert_eq!(atom.get("Bar"), None);
+ /// ```
+ pub fn get(&self, name: &str) -> Option<Property> {
+ let buffer = strings::to_c(name);
+ unsafe {
+ let handle = ffi::chfl_atom_get_property(self.as_ptr(), buffer.as_ptr());
+ if handle.is_null() {
+ None
+ } else {
+ let raw = RawProperty::from_ptr(handle);
+ let property = Property::from_raw(raw);
+ Some(property)
+ }
+ }
+ }
+
+ /// Get an iterator over all (name, property) pairs for this atom
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Atom, Property};
+ /// let mut atom = Atom::new("He");
+ /// atom.set("foo", Property::Double(22.2));
+ /// atom.set("bar", Property::Bool(false));
+ ///
+ /// for (name, property) in atom.properties() {
+ /// if name == "foo" {
+ /// assert_eq!(property, Property::Double(22.2));
+ /// } else if name == "bar" {
+ /// assert_eq!(property, Property::Bool(false));
+ /// }
+ /// }
+ /// ```
+ pub fn properties(&self) -> PropertiesIter {
+ let mut count = 0;
+ unsafe {
+ check_success(ffi::chfl_atom_properties_count(self.as_ptr(), &mut count));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = count as usize;
+ let mut c_names = vec![std::ptr::null_mut(); size];
+ unsafe {
+ check_success(ffi::chfl_atom_list_properties(
+ self.as_ptr(),
+ c_names.as_mut_ptr(),
+ count,
+ ));
+ }
+
+ let mut names = Vec::new();
+ for ptr in c_names {
+ names.push(strings::from_c(ptr));
+ }
+
+ PropertiesIter {
+ names: names.into_iter(),
+ getter: Box::new(move |name| self.get(name).expect("failed to get property")),
+ }
+ }
+}
+
+impl Drop for Atom {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = ffi::chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.name(), "He");
+
+ let copy = atom.clone();
+ assert_eq!(copy.name(), "He");
+
+ atom.set_name("Na");
+ assert_eq!(atom.name(), "Na");
+ assert_eq!(copy.name(), "He");
+ }
+
+ #[test]
+ fn mass() {
+ let mut atom = Atom::new("He");
+ approx::assert_ulps_eq!(atom.mass(), 4.002602);
+ atom.set_mass(15.0);
+ assert_eq!(atom.mass(), 15.0);
+ }
+
+ #[test]
+ fn charge() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.charge(), 0.0);
+ atom.set_charge(-1.5);
+ assert_eq!(atom.charge(), -1.5);
+ }
+
+ #[test]
+ fn name() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.name(), "He");
+ atom.set_name("Zn-12");
+ assert_eq!(atom.name(), "Zn-12");
+ }
+
+ #[test]
+ fn atomic_type() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.atomic_type(), "He");
+ atom.set_atomic_type("Zn");
+ assert_eq!(atom.atomic_type(), "Zn");
+ }
+
+ #[test]
+ fn full_name() {
+ let mut atom = Atom::new("He");
+ assert_eq!(atom.full_name(), "Helium");
+
+ atom.set_atomic_type("Zn");
+ assert_eq!(atom.full_name(), "Zinc");
+
+ let atom = Atom::new("Unknown");
+ assert_eq!(atom.full_name(), "");
+ }
+
+ #[test]
+ fn radii() {
+ let atom = Atom::new("He");
+ approx::assert_ulps_eq!(atom.vdw_radius(), 1.4);
+ approx::assert_ulps_eq!(atom.covalent_radius(), 0.32);
+
+ let atom = Atom::new("Unknown");
+ assert_eq!(atom.vdw_radius(), 0.0);
+ assert_eq!(atom.covalent_radius(), 0.0);
+ }
+
+ #[test]
+ fn atomic_number() {
+ let atom = Atom::new("He");
+ assert_eq!(atom.atomic_number(), 2);
+
+ let atom = Atom::new("Unknown");
+ assert_eq!(atom.atomic_number(), 0);
+ }
+
+ #[test]
+ fn property() {
+ let mut atom = Atom::new("F");
+
+ atom.set("foo", -22.0);
+ assert_eq!(atom.get("foo"), Some(Property::Double(-22.0)));
+ assert_eq!(atom.get("bar"), None);
+
+ atom.set("bar", Property::String("here".into()));
+ for (name, property) in atom.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(-22.0));
+ } else if name == "bar" {
+ assert_eq!(property, Property::String("here".into()));
+ }
+ }
+ }
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371 +372 +373 +374 +375 +376 +377 +378 +379 +380 +381 +382 +383 +384 +385 +386 +387 +388 +389 +390 +391 +392 +393 +394 +395 +396 +397 +398 +399 +400 +401 +402 +403 +404 +405 +406 +407 +408 +409 +410 +411 +412 +413 +414 +415 +416 +417 +418 +419 +420 +421 +422 +423 +424 +425 +426 +427 +428 +429 +430 +431 +432 +433 +434 +435 +436 +437 +438 +439 +440 +441 +442 +443 +444 +445 +446 +447 +448 +449 +450 +451 +452 +453 +454 +455 +456 +457 +458 +459 +460 +461 +462 +463 +464 +465 +466 +467 +468 +469 +470 +471 +472 +473 +474 +475 +476 +477 +478 +479 +480 +481 +482 +483 +484 +485 +486 +487 +488 +489 +490 +491 +492 +493 +494 +495 +496 +497 +498 +499 +500 +501 +502 +503 +504 +505 +506 +507 +508 +509 +510 +511 +512 +513 +514 +515 +516 +517 +518 +519 +520 +521 +522 +523 +524 +525 +526 +527 +528 +529 +530 +531 +532 +533 +534 +535 +536 +537 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::marker::PhantomData;
+
+#[allow(clippy::wildcard_imports)]
+use chemfiles_sys as ffi;
+
+use crate::errors::{check, check_not_null, check_success, Error};
+
+/// Available unit cell shapes.
+#[derive(Clone, Debug, PartialEq, Eq)]
+pub enum CellShape {
+ /// Orthorhombic cell, with the three angles equals to 90°.
+ Orthorhombic,
+ /// Triclinic cell, with any values for the angles.
+ Triclinic,
+ /// Infinite cell, to use when there is no cell.
+ Infinite,
+}
+
+impl From<ffi::chfl_cellshape> for CellShape {
+ fn from(celltype: ffi::chfl_cellshape) -> CellShape {
+ match celltype {
+ ffi::chfl_cellshape::CHFL_CELL_ORTHORHOMBIC => CellShape::Orthorhombic,
+ ffi::chfl_cellshape::CHFL_CELL_TRICLINIC => CellShape::Triclinic,
+ ffi::chfl_cellshape::CHFL_CELL_INFINITE => CellShape::Infinite,
+ }
+ }
+}
+
+impl From<CellShape> for ffi::chfl_cellshape {
+ fn from(celltype: CellShape) -> ffi::chfl_cellshape {
+ match celltype {
+ CellShape::Orthorhombic => ffi::chfl_cellshape::CHFL_CELL_ORTHORHOMBIC,
+ CellShape::Triclinic => ffi::chfl_cellshape::CHFL_CELL_TRICLINIC,
+ CellShape::Infinite => ffi::chfl_cellshape::CHFL_CELL_INFINITE,
+ }
+ }
+}
+
+/// An `UnitCell` represent the box containing the atoms, and its periodicity.
+///
+/// An unit cell is fully represented by three lengths (a, b, c); and three
+/// angles (alpha, beta, gamma). The angles are stored in degrees, and the
+/// lengths in Angstroms.
+///
+/// A cell also has a matricial representation, by projecting the three base
+/// vector into an orthonormal base. We choose to represent such matrix as an
+/// upper triangular matrix:
+///
+/// ```text
+/// | a_x b_x c_x |
+/// | 0 b_y c_y |
+/// | 0 0 c_z |
+/// ```
+#[derive(Debug)]
+pub struct UnitCell {
+ handle: *mut ffi::CHFL_CELL,
+}
+
+/// An analog to a reference to an unit cell (`&UnitCell`)
+#[derive(Debug)]
+pub struct UnitCellRef<'a> {
+ inner: UnitCell,
+ marker: PhantomData<&'a UnitCell>,
+}
+
+impl<'a> std::ops::Deref for UnitCellRef<'a> {
+ type Target = UnitCell;
+ fn deref(&self) -> &UnitCell {
+ &self.inner
+ }
+}
+
+/// An analog to a mutable reference to an unit cell (`&mut UnitCell`)
+#[derive(Debug)]
+pub struct UnitCellMut<'a> {
+ inner: UnitCell,
+ marker: PhantomData<&'a mut UnitCell>,
+}
+
+impl<'a> std::ops::Deref for UnitCellMut<'a> {
+ type Target = UnitCell;
+ fn deref(&self) -> &UnitCell {
+ &self.inner
+ }
+}
+
+impl<'a> std::ops::DerefMut for UnitCellMut<'a> {
+ fn deref_mut(&mut self) -> &mut UnitCell {
+ &mut self.inner
+ }
+}
+
+impl Clone for UnitCell {
+ fn clone(&self) -> UnitCell {
+ unsafe {
+ let new_handle = ffi::chfl_cell_copy(self.as_ptr());
+ UnitCell::from_ptr(new_handle)
+ }
+ }
+}
+
+impl UnitCell {
+ /// Create an owned `UnitCell` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut ffi::CHFL_CELL) -> UnitCell {
+ check_not_null(ptr);
+ UnitCell { handle: ptr }
+ }
+
+ /// Create a borrowed `UnitCell` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, and the caller is responsible for setting the right lifetime.
+ #[inline]
+ #[allow(clippy::ptr_cast_constness)]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const ffi::CHFL_CELL) -> UnitCellRef<'a> {
+ UnitCellRef {
+ inner: UnitCell::from_ptr(ptr as *mut ffi::CHFL_CELL),
+ marker: PhantomData,
+ }
+ }
+
+ /// Create a borrowed `UnitCell` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, except for it being non-null, and the caller is responsible for
+ /// setting the right lifetime
+ #[inline]
+ pub(crate) unsafe fn ref_mut_from_ptr<'a>(ptr: *mut ffi::CHFL_CELL) -> UnitCellMut<'a> {
+ UnitCellMut {
+ inner: UnitCell::from_ptr(ptr),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const ffi::CHFL_CELL {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut ffi::CHFL_CELL {
+ self.handle
+ }
+
+ /// Create an `Orthorhombic` `UnitCell` from the three lengths, in Angstroms.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::new([30.0, 30.0, 23.0]);
+ ///
+ /// assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// ```
+ pub fn new(lengths: [f64; 3]) -> UnitCell {
+ unsafe {
+ let handle = ffi::chfl_cell(lengths.as_ptr(), std::ptr::null());
+ UnitCell::from_ptr(handle)
+ }
+ }
+
+ /// Create an `Infinite` `UnitCell`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::infinite();
+ ///
+ /// assert_eq!(cell.lengths(), [0.0, 0.0, 0.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// assert_eq!(cell.shape(), CellShape::Infinite);
+ /// ```
+ pub fn infinite() -> UnitCell {
+ let mut cell = UnitCell::new([0.0, 0.0, 0.0]);
+ cell.set_shape(CellShape::Infinite).expect("could not set cell shape");
+ return cell;
+ }
+
+ /// Create an `Triclinic` `UnitCell` from the three lengths (in Angstroms)
+ /// and three angles (in degree). `alpha` is the angle between the vectors
+ /// `b` and `c`; `beta` is the between the vectors `a` and `c` and `gamma`
+ /// is the angle between the vectors `a` and `b`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::triclinic([10.0, 10.0, 10.0], [98.0, 99.0, 90.0]);
+ ///
+ /// assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);
+ /// assert_eq!(cell.angles()[0], 98.0);
+ /// // Rounding errors might occur due to internal representation
+ /// assert!((cell.angles()[1] - 99.0).abs() < 1e-12);
+ /// assert_eq!(cell.angles()[2], 90.0);
+ /// assert_eq!(cell.shape(), CellShape::Triclinic);
+ /// ```
+ pub fn triclinic(lengths: [f64; 3], angles: [f64; 3]) -> UnitCell {
+ unsafe {
+ let handle = ffi::chfl_cell(lengths.as_ptr(), angles.as_ptr());
+ UnitCell::from_ptr(handle)
+ }
+ }
+
+ /// Create an `UnitCell` from a cell matrix. If `matrix` contains only
+ /// zeros, then an `Infinite` cell is created. If only the diagonal of the
+ /// matrix is non-zero, then the cell is `Orthorhombic`. Else a
+ /// `Triclinic` cell is created. The matrix entries should be in Angstroms.
+ ///
+ /// # Panics
+ ///
+ /// If the matrix has a negative determinant, or more generally is not
+ /// representing a unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::from_matrix([
+ /// [1.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]
+ /// ]);
+ ///
+ /// assert_eq!(cell.lengths(), [1.0, 2.0, 3.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// ```
+ pub fn from_matrix(mut matrix: [[f64; 3]; 3]) -> UnitCell {
+ unsafe {
+ let handle = ffi::chfl_cell_from_matrix(matrix.as_mut_ptr());
+ UnitCell::from_ptr(handle)
+ }
+ }
+
+ /// Get the three lengths of the cell, in Angstroms.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([30.0, 30.0, 23.0]);
+ /// assert_eq!(cell.lengths(), [30.0, 30.0, 23.0]);
+ /// ```
+ pub fn lengths(&self) -> [f64; 3] {
+ let mut lengths = [0.0; 3];
+ unsafe {
+ check_success(ffi::chfl_cell_lengths(self.as_ptr(), lengths.as_mut_ptr()));
+ }
+ return lengths;
+ }
+
+ /// Set the three lengths of the cell, in Angstroms.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the unit cell is infinite, or if one of the
+ /// lengths is negative.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let mut cell = UnitCell::new([30.0, 30.0, 23.0]);
+ ///
+ /// cell.set_lengths([10.0, 30.0, 42.0]).unwrap();
+ /// assert_eq!(cell.lengths(), [10.0, 30.0, 42.0]);
+ ///
+ /// assert!(UnitCell::infinite().set_lengths([1.0, 1.0, 1.0]).is_err());
+ /// ```
+ pub fn set_lengths(&mut self, lengths: [f64; 3]) -> Result<(), Error> {
+ unsafe { check(ffi::chfl_cell_set_lengths(self.as_mut_ptr(), lengths.as_ptr())) }
+ }
+
+ /// Get the three angles of the cell, in degrees.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([20.0, 20.0, 20.0]);
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ ///
+ /// let cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+ /// assert_eq!(cell.angles()[0], 100.0);
+ /// // Rounding errors might occur due to internal representation
+ /// assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+ /// assert_eq!(cell.angles()[2], 90.0);
+ /// ```
+ pub fn angles(&self) -> [f64; 3] {
+ let mut angles = [0.0; 3];
+ unsafe {
+ check_success(ffi::chfl_cell_angles(self.as_ptr(), angles.as_mut_ptr()));
+ }
+ return angles;
+ }
+
+ /// Set the three angles of the cell, in degrees.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the unit cell is not `Triclinic`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let mut cell = UnitCell::triclinic([20.0, 20.0, 20.0], [100.0, 120.0, 90.0]);
+ /// assert_eq!(cell.angles()[0], 100.0);
+ /// // Rounding errors might occur due to internal representation
+ /// assert!((cell.angles()[1] - 120.0).abs() < 1e-12);
+ /// assert_eq!(cell.angles()[2], 90.0);
+ ///
+ /// cell.set_angles([90.0, 90.0, 90.0]).unwrap();
+ /// assert_eq!(cell.angles(), [90.0, 90.0, 90.0]);
+ /// ```
+ pub fn set_angles(&mut self, angles: [f64; 3]) -> Result<(), Error> {
+ unsafe { check(ffi::chfl_cell_set_angles(self.as_mut_ptr(), angles.as_ptr())) }
+ }
+
+ /// Get the unit cell matricial representation.
+ ///
+ /// The unit cell representation is obtained by aligning the a vector along
+ /// the *x* axis and putting the b vector in the *xy* plane. This make the
+ /// matrix an upper triangular matrix:
+ ///
+ /// ```text
+ /// | a_x b_x c_x |
+ /// | 0 b_y c_y |
+ /// | 0 0 c_z |
+ /// ```
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ ///
+ /// let matrix = cell.matrix();
+ ///
+ /// assert_eq!(matrix[0][0], 10.0);
+ /// assert_eq!(matrix[1][1], 20.0);
+ /// assert_eq!(matrix[2][2], 30.0);
+ ///
+ /// assert!(matrix[1][2].abs() < 1e-9);
+ /// ```
+ pub fn matrix(&self) -> [[f64; 3]; 3] {
+ let mut matrix = [[0.0; 3]; 3];
+ unsafe {
+ check_success(ffi::chfl_cell_matrix(self.as_ptr(), matrix.as_mut_ptr()));
+ }
+ return matrix;
+ }
+
+ /// Get the shape of the unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// ```
+ pub fn shape(&self) -> CellShape {
+ let mut shape = ffi::chfl_cellshape::CHFL_CELL_INFINITE;
+ unsafe {
+ check_success(ffi::chfl_cell_shape(self.as_ptr(), &mut shape));
+ }
+ return CellShape::from(shape);
+ }
+
+ /// Set the shape of the unit cell to `shape`.
+ ///
+ /// # Errors
+ ///
+ /// This can fail if the cell length or angles are incompatible with the
+ /// new shape.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{UnitCell, CellShape};
+ /// let mut cell = UnitCell::new([10.0, 20.0, 30.0]);
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ ///
+ /// cell.set_shape(CellShape::Triclinic).unwrap();
+ /// assert_eq!(cell.shape(), CellShape::Triclinic);
+ /// ```
+ pub fn set_shape(&mut self, shape: CellShape) -> Result<(), Error> {
+ unsafe { check(ffi::chfl_cell_set_shape(self.as_mut_ptr(), shape.into())) }
+ }
+
+ /// Get the volume of the unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ /// assert_eq!(cell.volume(), 10.0 * 20.0 * 30.0);
+ /// ```
+ pub fn volume(&self) -> f64 {
+ let mut volume = 0.0;
+ unsafe {
+ check_success(ffi::chfl_cell_volume(self.as_ptr(), &mut volume));
+ }
+ return volume;
+ }
+
+ /// Wrap a `vector` in this unit cell.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::UnitCell;
+ /// let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ ///
+ /// let mut vector = [12.0, 5.2, -45.3];
+ /// cell.wrap(&mut vector);
+ /// assert_eq!(vector, [2.0, 5.2, 14.700000000000003]);
+ /// ```
+ pub fn wrap(&self, vector: &mut [f64; 3]) {
+ unsafe {
+ check_success(ffi::chfl_cell_wrap(self.as_ptr(), vector.as_mut_ptr()));
+ }
+ }
+}
+
+impl Drop for UnitCell {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = ffi::chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.lengths(), [2.0, 3.0, 4.0]);
+
+ let copy = cell.clone();
+ assert_eq!(copy.lengths(), [2.0, 3.0, 4.0]);
+
+ cell.set_lengths([10.0, 12.0, 11.0]).unwrap();
+ assert_eq!(cell.lengths(), [10.0, 12.0, 11.0]);
+ assert_eq!(copy.lengths(), [2.0, 3.0, 4.0]);
+ }
+
+ #[test]
+ fn lengths() {
+ let mut cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.lengths(), [2.0, 3.0, 4.0]);
+ cell.set_lengths([10.0, 12.0, 11.0]).unwrap();
+ assert_eq!(cell.lengths(), [10.0, 12.0, 11.0]);
+ }
+
+ #[test]
+ fn angles() {
+ let mut cell = UnitCell::new([2.0, 3.0, 4.0]);
+ crate::assert_vector3d_eq(&cell.angles(), &[90.0, 90.0, 90.0], 1e-6);
+
+ cell.set_shape(CellShape::Triclinic).unwrap();
+ cell.set_angles([80.0, 89.0, 100.0]).unwrap();
+
+ crate::assert_vector3d_eq(&cell.angles(), &[80.0, 89.0, 100.0], 1e-6);
+
+ let cell = UnitCell::triclinic([1., 2., 3.], [80., 90., 100.]);
+ crate::assert_vector3d_eq(&cell.angles(), &[80.0, 90.0, 100.0], 1e-6);
+ }
+
+ #[test]
+ fn volume() {
+ let cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.volume(), 2.0 * 3.0 * 4.0);
+ }
+
+ #[test]
+ fn wrap() {
+ let cell = UnitCell::new([10.0, 20.0, 30.0]);
+ let mut vector = [12.0, 5.2, -45.3];
+ cell.wrap(&mut vector);
+ crate::assert_vector3d_eq(&vector, &[2.0, 5.2, 14.7], 1e-6);
+ }
+
+ #[test]
+ fn matrix() {
+ let cell = UnitCell::new([2.0, 3.0, 4.0]);
+
+ let matrix = cell.matrix();
+ let result = [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]];
+
+ for i in 0..3 {
+ for j in 0..3 {
+ approx::assert_ulps_eq!(matrix[i][j], result[i][j], epsilon = 1e-12);
+ }
+ }
+ }
+
+ #[test]
+ fn from_matrix() {
+ let cell = UnitCell::from_matrix([[10.0, 0.0, 0.0], [0.0, 21.0, 0.0], [0.0, 0.0, 32.0]]);
+ assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ assert_eq!(cell.lengths(), [10.0, 21.0, 32.0]);
+
+ let result_matrix = [[123.0, 4.08386, 71.7295], [0.0, 233.964, 133.571], [0.0, 0.0, 309.901]];
+ let cell = UnitCell::from_matrix(result_matrix);
+
+ assert_eq!(cell.shape(), CellShape::Triclinic);
+ for i in 0..3 {
+ approx::assert_ulps_eq!(cell.lengths()[i], [123.0, 234.0, 345.0][i], epsilon = 1e-3);
+ approx::assert_ulps_eq!(cell.angles()[i], [67.0, 78.0, 89.0][i], epsilon = 1e-3);
+ }
+
+ let matrix = cell.matrix();
+ for i in 0..3 {
+ for j in 0..3 {
+ approx::assert_ulps_eq!(matrix[i][j], result_matrix[i][j], epsilon = 1e-12);
+ }
+ }
+ }
+
+ #[test]
+ fn shape() {
+ let cell = UnitCell::new([2.0, 3.0, 4.0]);
+ assert_eq!(cell.shape(), CellShape::Orthorhombic);
+
+ let cell = UnitCell::infinite();
+ assert_eq!(cell.shape(), CellShape::Infinite);
+
+ let cell = UnitCell::triclinic([1.0, 2.0, 3.0], [80.0, 90.0, 100.0]);
+ assert_eq!(cell.shape(), CellShape::Triclinic);
+
+ let mut cell = UnitCell::new([10.0, 10.0, 10.0]);
+ assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ cell.set_shape(CellShape::Triclinic).unwrap();
+ assert_eq!(cell.shape(), CellShape::Triclinic);
+ }
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::os::raw::c_char;
+use std::panic::{self, RefUnwindSafe};
+use std::path::Path;
+
+use chemfiles_sys as ffi;
+
+use crate::strings;
+
+#[derive(Clone, Debug, PartialEq, Eq)]
+/// Error type for Chemfiles.
+pub struct Error {
+ /// The error status code
+ pub status: Status,
+ /// A message describing the error cause
+ pub message: String,
+}
+
+#[repr(C)]
+#[non_exhaustive]
+#[derive(Clone, Debug, PartialEq, Eq)]
+/// Possible causes of error in chemfiles
+pub enum Status {
+ /// No error
+ Success = ffi::chfl_status::CHFL_SUCCESS as isize,
+ /// Error in memory allocations
+ MemoryError = ffi::chfl_status::CHFL_MEMORY_ERROR as isize,
+ /// Error while reading or writing a file
+ FileError = ffi::chfl_status::CHFL_FILE_ERROR as isize,
+ /// Error in file formatting, *i.e.* the file is invalid
+ FormatError = ffi::chfl_status::CHFL_FORMAT_ERROR as isize,
+ /// Error in selection string syntax
+ SelectionError = ffi::chfl_status::CHFL_SELECTION_ERROR as isize,
+ /// Error in configuration files syntax
+ ConfigurationError = ffi::chfl_status::CHFL_CONFIGURATION_ERROR as isize,
+ /// Error for out of bounds indexing
+ OutOfBounds = ffi::chfl_status::CHFL_OUT_OF_BOUNDS as isize,
+ /// Error related to properties
+ PropertyError = ffi::chfl_status::CHFL_PROPERTY_ERROR as isize,
+ /// Exception in the C++ chemfiles library
+ ChemfilesError = ffi::chfl_status::CHFL_GENERIC_ERROR as isize,
+ /// Exception in the C++ standard library
+ StdCppError = ffi::chfl_status::CHFL_CXX_ERROR as isize,
+ /// The given path is not valid UTF8
+ // TODO: rename this to UTF8Error in the next breaking release
+ UTF8PathError,
+}
+
+impl From<ffi::chfl_status> for Error {
+ fn from(status: ffi::chfl_status) -> Error {
+ let status = match status {
+ ffi::chfl_status::CHFL_SUCCESS => Status::Success,
+ ffi::chfl_status::CHFL_CXX_ERROR => Status::StdCppError,
+ ffi::chfl_status::CHFL_GENERIC_ERROR => Status::ChemfilesError,
+ ffi::chfl_status::CHFL_MEMORY_ERROR => Status::MemoryError,
+ ffi::chfl_status::CHFL_FILE_ERROR => Status::FileError,
+ ffi::chfl_status::CHFL_FORMAT_ERROR => Status::FormatError,
+ ffi::chfl_status::CHFL_SELECTION_ERROR => Status::SelectionError,
+ ffi::chfl_status::CHFL_CONFIGURATION_ERROR => Status::ConfigurationError,
+ ffi::chfl_status::CHFL_OUT_OF_BOUNDS => Status::OutOfBounds,
+ ffi::chfl_status::CHFL_PROPERTY_ERROR => Status::PropertyError,
+ };
+
+ let message = Error::last_error();
+ Error { status, message }
+ }
+}
+
+impl From<std::str::Utf8Error> for Error {
+ fn from(_: std::str::Utf8Error) -> Self {
+ Error {
+ status: Status::UTF8PathError,
+ message: "failed to convert data to UTF8 string".into(),
+ }
+ }
+}
+
+impl Error {
+ /// Create a new error because the given `path` is invalid UTF-8 data
+ pub(crate) fn utf8_path_error(path: &Path) -> Error {
+ Error {
+ status: Status::UTF8PathError,
+ message: format!("Could not convert '{}' to UTF8", path.display()),
+ }
+ }
+
+ /// Get the last error message from the C++ library.
+ pub fn last_error() -> String {
+ unsafe { strings::from_c(ffi::chfl_last_error()) }
+ }
+
+ /// Clear any error from the C++ library
+ pub fn cleanup() {
+ unsafe {
+ check(ffi::chfl_clear_errors()).expect("error in ffi::chfl_clear_errors. Things went very bad");
+ }
+ }
+}
+
+/// Check return value of a C function, and get the error if needed.
+pub(crate) fn check(status: ffi::chfl_status) -> Result<(), Error> {
+ if status == ffi::chfl_status::CHFL_SUCCESS {
+ Ok(())
+ } else {
+ Err(Error::from(status))
+ }
+}
+
+/// Check return value of a C function, panic if it failed.
+pub(crate) fn check_success(status: ffi::chfl_status) {
+ assert!(
+ status == ffi::chfl_status::CHFL_SUCCESS,
+ "unexpected failure: {}",
+ Error::last_error()
+ );
+}
+
+/// Check a pointer for null.
+pub(crate) fn check_not_null<T>(ptr: *const T) {
+ assert!(!ptr.is_null(), "unexpected null pointer: {}", Error::last_error());
+}
+
+pub trait WarningCallback: RefUnwindSafe + Fn(&str) {}
+impl<T> WarningCallback for T where T: RefUnwindSafe + Fn(&str) {}
+
+static mut LOGGING_CALLBACK: Option<*mut dyn WarningCallback<Output = ()>> = None;
+
+extern "C" fn warning_callback(message: *const c_char) {
+ unsafe {
+ let callback = &*LOGGING_CALLBACK.expect("No callback provided, this is an internal bug");
+ // ignore result. If a panic happened, everything is going badly anyway
+ let _result = panic::catch_unwind(|| {
+ callback(&strings::from_c(message));
+ });
+ }
+}
+
+/// Use `callback` for every chemfiles warning. The callback will be passed
+/// the warning message. This will drop any previous warning callback.
+pub fn set_warning_callback<F>(callback: F)
+where
+ F: WarningCallback + 'static,
+{
+ // box callback to ensure it stays accessible
+ let callback = Box::into_raw(Box::new(callback));
+ unsafe {
+ if let Some(previous) = LOGGING_CALLBACK {
+ // drop the previous callback
+ let previous = Box::from_raw(previous);
+ std::mem::drop(previous);
+ // set the LOGGING_CALLBACK to the new one
+ LOGGING_CALLBACK = Some(callback);
+ } else {
+ // set the LOGGING_CALLBACK
+ LOGGING_CALLBACK = Some(callback);
+ // Tell C code to use Rust-provided callback
+ check_success(ffi::chfl_set_warning_callback(warning_callback));
+ }
+ }
+}
+
+impl std::fmt::Display for Error {
+ fn fmt(&self, fmt: &mut std::fmt::Formatter) -> Result<(), std::fmt::Error> {
+ write!(fmt, "{}", self.message)
+ }
+}
+
+impl std::error::Error for Error {
+ fn description(&self) -> &str {
+ match self.status {
+ Status::Success => "Success",
+ Status::StdCppError => "Exception from the C++ standard library",
+ Status::ChemfilesError => "Exception from the chemfiles library",
+ Status::MemoryError => "Error in memory allocations",
+ Status::FileError => "Error while reading or writing a file",
+ Status::FormatError => "Error in file formatting, i.e. the file is invalid",
+ Status::SelectionError => "Error in selection string syntax",
+ Status::UTF8PathError => "A string is not valid UTF8",
+ Status::ConfigurationError => "Error in configuration files",
+ Status::OutOfBounds => "Out of bounds indexing",
+ Status::PropertyError => "Error in property",
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+ use crate::Trajectory;
+
+ #[test]
+ fn errors() {
+ Error::cleanup();
+ assert_eq!(Error::last_error(), "");
+ assert!(Trajectory::open("nope", 'r').is_err());
+ assert_eq!(
+ Error::last_error(),
+ "file at \'nope\' does not have an extension, provide a format name to read it"
+ );
+ Error::cleanup();
+ assert_eq!(Error::last_error(), "");
+ }
+
+ #[test]
+ fn codes() {
+ assert_eq!(Error::from(ffi::chfl_status::CHFL_SUCCESS).status, Status::Success);
+ assert_eq!(
+ Error::from(ffi::chfl_status::CHFL_CXX_ERROR).status,
+ Status::StdCppError
+ );
+ assert_eq!(
+ Error::from(ffi::chfl_status::CHFL_GENERIC_ERROR).status,
+ Status::ChemfilesError
+ );
+ assert_eq!(
+ Error::from(ffi::chfl_status::CHFL_MEMORY_ERROR).status,
+ Status::MemoryError
+ );
+ assert_eq!(Error::from(ffi::chfl_status::CHFL_FILE_ERROR).status, Status::FileError);
+ assert_eq!(
+ Error::from(ffi::chfl_status::CHFL_FORMAT_ERROR).status,
+ Status::FormatError
+ );
+ assert_eq!(
+ Error::from(ffi::chfl_status::CHFL_SELECTION_ERROR).status,
+ Status::SelectionError
+ );
+ assert_eq!(
+ Error::from(ffi::chfl_status::CHFL_OUT_OF_BOUNDS).status,
+ Status::OutOfBounds
+ );
+ assert_eq!(
+ Error::from(ffi::chfl_status::CHFL_PROPERTY_ERROR).status,
+ Status::PropertyError
+ );
+ }
+}
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+1184 +1185 +1186 +1187 +1188 +1189 +1190 +1191 +1192 +1193 +1194 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+#[allow(clippy::wildcard_imports)]
+use chemfiles_sys as ffi;
+
+use crate::{Atom, AtomMut, AtomRef};
+use crate::{BondOrder, Residue, Topology, TopologyRef};
+use crate::{UnitCell, UnitCellMut, UnitCellRef};
+
+use crate::errors::{check, check_not_null, check_success, Error};
+use crate::property::{PropertiesIter, Property, RawProperty};
+use crate::strings;
+
+/// A `Frame` contains data from one simulation step: the current unit
+/// cell, the topology, the positions, and the velocities of the particles in
+/// the system. If some information is missing (topology or velocity or unit
+/// cell), the corresponding data is filled with a default value.
+#[derive(Debug)]
+pub struct Frame {
+ handle: *mut ffi::CHFL_FRAME,
+}
+
+impl Clone for Frame {
+ fn clone(&self) -> Frame {
+ unsafe {
+ let new_handle = ffi::chfl_frame_copy(self.as_ptr());
+ Frame::from_ptr(new_handle)
+ }
+ }
+}
+
+#[derive(Debug)]
+pub struct AtomIter<'a> {
+ frame: &'a Frame,
+ index: usize,
+ size: usize,
+}
+
+impl Frame {
+ /// Create a `Frame` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer,
+ /// except for it being non-null.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut ffi::CHFL_FRAME) -> Frame {
+ check_not_null(ptr);
+ Frame { handle: ptr }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const ffi::CHFL_FRAME {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut ffi::CHFL_FRAME {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer FROM A SHARED REFERENCE.
+ ///
+ /// For uses with functions of the C API using mut pointers for both read
+ /// and write access. Users should check that this does not lead to multiple
+ /// mutable borrows
+ #[inline]
+ #[allow(non_snake_case)]
+ pub(crate) fn as_mut_ptr_MANUALLY_CHECKING_BORROW(&self) -> *mut ffi::CHFL_FRAME {
+ self.handle
+ }
+
+ /// Create an empty frame. It will be resized by the library as needed.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let frame = Frame::new();
+ ///
+ /// assert_eq!(frame.size(), 0);
+ /// ```
+ pub fn new() -> Frame {
+ unsafe { Frame::from_ptr(ffi::chfl_frame()) }
+ }
+
+ /// Get a reference to the atom at the given `index` in this frame.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+ ///
+ /// let atom = frame.atom(0);
+ /// assert_eq!(atom.name(), "Zn");
+ /// ```
+ pub fn atom(&self, index: usize) -> AtomRef {
+ unsafe {
+ let handle = ffi::chfl_atom_from_frame(self.as_mut_ptr_MANUALLY_CHECKING_BORROW(), index as u64);
+ Atom::ref_from_ptr(handle)
+ }
+ }
+
+ /// Get a mutable reference to the atom at the given `index` in this frame.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+ ///
+ /// assert_eq!(frame.atom(0).name(), "Zn");
+ ///
+ /// frame.atom_mut(0).set_name("Fe");
+ /// assert_eq!(frame.atom(0).name(), "Fe");
+ /// ```
+ pub fn atom_mut(&mut self, index: usize) -> AtomMut {
+ unsafe {
+ let handle = ffi::chfl_atom_from_frame(self.as_mut_ptr(), index as u64);
+ Atom::ref_mut_from_ptr(handle)
+ }
+ }
+
+ /// Get the current number of atoms in this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.size(), 0);
+ ///
+ /// frame.resize(67);
+ /// assert_eq!(frame.size(), 67);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(ffi::chfl_frame_atoms_count(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Resize the positions and the velocities in this frame, to make space for
+ /// `natoms` atoms. Previous data is conserved, as well as the presence of
+ /// absence of velocities.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// assert_eq!(frame.size(), 67);
+ /// ```
+ pub fn resize(&mut self, natoms: usize) {
+ unsafe {
+ check_success(ffi::chfl_frame_resize(self.as_mut_ptr(), natoms as u64));
+ }
+ }
+
+ /// Add an `Atom` and the corresponding position and optionally velocity
+ /// data to this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [1.0, 1.0, 2.0], None);
+ ///
+ /// frame.add_velocities();
+ /// frame.add_atom(&Atom::new("Zn"), [-1.0, 1.0, 2.0], [0.2, 0.1, 0.0]);
+ /// ```
+ pub fn add_atom(&mut self, atom: &Atom, position: [f64; 3], velocity: impl Into<Option<[f64; 3]>>) {
+ let velocity = velocity.into();
+ let velocity_ptr = match velocity {
+ Some(ref data) => data.as_ptr(),
+ None => std::ptr::null(),
+ };
+
+ unsafe {
+ check_success(ffi::chfl_frame_add_atom(
+ self.as_mut_ptr(),
+ atom.as_ptr(),
+ position.as_ptr(),
+ velocity_ptr,
+ ));
+ }
+ }
+
+ /// Remove the atom at index `i` in this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("Zn"), [0.0; 3], None);
+ /// frame.add_atom(&Atom::new("Fe"), [0.0; 3], None);
+ /// frame.add_atom(&Atom::new("Sn"), [0.0; 3], None);
+ /// assert_eq!(frame.size(), 3);
+ ///
+ /// frame.remove(1);
+ /// assert_eq!(frame.size(), 2);
+ /// assert_eq!(frame.atom(1).name(), "Sn");
+ /// ```
+ pub fn remove(&mut self, i: usize) {
+ unsafe {
+ check_success(ffi::chfl_frame_remove(self.as_mut_ptr(), i as u64));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the frame.
+ ///
+ /// The bond order is set to `BondOrder::Unknown`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, BondOrder};
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.topology().bonds_count(), 0);
+ /// frame.resize(5);
+ ///
+ /// frame.add_bond(0, 1);
+ /// frame.add_bond(3, 1);
+ /// frame.add_bond(2, 4);
+ /// assert_eq!(frame.topology().bonds_count(), 3);
+ ///
+ /// assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown);
+ /// assert_eq!(frame.topology().bonds(), vec![[0, 1], [1, 3], [2, 4]]);
+ /// ```
+ pub fn add_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(ffi::chfl_frame_add_bond(self.as_mut_ptr(), i as u64, j as u64));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the frame
+ /// with the given bond `order`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, BondOrder};
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.topology().bonds_count(), 0);
+ /// frame.resize(2);
+ ///
+ /// frame.add_bond_with_order(0, 1, BondOrder::Double);
+ /// assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Double);
+ /// ```
+ pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder) {
+ unsafe {
+ check_success(ffi::chfl_frame_bond_with_order(
+ self.as_mut_ptr(),
+ i as u64,
+ j as u64,
+ order.as_raw(),
+ ));
+ }
+ }
+
+ /// Remove any existing bond between the atoms at indexes `i` and `j` in
+ /// the frame.
+ ///
+ /// This function does nothing if there is no bond between `i` and `j`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(5);
+ ///
+ /// frame.add_bond(0, 1);
+ /// frame.add_bond(3, 1);
+ /// frame.add_bond(2, 4);
+ ///
+ /// let bonds = frame.topology().bonds();
+ /// assert_eq!(bonds, vec![[0, 1], [1, 3], [2, 4]]);
+ ///
+ /// frame.remove_bond(2, 4);
+ /// let bonds = frame.topology().bonds();
+ /// assert_eq!(bonds, vec![[0, 1], [1, 3]]);
+ /// ```
+ pub fn remove_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(ffi::chfl_frame_remove_bond(self.as_mut_ptr(), i as u64, j as u64));
+ }
+ }
+
+ /// Add a copy of `residue` to this frame.
+ ///
+ /// # Errors
+ ///
+ /// This function fails is the residue id is already in this frame's
+ /// topology, or if the residue contain atoms that are already in another
+ /// residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Residue};
+ /// let mut frame = Frame::new();
+ ///
+ /// let residue = Residue::new("foo");
+ /// frame.add_residue(&residue).unwrap();
+ ///
+ /// let topology = frame.topology();
+ /// assert_eq!(topology.residues_count(), 1);
+ /// assert_eq!(topology.residue(0).unwrap().name(), "foo");
+ /// ```
+ pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error> {
+ unsafe { check(ffi::chfl_frame_add_residue(self.as_mut_ptr(), residue.as_ptr())) }
+ }
+
+ /// Get the distance between the atoms at indexes `i` and `j` in this frame,
+ /// accounting for periodic boundary conditions. The result is expressed in
+ /// Angstroms.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [1.0, 2.0, 3.0], None);
+ ///
+ /// assert_eq!(frame.distance(0, 1), f64::sqrt(14.0));
+ /// ```
+ pub fn distance(&self, i: usize, j: usize) -> f64 {
+ let mut distance = 0.0;
+ unsafe {
+ check_success(ffi::chfl_frame_distance(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ &mut distance,
+ ));
+ }
+ return distance;
+ }
+
+ /// Get the angle formed by the atoms at indexes `i`, `j` and `k` in this
+ /// frame, accounting for periodic boundary conditions. The result is
+ /// expressed in radians.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// # use std::f64;
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+ ///
+ /// assert_eq!(frame.angle(0, 1, 2), f64::consts::PI / 2.0);
+ /// ```
+ pub fn angle(&self, i: usize, j: usize, k: usize) -> f64 {
+ let mut angle = 0.0;
+ unsafe {
+ check_success(ffi::chfl_frame_angle(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ k as u64,
+ &mut angle,
+ ));
+ }
+ return angle;
+ }
+
+ /// Get the dihedral angle formed by the atoms at indexes `i`, `j`, `k` and
+ /// `m` in this frame, accounting for periodic boundary conditions. The
+ /// result is expressed in radians.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// # use std::f64;
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("C"), [0.0, 1.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("D"), [0.0, 1.0, 1.0], None);
+ ///
+ /// assert_eq!(frame.dihedral(0, 1, 2, 3), f64::consts::PI / 2.0);
+ /// ```
+ pub fn dihedral(&self, i: usize, j: usize, k: usize, m: usize) -> f64 {
+ let mut dihedral = 0.0;
+ unsafe {
+ check_success(ffi::chfl_frame_dihedral(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ k as u64,
+ m as u64,
+ &mut dihedral,
+ ));
+ }
+ return dihedral;
+ }
+
+ /// Get the out of plane distance formed by the atoms at indexes `i`, `j`,
+ /// `k` and `m` in this frame, accounting for periodic boundary conditions.
+ /// The result is expressed in angstroms.
+ ///
+ /// This is the distance between the atom j and the ikm plane. The j atom
+ /// is the center of the improper dihedral angle formed by i, j, k and m.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("A"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("B"), [0.0, 0.0, 2.0], None);
+ /// frame.add_atom(&Atom::new("C"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("D"), [0.0, 1.0, 0.0], None);
+ ///
+ /// assert_eq!(frame.out_of_plane(0, 1, 2, 3), 2.0);
+ /// ```
+ pub fn out_of_plane(&self, i: usize, j: usize, k: usize, m: usize) -> f64 {
+ let mut distance = 0.0;
+ unsafe {
+ check_success(ffi::chfl_frame_out_of_plane(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ k as u64,
+ m as u64,
+ &mut distance,
+ ));
+ }
+ return distance;
+ }
+
+ /// Get a view into the positions of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ ///
+ /// let positions = frame.positions();
+ /// assert_eq!(positions.len(), 67);
+ /// assert_eq!(positions[0], [0.0, 0.0, 0.0]);
+ /// ```
+ pub fn positions(&self) -> &[[f64; 3]] {
+ let mut ptr = std::ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(ffi::chfl_frame_positions(
+ self.as_mut_ptr_MANUALLY_CHECKING_BORROW(),
+ &mut ptr,
+ &mut natoms,
+ ));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return std::slice::from_raw_parts(ptr, size);
+ }
+ }
+
+ /// Get a mutable view into the positions of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// {
+ /// let positions = frame.positions_mut();
+ /// assert_eq!(positions[0], [0.0, 0.0, 0.0]);
+ /// positions[0] = [1.0, 2.0, 3.0];
+ /// }
+ ///
+ /// let positions = frame.positions();
+ /// assert_eq!(positions[0], [1.0, 2.0, 3.0]);
+ /// ```
+ pub fn positions_mut(&mut self) -> &mut [[f64; 3]] {
+ let mut ptr = std::ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(ffi::chfl_frame_positions(self.as_mut_ptr(), &mut ptr, &mut natoms));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return std::slice::from_raw_parts_mut(ptr, size);
+ }
+ }
+
+ /// Get a view into the velocities of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// frame.add_velocities();
+ ///
+ /// let velocities = frame.velocities().expect("missing velocities");
+ /// assert_eq!(velocities.len(), 67);
+ /// assert_eq!(velocities[0], [0.0, 0.0, 0.0]);
+ /// ```
+ pub fn velocities(&self) -> Option<&[[f64; 3]]> {
+ if !self.has_velocities() {
+ return None;
+ }
+
+ let mut ptr = std::ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(ffi::chfl_frame_velocities(
+ self.as_mut_ptr_MANUALLY_CHECKING_BORROW(),
+ &mut ptr,
+ &mut natoms,
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return Some(std::slice::from_raw_parts(ptr, size));
+ }
+ }
+
+ /// Get a mutable view into the velocities of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(67);
+ /// frame.add_velocities();
+ /// {
+ /// let velocities = frame.velocities_mut().expect("missing velocities");
+ /// assert_eq!(velocities[0], [0.0, 0.0, 0.0]);
+ /// velocities[0] = [1.0, 2.0, 3.0];
+ /// }
+ ///
+ /// let velocities = frame.velocities().expect("missing velocities");
+ /// assert_eq!(velocities[0], [1.0, 2.0, 3.0]);
+ /// ```
+ pub fn velocities_mut(&mut self) -> Option<&mut [[f64; 3]]> {
+ if !self.has_velocities() {
+ return None;
+ }
+
+ let mut ptr = std::ptr::null_mut();
+ let mut natoms = 0;
+ unsafe {
+ check_success(ffi::chfl_frame_velocities(self.as_mut_ptr(), &mut ptr, &mut natoms));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ let size = natoms as usize;
+ unsafe {
+ return Some(std::slice::from_raw_parts_mut(ptr, size));
+ }
+ }
+
+ /// Check if this frame contains velocity data.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.has_velocities(), false);
+ ///
+ /// frame.add_velocities();
+ /// assert_eq!(frame.has_velocities(), true);
+ /// ```
+ pub fn has_velocities(&self) -> bool {
+ let mut res = 0;
+ unsafe {
+ check_success(ffi::chfl_frame_has_velocities(self.as_ptr(), &mut res));
+ }
+ return res != 0;
+ }
+
+ /// Add velocity data to this frame. If the frame already have velocities,
+ /// this does nothing.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.has_velocities(), false);
+ ///
+ /// frame.add_velocities();
+ /// assert_eq!(frame.has_velocities(), true);
+ /// ```
+ pub fn add_velocities(&mut self) {
+ unsafe {
+ check_success(ffi::chfl_frame_add_velocities(self.as_mut_ptr()));
+ }
+ }
+
+ /// Get a reference to the `UnitCell` from this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, CellShape};
+ /// let frame = Frame::new();
+ ///
+ /// let cell = frame.cell();
+ /// assert_eq!(cell.shape(), CellShape::Infinite);
+ /// ```
+ pub fn cell(&self) -> UnitCellRef {
+ unsafe {
+ let handle = ffi::chfl_cell_from_frame(self.as_mut_ptr_MANUALLY_CHECKING_BORROW());
+ UnitCell::ref_from_ptr(handle)
+ }
+ }
+
+ /// Get a mutable reference to the `UnitCell` from this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, CellShape};
+ /// let mut frame = Frame::new();
+ ///
+ /// assert_eq!(frame.cell().shape(), CellShape::Infinite);
+ ///
+ /// frame.cell_mut().set_shape(CellShape::Triclinic).unwrap();
+ /// assert_eq!(frame.cell().shape(), CellShape::Triclinic);
+ /// ```
+ pub fn cell_mut(&mut self) -> UnitCellMut {
+ unsafe {
+ let handle = ffi::chfl_cell_from_frame(self.as_mut_ptr());
+ UnitCell::ref_mut_from_ptr(handle)
+ }
+ }
+
+ /// Set the `UnitCell` of this frame to `cell`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, UnitCell, CellShape};
+ /// let mut frame = Frame::new();
+ ///
+ /// frame.set_cell(&UnitCell::new([10.0, 10.0, 10.0]));
+ ///
+ /// let cell = frame.cell();
+ /// assert_eq!(cell.shape(), CellShape::Orthorhombic);
+ /// assert_eq!(cell.lengths(), [10.0, 10.0, 10.0]);
+ /// ```
+ pub fn set_cell(&mut self, cell: &UnitCell) {
+ unsafe {
+ check_success(ffi::chfl_frame_set_cell(self.as_mut_ptr(), cell.as_ptr()));
+ }
+ }
+
+ /// Get a reference to the `Topology` of this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// frame.resize(42);
+ ///
+ /// let topology = frame.topology();
+ /// assert_eq!(topology.size(), 42);
+ /// ```
+ pub fn topology(&self) -> TopologyRef {
+ unsafe {
+ let handle = ffi::chfl_topology_from_frame(self.as_ptr());
+ Topology::ref_from_ptr(handle)
+ }
+ }
+
+ /// Set the `Topology` of this frame to `topology`.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the topology contains a different number of atoms
+ /// than this frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Topology, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.resize(2);
+ ///
+ /// let mut topology = Topology::new();
+ /// topology.add_atom(&Atom::new("Cl"));
+ /// topology.add_atom(&Atom::new("Cl"));
+ /// topology.add_bond(0, 1);
+ ///
+ /// frame.set_topology(&topology).unwrap();
+ /// assert_eq!(frame.atom(0).name(), "Cl");
+ /// ```
+ pub fn set_topology(&mut self, topology: &Topology) -> Result<(), Error> {
+ unsafe { check(ffi::chfl_frame_set_topology(self.as_mut_ptr(), topology.as_ptr())) }
+ }
+
+ /// Get this frame step, i.e. the frame number in the trajectory
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let frame = Frame::new();
+ /// assert_eq!(frame.step(), 0);
+ /// ```
+ pub fn step(&self) -> usize {
+ let mut step = 0;
+ unsafe {
+ check_success(ffi::chfl_frame_step(self.as_ptr(), &mut step));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return step as usize;
+ }
+
+ /// Set this frame step to `step`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Frame;
+ /// let mut frame = Frame::new();
+ /// assert_eq!(frame.step(), 0);
+ ///
+ /// frame.set_step(10);
+ /// assert_eq!(frame.step(), 10);
+ /// ```
+ pub fn set_step(&mut self, step: usize) {
+ unsafe {
+ check_success(ffi::chfl_frame_set_step(self.as_mut_ptr(), step as u64));
+ }
+ }
+
+ /// Guess the bonds, angles and dihedrals in this `frame`.
+ ///
+ /// The bonds are guessed using a distance-based algorithm, and then angles
+ /// and dihedrals are guessed from the bonds.
+ ///
+ /// # Errors
+ ////
+ /// This function can fail if the covalent radius is unknown for some atoms
+ /// in the frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Frame, Atom};
+ /// let mut frame = Frame::new();
+ ///
+ /// frame.add_atom(&Atom::new("Cl"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("Cl"), [1.5, 0.0, 0.0], None);
+ /// assert_eq!(frame.topology().bonds_count(), 0);
+ ///
+ /// frame.guess_bonds().unwrap();
+ /// assert_eq!(frame.topology().bonds_count(), 1);
+ /// ```
+ pub fn guess_bonds(&mut self) -> Result<(), Error> {
+ unsafe { check(ffi::chfl_frame_guess_bonds(self.as_mut_ptr())) }
+ }
+
+ /// Remove all existing bonds, angles, dihedral angles and improper
+ /// dihedral angles in the topology of the frame.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Atom, Frame};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [0.0, 1.0, 0.0], None);
+ ///
+ /// frame.add_bond(0, 1);
+ /// frame.add_bond(1, 2);
+ ///
+ /// assert_eq!(frame.topology().bonds().len(), 2);
+ /// assert_eq!(frame.topology().angles().len(), 1);
+ ///
+ /// frame.clear_bonds();
+ /// assert!(frame.topology().bonds().is_empty());
+ /// assert!(frame.topology().angles().is_empty());
+ /// ```
+ pub fn clear_bonds(&mut self) {
+ unsafe {
+ check_success(ffi::chfl_frame_clear_bonds(self.as_mut_ptr()));
+ }
+ }
+
+ /// Add a new `property` with the given `name` to this frame.
+ ///
+ /// If a property with the same name already exists, this function override
+ /// the existing property with the new one.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Frame, Property};
+ /// let mut frame = Frame::new();
+ /// frame.set("a string", "hello");
+ /// frame.set("a double", 4.3);
+ ///
+ /// assert_eq!(frame.get("a string"), Some(Property::String("hello".into())));
+ /// assert_eq!(frame.get("a double"), Some(Property::Double(4.3)));
+ /// ```
+ pub fn set(&mut self, name: &str, property: impl Into<Property>) {
+ let buffer = strings::to_c(name);
+ let property = property.into().as_raw();
+ unsafe {
+ check_success(ffi::chfl_frame_set_property(
+ self.as_mut_ptr(),
+ buffer.as_ptr(),
+ property.as_ptr(),
+ ));
+ }
+ }
+
+ /// Get a property with the given `name` in this frame, if it exist.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Frame, Property};
+ /// let mut frame = Frame::new();
+ /// frame.set("foo", Property::Double(22.2));
+ ///
+ /// assert_eq!(frame.get("foo"), Some(Property::Double(22.2)));
+ /// assert_eq!(frame.get("Bar"), None);
+ /// ```
+ pub fn get(&self, name: &str) -> Option<Property> {
+ let buffer = strings::to_c(name);
+ unsafe {
+ let handle = ffi::chfl_frame_get_property(self.as_ptr(), buffer.as_ptr());
+ if handle.is_null() {
+ None
+ } else {
+ let raw = RawProperty::from_ptr(handle);
+ Some(Property::from_raw(raw))
+ }
+ }
+ }
+
+ /// Get an iterator over all (name, property) pairs for this frame
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Frame, Property};
+ /// let mut frame = Frame::new();
+ /// frame.set("foo", Property::Double(22.2));
+ /// frame.set("bar", Property::Bool(false));
+ ///
+ /// for (name, property) in frame.properties() {
+ /// if name == "foo" {
+ /// assert_eq!(property, Property::Double(22.2));
+ /// } else if name == "bar" {
+ /// assert_eq!(property, Property::Bool(false));
+ /// }
+ /// }
+ /// ```
+ pub fn properties(&self) -> PropertiesIter {
+ let mut count = 0;
+ unsafe {
+ check_success(ffi::chfl_frame_properties_count(self.as_ptr(), &mut count));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = count as usize;
+ let mut c_names = vec![std::ptr::null_mut(); size];
+ unsafe {
+ check_success(ffi::chfl_frame_list_properties(
+ self.as_ptr(),
+ c_names.as_mut_ptr(),
+ count,
+ ));
+ }
+
+ let mut names = Vec::new();
+ for ptr in c_names {
+ names.push(strings::from_c(ptr));
+ }
+
+ PropertiesIter {
+ names: names.into_iter(),
+ getter: Box::new(move |name| self.get(name).expect("failed to get property")),
+ }
+ }
+
+ /// Gets an iterator over atoms
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Atom, AtomRef, Frame};
+ /// let mut frame = Frame::new();
+ ///
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ ///
+ /// let mut atoms: Vec<AtomRef> = Vec::new();
+ ///
+ /// for atom in frame.iter_atoms() {
+ /// atoms.push(atom);
+ /// }
+ ///
+ /// assert_eq!(atoms.len(), 2);
+ /// ```
+ pub fn iter_atoms(&self) -> AtomIter<'_> {
+ AtomIter {
+ frame: self,
+ index: 0,
+ size: self.size(),
+ }
+ }
+}
+
+impl Drop for Frame {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = ffi::chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+impl<'a> Iterator for AtomIter<'a> {
+ type Item = AtomRef<'a>;
+
+ fn next(&mut self) -> Option<Self::Item> {
+ if self.size <= self.index {
+ return None;
+ }
+ let atom = self.frame.atom(self.index);
+ self.index += 1;
+ Some(atom)
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.size(), 0);
+ let copy = frame.clone();
+ assert_eq!(copy.size(), 0);
+
+ frame.resize(42);
+ assert_eq!(frame.size(), 42);
+ assert_eq!(copy.size(), 0);
+ }
+
+ #[test]
+ fn size() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.size(), 0);
+
+ frame.resize(12);
+ assert_eq!(frame.size(), 12);
+ }
+
+ #[test]
+ fn add_atom() {
+ let mut frame = Frame::new();
+
+ frame.add_atom(&Atom::new("U"), [1.0, 1.0, 2.0], None);
+ assert_eq!(frame.size(), 1);
+ assert_eq!(frame.atom(0).name(), "U");
+
+ let positions = &[[1.0, 1.0, 2.0]];
+ assert_eq!(frame.positions(), positions);
+
+ frame.add_velocities();
+ frame.add_atom(&Atom::new("F"), [1.0, 1.0, 2.0], [4.0, 3.0, 2.0]);
+ assert_eq!(frame.size(), 2);
+ assert_eq!(frame.atom(0).name(), "U");
+ assert_eq!(frame.atom(1).name(), "F");
+
+ let positions = &[[1.0, 1.0, 2.0], [1.0, 1.0, 2.0]];
+ assert_eq!(frame.positions(), positions);
+
+ let velocities = &[[0.0, 0.0, 0.0], [4.0, 3.0, 2.0]];
+ assert_eq!(frame.velocities().unwrap(), velocities);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_atom() {
+ let mut frame = Frame::new();
+ frame.resize(22);
+ let _atom = frame.atom(23);
+ }
+
+ #[test]
+ fn remove_atom() {
+ let mut frame = Frame::new();
+ frame.add_atom(&Atom::new("U"), [1.0, 1.0, 2.0], None);
+ frame.add_atom(&Atom::new("F"), [1.0, 1.0, 2.0], None);
+
+ assert_eq!(frame.size(), 2);
+ assert_eq!(frame.atom(0).name(), "U");
+
+ frame.remove(0);
+ assert_eq!(frame.size(), 1);
+ assert_eq!(frame.atom(0).name(), "F");
+ }
+
+ #[test]
+ #[should_panic]
+ fn remove_out_of_bounds() {
+ let mut frame = Frame::new();
+ frame.resize(32);
+
+ frame.remove(100);
+ }
+
+ #[test]
+ fn positions() {
+ let mut frame = Frame::new();
+ frame.resize(4);
+ let expected = &[[1.0, 2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0], [10.0, 11.0, 12.0]];
+
+ frame.positions_mut().clone_from_slice(expected);
+ assert_eq!(frame.positions(), expected);
+ }
+
+ #[test]
+ fn velocities() {
+ let mut frame = Frame::new();
+ frame.resize(4);
+ assert!(!frame.has_velocities());
+ frame.add_velocities();
+ assert!(frame.has_velocities());
+
+ let expected = &[[1.0, 2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0], [10.0, 11.0, 12.0]];
+
+ frame.velocities_mut().unwrap().clone_from_slice(expected);
+ assert_eq!(frame.velocities().unwrap(), expected);
+ }
+
+ #[test]
+ fn cell() {
+ let mut frame = Frame::new();
+ frame.set_cell(&UnitCell::new([3.0, 4.0, 5.0]));
+ let cell = frame.cell();
+ assert_eq!(cell.lengths(), [3.0, 4.0, 5.0]);
+ }
+
+ #[test]
+ fn topology() {
+ let mut frame = Frame::new();
+ frame.resize(2);
+ let mut topology = Topology::new();
+
+ topology.add_atom(&Atom::new("Zn"));
+ topology.add_atom(&Atom::new("Ar"));
+
+ assert!(frame.set_topology(&topology).is_ok());
+
+ let topology = frame.topology();
+
+ assert_eq!(topology.atom(0).name(), "Zn");
+ assert_eq!(topology.atom(1).name(), "Ar");
+
+ assert_eq!(frame.atom(0).name(), "Zn");
+ assert_eq!(frame.atom(1).name(), "Ar");
+ }
+
+ #[test]
+ fn bonds() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ assert_eq!(frame.topology().bonds_count(), 0);
+
+ frame.add_bond(0, 1);
+ frame.add_bond(9, 2);
+ frame.add_bond_with_order(3, 7, BondOrder::Aromatic);
+ assert_eq!(frame.topology().bonds_count(), 3);
+
+ assert_eq!(frame.topology().bonds(), vec![[0, 1], [2, 9], [3, 7]]);
+ let expected = vec![BondOrder::Unknown, BondOrder::Unknown, BondOrder::Aromatic];
+ assert_eq!(frame.topology().bond_orders(), expected);
+
+ assert_eq!(frame.topology().bond_order(0, 1), BondOrder::Unknown);
+ assert_eq!(frame.topology().bond_order(3, 7), BondOrder::Aromatic);
+
+ frame.remove_bond(3, 7);
+ // Removing unexisting bond is OK if both indexes are in bounds
+ frame.remove_bond(8, 7);
+ assert_eq!(frame.topology().bonds_count(), 2);
+
+ frame.clear_bonds();
+ assert_eq!(frame.topology().bonds_count(), 0);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ frame.add_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_remove_bond() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ frame.remove_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds_with_order() {
+ let mut frame = Frame::new();
+ frame.resize(12);
+ frame.add_bond_with_order(300, 7, BondOrder::Unknown);
+ }
+
+ #[test]
+ fn residues() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.topology().residues_count(), 0);
+
+ let residue = &Residue::new("foobar");
+ frame.add_residue(residue).unwrap();
+ frame.add_residue(residue).unwrap();
+ frame.add_residue(residue).unwrap();
+
+ assert_eq!(frame.topology().residues_count(), 3);
+ assert_eq!(frame.topology().residue(0).unwrap().name(), "foobar");
+ }
+
+ #[test]
+ fn step() {
+ let mut frame = Frame::new();
+ assert_eq!(frame.step(), 0);
+ frame.set_step(42);
+ assert_eq!(frame.step(), 42);
+ }
+
+ #[test]
+ fn property() {
+ let mut frame = Frame::new();
+ frame.set("foo", -22.0);
+ assert_eq!(frame.get("foo"), Some(Property::Double(-22.0)));
+ assert_eq!(frame.get("bar"), None);
+
+ frame.set("bar", Property::String("here".into()));
+ for (name, property) in frame.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(-22.0));
+ } else if name == "bar" {
+ assert_eq!(property, Property::String("here".into()));
+ }
+ }
+ }
+
+ #[test]
+ fn pbc_geometry() {
+ use std::f64::consts::PI;
+
+ let mut frame = Frame::new();
+ let atom = &Atom::new("");
+
+ frame.add_atom(atom, [1.0, 0.0, 0.0], None);
+ frame.add_atom(atom, [0.0, 0.0, 0.0], None);
+ frame.add_atom(atom, [0.0, 1.0, 0.0], None);
+ frame.add_atom(atom, [0.0, 1.0, 1.0], None);
+ frame.add_atom(atom, [0.0, 0.0, 2.0], None);
+
+ assert_eq!(frame.distance(0, 2), f64::sqrt(2.0));
+ assert_eq!(frame.angle(0, 1, 2), PI / 2.0);
+ assert_eq!(frame.dihedral(0, 1, 2, 3), PI / 2.0);
+ assert_eq!(frame.out_of_plane(1, 4, 0, 2), 2.0);
+ }
+
+ #[test]
+ fn atom_iterator() {
+ let mut frame = Frame::new();
+
+ frame.add_atom(&Atom::new("H1"), [1.0, 0.0, 0.0], None);
+ frame.add_atom(&Atom::new("H2"), [0.0, 1.0, 0.0], None);
+ frame.add_atom(&Atom::new("H3"), [0.0, 0.0, 1.0], None);
+ frame.add_atom(&Atom::new("H4"), [1.0, 1.0, 1.0], None);
+
+ let mut items: Vec<(AtomRef, &[f64; 3])> = Vec::new();
+
+ for item in frame.iter_atoms().zip(frame.positions()) {
+ items.push(item);
+ }
+
+ assert_eq!(items[0].0.name(), "H1");
+ assert_eq!(items[2].0.name(), "H3");
+
+ assert_eq!(items[1].1, &[0.0_f64, 1.0_f64, 0.0_f64]);
+ assert_eq!(items[3].1, &[1.0_f64, 1.0_f64, 1.0_f64]);
+ }
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+
+//! Chemfiles is a multi-language library written in modern C++ for reading and
+//! writing from and to molecular trajectory files. These files are created by
+//! your favorite theoretical chemistry program, and contains information about
+//! atomic or residues names and positions. Some format also have additional
+//! information, such as velocities, forces, energy, …
+//!
+//! This crate expose the C API of chemfiles to Rust, and make all the
+//! functionalities accessible. For more information on the C++ library,
+//! please see its [documentation][cxx_doc]. Specifically, the following pages
+//! are worth reading:
+//!
+//! - The [overview][overview] of the classes organization;
+//! - The list of [supported formats][formats];
+//! - The documentation for the [selection language][selections];
+//!
+//! [cxx_doc]: https://chemfiles.org/chemfiles
+//! [overview]: https://chemfiles.org/chemfiles/latest/overview.html
+//! [formats]: https://chemfiles.org/chemfiles/latest/formats.html
+//! [selections]: https://chemfiles.org/chemfiles/latest/selections.html
+
+#![deny(missing_docs)]
+#![warn(trivial_casts, unused_import_braces, variant_size_differences)]
+#![warn(unused_results)]
+// Configuration for clippy lints
+#![warn(clippy::all, clippy::pedantic)]
+#![allow(clippy::needless_return, clippy::module_name_repetitions)]
+#![allow(clippy::missing_panics_doc, clippy::must_use_candidate)]
+// Allow a few more clippy lints in test mode
+#![cfg_attr(test, allow(clippy::float_cmp, clippy::unreadable_literal, clippy::shadow_unrelated))]
+// deny(warnings) in doc tests
+#![doc(test(attr(deny(warnings))))]
+#![doc(test(attr(allow(unused_variables))))]
+
+use chemfiles_sys as ffi;
+
+mod strings;
+
+mod errors;
+pub use self::errors::set_warning_callback;
+pub use self::errors::{Error, Status};
+
+mod atom;
+pub use self::atom::Atom;
+pub use self::atom::AtomMut;
+pub use self::atom::AtomRef;
+
+mod cell;
+pub use self::cell::CellShape;
+pub use self::cell::UnitCell;
+pub use self::cell::UnitCellMut;
+pub use self::cell::UnitCellRef;
+
+mod residue;
+pub use self::residue::Residue;
+pub use self::residue::ResidueRef;
+
+mod topology;
+pub use self::topology::BondOrder;
+pub use self::topology::Topology;
+pub use self::topology::TopologyRef;
+
+mod frame;
+pub use self::frame::Frame;
+
+mod trajectory;
+pub use self::trajectory::MemoryTrajectoryReader;
+pub use self::trajectory::Trajectory;
+
+mod selection;
+pub use self::selection::{Match, Selection};
+
+mod property;
+pub use self::property::PropertiesIter;
+pub use self::property::Property;
+
+mod misc;
+pub use self::misc::{formats_list, guess_format, FormatMetadata};
+
+/// Get the version of the chemfiles library.
+///
+/// # Example
+/// ```
+/// let version = chemfiles::version();
+/// assert!(version.starts_with("0.10"));
+/// ```
+pub fn version() -> String {
+ unsafe { strings::from_c(ffi::chfl_version()) }
+}
+
+/// Read configuration data from the file at `path`.
+///
+/// By default, chemfiles reads configuration from any file named
+/// `.chemfiles.toml` in the current directory or any parent directory. This
+/// function can be used to add data from another configuration file. Data from
+/// the new configuration file will overwrite any existing data.
+///
+/// # Errors
+///
+/// This function will fail if there is no file at `path`, or if the file is
+/// incorrectly formatted.
+///
+/// # Example
+/// ```no_run
+/// chemfiles::add_configuration("local-config.toml").unwrap();
+/// // from now on, the data from "local-config.toml" will be used
+/// ```
+pub fn add_configuration<S>(path: S) -> Result<(), Error>
+where
+ S: AsRef<str>,
+{
+ let buffer = strings::to_c(path.as_ref());
+ unsafe { errors::check(ffi::chfl_add_configuration(buffer.as_ptr())) }
+}
+
+#[cfg(test)]
+fn assert_vector3d_eq(lhs: &[f64; 3], rhs: &[f64; 3], eps: f64) {
+ lhs.iter()
+ .zip(rhs)
+ .for_each(|(l, r)| approx::assert_ulps_eq!(l, r, epsilon = eps));
+}
+
+#[cfg(test)]
+mod tests {
+ #[test]
+ fn version() {
+ assert!(!crate::version().is_empty());
+ assert!(crate::version().starts_with("0.10"));
+ }
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2020 Guillaume Fraux -- BSD licensed
+use std::convert::TryInto;
+use std::ffi::CStr;
+use std::path::Path;
+
+use chemfiles_sys as ffi;
+
+use crate::errors::check_success;
+
+use crate::{errors::check, Error};
+
+/// `FormatMetadata` contains metadata associated with one format.
+#[allow(clippy::struct_excessive_bools)]
+#[derive(Debug, Clone, PartialEq, Eq)]
+pub struct FormatMetadata {
+ /// Name of the format.
+ pub name: &'static str,
+ /// Extension associated with the format.
+ pub extension: Option<&'static str>,
+ /// Extended, user-facing description of the format.
+ pub description: &'static str,
+ /// URL pointing to the format definition/reference.
+ pub reference: &'static str,
+ /// Is reading files in this format implemented?
+ pub read: bool,
+ /// Is writing files in this format implemented?
+ pub write: bool,
+ /// Does this format support in-memory IO?
+ pub memory: bool,
+ /// Does this format support storing atomic positions?
+ pub positions: bool,
+ /// Does this format support storing atomic velocities?
+ pub velocities: bool,
+ /// Does this format support storing unit cell information?
+ pub unit_cell: bool,
+ /// Does this format support storing atom names or types?
+ pub atoms: bool,
+ /// Does this format support storing bonds between atoms?
+ pub bonds: bool,
+ /// Does this format support storing residues?
+ pub residues: bool,
+}
+
+impl FormatMetadata {
+ pub(crate) fn from_raw(raw: &ffi::chfl_format_metadata) -> Self {
+ let str_from_ptr = |ptr| unsafe { CStr::from_ptr(ptr).to_str().expect("Invalid Rust str from C") };
+ let extension = if raw.extension.is_null() {
+ None
+ } else {
+ Some(str_from_ptr(raw.extension))
+ };
+ Self {
+ name: str_from_ptr(raw.name),
+ extension,
+ description: str_from_ptr(raw.description),
+ reference: str_from_ptr(raw.reference),
+ read: raw.read,
+ write: raw.write,
+ memory: raw.memory,
+ positions: raw.positions,
+ velocities: raw.velocities,
+ unit_cell: raw.unit_cell,
+ atoms: raw.atoms,
+ bonds: raw.bonds,
+ residues: raw.residues,
+ }
+ }
+}
+
+/// Get the list of formats known by chemfiles, as well as all associated metadata.
+///
+/// # Example
+/// ```
+/// let formats = chemfiles::formats_list();
+/// println!("chemfiles supports {} formats:", formats.len());
+/// for format in &formats {
+/// println!(
+/// " {:<15} {}",
+/// format.name,
+/// format.extension.as_deref().unwrap_or("")
+/// );
+/// }
+/// ```
+#[must_use]
+pub fn formats_list() -> Vec<FormatMetadata> {
+ let mut formats = std::ptr::null_mut();
+ let mut count: u64 = 0;
+ let formats_slice = unsafe {
+ check_success(ffi::chfl_formats_list(&mut formats, &mut count));
+ std::slice::from_raw_parts(formats, count.try_into().expect("failed to convert u64 to usize"))
+ };
+ let formats_vec = formats_slice.iter().map(FormatMetadata::from_raw).collect();
+ unsafe {
+ let _ = ffi::chfl_free(formats as *const _);
+ }
+ return formats_vec;
+}
+
+#[allow(clippy::doc_markdown)]
+/// Get the format that chemfiles would use to read a file at the given
+/// ``path``.
+///
+/// The format is mostly guessed from the path extension, chemfiles only tries
+/// to read the file to distinguish between CIF and mmCIF files. Opening the
+/// file using the returned format string might still fail. For example, it will
+/// fail if the file is not actually formatted according to the guessed format;
+/// or the format/compression combination is not supported (e.g. `XTC / GZ` will
+/// not work since the XTC reader does not support compressed files).
+///
+/// The returned format is represented in a way compatible with the various
+/// `Trajectory` constructors, i.e. `"<format name> [/ <compression>]"`, where
+/// compression is optional.
+///
+/// # Errors
+///
+/// This function returns an error if the file format couldn't be guessed.
+///
+/// # Panics
+///
+/// This function panics if the path can't be converted to a Unicode string.
+///
+/// # Examples
+/// ```
+/// let format = chemfiles::guess_format("trajectory.xyz.xz").unwrap();
+/// assert_eq!(format, "XYZ / XZ");
+///
+/// let format = chemfiles::guess_format("trajectory.nc").unwrap();
+/// assert_eq!(format, "Amber NetCDF");
+///
+/// let format = chemfiles::guess_format("trajectory.unknown.format");
+/// assert!(format.is_err());
+/// ```
+pub fn guess_format<P>(path: P) -> Result<String, Error>
+where
+ P: AsRef<Path>,
+{
+ let path = path.as_ref().to_str().expect("couldn't convert path to Unicode");
+ let path = crate::strings::to_c(path);
+ let mut buffer = vec![0; 128];
+ unsafe {
+ check(ffi::chfl_guess_format(
+ path.as_ptr(),
+ buffer.as_mut_ptr(),
+ buffer.len() as u64,
+ ))?;
+ }
+ Ok(crate::strings::from_c(buffer.as_ptr()))
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use chemfiles_sys as ffi;
+
+use crate::errors::{check, check_not_null, check_success, Error};
+use crate::strings;
+
+/// A thin wrapper around `ffi::CHFL_PROPERTY`
+#[derive(Debug)]
+pub(crate) struct RawProperty {
+ handle: *mut ffi::CHFL_PROPERTY,
+}
+
+impl RawProperty {
+ /// Create a `RawProperty` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ pub unsafe fn from_ptr(ptr: *mut ffi::CHFL_PROPERTY) -> RawProperty {
+ check_not_null(ptr);
+ RawProperty { handle: ptr }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ pub fn as_ptr(&self) -> *const ffi::CHFL_PROPERTY {
+ self.handle
+ }
+
+ fn double(value: f64) -> RawProperty {
+ unsafe {
+ let handle = ffi::chfl_property_double(value);
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn bool(value: bool) -> RawProperty {
+ unsafe {
+ let handle = ffi::chfl_property_bool(u8::from(value));
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn vector3d(value: [f64; 3]) -> RawProperty {
+ unsafe {
+ let handle = ffi::chfl_property_vector3d(value.as_ptr());
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn string(value: &str) -> RawProperty {
+ let buffer = strings::to_c(value);
+ unsafe {
+ let handle = ffi::chfl_property_string(buffer.as_ptr());
+ RawProperty::from_ptr(handle)
+ }
+ }
+
+ fn get_kind(&self) -> ffi::chfl_property_kind {
+ let mut kind = ffi::chfl_property_kind::CHFL_PROPERTY_BOOL;
+ unsafe {
+ check_success(ffi::chfl_property_get_kind(self.as_ptr(), &mut kind));
+ }
+ return kind;
+ }
+
+ fn get_bool(&self) -> Result<bool, Error> {
+ let mut value = 0;
+ unsafe {
+ check(ffi::chfl_property_get_bool(self.as_ptr(), &mut value))?;
+ }
+ return Ok(value != 0);
+ }
+
+ fn get_double(&self) -> Result<f64, Error> {
+ let mut value = 0.0;
+ unsafe {
+ check(ffi::chfl_property_get_double(self.as_ptr(), &mut value))?;
+ }
+ return Ok(value);
+ }
+
+ fn get_string(&self) -> Result<String, Error> {
+ let get_string = |ptr, len| unsafe { ffi::chfl_property_get_string(self.as_ptr(), ptr, len) };
+ let value = strings::call_autogrow_buffer(64, get_string)?;
+ return Ok(strings::from_c(value.as_ptr()));
+ }
+
+ fn get_vector3d(&self) -> Result<[f64; 3], Error> {
+ let mut value = [0.0; 3];
+ unsafe {
+ check(ffi::chfl_property_get_vector3d(self.as_ptr(), value.as_mut_ptr()))?;
+ }
+ return Ok(value);
+ }
+}
+
+impl Drop for RawProperty {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = ffi::chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+/// A `Property` is a piece of data that can be associated with an `Atom` or a
+/// `Frame`.
+#[derive(Debug, Clone, PartialEq, PartialOrd)]
+pub enum Property {
+ /// Boolean property
+ Bool(bool),
+ /// Floating point property
+ Double(f64),
+ /// String property
+ String(String),
+ /// 3-dimensional vector property
+ Vector3D([f64; 3]),
+}
+
+impl From<bool> for Property {
+ fn from(value: bool) -> Self {
+ Property::Bool(value)
+ }
+}
+
+impl From<f64> for Property {
+ fn from(value: f64) -> Self {
+ Property::Double(value)
+ }
+}
+
+impl From<String> for Property {
+ fn from(value: String) -> Self {
+ Property::String(value)
+ }
+}
+
+impl<'a> From<&'a str> for Property {
+ fn from(value: &'a str) -> Self {
+ Property::String(value.into())
+ }
+}
+
+impl From<[f64; 3]> for Property {
+ fn from(value: [f64; 3]) -> Self {
+ Property::Vector3D(value)
+ }
+}
+
+impl Property {
+ pub(crate) fn as_raw(&self) -> RawProperty {
+ match *self {
+ Property::Bool(value) => RawProperty::bool(value),
+ Property::Double(value) => RawProperty::double(value),
+ Property::String(ref value) => RawProperty::string(value),
+ Property::Vector3D(value) => RawProperty::vector3d(value),
+ }
+ }
+
+ #[allow(clippy::needless_pass_by_value)] // raw property
+ pub(crate) fn from_raw(raw: RawProperty) -> Property {
+ match raw.get_kind() {
+ ffi::chfl_property_kind::CHFL_PROPERTY_BOOL => Self::Bool(raw.get_bool().expect("should be a bool")),
+ ffi::chfl_property_kind::CHFL_PROPERTY_DOUBLE => {
+ Self::Double(raw.get_double().expect("should be a double"))
+ }
+ ffi::chfl_property_kind::CHFL_PROPERTY_STRING => {
+ Self::String(raw.get_string().expect("should be a string"))
+ }
+ ffi::chfl_property_kind::CHFL_PROPERTY_VECTOR3D => {
+ Property::Vector3D(raw.get_vector3d().expect("should be a vector3d"))
+ }
+ }
+ }
+}
+
+/// An iterator over the properties in an atom/frame/residue
+pub struct PropertiesIter<'a> {
+ pub(crate) names: std::vec::IntoIter<String>,
+ pub(crate) getter: Box<dyn Fn(&str) -> Property + 'a>,
+}
+
+impl<'a> Iterator for PropertiesIter<'a> {
+ type Item = (String, Property);
+ fn next(&mut self) -> Option<Self::Item> {
+ self.names.next().map(|name| {
+ let property = (self.getter)(&name);
+ (name, property)
+ })
+ }
+
+ fn size_hint(&self) -> (usize, Option<usize>) {
+ self.names.size_hint()
+ }
+
+ fn count(self) -> usize {
+ self.names.count()
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ mod raw {
+ use super::super::*;
+
+ #[test]
+ fn bool() {
+ let property = RawProperty::bool(false);
+ assert_eq!(property.get_kind(), ffi::chfl_property_kind::CHFL_PROPERTY_BOOL);
+ assert_eq!(property.get_bool(), Ok(false));
+ }
+
+ #[test]
+ fn double() {
+ let property = RawProperty::double(45.0);
+ assert_eq!(property.get_kind(), ffi::chfl_property_kind::CHFL_PROPERTY_DOUBLE);
+ assert_eq!(property.get_double(), Ok(45.0));
+ }
+
+ #[test]
+ fn string() {
+ let property = RawProperty::string("test");
+ assert_eq!(property.get_kind(), ffi::chfl_property_kind::CHFL_PROPERTY_STRING);
+ assert_eq!(property.get_string(), Ok("test".into()));
+ }
+
+ #[test]
+ fn vector3d() {
+ let property = RawProperty::vector3d([1.2, 3.4, 5.6]);
+ assert_eq!(property.get_kind(), ffi::chfl_property_kind::CHFL_PROPERTY_VECTOR3D);
+ assert_eq!(property.get_vector3d(), Ok([1.2, 3.4, 5.6]));
+ }
+ }
+
+ mod rust {
+ use super::super::*;
+
+ #[test]
+ fn bool() {
+ let property = Property::Bool(false);
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), ffi::chfl_property_kind::CHFL_PROPERTY_BOOL);
+ assert_eq!(raw.get_bool(), Ok(false));
+
+ assert_eq!(Property::from_raw(raw), property);
+ }
+
+ #[test]
+ fn double() {
+ let property = Property::Double(45.0);
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), ffi::chfl_property_kind::CHFL_PROPERTY_DOUBLE);
+ assert_eq!(raw.get_double(), Ok(45.0));
+
+ assert_eq!(Property::from_raw(raw), property);
+ }
+
+ #[test]
+ fn string() {
+ let property = Property::String("test".into());
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), ffi::chfl_property_kind::CHFL_PROPERTY_STRING);
+ assert_eq!(raw.get_string(), Ok("test".into()));
+
+ assert_eq!(Property::from_raw(raw), property);
+
+ let property = Property::String("long string ".repeat(128));
+ let raw = property.as_raw();
+ assert_eq!(raw.get_string(), Ok("long string ".repeat(128)));
+ }
+
+ #[test]
+ fn vector3d() {
+ let property = Property::Vector3D([1.2, 3.4, 5.6]);
+
+ let raw = property.as_raw();
+ assert_eq!(raw.get_kind(), ffi::chfl_property_kind::CHFL_PROPERTY_VECTOR3D);
+ assert_eq!(raw.get_vector3d(), Ok([1.2, 3.4, 5.6]));
+
+ assert_eq!(Property::from_raw(raw), property);
+ }
+ }
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371 +372 +373 +374 +375 +376 +377 +378 +379 +380 +381 +382 +383 +384 +385 +386 +387 +388 +389 +390 +391 +392 +393 +394 +395 +396 +397 +398 +399 +400 +401 +402 +403 +404 +405 +406 +407 +408 +409 +410 +411 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::marker::PhantomData;
+
+use chemfiles_sys as ffi;
+
+use crate::errors::{check_not_null, check_success};
+use crate::property::{PropertiesIter, Property, RawProperty};
+use crate::strings;
+
+/// A `Residue` is a group of atoms belonging to the same logical unit. They
+/// can be small molecules, amino-acids in a protein, monomers in polymers,
+/// *etc.*
+#[derive(Debug)]
+pub struct Residue {
+ handle: *mut ffi::CHFL_RESIDUE,
+}
+
+/// An analog to a reference to a residue (`&Residue`)
+#[derive(Debug)]
+pub struct ResidueRef<'a> {
+ inner: Residue,
+ marker: PhantomData<&'a Residue>,
+}
+
+impl<'a> std::ops::Deref for ResidueRef<'a> {
+ type Target = Residue;
+ fn deref(&self) -> &Residue {
+ &self.inner
+ }
+}
+
+impl Clone for Residue {
+ fn clone(&self) -> Residue {
+ unsafe {
+ let new_handle = ffi::chfl_residue_copy(self.as_ptr());
+ Residue::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Residue {
+ /// Create a `Residue` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut ffi::CHFL_RESIDUE) -> Residue {
+ check_not_null(ptr);
+ Residue { handle: ptr }
+ }
+
+ /// Create a borrowed `Residue` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, except for it being non-null, and the caller is responsible
+ /// for setting the right lifetime
+ #[inline]
+ #[allow(clippy::ptr_cast_constness)]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const ffi::CHFL_RESIDUE) -> ResidueRef<'a> {
+ ResidueRef {
+ inner: Residue::from_ptr(ptr as *mut ffi::CHFL_RESIDUE),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const ffi::CHFL_RESIDUE {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut ffi::CHFL_RESIDUE {
+ self.handle
+ }
+
+ /// Create a new residue with the given `name`
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::new("ALA");
+ /// assert_eq!(residue.name(), "ALA");
+ /// assert_eq!(residue.id(), None);
+ /// ```
+ pub fn new<'a>(name: impl Into<&'a str>) -> Residue {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ let handle = ffi::chfl_residue(buffer.as_ptr());
+ Residue::from_ptr(handle)
+ }
+ }
+
+ /// Create a new residue with the given `name` and `id` as identifier.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::with_id("ALA", 67);
+ /// assert_eq!(residue.name(), "ALA");
+ /// assert_eq!(residue.id(), Some(67));
+ /// ```
+ pub fn with_id<'a>(name: impl Into<&'a str>, id: i64) -> Residue {
+ let buffer = strings::to_c(name.into());
+ unsafe {
+ let handle = ffi::chfl_residue_with_id(buffer.as_ptr(), id);
+ Residue::from_ptr(handle)
+ }
+ }
+
+ /// Get the number of atoms in this residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.size(), 0);
+ ///
+ /// residue.add_atom(0);
+ /// residue.add_atom(1);
+ /// residue.add_atom(2);
+ /// assert_eq!(residue.size(), 3);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(ffi::chfl_residue_atoms_count(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Get the identifier of this residue in the initial topology file.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::with_id("", 42);
+ /// assert_eq!(residue.id(), Some(42));
+ /// ```
+ pub fn id(&self) -> Option<i64> {
+ let mut resid = 0;
+ let status = unsafe { ffi::chfl_residue_id(self.as_ptr(), &mut resid) };
+
+ if status == ffi::chfl_status::CHFL_SUCCESS {
+ return Some(resid);
+ } else if status == ffi::chfl_status::CHFL_GENERIC_ERROR {
+ return None;
+ }
+
+ // call check_success to panic in case of error
+ check_success(status);
+ unreachable!();
+ }
+
+ /// Get the name of this residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let residue = Residue::new("water");
+ /// assert_eq!(residue.name(), "water");
+ /// ```
+ pub fn name(&self) -> String {
+ let get_name = |ptr, len| unsafe { ffi::chfl_residue_name(self.as_ptr(), ptr, len) };
+ let name = strings::call_autogrow_buffer(64, get_name).expect("getting residue name failed");
+ return strings::from_c(name.as_ptr());
+ }
+
+ /// Add the atom at index `atom` in this residue.
+ ///
+ /// This will fail if the atom is already in the residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.size(), 0);
+ /// assert_eq!(residue.contains(56), false);
+ ///
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.size(), 1);
+ /// assert_eq!(residue.contains(56), true);
+ ///
+ /// // Adding the same atom twice is fine
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.size(), 1);
+ /// ```
+ pub fn add_atom(&mut self, atom: usize) {
+ unsafe {
+ check_success(ffi::chfl_residue_add_atom(self.as_mut_ptr(), atom as u64));
+ }
+ }
+
+ /// Check if the atom at index `i` is in this residue
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.contains(56), false);
+ ///
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.contains(56), true);
+ /// ```
+ pub fn contains(&self, atom: usize) -> bool {
+ let mut inside = 0;
+ unsafe {
+ check_success(ffi::chfl_residue_contains(self.as_ptr(), atom as u64, &mut inside));
+ }
+ return inside != 0;
+ }
+
+ /// Get the list of atoms of this residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Residue;
+ /// let mut residue = Residue::new("water");
+ /// assert_eq!(residue.atoms(), vec![]);
+ ///
+ /// residue.add_atom(56);
+ /// assert_eq!(residue.atoms(), vec![56]);
+ /// ```
+ pub fn atoms(&self) -> Vec<usize> {
+ let size = self.size();
+ let count = size as u64;
+ let mut indices = vec![u64::max_value(); size];
+ unsafe {
+ check_success(ffi::chfl_residue_atoms(self.as_ptr(), indices.as_mut_ptr(), count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return indices.into_iter().map(|idx| idx as usize).collect();
+ }
+
+ /// Add a new `property` with the given `name` to this residue.
+ ///
+ /// If a property with the same name already exists, this function override
+ /// the existing property with the new one.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Residue, Property};
+ /// let mut residue = Residue::new("ALA");
+ /// residue.set("a string", "hello");
+ /// residue.set("a double", 3.2);
+ ///
+ /// assert_eq!(residue.get("a string"), Some(Property::String("hello".into())));
+ /// assert_eq!(residue.get("a double"), Some(Property::Double(3.2)));
+ /// ```
+ pub fn set(&mut self, name: &str, property: impl Into<Property>) {
+ let buffer = strings::to_c(name);
+ let property = property.into().as_raw();
+ unsafe {
+ check_success(ffi::chfl_residue_set_property(
+ self.as_mut_ptr(),
+ buffer.as_ptr(),
+ property.as_ptr(),
+ ));
+ }
+ }
+
+ /// Get a property with the given `name` in this frame, if it exist.
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Residue, Property};
+ /// let mut residue = Residue::new("ALA");
+ /// residue.set("foo", Property::Double(22.2));
+ ///
+ /// assert_eq!(residue.get("foo"), Some(Property::Double(22.2)));
+ /// assert_eq!(residue.get("Bar"), None);
+ /// ```
+ pub fn get(&self, name: &str) -> Option<Property> {
+ let buffer = strings::to_c(name);
+ unsafe {
+ let handle = ffi::chfl_residue_get_property(self.as_ptr(), buffer.as_ptr());
+ if handle.is_null() {
+ None
+ } else {
+ let raw = RawProperty::from_ptr(handle);
+ Some(Property::from_raw(raw))
+ }
+ }
+ }
+
+ /// Get an iterator over all (name, property) pairs for this frame
+ ///
+ /// # Examples
+ /// ```
+ /// # use chemfiles::{Residue, Property};
+ /// let mut residue = Residue::new("ALA");
+ /// residue.set("foo", Property::Double(22.2));
+ /// residue.set("bar", Property::Bool(false));
+ ///
+ /// for (name, property) in residue.properties() {
+ /// if name == "foo" {
+ /// assert_eq!(property, Property::Double(22.2));
+ /// } else if name == "bar" {
+ /// assert_eq!(property, Property::Bool(false));
+ /// }
+ /// }
+ /// ```
+ pub fn properties(&self) -> PropertiesIter {
+ let mut count = 0;
+ unsafe {
+ check_success(ffi::chfl_residue_properties_count(self.as_ptr(), &mut count));
+ }
+
+ #[allow(clippy::cast_possible_truncation)]
+ let size = count as usize;
+ let mut c_names = vec![std::ptr::null_mut(); size];
+ unsafe {
+ check_success(ffi::chfl_residue_list_properties(
+ self.as_ptr(),
+ c_names.as_mut_ptr(),
+ count,
+ ));
+ }
+
+ let mut names = Vec::new();
+ for ptr in c_names {
+ names.push(strings::from_c(ptr));
+ }
+
+ PropertiesIter {
+ names: names.into_iter(),
+ getter: Box::new(move |name| self.get(name).expect("failed to get property")),
+ }
+ }
+}
+
+impl Drop for Residue {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = ffi::chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut residue = Residue::new("A");
+ assert_eq!(residue.size(), 0);
+
+ let copy = residue.clone();
+ assert_eq!(copy.size(), 0);
+
+ residue.add_atom(3);
+ residue.add_atom(7);
+ assert_eq!(residue.size(), 2);
+ assert_eq!(copy.size(), 0);
+ }
+
+ #[test]
+ fn name() {
+ let residue = Residue::new("A");
+ assert_eq!(residue.name(), "A");
+ }
+
+ #[test]
+ fn id() {
+ let residue = Residue::new("A");
+ assert_eq!(residue.id(), None);
+
+ let residue = Residue::with_id("A", 42);
+ assert_eq!(residue.id(), Some(42));
+
+ let residue = Residue::with_id("A", -3);
+ assert_eq!(residue.id(), Some(-3));
+ }
+
+ #[test]
+ fn atoms() {
+ let mut residue = Residue::new("A");
+ assert_eq!(residue.size(), 0);
+
+ residue.add_atom(0);
+ residue.add_atom(3);
+ residue.add_atom(45);
+ assert_eq!(residue.size(), 3);
+
+ assert!(residue.contains(3));
+ assert!(!residue.contains(5));
+
+ assert_eq!(residue.atoms(), vec![0, 3, 45]);
+ }
+
+ #[test]
+ fn property() {
+ let mut residue = Residue::new("ALA");
+
+ residue.set("foo", -22.0);
+ assert_eq!(residue.get("foo"), Some(Property::Double(-22.0)));
+ assert_eq!(residue.get("bar"), None);
+
+ residue.set("bar", Property::String("here".into()));
+ for (name, property) in residue.properties() {
+ if name == "foo" {
+ assert_eq!(property, Property::Double(-22.0));
+ } else if name == "bar" {
+ assert_eq!(property, Property::String("here".into()));
+ }
+ }
+ }
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371 +372 +373 +374 +375 +376 +377 +378 +379 +380 +381 +382 +383 +384 +385 +386 +387 +388 +389 +390 +391 +392 +393 +394 +395 +396 +397 +398 +399 +400 +401 +402 +403 +404 +405 +406 +407 +408 +409 +410 +411 +412 +413 +414 +415 +416 +417 +418 +419 +420 +421 +422 +423 +424 +425 +426 +427 +428 +429 +430 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use chemfiles_sys as ffi;
+
+use crate::errors::{check, check_not_null, check_success, Error, Status};
+use crate::frame::Frame;
+use crate::strings;
+
+#[derive(Debug, Clone, PartialEq, Eq)]
+/// A `Match` is a set of atomic indexes matching a given selection. It can
+/// mostly be used like a `&[usize]`.
+pub struct Match {
+ size: usize,
+ atoms: [usize; 4],
+}
+
+#[allow(clippy::len_without_is_empty)]
+impl Match {
+ /// Get the length of the Match.
+ ///
+ /// # Example
+ ///
+ /// ```
+ /// # use chemfiles::Match;
+ /// let atomic_match = Match::new(&[3, 4, 5]);
+ /// assert_eq!(atomic_match.len(), 3);
+ /// ```
+ pub fn len(&self) -> usize {
+ self.size
+ }
+
+ /// Create a new match containing the atoms in the `atoms` slice.
+ ///
+ /// # Panics
+ ///
+ /// If the slice contains more than 4 elements, which is the maximal size
+ /// of a match.
+ ///
+ /// # Example
+ ///
+ /// ```
+ /// # use chemfiles::Match;
+ /// let atomic_match = Match::new(&[3, 4, 5]);
+ /// assert_eq!(atomic_match.len(), 3);
+ /// assert_eq!(atomic_match[0], 3);
+ /// assert_eq!(atomic_match[1], 4);
+ /// assert_eq!(atomic_match[2], 5);
+ /// ```
+ pub fn new(atoms: &[usize]) -> Match {
+ assert!(atoms.len() <= 4);
+ let size = atoms.len();
+ let mut matches = [usize::max_value(); 4];
+ for (i, atom) in atoms.iter().enumerate() {
+ matches[i] = *atom;
+ }
+ Match { size, atoms: matches }
+ }
+
+ /// Iterate over the atomic indexes in the match.
+ ///
+ /// # Example
+ ///
+ /// ```
+ /// # use chemfiles::Match;
+ /// let atomic_match = Match::new(&[3, 4, 5]);
+ /// let mut iter = atomic_match.iter();
+ ///
+ /// assert_eq!(iter.next(), Some(&3));
+ /// assert_eq!(iter.next(), Some(&4));
+ /// assert_eq!(iter.next(), Some(&5));
+ /// assert_eq!(iter.next(), None);
+ /// ```
+ pub fn iter(&self) -> std::slice::Iter<usize> {
+ self.atoms[..self.len()].iter()
+ }
+}
+
+impl std::ops::Index<usize> for Match {
+ type Output = usize;
+ fn index(&self, i: usize) -> &Self::Output {
+ assert!(i < self.len());
+ &self.atoms[i]
+ }
+}
+
+impl<'a> IntoIterator for &'a Match {
+ type Item = &'a usize;
+ type IntoIter = std::slice::Iter<'a, usize>;
+
+ fn into_iter(self) -> Self::IntoIter {
+ self.atoms[..self.len()].iter()
+ }
+}
+
+/// A `Selection` allow to select atoms in a `Frame`, from a selection
+/// language. The selection language is built by combining basic operations.
+/// Each basic operation follows the `<selector>[(<variable>)] <operator>
+/// <value>` structure, where `<operator>` is a comparison operator in
+/// `== != < <= > >=`.
+#[derive(Debug)]
+pub struct Selection {
+ handle: *mut ffi::CHFL_SELECTION,
+}
+
+impl Clone for Selection {
+ fn clone(&self) -> Selection {
+ unsafe {
+ let new_handle = ffi::chfl_selection_copy(self.as_ptr());
+ Selection::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Drop for Selection {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = ffi::chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+impl Selection {
+ /// Create a `Selection` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut ffi::CHFL_SELECTION) -> Selection {
+ check_not_null(ptr);
+ Selection { handle: ptr }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const ffi::CHFL_SELECTION {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut ffi::CHFL_SELECTION {
+ self.handle
+ }
+
+ /// Create a new selection from the given selection string.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the selection string is invalid.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Selection;
+ /// let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+ /// ```
+ pub fn new<'a, S: Into<&'a str>>(selection: S) -> Result<Selection, Error> {
+ let buffer = strings::to_c(selection.into());
+ unsafe {
+ let handle = ffi::chfl_selection(buffer.as_ptr());
+ if handle.is_null() {
+ Err(Error {
+ status: Status::SelectionError,
+ message: Error::last_error(),
+ })
+ } else {
+ Ok(Selection::from_ptr(handle))
+ }
+ }
+ }
+
+ /// Get the size of the selection, i.e. the number of atoms we are selecting
+ /// together.
+ ///
+ /// This value is 1 for the 'atom' context, 2 for the 'pair' and 'bond'
+ /// context, 3 for the 'three' and 'angles' context and 4 for the 'four'
+ /// and 'dihedral' context.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Selection;
+ /// let selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+ /// assert_eq!(selection.size(), 2);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(ffi::chfl_selection_size(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Get the selection string used to create this selection.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Selection;
+ /// let selection = Selection::new("name H").unwrap();
+ /// assert_eq!(selection.string(), "name H");
+ /// ```
+ pub fn string(&self) -> String {
+ let get_string = |ptr, len| unsafe { ffi::chfl_selection_string(self.as_ptr(), ptr, len) };
+ let selection = strings::call_autogrow_buffer(1024, get_string).expect("failed to get selection string");
+ return strings::from_c(selection.as_ptr());
+ }
+
+ /// Evaluate a selection for a given frame, and return the corresponding
+ /// matches.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Selection, Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+ ///
+ /// let mut selection = Selection::new("pairs: name(#1) H and name(#2) O").unwrap();
+ /// let matches = selection.evaluate(&frame);
+ ///
+ /// assert_eq!(matches.len(), 2);
+ ///
+ /// assert_eq!(matches[0].len(), 2);
+ /// assert_eq!(matches[0][0], 0);
+ /// assert_eq!(matches[0][1], 1);
+ ///
+ /// assert_eq!(matches[1].len(), 2);
+ /// assert_eq!(matches[1][0], 2);
+ /// assert_eq!(matches[1][1], 1);
+ /// ```
+ pub fn evaluate(&mut self, frame: &Frame) -> Vec<Match> {
+ #![allow(clippy::cast_possible_truncation)]
+ let mut count = 0;
+ unsafe {
+ check(ffi::chfl_selection_evaluate(
+ self.as_mut_ptr(),
+ frame.as_ptr(),
+ &mut count,
+ ))
+ .expect("failed to evaluate selection");
+ }
+
+ let size = count as usize;
+ let mut chfl_matches = vec![ffi::chfl_match { size: 0, atoms: [0; 4] }; size];
+ unsafe {
+ check(ffi::chfl_selection_matches(
+ self.handle,
+ chfl_matches.as_mut_ptr(),
+ count,
+ ))
+ .expect("failed to extract matches");
+ }
+
+ return chfl_matches
+ .into_iter()
+ .map(|chfl_match| Match {
+ size: chfl_match.size as usize,
+ atoms: [
+ chfl_match.atoms[0] as usize,
+ chfl_match.atoms[1] as usize,
+ chfl_match.atoms[2] as usize,
+ chfl_match.atoms[3] as usize,
+ ],
+ })
+ .collect();
+ }
+
+ /// Evaluates a selection of size 1 on a given `frame`. This function
+ /// returns the list of atomic indexes in the frame matching this selection.
+ ///
+ /// # Panics
+ ///
+ /// If the selection size is not 1
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Selection, Frame, Atom};
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("H"), [1.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("O"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("H"), [-1.0, 0.0, 0.0], None);
+ ///
+ /// let mut selection = Selection::new("name H").unwrap();
+ /// let matches = selection.list(&frame);
+ ///
+ /// assert_eq!(matches.len(), 2);
+ /// assert_eq!(matches[0], 0);
+ /// assert_eq!(matches[1], 2);
+ /// ```
+ pub fn list(&mut self, frame: &Frame) -> Vec<usize> {
+ assert!(
+ self.size() == 1,
+ "can not call `Selection::list` on a multiple selection"
+ );
+ return self.evaluate(frame).into_iter().map(|m| m[0]).collect();
+ }
+}
+
+#[cfg(test)]
+mod tests {
+ use super::*;
+ use crate::{Atom, Topology};
+
+ #[test]
+ fn clone() {
+ let selection = Selection::new("name H").unwrap();
+
+ let copy = selection.clone();
+ assert_eq!(selection.size(), 1);
+ assert_eq!(copy.size(), 1);
+ }
+
+ fn testing_frame() -> Frame {
+ let mut topology = Topology::new();
+
+ topology.add_atom(&Atom::new("H"));
+ topology.add_atom(&Atom::new("O"));
+ topology.add_atom(&Atom::new("O"));
+ topology.add_atom(&Atom::new("H"));
+
+ topology.add_bond(0, 1);
+ topology.add_bond(1, 2);
+ topology.add_bond(2, 3);
+
+ let mut frame = Frame::new();
+ frame.resize(4);
+ frame.set_topology(&topology).unwrap();
+ return frame;
+ }
+
+ mod matches {
+ use super::*;
+
+ #[test]
+ fn index() {
+ let m = Match::new(&[1, 2, 3, 4]);
+ assert_eq!(m[0], 1);
+ assert_eq!(m[1], 2);
+ assert_eq!(m[2], 3);
+ assert_eq!(m[3], 4);
+
+ let m = Match::new(&[1, 2]);
+ assert_eq!(m[0], 1);
+ assert_eq!(m[1], 2);
+ }
+
+ #[test]
+ fn iter() {
+ let match_ = Match::new(&[1, 2, 3, 4]);
+ assert_eq!(match_.iter().copied().collect::<Vec<usize>>(), vec![1, 2, 3, 4]);
+
+ let v = [1, 2, 3, 4];
+ for (i, &m) in match_.iter().enumerate() {
+ assert_eq!(v[i], m);
+ }
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bound() {
+ let m = Match::new(&[1, 2]);
+ let _ = m[2];
+ }
+
+ #[test]
+ #[should_panic]
+ fn too_big() {
+ let _ = Match::new(&[1, 2, 3, 5, 4]);
+ }
+ }
+
+ #[test]
+ fn size() {
+ let selection = Selection::new("name H").unwrap();
+ assert_eq!(selection.size(), 1);
+
+ let selection = Selection::new("angles: name(#1) H").unwrap();
+ assert_eq!(selection.size(), 3);
+
+ let selection = Selection::new("four: name(#1) H").unwrap();
+ assert_eq!(selection.size(), 4);
+ }
+
+ #[test]
+ fn string() {
+ let selection = Selection::new("name H").unwrap();
+ assert_eq!(selection.string(), "name H");
+
+ let selection = Selection::new("angles: name(#1) H").unwrap();
+ assert_eq!(selection.string(), "angles: name(#1) H");
+ }
+
+ #[test]
+ fn invalid() {
+ let error = Selection::new("foo").unwrap_err();
+ assert_eq!(error.message, "unexpected identifier 'foo' in mathematical expression");
+ assert_eq!(error.status, Status::SelectionError);
+ }
+
+ #[test]
+ fn evaluate() {
+ let frame = testing_frame();
+
+ let mut selection = Selection::new("name H").unwrap();
+ let res = selection.evaluate(&frame);
+ assert_eq!(res, &[Match::new(&[0]), Match::new(&[3])]);
+
+ let mut selection = Selection::new("angles: all").unwrap();
+ let res = selection.evaluate(&frame);
+ for m in &[Match::new(&[0, 1, 2]), Match::new(&[1, 2, 3])] {
+ assert!(res.iter().any(|r| r == m));
+ }
+ }
+
+ #[test]
+ fn list() {
+ let frame = testing_frame();
+
+ let mut selection = Selection::new("name H").unwrap();
+ let res = selection.list(&frame);
+ assert_eq!(res, vec![0, 3]);
+ }
+
+ #[test]
+ #[should_panic = "can not call `Selection::list` on a multiple selection"]
+ fn list_on_size_1_selection() {
+ let frame = testing_frame();
+ let mut selection = Selection::new("pairs: name(#1) H").unwrap();
+ let _list = selection.list(&frame);
+ }
+}
+1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +
// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+
+//! String conversions between C and Rust
+use std::ffi::{CStr, CString};
+use std::os::raw::c_char;
+
+use crate::errors::{check, Error};
+
+/// Create a Rust string from a C string. Clones all characters in `buffer`.
+pub fn from_c(buffer: *const c_char) -> String {
+ unsafe {
+ let rust_str = CStr::from_ptr(buffer).to_str().expect("Invalid Rust string from C");
+ return String::from(rust_str);
+ }
+}
+
+/// Create a C string from a Rust string.
+pub fn to_c<S>(string: S) -> CString
+where
+ S: Into<Vec<u8>>,
+{
+ CString::new(string).expect("Invalid C string from Rust")
+}
+
+/// Check if a string buffer was big enough when passed to a C function
+fn buffer_was_big_enough(buffer: &[c_char]) -> bool {
+ let len = buffer.len();
+ if len < 2 {
+ false
+ } else {
+ // The C code should always set the last element to 0
+ debug_assert_eq!(buffer[len - 1], 0);
+ buffer[len - 2] == 0
+ }
+}
+
+/// Call `callback` C function with a string buffer and it length, using
+/// `initial` as the buffer initial size. If the buffer was filled and the
+/// result truncated by the C library, grow the buffer and try again until we
+/// get all the data. Then return the filled buffer to the caller.
+pub fn call_autogrow_buffer<F>(initial: usize, callback: F) -> Result<Vec<c_char>, Error>
+where
+ F: Fn(*mut c_char, u64) -> chemfiles_sys::chfl_status,
+{
+ let mut size = initial;
+ let mut buffer = vec![0; size];
+ check(callback(buffer.as_mut_ptr(), buffer.len() as u64))?;
+
+ while !buffer_was_big_enough(&buffer) {
+ // Grow the buffer and retry
+ size *= 2;
+ buffer.resize(size, 0);
+ check(callback(buffer.as_mut_ptr(), buffer.len() as u64))?;
+ }
+
+ Ok(buffer)
+}
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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::marker::PhantomData;
+use std::ops::{Deref, Drop};
+
+use chemfiles_sys as ffi;
+
+use crate::errors::{check, check_not_null, check_success, Error};
+use crate::{Atom, AtomMut, AtomRef};
+use crate::{Residue, ResidueRef};
+
+/// Possible bond order associated with bonds
+#[repr(C)]
+#[non_exhaustive]
+#[derive(Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord)]
+pub enum BondOrder {
+ /// Unknown or unspecified bond order
+ Unknown = ffi::chfl_bond_order::CHFL_BOND_UNKNOWN as isize,
+ /// Single bond
+ Single = ffi::chfl_bond_order::CHFL_BOND_SINGLE as isize,
+ /// Double bond
+ Double = ffi::chfl_bond_order::CHFL_BOND_DOUBLE as isize,
+ /// Triple bond
+ Triple = ffi::chfl_bond_order::CHFL_BOND_TRIPLE as isize,
+ /// Quadruple bond (present in some metals)
+ Quadruple = ffi::chfl_bond_order::CHFL_BOND_QUADRUPLE as isize,
+ /// Quintuplet bond (present in some metals)
+ Quintuplet = ffi::chfl_bond_order::CHFL_BOND_QUINTUPLET as isize,
+ /// Amide bond (required by some file formats)
+ Amide = ffi::chfl_bond_order::CHFL_BOND_AMIDE as isize,
+ /// Aromatic bond (required by some file formats)
+ Aromatic = ffi::chfl_bond_order::CHFL_BOND_AROMATIC as isize,
+}
+
+impl BondOrder {
+ pub(crate) fn as_raw(self) -> ffi::chfl_bond_order {
+ match self {
+ BondOrder::Unknown => ffi::chfl_bond_order::CHFL_BOND_UNKNOWN,
+ BondOrder::Single => ffi::chfl_bond_order::CHFL_BOND_SINGLE,
+ BondOrder::Double => ffi::chfl_bond_order::CHFL_BOND_DOUBLE,
+ BondOrder::Triple => ffi::chfl_bond_order::CHFL_BOND_TRIPLE,
+ BondOrder::Quadruple => ffi::chfl_bond_order::CHFL_BOND_QUADRUPLE,
+ BondOrder::Quintuplet => ffi::chfl_bond_order::CHFL_BOND_QUINTUPLET,
+ BondOrder::Amide => ffi::chfl_bond_order::CHFL_BOND_AMIDE,
+ BondOrder::Aromatic => ffi::chfl_bond_order::CHFL_BOND_AROMATIC,
+ }
+ }
+}
+
+impl From<ffi::chfl_bond_order> for BondOrder {
+ fn from(order: ffi::chfl_bond_order) -> BondOrder {
+ match order {
+ ffi::chfl_bond_order::CHFL_BOND_UNKNOWN => BondOrder::Unknown,
+ ffi::chfl_bond_order::CHFL_BOND_SINGLE => BondOrder::Single,
+ ffi::chfl_bond_order::CHFL_BOND_DOUBLE => BondOrder::Double,
+ ffi::chfl_bond_order::CHFL_BOND_TRIPLE => BondOrder::Triple,
+ ffi::chfl_bond_order::CHFL_BOND_QUADRUPLE => BondOrder::Quadruple,
+ ffi::chfl_bond_order::CHFL_BOND_QUINTUPLET => BondOrder::Quintuplet,
+ ffi::chfl_bond_order::CHFL_BOND_AMIDE => BondOrder::Amide,
+ ffi::chfl_bond_order::CHFL_BOND_AROMATIC => BondOrder::Aromatic,
+ }
+ }
+}
+
+/// A `Topology` contains the definition of all the atoms in the system, and
+/// the liaisons between the atoms (bonds, angles, dihedrals, ...). It will
+/// also contain all the residues information if it is available.
+#[derive(Debug)]
+pub struct Topology {
+ handle: *mut ffi::CHFL_TOPOLOGY,
+}
+
+/// An analog to a reference to a topology (`&Topology`)
+#[derive(Debug)]
+pub struct TopologyRef<'a> {
+ inner: Topology,
+ marker: PhantomData<&'a Topology>,
+}
+
+impl<'a> Deref for TopologyRef<'a> {
+ type Target = Topology;
+ fn deref(&self) -> &Topology {
+ &self.inner
+ }
+}
+
+impl Clone for Topology {
+ fn clone(&self) -> Topology {
+ unsafe {
+ let new_handle = ffi::chfl_topology_copy(self.as_ptr());
+ Topology::from_ptr(new_handle)
+ }
+ }
+}
+
+impl Topology {
+ /// Create a `Topology` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer,
+ /// except for it being non-null.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut ffi::CHFL_TOPOLOGY) -> Topology {
+ check_not_null(ptr);
+ Topology { handle: ptr }
+ }
+
+ /// Create a borrowed `Topology` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the
+ /// pointer, except for it being non-null, and the caller is responsible
+ /// for setting the right lifetime
+ #[inline]
+ #[allow(clippy::ptr_cast_constness)]
+ pub(crate) unsafe fn ref_from_ptr<'a>(ptr: *const ffi::CHFL_TOPOLOGY) -> TopologyRef<'a> {
+ TopologyRef {
+ inner: Topology::from_ptr(ptr as *mut ffi::CHFL_TOPOLOGY),
+ marker: PhantomData,
+ }
+ }
+
+ /// Get the underlying C pointer as a const pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const ffi::CHFL_TOPOLOGY {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut ffi::CHFL_TOPOLOGY {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer FROM A SHARED REFERENCE.
+ ///
+ /// For uses with functions of the C API using mut pointers for both read
+ /// and write access. Users should check that this does not lead to multiple
+ /// mutable borrows
+ #[inline]
+ #[allow(non_snake_case)]
+ pub(crate) fn as_mut_ptr_MANUALLY_CHECKING_BORROW(&self) -> *mut ffi::CHFL_TOPOLOGY {
+ self.handle
+ }
+
+ /// Create a new empty topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let topology = Topology::new();
+ /// assert_eq!(topology.size(), 0);
+ /// ```
+ pub fn new() -> Topology {
+ unsafe { Topology::from_ptr(ffi::chfl_topology()) }
+ }
+
+ /// Get a reference of the atom at the given `index` in this topology.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(6);
+ ///
+ /// let atom = topology.atom(4);
+ /// assert_eq!(atom.name(), "");
+ /// ```
+ pub fn atom(&self, index: usize) -> AtomRef {
+ unsafe {
+ let handle = ffi::chfl_atom_from_topology(self.as_mut_ptr_MANUALLY_CHECKING_BORROW(), index as u64);
+ Atom::ref_from_ptr(handle)
+ }
+ }
+
+ /// Get a mutable reference to the atom at the given `index` in this topology.
+ ///
+ /// # Panics
+ ///
+ /// If `index` is out of bounds.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(6);
+ ///
+ /// assert_eq!(topology.atom(4).name(), "");
+ ///
+ /// topology.atom_mut(4).set_name("Fe");
+ /// assert_eq!(topology.atom(4).name(), "Fe");
+ /// ```
+ pub fn atom_mut(&mut self, index: usize) -> AtomMut {
+ unsafe {
+ let handle = ffi::chfl_atom_from_topology(self.as_mut_ptr(), index as u64);
+ Atom::ref_mut_from_ptr(handle)
+ }
+ }
+
+ /// Get the current number of atoms in this topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.size(), 0);
+ ///
+ /// topology.resize(6);
+ /// assert_eq!(topology.size(), 6);
+ /// ```
+ pub fn size(&self) -> usize {
+ let mut size = 0;
+ unsafe {
+ check_success(ffi::chfl_topology_atoms_count(self.as_ptr(), &mut size));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return size as usize;
+ }
+
+ /// Resize this topology to hold `natoms` atoms, inserting dummy atoms if
+ /// the new size if bigger than the old one.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.size(), 0);
+ ///
+ /// topology.resize(6);
+ /// assert_eq!(topology.size(), 6);
+ /// ```
+ pub fn resize(&mut self, natoms: usize) {
+ unsafe {
+ check_success(ffi::chfl_topology_resize(self.as_mut_ptr(), natoms as u64));
+ }
+ }
+
+ /// Add an `Atom` at the end of this topology
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Atom};
+ /// let mut topology = Topology::new();
+ /// topology.add_atom(&Atom::new("Mg"));
+ ///
+ /// let atom = topology.atom(0);
+ /// assert_eq!(atom.name(), "Mg");
+ /// ```
+ pub fn add_atom(&mut self, atom: &Atom) {
+ unsafe {
+ check_success(ffi::chfl_topology_add_atom(self.as_mut_ptr(), atom.as_ptr()));
+ }
+ }
+
+ /// Remove an `Atom` from this topology by `index`. This modify all the
+ /// other atoms indexes.
+ ///
+ /// # Panics
+ ///
+ /// If the `index` is out of bounds
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(9);
+ /// assert_eq!(topology.size(), 9);
+ ///
+ /// topology.remove(7);
+ /// assert_eq!(topology.size(), 8);
+ /// ```
+ pub fn remove(&mut self, index: usize) {
+ unsafe {
+ check_success(ffi::chfl_topology_remove(self.as_mut_ptr(), index as u64));
+ }
+ }
+
+ /// Get the number of bonds in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.bonds_count(), 3);
+ /// ```
+ pub fn bonds_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(ffi::chfl_topology_bonds_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the number of angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.angles_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.angles_count(), 2);
+ /// ```
+ pub fn angles_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(ffi::chfl_topology_angles_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the number of dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.dihedrals_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.dihedrals_count(), 1);
+ /// ```
+ pub fn dihedrals_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(ffi::chfl_topology_dihedrals_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the number of improper dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.dihedrals_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// topology.add_bond(0, 3);
+ /// assert_eq!(topology.impropers_count(), 1);
+ /// ```
+ pub fn impropers_count(&self) -> usize {
+ let mut count = 0;
+ unsafe {
+ check_success(ffi::chfl_topology_impropers_count(self.as_ptr(), &mut count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return count as usize;
+ }
+
+ /// Get the list of bonds in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.bonds(), vec![[0, 1], [1, 2], [2, 3]]);
+ /// ```
+ pub fn bonds(&self) -> Vec<[usize; 2]> {
+ let size = self.bonds_count();
+ let count = size as u64;
+ let mut bonds = vec![[u64::max_value(); 2]; size];
+ unsafe {
+ check_success(ffi::chfl_topology_bonds(self.as_ptr(), bonds.as_mut_ptr(), count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return bonds
+ .into_iter()
+ .map(|bond| [bond[0] as usize, bond[1] as usize])
+ .collect();
+ }
+
+ /// Get the list of angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ /// assert_eq!(topology.angles(), vec![[0, 1, 2], [1, 2, 3]]);
+ /// ```
+ pub fn angles(&self) -> Vec<[usize; 3]> {
+ let size = self.angles_count();
+ let count = size as u64;
+ let mut angles = vec![[u64::max_value(); 3]; size];
+ unsafe {
+ check_success(ffi::chfl_topology_angles(self.as_ptr(), angles.as_mut_ptr(), count));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return angles
+ .into_iter()
+ .map(|angle| [angle[0] as usize, angle[1] as usize, angle[2] as usize])
+ .collect();
+ }
+
+ /// Get the list of dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(2, 1);
+ /// topology.add_bond(2, 3);
+ ///
+ /// assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3]]);
+ /// ```
+ pub fn dihedrals(&self) -> Vec<[usize; 4]> {
+ let size = self.dihedrals_count();
+ let count = size as u64;
+ let mut dihedrals = vec![[u64::max_value(); 4]; size];
+ unsafe {
+ check_success(ffi::chfl_topology_dihedrals(
+ self.as_ptr(),
+ dihedrals.as_mut_ptr(),
+ count,
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return dihedrals
+ .into_iter()
+ .map(|dihedral| {
+ [
+ dihedral[0] as usize,
+ dihedral[1] as usize,
+ dihedral[2] as usize,
+ dihedral[3] as usize,
+ ]
+ })
+ .collect();
+ }
+
+ /// Get the list of improper dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// topology.add_bond(0, 3);
+ ///
+ /// assert_eq!(topology.impropers(), vec![[1, 0, 2, 3]]);
+ /// ```
+ pub fn impropers(&self) -> Vec<[usize; 4]> {
+ let size = self.impropers_count();
+ let count = size as u64;
+ let mut impropers = vec![[u64::max_value(); 4]; size];
+ unsafe {
+ check_success(ffi::chfl_topology_impropers(
+ self.as_ptr(),
+ impropers.as_mut_ptr(),
+ count,
+ ));
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return impropers
+ .into_iter()
+ .map(|improper| {
+ [
+ improper[0] as usize,
+ improper[1] as usize,
+ improper[2] as usize,
+ improper[3] as usize,
+ ]
+ })
+ .collect();
+ }
+
+ /// Remove all existing bonds, angles, dihedral angles and improper
+ /// dihedral angles in the topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// assert_eq!(topology.bonds_count(), 2);
+ /// assert_eq!(topology.angles().len(), 1);
+ ///
+ /// topology.clear_bonds();
+ /// assert!(topology.bonds().is_empty());
+ /// assert!(topology.angles().is_empty());
+ /// ```
+ pub fn clear_bonds(&mut self) {
+ unsafe {
+ check_success(ffi::chfl_topology_clear_bonds(self.as_mut_ptr()));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the topology.
+ ///
+ /// The bond order is set to `BondOrder::Unknown`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(0, 2);
+ /// assert_eq!(topology.bonds_count(), 2);
+ ///
+ /// assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);
+ /// ```
+ pub fn add_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(ffi::chfl_topology_add_bond(self.as_mut_ptr(), i as u64, j as u64));
+ }
+ }
+
+ /// Add a bond between the atoms at indexes `i` and `j` in the topology
+ /// with the given bond `order`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(2);
+ ///
+ /// topology.add_bond_with_order(0, 1, BondOrder::Double);
+ /// assert_eq!(topology.bond_order(0, 1), BondOrder::Double);
+ /// ```
+ pub fn add_bond_with_order(&mut self, i: usize, j: usize, order: BondOrder) {
+ unsafe {
+ check_success(ffi::chfl_topology_bond_with_order(
+ self.as_mut_ptr(),
+ i as u64,
+ j as u64,
+ order.as_raw(),
+ ));
+ }
+ }
+
+ /// Get the bond order for the bond between the atoms at indexes `i` and
+ /// `j`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(2);
+ ///
+ /// topology.add_bond_with_order(0, 1, BondOrder::Double);
+ /// assert_eq!(topology.bond_order(0, 1), BondOrder::Double);
+ /// ```
+ pub fn bond_order(&self, i: usize, j: usize) -> BondOrder {
+ let mut order = ffi::chfl_bond_order::CHFL_BOND_UNKNOWN;
+ unsafe {
+ check_success(ffi::chfl_topology_bond_order(
+ self.as_ptr(),
+ i as u64,
+ j as u64,
+ &mut order,
+ ));
+ }
+ return order.into();
+ }
+
+ /// Get the bond order for all the bonds in the topology
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, BondOrder};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(3);
+ ///
+ /// topology.add_bond_with_order(0, 1, BondOrder::Double);
+ /// topology.add_bond_with_order(0, 2, BondOrder::Single);
+ ///
+ /// assert_eq!(topology.bond_orders(), &[BondOrder::Double, BondOrder::Single]);
+ /// ```
+ pub fn bond_orders(&self) -> Vec<BondOrder> {
+ let size = self.bonds_count();
+ let count = size as u64;
+ let mut bonds = vec![BondOrder::Unknown; size];
+ unsafe {
+ check_success(ffi::chfl_topology_bond_orders(
+ self.as_ptr(),
+ // Casting BondOrder to ffi::chfl_bond_order is safe, as they are
+ // both `repr(C)` enums with the same values.
+ bonds.as_mut_ptr().cast(),
+ count,
+ ));
+ }
+ return bonds;
+ }
+
+ /// Remove any existing bond between the atoms at indexes `i` and `j` in
+ /// this topology.
+ ///
+ /// This function does nothing if there is no bond between `i` and `j`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Topology;
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.bonds_count(), 0);
+ /// topology.resize(4);
+ ///
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(1, 2);
+ /// assert_eq!(topology.bonds_count(), 2);
+ ///
+ /// topology.remove_bond(0, 1);
+ /// assert_eq!(topology.bonds_count(), 1);
+ ///
+ /// // Removing a bond that does not exists is fine
+ /// topology.remove_bond(0, 2);
+ /// assert_eq!(topology.bonds_count(), 1);
+ /// ```
+ pub fn remove_bond(&mut self, i: usize, j: usize) {
+ unsafe {
+ check_success(ffi::chfl_topology_remove_bond(self.as_mut_ptr(), i as u64, j as u64));
+ }
+ }
+
+ /// Get a reference to the residue at index `index` from this topology.
+ ///
+ /// The residue index in the topology is not always the same as the residue
+ /// `id`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// topology.add_residue(&Residue::new("water")).unwrap();
+ ///
+ /// let residue = topology.residue(0).unwrap();
+ /// assert_eq!(residue.name(), "water");
+ /// ```
+ pub fn residue(&self, index: usize) -> Option<ResidueRef> {
+ unsafe {
+ let handle = ffi::chfl_residue_from_topology(self.as_ptr(), index as u64);
+ if handle.is_null() {
+ None
+ } else {
+ Some(Residue::ref_from_ptr(handle))
+ }
+ }
+ }
+
+ /// Get a copy of the residue containing the atom at index `index` in this
+ /// topology, if any.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// topology.resize(8);
+ ///
+ /// let mut residue = Residue::new("water");
+ /// residue.add_atom(0);
+ /// residue.add_atom(1);
+ /// residue.add_atom(2);
+ /// topology.add_residue(&residue).unwrap();
+ ///
+ /// let residue = topology.residue_for_atom(0).unwrap();
+ /// assert_eq!(residue.name(), "water");
+ ///
+ /// assert!(topology.residue_for_atom(6).is_none());
+ /// ```
+ pub fn residue_for_atom(&self, index: usize) -> Option<ResidueRef> {
+ let handle = unsafe { ffi::chfl_residue_for_atom(self.as_ptr(), index as u64) };
+ if handle.is_null() {
+ None
+ } else {
+ unsafe { Some(Residue::ref_from_ptr(handle)) }
+ }
+ }
+
+ /// Get the number of residues in this topology.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// assert_eq!(topology.residues_count(), 0);
+ ///
+ /// topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+ /// topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+ /// assert_eq!(topology.residues_count(), 2);
+ /// ```
+ pub fn residues_count(&self) -> u64 {
+ let mut count = 0;
+ unsafe {
+ check_success(ffi::chfl_topology_residues_count(self.as_ptr(), &mut count));
+ }
+ return count;
+ }
+
+ /// Add a residue to this topology.
+ ///
+ /// # Errors
+ ///
+ /// This function fails is the residue `id` is not already in the topology,
+ /// or if the residue contains atoms that are already in another residue.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ /// topology.add_residue(&Residue::new("water")).unwrap();
+ ///
+ /// let residue = topology.residue(0).unwrap();
+ /// assert_eq!(residue.name(), "water");
+ /// ```
+ pub fn add_residue(&mut self, residue: &Residue) -> Result<(), Error> {
+ unsafe { check(ffi::chfl_topology_add_residue(self.as_mut_ptr(), residue.as_ptr())) }
+ }
+
+ /// Check if the two residues `first` and `second` from the `topology` are
+ /// linked together, *i.e.* if there is a bond between one atom in the
+ /// first residue and one atom in the second one.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Topology, Residue};
+ /// let mut topology = Topology::new();
+ ///
+ /// topology.add_residue(&Residue::with_id("water", 0)).unwrap();
+ /// topology.add_residue(&Residue::with_id("protein", 1)).unwrap();
+ ///
+ /// let first = topology.residue(0).unwrap();
+ /// let second = topology.residue(1).unwrap();
+ /// assert_eq!(topology.are_linked(&first, &second), false);
+ /// ```
+ pub fn are_linked(&self, first: &Residue, second: &Residue) -> bool {
+ let mut linked = 0;
+ unsafe {
+ check_success(ffi::chfl_topology_residues_linked(
+ self.as_ptr(),
+ first.as_ptr(),
+ second.as_ptr(),
+ &mut linked,
+ ));
+ }
+ return linked != 0;
+ }
+}
+
+impl Drop for Topology {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = ffi::chfl_free(self.as_ptr().cast());
+ }
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ #[test]
+ fn clone() {
+ let mut topology = Topology::new();
+ assert_eq!(topology.size(), 0);
+
+ let copy = topology.clone();
+ assert_eq!(copy.size(), 0);
+
+ topology.resize(10);
+ assert_eq!(topology.size(), 10);
+ assert_eq!(copy.size(), 0);
+ }
+
+ #[test]
+ fn size() {
+ let mut topology = Topology::new();
+ assert_eq!(topology.size(), 0);
+
+ topology.resize(10);
+ assert_eq!(topology.size(), 10);
+
+ topology.remove(7);
+ assert_eq!(topology.size(), 9);
+
+ topology.add_atom(&Atom::new("Hg"));
+ assert_eq!(topology.size(), 10);
+ }
+
+ #[test]
+ fn atoms() {
+ let mut topology = Topology::new();
+
+ topology.add_atom(&Atom::new("Hg"));
+ topology.add_atom(&Atom::new("Mn"));
+ topology.add_atom(&Atom::new("W"));
+ topology.add_atom(&Atom::new("Fe"));
+
+ assert_eq!(topology.atom(0).name(), "Hg");
+ assert_eq!(topology.atom(3).name(), "Fe");
+ }
+
+ #[test]
+ fn remove() {
+ let mut topology = Topology::new();
+ topology.add_atom(&Atom::new("Hg"));
+ topology.add_atom(&Atom::new("Mn"));
+ topology.add_atom(&Atom::new("W"));
+ topology.add_atom(&Atom::new("Fe"));
+
+ assert_eq!(topology.atom(0).name(), "Hg");
+ assert_eq!(topology.atom(2).name(), "W");
+
+ topology.remove(1);
+ assert_eq!(topology.atom(0).name(), "Hg");
+ assert_eq!(topology.atom(2).name(), "Fe");
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_remove() {
+ let mut topology = Topology::new();
+ topology.resize(18);
+ topology.remove(33);
+ }
+
+ #[test]
+ fn bonds() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.bonds_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(9, 2);
+ topology.add_bond_with_order(3, 7, BondOrder::Aromatic);
+ assert_eq!(topology.bonds_count(), 3);
+
+ assert_eq!(topology.bonds(), vec![[0, 1], [2, 9], [3, 7]]);
+ let expected = vec![BondOrder::Unknown, BondOrder::Unknown, BondOrder::Aromatic];
+ assert_eq!(topology.bond_orders(), expected);
+
+ assert_eq!(topology.bond_order(0, 1), BondOrder::Unknown);
+ assert_eq!(topology.bond_order(3, 7), BondOrder::Aromatic);
+
+ topology.remove_bond(3, 7);
+ // Removing unexisting bond is OK if both indexes are in bounds
+ topology.remove_bond(8, 7);
+ assert_eq!(topology.bonds_count(), 2);
+
+ topology.clear_bonds();
+ assert_eq!(topology.bonds_count(), 0);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ topology.add_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_remove_bond() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ topology.remove_bond(300, 7);
+ }
+
+ #[test]
+ #[should_panic]
+ fn out_of_bounds_bonds_with_order() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ topology.add_bond_with_order(300, 7, BondOrder::Unknown);
+ }
+
+ #[test]
+ fn angles() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.angles_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(1, 2);
+ topology.add_bond(3, 7);
+ topology.add_bond(3, 5);
+ assert_eq!(topology.angles_count(), 2);
+
+ assert_eq!(topology.angles(), vec![[0, 1, 2], [5, 3, 7]]);
+
+ topology.clear_bonds();
+ assert_eq!(topology.angles_count(), 0);
+ }
+
+ #[test]
+ fn dihedrals() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.dihedrals_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(1, 2);
+ topology.add_bond(3, 2);
+ topology.add_bond(4, 7);
+ topology.add_bond(4, 5);
+ topology.add_bond(7, 10);
+ assert_eq!(topology.dihedrals_count(), 2);
+
+ assert_eq!(topology.dihedrals(), vec![[0, 1, 2, 3], [5, 4, 7, 10]]);
+
+ topology.clear_bonds();
+ assert_eq!(topology.dihedrals_count(), 0);
+ }
+
+ #[test]
+ fn impropers() {
+ let mut topology = Topology::new();
+ topology.resize(12);
+ assert_eq!(topology.impropers_count(), 0);
+
+ topology.add_bond(0, 1);
+ topology.add_bond(0, 2);
+ topology.add_bond(0, 3);
+ topology.add_bond(4, 7);
+ topology.add_bond(4, 5);
+ topology.add_bond(4, 8);
+ assert_eq!(topology.impropers_count(), 2);
+
+ assert_eq!(topology.impropers(), vec![[1, 0, 2, 3], [5, 4, 7, 8]]);
+
+ topology.clear_bonds();
+ assert_eq!(topology.impropers_count(), 0);
+ }
+
+ #[test]
+ fn residues() {
+ let mut topology = Topology::new();
+ topology.resize(4);
+ assert_eq!(topology.residues_count(), 0);
+
+ let mut residue = Residue::new("Foo");
+ residue.add_atom(0);
+ residue.add_atom(2);
+
+ topology.add_residue(&residue).unwrap();
+ assert_eq!(topology.residues_count(), 1);
+
+ assert_eq!(topology.residue(0).unwrap().name(), "Foo");
+ {
+ let residue = topology.residue_for_atom(2).unwrap();
+ assert_eq!(residue.name(), "Foo");
+ }
+
+ let mut residue = Residue::new("Bar");
+ residue.add_atom(3);
+ topology.add_residue(&residue).unwrap();
+ assert_eq!(topology.residues_count(), 2);
+
+ let first = topology.residue(0).unwrap();
+ let second = topology.residue(0).unwrap();
+ assert!(topology.are_linked(&first, &second));
+
+ // missing residue
+ assert!(topology.residue_for_atom(1).is_none());
+ // out of bounds
+ assert!(topology.residue_for_atom(67).is_none());
+ }
+}
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// Chemfiles, a modern library for chemistry file reading and writing
+// Copyright (C) 2015-2018 Guillaume Fraux -- BSD licensed
+use std::convert::TryInto;
+use std::os::raw::c_char;
+use std::path::Path;
+
+use chemfiles_sys as ffi;
+
+use crate::errors::{check, check_success, Error, Status};
+use crate::strings;
+use crate::{Frame, Topology, UnitCell};
+
+/// The `Trajectory` type is the main entry point when using chemfiles. A
+/// `Trajectory` behave a bit like a file, allowing to read and/or write
+/// `Frame`.
+#[derive(Debug)]
+pub struct Trajectory {
+ handle: *mut ffi::CHFL_TRAJECTORY,
+}
+
+impl Drop for Trajectory {
+ fn drop(&mut self) {
+ unsafe {
+ let _ = ffi::chfl_trajectory_close(self.as_ptr());
+ }
+ }
+}
+
+impl Trajectory {
+ /// Create a `Trajectory` from a C pointer.
+ ///
+ /// This function is unsafe because no validity check is made on the pointer.
+ #[inline]
+ pub(crate) unsafe fn from_ptr(ptr: *mut ffi::CHFL_TRAJECTORY) -> Result<Trajectory, Error> {
+ if ptr.is_null() {
+ Err(Error {
+ status: Status::FileError,
+ message: Error::last_error(),
+ })
+ } else {
+ Ok(Trajectory { handle: ptr })
+ }
+ }
+
+ /// Get the underlying C pointer as a pointer.
+ #[inline]
+ pub(crate) fn as_ptr(&self) -> *const ffi::CHFL_TRAJECTORY {
+ self.handle
+ }
+
+ /// Get the underlying C pointer as a mutable pointer.
+ #[inline]
+ pub(crate) fn as_mut_ptr(&mut self) -> *mut ffi::CHFL_TRAJECTORY {
+ self.handle
+ }
+
+ /// Open the file at the given `path` in the given `mode`.
+ ///
+ /// Valid modes are `'r'` for read, `'w'` for write and `'a'` for append.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the file is not accessible for the given mode, if
+ /// it is incorrectly formatted for the corresponding format, or in case of
+ /// I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// ```
+ pub fn open<P>(path: P, mode: char) -> Result<Trajectory, Error>
+ where
+ P: AsRef<Path>,
+ {
+ let path = path
+ .as_ref()
+ .to_str()
+ .ok_or_else(|| Error::utf8_path_error(path.as_ref()))?;
+
+ let path = strings::to_c(path);
+ unsafe {
+ #[allow(clippy::cast_possible_wrap)]
+ let handle = ffi::chfl_trajectory_open(path.as_ptr(), mode as c_char);
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Open the file at the given `path` using a specific file `format` and the
+ /// given `mode`.
+ ///
+ /// Valid modes are `'r'` for read, `'w'` for write and `'a'` for append.
+ ///
+ /// Specifying a format is needed when the file format does not match the
+ /// extension, or when there is not standard extension for this format. If
+ /// `format` is an empty string, the format will be guessed from the
+ /// extension.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the file is not accessible for the given mode, if
+ /// it is incorrectly formatted for the corresponding format, or in case of
+ /// I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let trajectory = Trajectory::open_with_format("water.zeo", 'r', "XYZ").unwrap();
+ /// ```
+ pub fn open_with_format<'a, P, S>(filename: P, mode: char, format: S) -> Result<Trajectory, Error>
+ where
+ P: AsRef<Path>,
+ S: Into<&'a str>,
+ {
+ let filename = filename
+ .as_ref()
+ .to_str()
+ .ok_or_else(|| Error::utf8_path_error(filename.as_ref()))?;
+
+ let filename = strings::to_c(filename);
+ let format = strings::to_c(format.into());
+ unsafe {
+ #[allow(clippy::cast_possible_wrap)]
+ let handle = ffi::chfl_trajectory_with_format(filename.as_ptr(), mode as c_char, format.as_ptr());
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Write to a memory buffer as though it was a formatted file.
+ ///
+ /// The `format` parameter should follow the same rules as in the main
+ /// `Trajectory` constructor, except that compression specification
+ /// is not supported.
+ ///
+ /// The `memory_buffer` function can be used to retrieve the data written
+ /// to memory of the `Trajectory`.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the format do not support in-memory writers.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::Trajectory;
+ /// let trajectory_memory = Trajectory::memory_writer("SMI");
+ ///
+ /// // Binary formats typically do not support this feature
+ /// assert!(Trajectory::memory_writer("XTC").is_err());
+ /// ```
+ pub fn memory_writer<'a, S>(format: S) -> Result<Trajectory, Error>
+ where
+ S: Into<&'a str>,
+ {
+ let format = strings::to_c(format.into());
+ unsafe {
+ let handle = ffi::chfl_trajectory_memory_writer(format.as_ptr());
+ Trajectory::from_ptr(handle)
+ }
+ }
+
+ /// Read the next step of this trajectory into a `frame`.
+ ///
+ /// If the number of atoms in frame does not correspond to the number of atom
+ /// in the next step, the frame is resized.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format, or in case of I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// let mut frame = Frame::new();
+ ///
+ /// trajectory.read(&mut frame).unwrap();
+ /// ```
+ pub fn read(&mut self, frame: &mut Frame) -> Result<(), Error> {
+ unsafe { check(ffi::chfl_trajectory_read(self.as_mut_ptr(), frame.as_mut_ptr())) }
+ }
+
+ /// Read a specific `step` of this trajectory into a `frame`.
+ ///
+ /// If the number of atoms in frame does not correspond to the number of
+ /// atom at this step, the frame is resized.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// let mut frame = Frame::new();
+ ///
+ /// trajectory.read_step(10, &mut frame).unwrap();
+ /// ```
+ pub fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error> {
+ unsafe {
+ check(ffi::chfl_trajectory_read_step(
+ self.as_mut_ptr(),
+ step as u64,
+ frame.as_mut_ptr(),
+ ))
+ }
+ }
+
+ /// Write a `frame` to this trajectory.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Frame};
+ /// let mut trajectory = Trajectory::open("water.pdb", 'w').unwrap();
+ /// let mut frame = Frame::new();
+ ///
+ /// trajectory.write(&mut frame).unwrap();
+ /// ```
+ pub fn write(&mut self, frame: &Frame) -> Result<(), Error> {
+ unsafe { check(ffi::chfl_trajectory_write(self.as_mut_ptr(), frame.as_ptr())) }
+ }
+
+ /// Set the `topology` associated with this trajectory. This topology will
+ /// be used when reading and writing the files, replacing any topology in
+ /// the frames or files.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, Atom, Topology};
+ /// let mut topology = Topology::new();
+ /// topology.add_atom(&Atom::new("H"));
+ /// topology.add_atom(&Atom::new("O"));
+ /// topology.add_atom(&Atom::new("H"));
+ /// topology.add_bond(0, 1);
+ /// topology.add_bond(1, 2);
+ ///
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// trajectory.set_topology(&topology);
+ /// ```
+ pub fn set_topology(&mut self, topology: &Topology) {
+ unsafe {
+ check_success(ffi::chfl_trajectory_set_topology(self.as_mut_ptr(), topology.as_ptr()));
+ }
+ }
+
+ /// Set the topology associated with this trajectory by reading the first
+ /// frame of the file at the given `path` using the file format in `format`;
+ /// and extracting the topology of this frame.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the topology file is incorrectly formatted for
+ /// the corresponding format, or in case of I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+ /// trajectory.set_topology_file("topology.pdb").unwrap();
+ /// ```
+ pub fn set_topology_file<P>(&mut self, path: P) -> Result<(), Error>
+ where
+ P: AsRef<Path>,
+ {
+ let path = path
+ .as_ref()
+ .to_str()
+ .ok_or_else(|| Error::utf8_path_error(path.as_ref()))?;
+
+ let path = strings::to_c(path);
+ unsafe {
+ check(ffi::chfl_trajectory_topology_file(
+ self.as_mut_ptr(),
+ path.as_ptr(),
+ std::ptr::null(),
+ ))
+ }
+ }
+
+ /// Set the topology associated with this trajectory by reading the first
+ /// frame of the file at the given `path` using the file format in
+ /// `format`; and extracting the topology of this frame.
+ ///
+ /// If `format` is an empty string, the format will be guessed from the
+ /// `path` extension.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the topology file is incorrectly formatted for
+ /// the corresponding format, or in case of I/O errors from the OS.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let mut trajectory = Trajectory::open("water.nc", 'r').unwrap();
+ /// trajectory.set_topology_with_format("topology.mol", "PDB").unwrap();
+ /// ```
+ pub fn set_topology_with_format<'a, P, S>(&mut self, path: P, format: S) -> Result<(), Error>
+ where
+ P: AsRef<Path>,
+ S: Into<&'a str>,
+ {
+ let path = path
+ .as_ref()
+ .to_str()
+ .ok_or_else(|| Error::utf8_path_error(path.as_ref()))?;
+
+ let format = strings::to_c(format.into());
+ let path = strings::to_c(path);
+ unsafe {
+ check(ffi::chfl_trajectory_topology_file(
+ self.as_mut_ptr(),
+ path.as_ptr(),
+ format.as_ptr(),
+ ))
+ }
+ }
+
+ /// Set the unit `cell` associated with a trajectory. This cell will be
+ /// used when reading and writing the files, replacing any unit cell in the
+ /// frames or files.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::{Trajectory, UnitCell};
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ /// trajectory.set_cell(&UnitCell::new([10.0, 11.0, 12.5]));
+ /// ```
+ pub fn set_cell(&mut self, cell: &UnitCell) {
+ unsafe {
+ check_success(ffi::chfl_trajectory_set_cell(self.as_mut_ptr(), cell.as_ptr()));
+ }
+ }
+
+ /// Get the number of steps (the number of frames) in a trajectory.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let mut trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ ///
+ /// println!("This trajectory contains {} steps", trajectory.nsteps());
+ /// ```
+ // FIXME should this take &self instead? The file can be modified by this
+ // function, but the format should reset the state.
+ pub fn nsteps(&mut self) -> usize {
+ let mut res = 0;
+ unsafe {
+ check(ffi::chfl_trajectory_nsteps(self.as_mut_ptr(), &mut res))
+ .expect("failed to get the number of steps in this trajectory");
+ }
+ #[allow(clippy::cast_possible_truncation)]
+ return res as usize;
+ }
+
+ /// Obtain the memory buffer written to by the trajectory.
+ ///
+ /// # Errors
+ ///
+ /// This fails if the trajectory was not opened with
+ /// `Trajectory::memory_writer`.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{Atom, BondOrder, Frame, Trajectory};
+ /// let mut trajectory_memory = Trajectory::memory_writer("SMI").unwrap();
+ ///
+ /// let mut frame = Frame::new();
+ /// frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+ /// frame.add_atom(&Atom::new("C"), [0.0, 0.0, 0.0], None);
+ /// frame.add_bond_with_order(0, 1, BondOrder::Single);
+ ///
+ /// trajectory_memory.write(&frame).unwrap();
+ ///
+ /// let result = trajectory_memory.memory_buffer();
+ /// assert_eq!(result.unwrap(), "CC\n");
+ /// ```
+ #[allow(clippy::cast_possible_truncation)]
+ pub fn memory_buffer(&self) -> Result<&str, Error> {
+ let mut ptr: *const c_char = std::ptr::null();
+ let mut count: u64 = 0;
+ let buffer = unsafe {
+ check(ffi::chfl_trajectory_memory_buffer(self.as_ptr(), &mut ptr, &mut count))?;
+ std::slice::from_raw_parts(ptr.cast(), count.try_into().expect("failed to convert u64 to usize"))
+ };
+
+ let string = std::str::from_utf8(buffer)?;
+ Ok(string)
+ }
+
+ /// Get file path for this trajectory.
+ ///
+ /// # Example
+ /// ```no_run
+ /// # use chemfiles::Trajectory;
+ /// let trajectory = Trajectory::open("water.xyz", 'r').unwrap();
+ ///
+ /// assert_eq!(trajectory.path(), "water.xyz");
+ /// ```
+ pub fn path(&self) -> String {
+ let get_string = |ptr, len| unsafe { ffi::chfl_trajectory_path(self.as_ptr(), ptr, len) };
+ let path = strings::call_autogrow_buffer(1024, get_string).expect("failed to get path string");
+ return strings::from_c(path.as_ptr());
+ }
+}
+
+/// `MemoryTrajectoryReader` is a handle for a `Trajectory` in memory.
+pub struct MemoryTrajectoryReader<'data> {
+ inner: Trajectory,
+ phantom: std::marker::PhantomData<&'data [u8]>,
+}
+
+impl<'data> MemoryTrajectoryReader<'data> {
+ /// Read a memory buffer as though it was a formatted file.
+ ///
+ /// The memory buffer used to store the file is given using the `data`
+ /// argument. The `format` parameter is required and should follow the same
+ /// rules as in the main `Trajectory` constructor.
+ ///
+ /// # Errors
+ ///
+ /// This function fails if the data is incorrectly formatted for the
+ /// corresponding format, or if the format do not support in-memory readers.
+ ///
+ /// # Example
+ /// ```
+ /// # use chemfiles::{MemoryTrajectoryReader, Frame};
+ /// let aromatics = "c1ccccc1\nc1ccco1\nc1ccccn1\n";
+ /// let mut trajectory = MemoryTrajectoryReader::new(aromatics.as_bytes(), "SMI").unwrap();
+ /// let mut frame = Frame::new();
+ /// trajectory.read(&mut frame).unwrap();
+ /// assert_eq!(frame.size(), 6);
+ /// ```
+ pub fn new<Data, Format>(data: Data, format: Format) -> Result<MemoryTrajectoryReader<'data>, Error>
+ where
+ Data: Into<&'data [u8]>,
+ Format: AsRef<str>,
+ {
+ let data = data.into();
+ let format = strings::to_c(format.as_ref());
+ let trajectory = unsafe {
+ let handle = ffi::chfl_trajectory_memory_reader(data.as_ptr().cast(), data.len() as u64, format.as_ptr());
+ Trajectory::from_ptr(handle)
+ };
+ Ok(MemoryTrajectoryReader {
+ inner: trajectory?,
+ phantom: std::marker::PhantomData,
+ })
+ }
+}
+
+impl<'a> std::ops::Deref for MemoryTrajectoryReader<'a> {
+ type Target = Trajectory;
+
+ #[inline]
+ fn deref(&self) -> &Self::Target {
+ &self.inner
+ }
+}
+
+impl<'a> std::ops::DerefMut for MemoryTrajectoryReader<'a> {
+ #[inline]
+ fn deref_mut(&mut self) -> &mut Self::Target {
+ &mut self.inner
+ }
+}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+
+ use std::io::Read;
+ use std::path::Path;
+
+ use approx::assert_ulps_eq;
+
+ use crate::{Atom, CellShape, Frame, Topology, UnitCell};
+
+ #[test]
+ fn read() {
+ let root = Path::new(file!()).parent().unwrap().join("..");
+ let filename = root.join("data").join("water.xyz");
+ let mut file = Trajectory::open(filename.to_str().unwrap(), 'r').unwrap();
+
+ if cfg!(target_family = "unix") {
+ assert_eq!(file.path(), "src/../data/water.xyz");
+ } else if cfg!(target_family = "windows") {
+ assert_eq!(file.path(), "src\\..\\data\\water.xyz");
+ } else {
+ panic!("please add test for this OS!");
+ }
+
+ assert_eq!(file.nsteps(), 100);
+
+ let mut frame = Frame::new();
+ assert!(file.read(&mut frame).is_ok());
+
+ assert_eq!(frame.size(), 297);
+ assert_ulps_eq!(frame.positions()[0][0], 0.417219);
+ assert_ulps_eq!(frame.positions()[0][1], 8.303366);
+ assert_ulps_eq!(frame.positions()[0][2], 11.737172);
+ assert_ulps_eq!(frame.positions()[124][0], 5.099554);
+ assert_ulps_eq!(frame.positions()[124][1], -0.045104);
+ assert_ulps_eq!(frame.positions()[124][2], 14.153846);
+
+ assert_eq!(frame.atom(0).name(), "O");
+
+ file.set_cell(&UnitCell::new([30.0, 30.0, 30.0]));
+ assert!(file.read_step(41, &mut frame).is_ok());
+ let cell = frame.cell().clone();
+ assert_eq!(cell.lengths(), [30.0, 30.0, 30.0]);
+
+ assert_ulps_eq!(frame.positions()[0][0], 0.761277);
+ assert_ulps_eq!(frame.positions()[0][1], 8.106125);
+ assert_ulps_eq!(frame.positions()[0][2], 10.622949);
+ assert_ulps_eq!(frame.positions()[124][0], 5.13242);
+ assert_ulps_eq!(frame.positions()[124][1], 0.079862);
+ assert_ulps_eq!(frame.positions()[124][2], 14.194161);
+
+ {
+ let topology = frame.topology();
+ assert_eq!(topology.size(), 297);
+ assert_eq!(topology.bonds_count(), 0);
+ }
+
+ assert!(frame.guess_bonds().is_ok());
+ {
+ let topology = frame.topology();
+ assert_eq!(topology.size(), 297);
+ assert_eq!(topology.bonds_count(), 180);
+ assert_eq!(topology.angles_count(), 84);
+ }
+
+ let mut topology = Topology::new();
+ let atom = Atom::new("Cs");
+ for _ in 0..297 {
+ topology.add_atom(&atom);
+ }
+
+ file.set_topology(&topology);
+ assert!(file.read_step(10, &mut frame).is_ok());
+ assert_eq!(frame.atom(42).name(), "Cs");
+
+ let filename = root.join("data").join("topology.xyz");
+ assert!(file.set_topology_file(filename.to_str().unwrap()).is_ok());
+ assert!(file.read(&mut frame).is_ok());
+ assert_eq!(frame.atom(100).name(), "Rd");
+
+ let filename = root.join("data").join("helium.xyz.but.not.really");
+ let filename = filename.to_str().unwrap();
+ let mut file = Trajectory::open_with_format(filename, 'r', "XYZ").unwrap();
+ assert!(file.read(&mut frame).is_ok());
+ assert_eq!(frame.size(), 125);
+ }
+
+ fn write_file<P>(path: P)
+ where
+ P: AsRef<Path>,
+ {
+ let mut file = Trajectory::open(path, 'w').unwrap();
+ let mut frame = Frame::new();
+ frame.resize(4);
+
+ for position in frame.positions_mut() {
+ *position = [1.0, 2.0, 3.0];
+ }
+
+ let mut topology = Topology::new();
+ let atom = Atom::new("X");
+ for _ in 0..4 {
+ topology.add_atom(&atom);
+ }
+ frame.set_topology(&topology).unwrap();
+ assert!(file.write(&frame).is_ok());
+ }
+
+ #[test]
+ fn write() {
+ let filename = "test-tmp.xyz";
+ write_file(filename);
+
+ let expected_content = "4
+Properties=species:S:1:pos:R:3
+X 1 2 3
+X 1 2 3
+X 1 2 3
+X 1 2 3"
+ .lines()
+ .collect::<Vec<_>>();
+
+ let mut file = std::fs::File::open(filename).unwrap();
+ let mut content = String::new();
+ let _ = file.read_to_string(&mut content).unwrap();
+
+ assert_eq!(expected_content, content.lines().collect::<Vec<_>>());
+ std::fs::remove_file(filename).unwrap();
+ }
+
+ #[test]
+ fn memory() {
+ // formats in decreasing order of their memory buffer length to check null termination
+ for format in &["CSSR", "GRO", "XYZ"] {
+ let mut frame_write = Frame::new();
+ frame_write.add_atom(&Atom::new("H"), [1.5, 3.0, -10.0], None);
+ frame_write.add_atom(&Atom::new("O"), [2.3, -1.4, 50.0], None);
+ frame_write.add_atom(&Atom::new("H"), [-1.5, 10.0, 0.0], None);
+ let cell = UnitCell::new([10.0, 11.0, 12.5]);
+
+ let mut trajectory_write = Trajectory::memory_writer(*format).unwrap();
+ trajectory_write.set_cell(&cell);
+ trajectory_write.write(&frame_write).unwrap();
+
+ let buffer = trajectory_write.memory_buffer().unwrap();
+ let mut trajectory_read = MemoryTrajectoryReader::new(buffer.as_bytes(), *format).unwrap();
+ let mut frame_read = Frame::new();
+ trajectory_read.read(&mut frame_read).unwrap();
+
+ assert_eq!(trajectory_read.nsteps(), 1);
+ assert_eq!(frame_read.cell().shape(), CellShape::Orthorhombic);
+ assert_eq!(frame_read.size(), 3);
+ assert_eq!(frame_read.atom(1).name(), "O");
+ crate::assert_vector3d_eq(&frame_read.positions()[2], &[-1.5, 10.0, 0.0], 1e-4);
+ }
+ }
+}
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a/0.10.40/static.files/scrape-examples-ef1e698c1d417c0c.js b/0.10.40/static.files/scrape-examples-ef1e698c1d417c0c.js new file mode 100644 index 000000000..ba830e374 --- /dev/null +++ b/0.10.40/static.files/scrape-examples-ef1e698c1d417c0c.js @@ -0,0 +1 @@ +"use strict";(function(){const DEFAULT_MAX_LINES=5;const HIDDEN_MAX_LINES=10;function scrollToLoc(elt,loc,isHidden){const lines=elt.querySelector(".src-line-numbers");let scrollOffset;const maxLines=isHidden?HIDDEN_MAX_LINES:DEFAULT_MAX_LINES;if(loc[1]-loc[0]>maxLines){const line=Math.max(0,loc[0]-1);scrollOffset=lines.children[line].offsetTop}else{const wrapper=elt.querySelector(".code-wrapper");const halfHeight=wrapper.offsetHeight/2;const offsetTop=lines.children[loc[0]].offsetTop;const lastLine=lines.children[loc[1]];const offsetBot=lastLine.offsetTop+lastLine.offsetHeight;const 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b/0.10.40/static.files/search-f6292fe389d70017.js new file mode 100644 index 000000000..c91355a61 --- /dev/null +++ b/0.10.40/static.files/search-f6292fe389d70017.js @@ -0,0 +1,5 @@ +"use strict";(function(){const itemTypes=["mod","externcrate","import","struct","enum","fn","type","static","trait","impl","tymethod","method","structfield","variant","macro","primitive","associatedtype","constant","associatedconstant","union","foreigntype","keyword","existential","attr","derive","traitalias",];const longItemTypes=["module","extern crate","re-export","struct","enum","function","type alias","static","trait","","trait method","method","struct field","enum variant","macro","primitive type","assoc type","constant","assoc const","union","foreign type","keyword","existential type","attribute macro","derive macro","trait alias",];const TY_PRIMITIVE=itemTypes.indexOf("primitive");const TY_KEYWORD=itemTypes.indexOf("keyword");const ROOT_PATH=typeof window!=="undefined"?window.rootPath:"../";function hasOwnPropertyRustdoc(obj,property){return Object.prototype.hasOwnProperty.call(obj,property)}function printTab(nb){let iter=0;let foundCurrentTab=false;let foundCurrentResultSet=false;onEachLazy(document.getElementById("search-tabs").childNodes,elem=>{if(nb===iter){addClass(elem,"selected");foundCurrentTab=true}else{removeClass(elem,"selected")}iter+=1});const isTypeSearch=(nb>0||iter===1);iter=0;onEachLazy(document.getElementById("results").childNodes,elem=>{if(nb===iter){addClass(elem,"active");foundCurrentResultSet=true}else{removeClass(elem,"active")}iter+=1});if(foundCurrentTab&&foundCurrentResultSet){searchState.currentTab=nb;const correctionsElem=document.getElementsByClassName("search-corrections");if(isTypeSearch){removeClass(correctionsElem[0],"hidden")}else{addClass(correctionsElem[0],"hidden")}}else if(nb!==0){printTab(0)}}const editDistanceState={current:[],prev:[],prevPrev:[],calculate:function calculate(a,b,limit){if(a.length\
+ ${item.displayPath}${name}\
+
`);link.appendChild(resultName);const description=document.createElement("div");description.className="desc";description.insertAdjacentHTML("beforeend",item.desc);link.appendChild(description);output.appendChild(link)})}else if(query.error===null){output.className="search-failed"+extraClass;output.innerHTML="No results :("+"Try on DuckDuckGo?
"+"Or try looking in one of these:
- The Rust Reference "+" for technical details about the language.
- Rust By "+"Example for expository code examples.
- The Rust Book for "+"introductions to language features and the language itself.
- Docs.rs for documentation of crates released on"+" crates.io.
Results${crates}
`;if(results.query.error!==null){const error=results.query.error;error.forEach((value,index)=>{value=value.split("<").join("<").split(">").join(">");if(index%2!==0){error[index]=`${value.replaceAll(" ", " ")}`}else{error[index]=value}});output+=`Query parser error: "${error.join("")}".
`;output+=""+makeTabHeader(0,"In Names",ret_others[1])+"
";currentTab=0}else if(results.query.foundElems<=1&&results.query.returned.length===0){output+=""+makeTabHeader(0,"In Names",ret_others[1])+makeTabHeader(1,"In Parameters",ret_in_args[1])+makeTabHeader(2,"In Return Types",ret_returned[1])+"
"}else{const signatureTabTitle=results.query.elems.length===0?"In Function Return Types":results.query.returned.length===0?"In Function Parameters":"In Function Signatures";output+=""+makeTabHeader(0,signatureTabTitle,ret_others[1])+"
";currentTab=0}if(results.query.correction!==null){const orig=results.query.returned.length>0?results.query.returned[0].name:results.query.elems[0].name;output+=""+`Type "${orig}" not found. `+"Showing results for closest type name "+`"${results.query.correction}" instead.
`}const resultsElem=document.createElement("div");resultsElem.id="results";resultsElem.appendChild(ret_others[0]);resultsElem.appendChild(ret_in_args[0]);resultsElem.appendChild(ret_returned[0]);search.innerHTML=output;const crateSearch=document.getElementById("crate-search");if(crateSearch){crateSearch.addEventListener("input",updateCrate)}search.appendChild(resultsElem);searchState.showResults(search);const elems=document.getElementById("search-tabs").childNodes;searchState.focusedByTab=[];let i=0;for(const elem of elems){const j=i;elem.onclick=()=>printTab(j);searchState.focusedByTab.push(null);i+=1}printTab(currentTab)}function updateSearchHistory(url){if(!browserSupportsHistoryApi()){return}const params=searchState.getQueryStringParams();if(!history.state&&!params.search){history.pushState(null,"",url)}else{history.replaceState(null,"",url)}}function search(e,forced){if(e){e.preventDefault()}const query=parseQuery(searchState.input.value.trim());let filterCrates=getFilterCrates();if(!forced&&query.userQuery===currentResults){if(query.userQuery.length>0){putBackSearch()}return}searchState.setLoadingSearch();const params=searchState.getQueryStringParams();if(filterCrates===null&¶ms["filter-crate"]!==undefined){filterCrates=params["filter-crate"]}searchState.title="Results for "+query.original+" - Rust";updateSearchHistory(buildUrl(query.original,filterCrates));showResults(execQuery(query,searchWords,filterCrates,window.currentCrate),params.go_to_first,filterCrates)}function buildItemSearchTypeAll(types,lowercasePaths){const PATH_INDEX_DATA=0;const GENERICS_DATA=1;return types.map(type=>{let pathIndex,generics;if(typeof type==="number"){pathIndex=type;generics=[]}else{pathIndex=type[PATH_INDEX_DATA];generics=buildItemSearchTypeAll(type[GENERICS_DATA],lowercasePaths)}return{id:pathIndex===0?-1:buildTypeMapIndex(lowercasePaths[pathIndex-1].name),ty:pathIndex===0?null:lowercasePaths[pathIndex-1].ty,generics:generics,}})}function buildFunctionSearchType(functionSearchType,lowercasePaths){const INPUTS_DATA=0;const OUTPUT_DATA=1;if(functionSearchType===0){return null}let inputs,output;if(typeof functionSearchType[INPUTS_DATA]==="number"){const pathIndex=functionSearchType[INPUTS_DATA];inputs=[{id:pathIndex===0?-1:buildTypeMapIndex(lowercasePaths[pathIndex-1].name),ty:pathIndex===0?null:lowercasePaths[pathIndex-1].ty,generics:[],}]}else{inputs=buildItemSearchTypeAll(functionSearchType[INPUTS_DATA],lowercasePaths)}if(functionSearchType.length>1){if(typeof functionSearchType[OUTPUT_DATA]==="number"){const pathIndex=functionSearchType[OUTPUT_DATA];output=[{id:pathIndex===0?-1:buildTypeMapIndex(lowercasePaths[pathIndex-1].name),ty:pathIndex===0?null:lowercasePaths[pathIndex-1].ty,generics:[],}]}else{output=buildItemSearchTypeAll(functionSearchType[OUTPUT_DATA],lowercasePaths)}}else{output=[]}return{inputs,output,}}function buildIndex(rawSearchIndex){searchIndex=[];const searchWords=[];typeNameIdMap=new Map();const charA="A".charCodeAt(0);let currentIndex=0;let id=0;typeNameIdOfArray=buildTypeMapIndex("array");typeNameIdOfSlice=buildTypeMapIndex("slice");typeNameIdOfArrayOrSlice=buildTypeMapIndex("[]");for(const crate in rawSearchIndex){if(!hasOwnPropertyRustdoc(rawSearchIndex,crate)){continue}let crateSize=0;const crateCorpus=rawSearchIndex[crate];searchWords.push(crate);const crateRow={crate:crate,ty:1,name:crate,path:"",desc:crateCorpus.doc,parent:undefined,type:null,id:id,normalizedName:crate.indexOf("_")===-1?crate:crate.replace(/_/g,""),deprecated:null,};id+=1;searchIndex.push(crateRow);currentIndex+=1;const itemTypes=crateCorpus.t;const itemNames=crateCorpus.n;const itemPaths=new Map(crateCorpus.q);const itemDescs=crateCorpus.d;const itemParentIdxs=crateCorpus.i;const itemFunctionSearchTypes=crateCorpus.f;const deprecatedItems=new Set(crateCorpus.c);const paths=crateCorpus.p;const aliases=crateCorpus.a;const lowercasePaths=[];let len=paths.length;for(let i=0;i
+
`}else{const checked=setting["default"]===true?" checked":"";output+=`\
+${setting_name}
+ `;onEach(setting["options"],option=>{const checked=option===setting["default"]?" checked":"";const full=`${js_data_name}-${option.replace(/ /g,"-")}`;output+=`\
+ `});output+=`\
+
+\
+ \
+
`}}return output}function buildSettingsPage(){const theme_names=getVar("themes").split(",").filter(t=>t);theme_names.push("light","dark","ayu");const settings=[{"name":"Theme","js_name":"theme","default":"system preference","options":theme_names.concat("system preference"),},{"name":"Preferred light theme","js_name":"preferred-light-theme","default":"light","options":theme_names,},{"name":"Preferred dark theme","js_name":"preferred-dark-theme","default":"dark","options":theme_names,},{"name":"Auto-hide item contents for large items","js_name":"auto-hide-large-items","default":true,},{"name":"Auto-hide item methods' documentation","js_name":"auto-hide-method-docs","default":false,},{"name":"Auto-hide trait implementation documentation","js_name":"auto-hide-trait-implementations","default":false,},{"name":"Directly go to item in search if there is only one result","js_name":"go-to-only-result","default":false,},{"name":"Show line numbers on code examples","js_name":"line-numbers","default":false,},{"name":"Disable keyboard shortcuts","js_name":"disable-shortcuts","default":false,},];const elementKind=isSettingsPage?"section":"div";const innerHTML=`${buildSettingsPageSections(settings)}
`;const el=document.createElement(elementKind);el.id="settings";if(!isSettingsPage){el.className="popover"}el.innerHTML=innerHTML;if(isSettingsPage){document.getElementById(MAIN_ID).appendChild(el)}else{el.setAttribute("tabindex","-1");getSettingsButton().appendChild(el)}return el}const settingsMenu=buildSettingsPage();function displaySettings(){settingsMenu.style.display=""}function settingsBlurHandler(event){blurHandler(event,getSettingsButton(),window.hidePopoverMenus)}if(isSettingsPage){getSettingsButton().onclick=function(event){event.preventDefault()}}else{const settingsButton=getSettingsButton();const settingsMenu=document.getElementById("settings");settingsButton.onclick=function(event){if(elemIsInParent(event.target,settingsMenu)){return}event.preventDefault();const shouldDisplaySettings=settingsMenu.style.display==="none";window.hideAllModals();if(shouldDisplaySettings){displaySettings()}};settingsButton.onblur=settingsBlurHandler;settingsButton.querySelector("a").onblur=settingsBlurHandler;onEachLazy(settingsMenu.querySelectorAll("input"),el=>{el.onblur=settingsBlurHandler});settingsMenu.onblur=settingsBlurHandler}setTimeout(()=>{setEvents(settingsMenu);if(!isSettingsPage){displaySettings()}removeClass(getSettingsButton(),"rotate")},0)})()
\ No newline at end of file
diff --git a/0.10.40/static.files/source-script-106908c7a7964ba4.js b/0.10.40/static.files/source-script-106908c7a7964ba4.js
new file mode 100644
index 000000000..191bf6d99
--- /dev/null
+++ b/0.10.40/static.files/source-script-106908c7a7964ba4.js
@@ -0,0 +1 @@
+"use strict";(function(){const rootPath=getVar("root-path");const NAME_OFFSET=0;const DIRS_OFFSET=1;const FILES_OFFSET=2;const RUSTDOC_MOBILE_BREAKPOINT=700;function closeSidebarIfMobile(){if(window.innerWidthRedirecting to ../../chemfiles/enum.AtomType.html...
+ + + \ No newline at end of file diff --git a/0.4.0/chemfiles/atom/index.html b/0.4.0/chemfiles/atom/index.html new file mode 100644 index 000000000..e69de29bb diff --git a/0.4.0/chemfiles/atom/sidebar-items.js b/0.4.0/chemfiles/atom/sidebar-items.js new file mode 100644 index 000000000..424895982 --- /dev/null +++ b/0.4.0/chemfiles/atom/sidebar-items.js @@ -0,0 +1 @@ +initSidebarItems({"enum":[["AtomType","Available types of atoms"]],"struct":[["Atom","An Atom is a particle in the current Frame. It can be used to store and retrieve informations about a particle, such as mass, name, atomic number, *etc.*"]]}); \ No newline at end of file diff --git a/0.4.0/chemfiles/atom/struct.Atom.html b/0.4.0/chemfiles/atom/struct.Atom.html new file mode 100644 index 000000000..fce480c69 --- /dev/null +++ b/0.4.0/chemfiles/atom/struct.Atom.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.Atom.html...
+ + + \ No newline at end of file diff --git a/0.4.0/chemfiles/cell/enum.CellType.html b/0.4.0/chemfiles/cell/enum.CellType.html new file mode 100644 index 000000000..6b1bd07a6 --- /dev/null +++ b/0.4.0/chemfiles/cell/enum.CellType.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/enum.CellType.html...
+ + + \ No newline at end of file diff --git a/0.4.0/chemfiles/cell/index.html b/0.4.0/chemfiles/cell/index.html new file mode 100644 index 000000000..e69de29bb diff --git a/0.4.0/chemfiles/cell/sidebar-items.js b/0.4.0/chemfiles/cell/sidebar-items.js new file mode 100644 index 000000000..71dc4b23c --- /dev/null +++ b/0.4.0/chemfiles/cell/sidebar-items.js @@ -0,0 +1 @@ +initSidebarItems({"enum":[["CellType","Available unit cell types"]],"struct":[["UnitCell","An `UnitCell` represent the box containing the atoms in the system, and its periodicity."]]}); \ No newline at end of file diff --git a/0.4.0/chemfiles/cell/struct.UnitCell.html b/0.4.0/chemfiles/cell/struct.UnitCell.html new file mode 100644 index 000000000..cddcfc6bf --- /dev/null +++ b/0.4.0/chemfiles/cell/struct.UnitCell.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.UnitCell.html...
+ + + \ No newline at end of file diff --git a/0.4.0/chemfiles/enum.AtomType.html b/0.4.0/chemfiles/enum.AtomType.html new file mode 100644 index 000000000..087f28cf2 --- /dev/null +++ b/0.4.0/chemfiles/enum.AtomType.html @@ -0,0 +1,130 @@ + + + + + + + + + +Enum chemfiles::AtomType
+
+ [−]
+
+ [src]
+pub enum AtomType {
+ Element,
+ CorseGrain,
+ Dummy,
+ Undefined,
+}Available types of atoms
+Variants
+Element | Element from the periodic table of elements + | |
CorseGrain | Corse-grained atom are composed of more than one element: CH3 groups, +amino-acids are corse-grained atoms. + | |
Dummy | Dummy site, with no physical reality + | |
Undefined | Undefined atom type + |
Trait Implementations
impl From<CHFL_ATOM_TYPE> for AtomType
fn from(atomtype: CHFL_ATOM_TYPE) -> AtomType
+Derived Implementations
impl Eq for AtomType
impl PartialEq for AtomType
impl Debug for AtomType
impl Clone for AtomType
fn clone(&self) -> AtomType
+1.0.0fn clone_from(&mut self, source: &Self)
+Enum chemfiles::CellType
+
+ [−]
+
+ [src]
+pub enum CellType {
+ Orthorombic,
+ Triclinic,
+ Infinite,
+}Available unit cell types
+Variants
+Orthorombic | Orthorombic cell, with the three angles equals to 90° + | |
Triclinic | Triclinic cell, with any values for the angles. + | |
Infinite | Infinite cell, to use when there is no cell. + |
Trait Implementations
impl From<CHFL_CELL_TYPE> for CellType
fn from(celltype: CHFL_CELL_TYPE) -> CellType
+Derived Implementations
impl Eq for CellType
impl PartialEq for CellType
impl Debug for CellType
impl Clone for CellType
fn clone(&self) -> CellType
+1.0.0fn clone_from(&mut self, source: &Self)
+Enum chemfiles::Error
+
+ [−]
+
+ [src]
+pub enum Error {
+ CppStdError {
+ message: String,
+ },
+ ChemfilesCppError {
+ message: String,
+ },
+ MemoryError,
+ FileError,
+ FormatError,
+ UTF8PathError {
+ message: String,
+ },
+}Possible causes of error in chemfiles
+Variants
+CppStdError | Exception in the C++ standard library +Fields+ +
| |||
ChemfilesCppError | Exception in the C++ chemfiles library +Fields+ +
| |||
MemoryError | Error in memory allocations + | |||
FileError | Error while reading or writing a file + | |||
FormatError | Error in file formatting, i.e. the file is invalid + | |||
UTF8PathError | The given path is not valid UTF8 +Fields+ +
|
Methods
impl Error
fn message(&self) -> String
+Get the message associated with this error.
+fn last_error() -> String
+Get the last error message.
+Trait Implementations
impl From<CHFL_STATUS> for Error
fn from(status: CHFL_STATUS) -> Error
+Derived Implementations
impl PartialEq for Error
impl Debug for Error
impl Clone for Error
fn clone(&self) -> Error
+1.0.0fn clone_from(&mut self, source: &Self)
+Enum chemfiles::ErrorKind
+
+ [−]
+
+ [src]
+pub enum ErrorKind {
+ CppStdError,
+ ChemfilesCppError,
+ MemoryError,
+ FileError,
+ FormatError,
+ SelectionError,
+ UTF8PathError,
+ NullPtr,
+}Possible causes of error in chemfiles
+Variants
+CppStdError | Exception in the C++ standard library + | |
ChemfilesCppError | Exception in the C++ chemfiles library + | |
MemoryError | Error in memory allocations + | |
FileError | Error while reading or writing a file + | |
FormatError | Error in file formatting, i.e. the file is invalid + | |
SelectionError | Error in selection string syntax + | |
UTF8PathError | The given path is not valid UTF8 + | |
NullPtr | We got a null pointer from C++ + |
Trait Implementations
Derived Implementations
impl PartialEq for ErrorKind
impl Debug for ErrorKind
impl Clone for ErrorKind
fn clone(&self) -> ErrorKind
+1.0.0fn clone_from(&mut self, source: &Self)
+Enum chemfiles::LogLevel
+
+ [−]
+
+ [src]
+pub enum LogLevel {
+ Error,
+ Warning,
+ Info,
+ Debug,
+}Available log levels
+Variants
+Error | Only log errors + | |
Warning | Log errors and warnings + | |
Info | Log errors, warnings and informations + | |
Debug | Log everything (errors, warnings, informations and debug informations) + |
Trait Implementations
impl From<CHFL_LOG_LEVEL> for LogLevel
fn from(level: CHFL_LOG_LEVEL) -> LogLevel
+Derived Implementations
impl PartialEq for LogLevel
impl Debug for LogLevel
impl Clone for LogLevel
fn clone(&self) -> LogLevel
+1.0.0fn clone_from(&mut self, source: &Self)
+Redirecting to ../../chemfiles/enum.Error.html...
+ + + \ No newline at end of file diff --git a/0.4.0/chemfiles/errors/enum.ErrorKind.html b/0.4.0/chemfiles/errors/enum.ErrorKind.html new file mode 100644 index 000000000..cd236a770 --- /dev/null +++ b/0.4.0/chemfiles/errors/enum.ErrorKind.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/enum.ErrorKind.html...
+ + + \ No newline at end of file diff --git a/0.4.0/chemfiles/errors/index.html b/0.4.0/chemfiles/errors/index.html new file mode 100644 index 000000000..e69de29bb diff --git a/0.4.0/chemfiles/errors/sidebar-items.js b/0.4.0/chemfiles/errors/sidebar-items.js new file mode 100644 index 000000000..2b0a9b1b1 --- /dev/null +++ b/0.4.0/chemfiles/errors/sidebar-items.js @@ -0,0 +1 @@ +initSidebarItems({"enum":[["Error","Possible causes of error in chemfiles"]]}); \ No newline at end of file diff --git a/0.4.0/chemfiles/errors/struct.Error.html b/0.4.0/chemfiles/errors/struct.Error.html new file mode 100644 index 000000000..413e6df25 --- /dev/null +++ b/0.4.0/chemfiles/errors/struct.Error.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.Error.html...
+ + + \ No newline at end of file diff --git a/0.4.0/chemfiles/fn.version.html b/0.4.0/chemfiles/fn.version.html new file mode 100644 index 000000000..69c870a2d --- /dev/null +++ b/0.4.0/chemfiles/fn.version.html @@ -0,0 +1,113 @@ + + + + + + + + + +Function chemfiles::version
+
+ [−]
+
+ [src]
+pub fn version() -> String
Get the version of the chemfiles library
+Redirecting to ../../chemfiles/struct.Frame.html...
+ + + \ No newline at end of file diff --git a/0.4.0/chemfiles/index.html b/0.4.0/chemfiles/index.html new file mode 100644 index 000000000..735e392fa --- /dev/null +++ b/0.4.0/chemfiles/index.html @@ -0,0 +1,203 @@ + + + + + + + + + +Crate chemfiles + + [−] + + [src]
+Chemfiles is a multi-language library written in modern C++ for reading and +writing from and to molecular trajectory files. These files are created by +your favorite theoretical chemistry program, and contains informations about +atomic or residues names and positions. Some format also have additional +informations, such as velocities, forces, energy, …
+ +This crate expose the C API of chemfiles to Rust, and make all the +functionalities accessibles. For more informations on the C++ library, +please see its documentation. Specifically, the +following pages are worth reading:
+ +-
+
- The overview of the +classes organisation; +
- The supported formats; +
As all the function call the underlying C library, they all can fail and
+thus all return a Result<_, Error> value.
Modules
+| logging | +
+ Logging utilities + |
+
Structs
+| Atom | +
+ An Atom is a particle in the current Frame. It can be used to store and +retrieve informations about a particle, such as mass, name, atomic number, +etc. + |
+
| Frame | +
+ A |
+
| Topology | +
+ A |
+
| Trajectory | +
+ A Trajectory is a chemistry file on the hard drive. It is the main entry +point of chemfiles. + |
+
| UnitCell | +
+ An |
+
Enums
+| AtomType | +
+ Available types of atoms + |
+
| CellType | +
+ Available unit cell types + |
+
| Error | +
+ Possible causes of error in chemfiles + |
+
Enum chemfiles::logging::LogLevel
+
+ [−]
+
+ [src]
+pub enum LogLevel {
+ NONE,
+ ERROR,
+ WARNING,
+ INFO,
+ DEBUG,
+}Available log levels
+Variants
+NONE | Do not log anything + | |
ERROR | Only log errors + | |
WARNING | Log errors and warnings + | |
INFO | Log errors, warnings and informations + | |
DEBUG | Log everything (errors, warnings, informations and debug informations) + |
Trait Implementations
impl From<CHFL_LOG_LEVEL> for LogLevel
fn from(level: CHFL_LOG_LEVEL) -> LogLevel
+Derived Implementations
impl PartialEq for LogLevel
impl Debug for LogLevel
impl Clone for LogLevel
fn clone(&self) -> LogLevel
+1.0.0fn clone_from(&mut self, source: &Self)
+Function chemfiles::logging::level
+
+ [−]
+
+ [src]
+pub fn level() -> Result<LogLevel, Error>
Get current logging level
+Function chemfiles::logging::log_to_file
+
+ [−]
+
+ [src]
+pub fn log_to_file<P>(filename: P) -> Result<(), Error> where P: AsRef<Path>
Write logs to the file at path, creating it if needed.
Function chemfiles::logging::log_to_stderr
+
+ [−]
+
+ [src]
+pub fn log_to_stderr() -> Result<(), Error>
Write logs to the standard error stream. This is the default.
+Function chemfiles::logging::set_level
+
+ [−]
+
+ [src]
+pub fn set_level(level: LogLevel) -> Result<(), Error>
Set the logging level to level
Module chemfiles::logging
+
+ [−]
+
+ [src]
+Logging utilities
+Enums
+| LogLevel | +
+ Available log levels + |
+
Functions
+| level | +
+ Get current logging level + |
+
| log_to_file | +
+ Write logs to the file at |
+
| log_to_stderr | +
+ Write logs to the standard error stream. This is the default. + |
+
| set_level | +
+ Set the logging level to |
+
Redirecting to ../../chemfiles/struct.Logger.html...
+ + + \ No newline at end of file diff --git a/0.4.0/chemfiles/selection/index.html b/0.4.0/chemfiles/selection/index.html new file mode 100644 index 000000000..e69de29bb diff --git a/0.4.0/chemfiles/selection/sidebar-items.js b/0.4.0/chemfiles/selection/sidebar-items.js new file mode 100644 index 000000000..4e66c8dc8 --- /dev/null +++ b/0.4.0/chemfiles/selection/sidebar-items.js @@ -0,0 +1 @@ +initSidebarItems({"struct":[["Match","A `Match` is a set of atomic indexes matching a given selection. It should be used like a `&[usize]`."],["Selection","Select atoms in a `Frame` with a selection language."]]}); \ No newline at end of file diff --git a/0.4.0/chemfiles/selection/struct.Match.html b/0.4.0/chemfiles/selection/struct.Match.html new file mode 100644 index 000000000..848ab37f8 --- /dev/null +++ b/0.4.0/chemfiles/selection/struct.Match.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.Match.html...
+ + + \ No newline at end of file diff --git a/0.4.0/chemfiles/selection/struct.Selection.html b/0.4.0/chemfiles/selection/struct.Selection.html new file mode 100644 index 000000000..2268a4ddb --- /dev/null +++ b/0.4.0/chemfiles/selection/struct.Selection.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.Selection.html...
+ + + \ No newline at end of file diff --git a/0.4.0/chemfiles/sidebar-items.js b/0.4.0/chemfiles/sidebar-items.js new file mode 100644 index 000000000..4ff599f70 --- /dev/null +++ b/0.4.0/chemfiles/sidebar-items.js @@ -0,0 +1 @@ +initSidebarItems({"enum":[["AtomType","Available types of atoms"],["CellType","Available unit cell types"],["Error","Possible causes of error in chemfiles"]],"mod":[["logging","Logging utilities"]],"struct":[["Atom","An Atom is a particle in the current Frame. It can be used to store and retrieve informations about a particle, such as mass, name, atomic number, *etc.*"],["Frame","A `Frame` holds data from one step of a simulation: the current `Topology`, the positions, and maybe the velocities of the particles in the system."],["Topology","A `Topology` contains the definition of all the particles in the system, and the liaisons between the particles (bonds, angles, dihedrals, ...)."],["Trajectory","A Trajectory is a chemistry file on the hard drive. It is the main entry point of chemfiles."],["UnitCell","An `UnitCell` represent the box containing the atoms in the system, and its periodicity."]]}); \ No newline at end of file diff --git a/0.4.0/chemfiles/string/index.html b/0.4.0/chemfiles/string/index.html new file mode 100644 index 000000000..e69de29bb diff --git a/0.4.0/chemfiles/string/sidebar-items.js b/0.4.0/chemfiles/string/sidebar-items.js new file mode 100644 index 000000000..48333d31f --- /dev/null +++ b/0.4.0/chemfiles/string/sidebar-items.js @@ -0,0 +1 @@ +initSidebarItems({}); \ No newline at end of file diff --git a/0.4.0/chemfiles/struct.Atom.html b/0.4.0/chemfiles/struct.Atom.html new file mode 100644 index 000000000..aa3451bd6 --- /dev/null +++ b/0.4.0/chemfiles/struct.Atom.html @@ -0,0 +1,155 @@ + + + + + + + + + +Struct chemfiles::Atom
+
+ [−]
+
+ [src]
+pub struct Atom {
+ // some fields omitted
+}An Atom is a particle in the current Frame. It can be used to store and +retrieve informations about a particle, such as mass, name, atomic number, +etc.
+Methods
impl Atom
fn new<'a, S>(name: S) -> Result<Atom, Error> where S: Into<&'a str>
+Create a new Atom from a name.
fn mass(&self) -> Result<f32, Error>
+Get the Atom mass, in atomic mass units
fn set_mass(&mut self, mass: f32) -> Result<(), Error>
+Set the Atom mass, in atomic mass units
fn charge(&self) -> Result<f32, Error>
+Get the Atom charge, in number of the electron charge e
fn set_charge(&mut self, charge: f32) -> Result<(), Error>
+Set the Atom charge, in number of the electron charge e
fn name(&self) -> Result<String, Error>
+Get the Atom name
fn set_name<'a, S>(&mut self, name: S) -> Result<(), Error> where S: Into<&'a str>
+Set the Atom name
fn full_name(&mut self) -> Result<String, Error>
+Try to get the full name of the Atom. The full name of "He" is
+"Helium", and so on. If the name can not be found, returns the empty
+string.
fn vdw_radius(&self) -> Result<f64, Error>
+Try to get the Van der Waals radius of the Atom. If the radius can not
+be found, returns -1.
fn covalent_radius(&self) -> Result<f64, Error>
+Try to get the covalent radius of the Atom. If the radius can not be
+found, returns -1.
fn atomic_number(&self) -> Result<i32, Error>
+Try to get the atomic number of the Atom. If the number can not be
+found, returns -1.
fn atom_type(&self) -> Result<AtomType, Error>
+Get the type of the atom
+fn set_atom_type(&mut self, atom_type: AtomType) -> Result<(), Error>
+Set the type of the atom
+unsafe fn from_ptr(ptr: *const CHFL_ATOM) -> Atom
+Create an Atom from a C pointer. This function is unsafe because no
+validity check is made on the pointer.
unsafe fn as_ptr(&self) -> *const CHFL_ATOM
+Get the underlying C pointer. This function is unsafe because no +lifetime guarantee is made on the pointer.
+Trait Implementations
impl Drop for Atom
fn drop(&mut self)
+Struct chemfiles::Error
+
+ [−]
+
+ [src]
+pub struct Error {
+ pub kind: ErrorKind,
+ pub message: String,
+}Error type for Chemfiles.
+Fields
+kind | The error kind + |
message | A message describing the error cause + |
Methods
impl Error
fn last_error() -> String
+Get the last error message from the C++ library.
+fn cleaup()
+Clear any error from the C++ library
+Trait Implementations
impl From<CHFL_STATUS> for Error
fn from(status: CHFL_STATUS) -> Error
+impl Display for Error
impl Error for Error
fn description(&self) -> &str
+1.0.0fn cause(&self) -> Option<&Error>
+Derived Implementations
impl PartialEq for Error
impl Debug for Error
impl Clone for Error
fn clone(&self) -> Error
+1.0.0fn clone_from(&mut self, source: &Self)
+Struct chemfiles::Frame
+
+ [−]
+
+ [src]
+pub struct Frame {
+ // some fields omitted
+}A Frame holds data from one step of a simulation: the current Topology,
+the positions, and maybe the velocities of the particles in the system.
Methods
impl Frame
fn new(natoms: usize) -> Result<Frame, Error>
+Create an empty frame with initial capacity of natoms. It will be
+resized by the library as needed.
fn atom(&self, index: usize) -> Result<Atom, Error>
+Get a specific Atom from a frame, given its index in the frame
fn natoms(&self) -> Result<usize, Error>
+Get the current number of atoms in the Frame.
fn positions(&self) -> Result<Vec<[f32; 3]>, Error>
+Get the positions from the Frame.
fn set_positions(&mut self, positions: Vec<[f32; 3]>) -> Result<(), Error>
+Set the positions in the Frame.
fn velocities(&self) -> Result<Vec<[f32; 3]>, Error>
+Get the velocities from the Frame.
fn set_velocities(&mut self, velocities: Vec<[f32; 3]>) -> Result<(), Error>
+Set the velocities in the Frame.
fn has_velocities(&self) -> Result<bool, Error>
+Check if the Frame has velocity information.
fn cell(&self) -> Result<UnitCell, Error>
+Get the UnitCell from the Frame
fn set_cell(&mut self, cell: &UnitCell) -> Result<(), Error>
+Set the UnitCell of the Frame
fn topology(&self) -> Result<Topology, Error>
+Get the Topology from the Frame
fn set_topology(&mut self, topology: &Topology) -> Result<(), Error>
+Set the Topology of the Frame
fn step(&self) -> Result<usize, Error>
+Get the Frame step, i.e. the frame number in the trajectory
fn set_step(&mut self, step: usize) -> Result<(), Error>
+Set the Frame step
fn guess_topology(&self, bonds: bool) -> Result<(), Error>
+Try to guess the bonds, angles and dihedrals in the system. If bonds
+is true, guess everything; else only guess the angles and dihedrals from
+the topology bond list.
unsafe fn from_ptr(ptr: *const CHFL_FRAME) -> Frame
+Create a Frame from a C pointer. This function is unsafe because
+no validity check is made on the pointer.
unsafe fn as_ptr(&self) -> *const CHFL_FRAME
+Get the underlying C pointer. This function is unsafe because no +lifetime guarantee is made on the pointer.
+Trait Implementations
impl Drop for Frame
fn drop(&mut self)
+Struct chemfiles::Logger
+
+ [−]
+
+ [src]
+pub struct Logger<'a> {
+ // some fields omitted
+}This struct give access to the logging system.
+ +As it is a global system, it must be aquired before any operations.
+Methods
impl<'a> Logger<'a>
fn get() -> Logger<'a>
+Get an handle to the logging system. This function blocks, waiting for a +mutex to be available. You should probably call this function from one +thread only.
+fn level(&self) -> Result<LogLevel>
+Get the current maximal logging level
+fn set_level(&self, level: LogLevel) -> Result<()>
+Set the maximal logging level to level
fn log_to_file<P>(&self, filename: P) -> Result<()> where P: AsRef<Path>
+Write logs to the file at path, creating it if needed.
fn log_to_stderr(&self) -> Result<()>
+Redirect the logs to the standard error stream. This is the default.
+fn log_to_stdout(&self) -> Result<()>
+Redirect the logs to the standard output.
+fn log_silent(&self) -> Result<()>
+Remove all logging output.
+fn log_callback<F>(&self, callback: F) -> Result<()> where F: Fn(LogLevel, &str) + 'static
+Redirect all logging to user-provided logging. The callback function will
+be called at each loggin operation with the level of the message, and the
+the message itself.
Struct chemfiles::Match
+
+ [−]
+
+ [src]
+pub struct Match(_);
A Match is a set of atomic indexes matching a given selection. It should
+be used like a &[usize].
Methods
impl Match
fn new(atoms: &[usize]) -> Match
+Create a new match containing the atoms in the atoms slice.
Panics
+If the slice contains more than 4 elements, which is the maximal size +of a match.
+fn iter<'a>(&'a self) -> Iter<'a, usize>
+Iterate over the atomic indexes in the match.
+Trait Implementations
impl Index<usize> for Match
impl<'a> IntoIterator for &'a Match
Derived Implementations
impl Eq for Match
impl PartialEq for Match
impl Copy for Match
impl Clone for Match
fn clone(&self) -> Match
+1.0.0fn clone_from(&mut self, source: &Self)
+impl Debug for Match
Struct chemfiles::Selection
+
+ [−]
+
+ [src]
+pub struct Selection {
+ // some fields omitted
+}Select atoms in a Frame with a selection language.
The selection language is built by combining basic operations. Each basic
+operation follows the <selector>[(<variable>)] <operator> <value>
+structure, where <operator> is a comparison operator in == != < <= > >=.
+Refer to the full
+documentation to know
+the allowed selectors and how to use them.
Methods
impl Selection
fn new<'a, S: Into<&'a str>>(selection: S) -> Result<Selection>
+Create a new selection from the given selection string.
+fn size(&self) -> Result<usize>
+Get the size of the selection, i.e. the number of atoms we are selecting +together.
+ +This value is 1 for the 'atom' context, 2 for the 'pair' and 'bond' +context, 3 for the 'three' and 'angles' contextes and 4 for the 'four' +and 'dihedral' contextes.
+fn evaluate(&mut self, frame: &Frame) -> Result<Vec<Match>>
+Evaluate a selection for a given frame, and return the corresponding +matches.
+fn list(&mut self, frame: &Frame) -> Result<Vec<usize>>
+Evaluates a selection of size 1 on a given frame. This function
+returns the list of atomic indexes in the frame matching this selection.
Panics
+If the selection size is not 1.
+Trait Implementations
impl Drop for Selection
fn drop(&mut self)
+Struct chemfiles::Topology
+
+ [−]
+
+ [src]
+pub struct Topology {
+ // some fields omitted
+}A Topology contains the definition of all the particles in the system, and
+the liaisons between the particles (bonds, angles, dihedrals, ...).
Only the atoms and the bonds are stored, the angles and the dihedrals are +computed automaticaly.
+Methods
impl Topology
fn new() -> Result<Topology, Error>
+Create a new empty topology
+fn atom(&self, index: usize) -> Result<Atom, Error>
+Get a specific Atom from a topology, given its index in the topology
fn natoms(&self) -> Result<usize, Error>
+Get the current number of atoms in the topology.
+fn push(&mut self, atom: &Atom) -> Result<(), Error>
+Add an Atom at the end of a topology
fn remove(&mut self, index: usize) -> Result<(), Error>
+Remove an Atom from a topology by index. This modify all the other
+atoms indexes.
fn is_bond(&self, i: usize, j: usize) -> Result<bool, Error>
+Tell if the atoms at indexes i and j are bonded together
fn is_angle(&self, i: usize, j: usize, k: usize) -> Result<bool, Error>
+Tell if the atoms at indexes i, j and k constitues an angle
fn is_dihedral(&self, i: usize, j: usize, k: usize, m: usize) -> Result<bool, Error>
+Tell if the atoms at indexes i, j, k and m constitues a dihedral
+angle
fn bonds_count(&self) -> Result<usize, Error>
+Get the number of bonds in the system
+fn angles_count(&self) -> Result<usize, Error>
+Get the number of angles in the system
+fn dihedrals_count(&self) -> Result<usize, Error>
+Get the number of dihedral angles in the system
+fn bonds(&self) -> Result<Vec<[usize; 2]>, Error>
+Get the list of bonds in the system
+fn angles(&self) -> Result<Vec<[usize; 3]>, Error>
+Get the list of angles in the system
+fn dihedrals(&self) -> Result<Vec<[usize; 4]>, Error>
+Get the list of dihedral angles in the system
+fn add_bond(&mut self, i: usize, j: usize) -> Result<(), Error>
+Add a bond between the atoms at indexes i and j in the system
fn remove_bond(&mut self, i: usize, j: usize) -> Result<(), Error>
+Remove any existing bond between the atoms at indexes i and j in
+the system
unsafe fn from_ptr(ptr: *const CHFL_TOPOLOGY) -> Topology
+Create a Topology from a C pointer. This function is unsafe because no
+validity check is made on the pointer.
unsafe fn as_ptr(&self) -> *const CHFL_TOPOLOGY
+Get the underlying C pointer. This function is unsafe because no +lifetime guarantee is made on the pointer.
+Trait Implementations
impl Drop for Topology
fn drop(&mut self)
+Struct chemfiles::Trajectory
+
+ [−]
+
+ [src]
+pub struct Trajectory {
+ // some fields omitted
+}A Trajectory is a chemistry file on the hard drive. It is the main entry +point of chemfiles.
+Methods
impl Trajectory
fn open<P>(filename: P) -> Result<Trajectory, Error> where P: AsRef<Path>
+Open a trajectory file in read mode.
+fn create<P>(filename: P) -> Result<Trajectory, Error> where P: AsRef<Path>
+Open a trajectory file in write mode.
+fn open_with_format<'a, P, S>(filename: P, format: S) -> Result<Trajectory, Error> where P: AsRef<Path>, S: Into<&'a str>
+Open a trajectory file in read mode using a specific format.
fn create_with_format<'a, P, S>(filename: P, format: S) -> Result<Trajectory, Error> where P: AsRef<Path>, S: Into<&'a str>
+Open a trajectory file in write mode.
+fn read(&mut self, frame: &mut Frame) -> Result<(), Error>
+Read the next step of the trajectory into a frame
+fn read_step(&mut self, step: usize, frame: &mut Frame) -> Result<(), Error>
+Read a specific step of the trajectory in a frame
+fn write(&mut self, frame: &Frame) -> Result<(), Error>
+Write a frame to the trajectory.
+fn set_topology(&mut self, topology: Topology) -> Result<(), Error>
+Set the topology associated with a trajectory. This topology will be +used when reading and writing the files, replacing any topology in the +frames or files.
+fn set_topology_file<P>(&mut self, filename: P) -> Result<(), Error> where P: AsRef<Path>
+Set the topology associated with a trajectory by reading the first frame
+of filename; and extracting the topology of this frame.
fn set_cell(&mut self, cell: UnitCell) -> Result<(), Error>
+Set the unit cell associated with a trajectory. This cell will be used +when reading and writing the files, replacing any unit cell in the +frames or files.
+fn nsteps(&mut self) -> Result<usize, Error>
+Get the number of steps (the number of frames) in a trajectory.
+fn sync(&mut self) -> Result<(), Error>
+Synchronize any buffered content to the hard drive.
+unsafe fn from_ptr(ptr: *mut CHFL_TRAJECTORY) -> Trajectory
+Create a Trajectory from a C pointer. This function is unsafe because
+no validity check is made on the pointer.
unsafe fn as_ptr(&self) -> *const CHFL_TRAJECTORY
+Get the underlying C pointer. This function is unsafe because no +lifetime guarantee is made on the pointer.
+Trait Implementations
impl Drop for Trajectory
fn drop(&mut self)
+Struct chemfiles::UnitCell
+
+ [−]
+
+ [src]
+pub struct UnitCell {
+ // some fields omitted
+}An UnitCell represent the box containing the atoms in the system, and its
+periodicity.
A unit cell is fully represented by three lenghts (a, b, c); and three +angles (alpha, beta, gamma). The angles are stored in degrees, and the +lenghts in Angstroms. A cell also has a matricial representation, by +projecting the three base vector into an orthonormal base. We choose to +represent such matrix as an upper triangular matrix:
+ ++ | a_x b_x c_x | + | 0 b_y c_y | + | 0 0 c_z |+ +
An unit cell also have a cell type, represented by the CellType enum.
Methods
impl UnitCell
fn new(a: f64, b: f64, c: f64) -> Result<UnitCell, Error>
+Create an Orthorombic UnitCell from the three lenghts
fn infinite() -> Result<UnitCell, Error>
+Create an Infinite UnitCell
fn triclinic(a: f64, b: f64, c: f64, alpha: f64, beta: f64, gamma: f64) -> Result<UnitCell, Error>
+Create an Triclinic UnitCell from the three lenghts and three angles
fn lengths(&self) -> Result<(f64, f64, f64), Error>
+Get the three lenghts of an UnitCell, in Angstroms.
fn set_lengths(&mut self, a: f64, b: f64, c: f64) -> Result<(), Error>
+Set the three lenghts of an UnitCell, in Angstroms.
fn angles(&self) -> Result<(f64, f64, f64), Error>
+Get the three angles of an UnitCell, in degrees.
fn set_angles(&mut self, alpha: f64, beta: f64, gamma: f64) -> Result<(), Error>
+Set the three angles of an UnitCell, in degrees. This is only possible
+with Triclinic cells.
fn matrix(&self) -> Result<[[f64; 3]; 3], Error>
+Get the unit cell matricial representation.
+fn cell_type(&self) -> Result<CellType, Error>
+Get the type of the unit cell
+fn set_cell_type(&mut self, cell_type: CellType) -> Result<(), Error>
+Set the type of the unit cell
+fn periodicity(&self) -> Result<(bool, bool, bool), Error>
+Get the cell periodic boundary conditions along the three axis
+fn set_periodicity(&mut self, x: bool, y: bool, z: bool) -> Result<(), Error>
+Set the cell periodic boundary conditions along the three axis
+fn volume(&self) -> Result<f64, Error>
+Get the volume of the unit cell
+unsafe fn from_ptr(ptr: *const CHFL_CELL) -> UnitCell
+Create an UnitCell from a C pointer. This function is unsafe because
+no validity check is made on the pointer.
unsafe fn as_ptr(&self) -> *const CHFL_CELL
+Get the underlying C pointer. This function is unsafe because no +lifetime guarantee is made on the pointer.
+Trait Implementations
impl Drop for UnitCell
fn drop(&mut self)
+Redirecting to ../../chemfiles/struct.Topology.html...
+ + + \ No newline at end of file diff --git a/0.4.0/chemfiles/trajectory/index.html b/0.4.0/chemfiles/trajectory/index.html new file mode 100644 index 000000000..e69de29bb diff --git a/0.4.0/chemfiles/trajectory/sidebar-items.js b/0.4.0/chemfiles/trajectory/sidebar-items.js new file mode 100644 index 000000000..7bd8162bc --- /dev/null +++ b/0.4.0/chemfiles/trajectory/sidebar-items.js @@ -0,0 +1 @@ +initSidebarItems({"struct":[["Trajectory","A Trajectory is a chemistry file on the hard drive. It is the main entry point of chemfiles."]]}); \ No newline at end of file diff --git a/0.4.0/chemfiles/trajectory/struct.Trajectory.html b/0.4.0/chemfiles/trajectory/struct.Trajectory.html new file mode 100644 index 000000000..8d4845dd3 --- /dev/null +++ b/0.4.0/chemfiles/trajectory/struct.Trajectory.html @@ -0,0 +1,10 @@ + + + + + + +Redirecting to ../../chemfiles/struct.Trajectory.html...
+ + + \ No newline at end of file diff --git a/0.4.0/chemfiles/type.Result.html b/0.4.0/chemfiles/type.Result.html new file mode 100644 index 000000000..3d5b5ba4a --- /dev/null +++ b/0.4.0/chemfiles/type.Result.html @@ -0,0 +1,113 @@ + + + + + + + + + +chemfiles::Result
+
+ [−]
+
+ [src]
+type Result<T> = Result<T, Error>;
Custom result type for working with errors in chemfiles
+chemfiles_sys::CHFL_ATOM_COARSE_GRAINED
+
+ [−]
+
+ [src]
+pub const CHFL_ATOM_COARSE_GRAINED: CHFL_ATOM_TYPES=1
chemfiles_sys::CHFL_ATOM_DUMMY
+
+ [−]
+
+ [src]
+pub const CHFL_ATOM_DUMMY: CHFL_ATOM_TYPES=2
chemfiles_sys::CHFL_ATOM_ELEMENT
+
+ [−]
+
+ [src]
+pub const CHFL_ATOM_ELEMENT: CHFL_ATOM_TYPES=0
chemfiles_sys::CHFL_ATOM_UNDEFINED
+
+ [−]
+
+ [src]
+pub const CHFL_ATOM_UNDEFINED: CHFL_ATOM_TYPES=3
chemfiles_sys::CHFL_CELL_INFINITE
+
+ [−]
+
+ [src]
+pub const CHFL_CELL_INFINITE: CHFL_CELL_TYPES=2
chemfiles_sys::CHFL_CELL_ORTHORHOMBIC
+
+ [−]
+
+ [src]
+pub const CHFL_CELL_ORTHORHOMBIC: CHFL_CELL_TYPES=0
chemfiles_sys::CHFL_CELL_TRICLINIC
+
+ [−]
+
+ [src]
+pub const CHFL_CELL_TRICLINIC: CHFL_CELL_TYPES=1
chemfiles_sys::CHFL_CXX_ERROR
+
+ [−]
+
+ [src]
+pub const CHFL_CXX_ERROR: CHFL_STATUS=6
chemfiles_sys::CHFL_FILE_ERROR
+
+ [−]
+
+ [src]
+pub const CHFL_FILE_ERROR: CHFL_STATUS=2
chemfiles_sys::CHFL_FORMAT_ERROR
+
+ [−]
+
+ [src]
+pub const CHFL_FORMAT_ERROR: CHFL_STATUS=3
chemfiles_sys::CHFL_GENERIC_ERROR
+
+ [−]
+
+ [src]
+pub const CHFL_GENERIC_ERROR: CHFL_STATUS=5
chemfiles_sys::CHFL_LOG_DEBUG
+
+ [−]
+
+ [src]
+pub const CHFL_LOG_DEBUG: CHFL_LOG_LEVEL=3
chemfiles_sys::CHFL_LOG_ERROR
+
+ [−]
+
+ [src]
+pub const CHFL_LOG_ERROR: CHFL_LOG_LEVEL=0
chemfiles_sys::CHFL_LOG_INFO
+
+ [−]
+
+ [src]
+pub const CHFL_LOG_INFO: CHFL_LOG_LEVEL=2
chemfiles_sys::CHFL_LOG_WARNING
+
+ [−]
+
+ [src]
+pub const CHFL_LOG_WARNING: CHFL_LOG_LEVEL=1
chemfiles_sys::CHFL_MEMORY_ERROR
+
+ [−]
+
+ [src]
+pub const CHFL_MEMORY_ERROR: CHFL_STATUS=1
chemfiles_sys::CHFL_SELECTION_ERROR
+
+ [−]
+
+ [src]
+pub const CHFL_SELECTION_ERROR: CHFL_STATUS=4
chemfiles_sys::CHFL_SUCCESS
+
+ [−]
+
+ [src]
+pub const CHFL_SUCCESS: CHFL_STATUS=0
chemfiles_sys::CORSE_GRAIN
+
+ [−]
+
+ [src]
+pub const CORSE_GRAIN: c_uint=1
chemfiles_sys::DEBUG
+
+ [−]
+
+ [src]
+pub const DEBUG: c_uint=4
chemfiles_sys::DUMMY
+
+ [−]
+
+ [src]
+pub const DUMMY: c_uint=2
chemfiles_sys::ELEMENT
+
+ [−]
+
+ [src]
+pub const ELEMENT: c_uint=0
chemfiles_sys::ERROR
+
+ [−]
+
+ [src]
+pub const ERROR: c_uint=1
chemfiles_sys::INFINITE
+
+ [−]
+
+ [src]
+pub const INFINITE: c_uint=2
chemfiles_sys::INFO
+
+ [−]
+
+ [src]
+pub const INFO: c_uint=3
chemfiles_sys::NONE
+
+ [−]
+
+ [src]
+pub const NONE: c_uint=0
chemfiles_sys::ORTHOROMBIC
+
+ [−]
+
+ [src]
+pub const ORTHOROMBIC: c_uint=0
chemfiles_sys::TRICLINIC
+
+ [−]
+
+ [src]
+pub const TRICLINIC: c_uint=1
chemfiles_sys::UNDEFINED
+
+ [−]
+
+ [src]
+pub const UNDEFINED: c_uint=3
chemfiles_sys::WARNING
+
+ [−]
+
+ [src]
+pub const WARNING: c_uint=2
Enum chemfiles_sys::CHFL_ATOM
+
+ [−]
+
+ [src]
+pub enum CHFL_ATOM {}Enum chemfiles_sys::CHFL_CELL
+
+ [−]
+
+ [src]
+pub enum CHFL_CELL {}Enum chemfiles_sys::CHFL_FRAME
+
+ [−]
+
+ [src]
+pub enum CHFL_FRAME {}Enum chemfiles_sys::CHFL_SELECTION
+
+ [−]
+
+ [src]
+pub enum CHFL_SELECTION {}Enum chemfiles_sys::CHFL_TOPOLOGY
+
+ [−]
+
+ [src]
+pub enum CHFL_TOPOLOGY {}Enum chemfiles_sys::CHFL_TRAJECTORY
+
+ [−]
+
+ [src]
+pub enum CHFL_TRAJECTORY {}chemfiles_sys::chfl_atom
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_atom(name: *const c_char) -> *mut CHFL_ATOM
chemfiles_sys::chfl_atom_atomic_number
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_atom_atomic_number(atom: *const CHFL_ATOM, number: *mut c_int) -> CHFL_STATUS
chemfiles_sys::chfl_atom_charge
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_atom_charge(atom: *const CHFL_ATOM, charge: *mut c_float) -> CHFL_STATUS
chemfiles_sys::chfl_atom_covalent_radius
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_atom_covalent_radius(atom: *const CHFL_ATOM, radius: *mut c_double) -> CHFL_STATUS
chemfiles_sys::chfl_atom_free
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_atom_free(atom: *mut CHFL_ATOM) -> CHFL_STATUS
chemfiles_sys::chfl_atom_from_frame
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_atom_from_frame(frame: *const CHFL_FRAME, idx: size_t) -> *mut CHFL_ATOM
chemfiles_sys::chfl_atom_from_topology
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_atom_from_topology(topology: *const CHFL_TOPOLOGY, idx: size_t) -> *mut CHFL_ATOM
chemfiles_sys::chfl_atom_full_name
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_atom_full_name(atom: *const CHFL_ATOM, name: *mut c_char, buffsize: size_t) -> CHFL_STATUS
chemfiles_sys::chfl_atom_mass
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_atom_mass(atom: *const CHFL_ATOM, mass: *mut c_float) -> CHFL_STATUS
chemfiles_sys::chfl_atom_name
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_atom_name(atom: *const CHFL_ATOM, name: *mut c_char, buffsize: size_t) -> CHFL_STATUS
chemfiles_sys::chfl_atom_set_charge
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_atom_set_charge(atom: *mut CHFL_ATOM, charge: c_float) -> CHFL_STATUS
chemfiles_sys::chfl_atom_set_mass
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_atom_set_mass(atom: *mut CHFL_ATOM, mass: c_float) -> CHFL_STATUS
chemfiles_sys::chfl_atom_set_name
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_atom_set_name(atom: *mut CHFL_ATOM, name: *const c_char) -> CHFL_STATUS
chemfiles_sys::chfl_atom_set_type
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_atom_set_type(cell: *mut CHFL_ATOM, _type: CHFL_ATOM_TYPE) -> CHFL_STATUS
chemfiles_sys::chfl_atom_type
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_atom_type(cell: *const CHFL_ATOM, _type: *mut CHFL_ATOM_TYPE) -> CHFL_STATUS
chemfiles_sys::chfl_atom_vdw_radius
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_atom_vdw_radius(atom: *const CHFL_ATOM, radius: *mut c_double) -> CHFL_STATUS
chemfiles_sys::chfl_cell
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_cell(a: c_double, b: c_double, c: c_double) -> *mut CHFL_CELL
chemfiles_sys::chfl_cell_angles
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_cell_angles(cell: *const CHFL_CELL, alpha: *mut c_double, beta: *mut c_double, gamma: *mut c_double) -> CHFL_STATUS
chemfiles_sys::chfl_cell_free
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_cell_free(cell: *mut CHFL_CELL) -> CHFL_STATUS
chemfiles_sys::chfl_cell_from_frame
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_cell_from_frame(frame: *mut CHFL_FRAME) -> *mut CHFL_CELL
chemfiles_sys::chfl_cell_lengths
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_cell_lengths(cell: *const CHFL_CELL, a: *mut c_double, b: *mut c_double, c: *mut c_double) -> CHFL_STATUS
chemfiles_sys::chfl_cell_matrix
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_cell_matrix(cell: *const CHFL_CELL, mat: *mut [c_double; 3usize]) -> CHFL_STATUS
chemfiles_sys::chfl_cell_periodicity
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_cell_periodicity(cell: *const CHFL_CELL, x: *mut u8, y: *mut u8, z: *mut u8) -> CHFL_STATUS
chemfiles_sys::chfl_cell_set_angles
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_cell_set_angles(cell: *mut CHFL_CELL, alpha: c_double, beta: c_double, gamma: c_double) -> CHFL_STATUS
chemfiles_sys::chfl_cell_set_lengths
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_cell_set_lengths(cell: *mut CHFL_CELL, a: c_double, b: c_double, c: c_double) -> CHFL_STATUS
chemfiles_sys::chfl_cell_set_periodicity
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_cell_set_periodicity(cell: *mut CHFL_CELL, x: u8, y: u8, z: u8) -> CHFL_STATUS
chemfiles_sys::chfl_cell_set_type
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_cell_set_type(cell: *mut CHFL_CELL, _type: CHFL_CELL_TYPE) -> CHFL_STATUS
chemfiles_sys::chfl_cell_triclinic
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_cell_triclinic(a: c_double, b: c_double, c: c_double, alpha: c_double, beta: c_double, gamma: c_double) -> *mut CHFL_CELL
chemfiles_sys::chfl_cell_type
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_cell_type(cell: *const CHFL_CELL, _type: *mut CHFL_CELL_TYPE) -> CHFL_STATUS
chemfiles_sys::chfl_cell_volume
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_cell_volume(cell: *const CHFL_CELL, V: *mut c_double) -> CHFL_STATUS
chemfiles_sys::chfl_clear_errors
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_clear_errors() -> CHFL_STATUS
chemfiles_sys::chfl_frame
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_frame(natoms: size_t) -> *mut CHFL_FRAME
chemfiles_sys::chfl_frame_add_velocities
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_frame_add_velocities(frame: *mut CHFL_FRAME) -> CHFL_STATUS
chemfiles_sys::chfl_frame_atoms_count
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_frame_atoms_count(frame: *const CHFL_FRAME, natoms: *mut size_t) -> CHFL_STATUS
chemfiles_sys::chfl_frame_free
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_frame_free(frame: *mut CHFL_FRAME) -> CHFL_STATUS
chemfiles_sys::chfl_frame_guess_topology
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_frame_guess_topology(frame: *mut CHFL_FRAME, bonds: u8) -> CHFL_STATUS
chemfiles_sys::chfl_frame_has_velocities
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_frame_has_velocities(frame: *const CHFL_FRAME, has_vel: *mut u8) -> CHFL_STATUS
chemfiles_sys::chfl_frame_positions
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_frame_positions(frame: *const CHFL_FRAME, data: *mut c_float, size: size_t) -> CHFL_STATUS
chemfiles_sys::chfl_frame_resize
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_frame_resize(frame: *mut CHFL_FRAME, natoms: size_t) -> CHFL_STATUS
chemfiles_sys::chfl_frame_set_cell
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_frame_set_cell(frame: *mut CHFL_FRAME, cell: *const CHFL_CELL) -> CHFL_STATUS
chemfiles_sys::chfl_frame_set_positions
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_frame_set_positions(frame: *mut CHFL_FRAME, data: *const c_float, size: size_t) -> CHFL_STATUS
chemfiles_sys::chfl_frame_set_step
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_frame_set_step(frame: *mut CHFL_FRAME, step: size_t) -> CHFL_STATUS
chemfiles_sys::chfl_frame_set_topology
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_frame_set_topology(frame: *mut CHFL_FRAME, topology: *const CHFL_TOPOLOGY) -> CHFL_STATUS
chemfiles_sys::chfl_frame_set_velocities
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_frame_set_velocities(frame: *mut CHFL_FRAME, data: *const c_float, size: size_t) -> CHFL_STATUS
chemfiles_sys::chfl_frame_step
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_frame_step(frame: *const CHFL_FRAME, step: *mut size_t) -> CHFL_STATUS
chemfiles_sys::chfl_frame_velocities
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_frame_velocities(frame: *const CHFL_FRAME, data: *mut c_float, size: size_t) -> CHFL_STATUS
chemfiles_sys::chfl_last_error
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_last_error() -> *const c_char
chemfiles_sys::chfl_log_callback
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_log_callback(callback: chfl_logging_callback_t) -> CHFL_STATUS
chemfiles_sys::chfl_log_silent
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_log_silent() -> CHFL_STATUS
chemfiles_sys::chfl_log_stderr
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_log_stderr() -> CHFL_STATUS
chemfiles_sys::chfl_log_stdout
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_log_stdout() -> CHFL_STATUS
chemfiles_sys::chfl_logfile
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_logfile(file: *const c_char) -> CHFL_STATUS
chemfiles_sys::chfl_loglevel
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_loglevel(level: *mut CHFL_LOG_LEVEL) -> CHFL_STATUS
chemfiles_sys::chfl_selection
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_selection(selection: *const c_char) -> *mut CHFL_SELECTION
chemfiles_sys::chfl_selection_evalutate
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_selection_evalutate(selection: *mut CHFL_SELECTION, frame: *const CHFL_FRAME, n_matches: *mut size_t) -> CHFL_STATUS
chemfiles_sys::chfl_selection_free
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_selection_free(selection: *mut CHFL_SELECTION) -> CHFL_STATUS
chemfiles_sys::chfl_selection_matches
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_selection_matches(selection: *const CHFL_SELECTION, matches: *mut chfl_match_t, n_matches: size_t) -> CHFL_STATUS
chemfiles_sys::chfl_selection_size
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_selection_size(selection: *const CHFL_SELECTION, size: *mut size_t) -> CHFL_STATUS
chemfiles_sys::chfl_set_loglevel
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_set_loglevel(level: CHFL_LOG_LEVEL) -> CHFL_STATUS
chemfiles_sys::chfl_strerror
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_strerror(status: c_int) -> *const c_char
chemfiles_sys::chfl_topology
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_topology() -> *mut CHFL_TOPOLOGY
chemfiles_sys::chfl_topology_add_bond
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_topology_add_bond(topology: *mut CHFL_TOPOLOGY, i: size_t, j: size_t) -> CHFL_STATUS
chemfiles_sys::chfl_topology_angles
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_topology_angles(topology: *const CHFL_TOPOLOGY, data: *mut size_t, nangles: size_t) -> CHFL_STATUS
chemfiles_sys::chfl_topology_angles_count
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_topology_angles_count(topology: *const CHFL_TOPOLOGY, nangles: *mut size_t) -> CHFL_STATUS
chemfiles_sys::chfl_topology_append
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_topology_append(topology: *mut CHFL_TOPOLOGY, atom: *const CHFL_ATOM) -> CHFL_STATUS
chemfiles_sys::chfl_topology_atoms_count
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_topology_atoms_count(topology: *const CHFL_TOPOLOGY, natoms: *mut size_t) -> CHFL_STATUS
chemfiles_sys::chfl_topology_bonds
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_topology_bonds(topology: *const CHFL_TOPOLOGY, data: *mut size_t, nbonds: size_t) -> CHFL_STATUS
chemfiles_sys::chfl_topology_bonds_count
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_topology_bonds_count(topology: *const CHFL_TOPOLOGY, nbonds: *mut size_t) -> CHFL_STATUS
chemfiles_sys::chfl_topology_dihedrals
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_topology_dihedrals(topology: *const CHFL_TOPOLOGY, data: *mut size_t, ndihedrals: size_t) -> CHFL_STATUS
chemfiles_sys::chfl_topology_dihedrals_count
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_topology_dihedrals_count(topology: *const CHFL_TOPOLOGY, ndihedrals: *mut size_t) -> CHFL_STATUS
chemfiles_sys::chfl_topology_free
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_topology_free(topology: *mut CHFL_TOPOLOGY) -> CHFL_STATUS
chemfiles_sys::chfl_topology_from_frame
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_topology_from_frame(frame: *mut CHFL_FRAME) -> *mut CHFL_TOPOLOGY
chemfiles_sys::chfl_topology_isangle
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_topology_isangle(topology: *const CHFL_TOPOLOGY, i: size_t, j: size_t, k: size_t, result: *mut u8) -> CHFL_STATUS
chemfiles_sys::chfl_topology_isbond
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_topology_isbond(topology: *const CHFL_TOPOLOGY, i: size_t, j: size_t, result: *mut u8) -> CHFL_STATUS
chemfiles_sys::chfl_topology_isdihedral
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_topology_isdihedral(topology: *const CHFL_TOPOLOGY, i: size_t, j: size_t, k: size_t, m: size_t, result: *mut u8) -> CHFL_STATUS
chemfiles_sys::chfl_topology_remove
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_topology_remove(topology: *mut CHFL_TOPOLOGY, i: size_t) -> CHFL_STATUS
chemfiles_sys::chfl_topology_remove_bond
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_topology_remove_bond(topology: *mut CHFL_TOPOLOGY, i: size_t, j: size_t) -> CHFL_STATUS
chemfiles_sys::chfl_trajectory_close
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_trajectory_close(file: *mut CHFL_TRAJECTORY) -> CHFL_STATUS
chemfiles_sys::chfl_trajectory_nsteps
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_trajectory_nsteps(file: *mut CHFL_TRAJECTORY, nsteps: *mut size_t) -> CHFL_STATUS
chemfiles_sys::chfl_trajectory_open
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_trajectory_open(filename: *const c_char, mode: *const c_char) -> *mut CHFL_TRAJECTORY
chemfiles_sys::chfl_trajectory_read
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_trajectory_read(file: *mut CHFL_TRAJECTORY, frame: *mut CHFL_FRAME) -> CHFL_STATUS
chemfiles_sys::chfl_trajectory_read_step
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_trajectory_read_step(file: *mut CHFL_TRAJECTORY, step: size_t, frame: *mut CHFL_FRAME) -> CHFL_STATUS
chemfiles_sys::chfl_trajectory_set_cell
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_trajectory_set_cell(file: *mut CHFL_TRAJECTORY, cell: *const CHFL_CELL) -> CHFL_STATUS
chemfiles_sys::chfl_trajectory_set_topology
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_trajectory_set_topology(file: *mut CHFL_TRAJECTORY, topology: *const CHFL_TOPOLOGY) -> CHFL_STATUS
chemfiles_sys::chfl_trajectory_set_topology_file
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_trajectory_set_topology_file(file: *mut CHFL_TRAJECTORY, filename: *const c_char) -> CHFL_STATUS
chemfiles_sys::chfl_trajectory_set_topology_with_format
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_trajectory_set_topology_with_format(file: *mut CHFL_TRAJECTORY, filename: *const c_char, format: *const c_char) -> CHFL_STATUS
chemfiles_sys::chfl_trajectory_sync
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_trajectory_sync(file: *mut CHFL_TRAJECTORY) -> CHFL_STATUS
chemfiles_sys::chfl_trajectory_with_format
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_trajectory_with_format(filename: *const c_char, mode: *const c_char, format: *const c_char) -> *mut CHFL_TRAJECTORY
chemfiles_sys::chfl_trajectory_write
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_trajectory_write(file: *mut CHFL_TRAJECTORY, frame: *const CHFL_FRAME) -> CHFL_STATUS
chemfiles_sys::chfl_version
+
+ [−]
+
+ [src]
+pub unsafe extern fn chfl_version() -> *const c_char
Crate chemfiles_sys + + [−] + + [src]
+Enums
+| CHFL_ATOM | ++ + | +
| CHFL_CELL | ++ + | +
| CHFL_FRAME | ++ + | +
| CHFL_TOPOLOGY | ++ + | +
| CHFL_TRAJECTORY | ++ + | +
Constants
+| CORSE_GRAIN | ++ + | +
| DEBUG | ++ + | +
| DUMMY | ++ + | +
| ELEMENT | ++ + | +
| ERROR | ++ + | +
| INFINITE | ++ + | +
| INFO | ++ + | +
| NONE | ++ + | +
| ORTHOROMBIC | ++ + | +
| TRICLINIC | ++ + | +
| UNDEFINED | ++ + | +
| WARNING | ++ + | +
Functions
+Type Definitions
+| CHFL_ATOM_TYPE | ++ + | +
| CHFL_CELL_TYPE | ++ + | +
| CHFL_LOG_LEVEL | ++ + | +
| CHFL_STATUS | ++ + | +
| size_t | ++ + | +
Struct chemfiles_sys::chfl_match_t
+
+ [−]
+
+ [src]
+pub struct chfl_match_t {
+ pub size: c_char,
+ pub atoms: [size_t; 4],
+}Fields
+size | |
atoms |
Trait Implementations
Derived Implementations
impl Eq for chfl_match_t
impl PartialEq for chfl_match_t
fn eq(&self, __arg_0: &chfl_match_t) -> bool
+fn ne(&self, __arg_0: &chfl_match_t) -> bool
+impl Debug for chfl_match_t
impl Copy for chfl_match_t
impl Clone for chfl_match_t
fn clone(&self) -> chfl_match_t
+1.0.0fn clone_from(&mut self, source: &Self)
+chemfiles_sys::CHFL_ATOM_TYPE
+
+ [−]
+
+ [src]
+type CHFL_ATOM_TYPE = c_uint;
chemfiles_sys::CHFL_ATOM_TYPES
+
+ [−]
+
+ [src]
+type CHFL_ATOM_TYPES = c_uint;
chemfiles_sys::CHFL_CELL_TYPE
+
+ [−]
+
+ [src]
+type CHFL_CELL_TYPE = c_uint;
chemfiles_sys::CHFL_CELL_TYPES
+
+ [−]
+
+ [src]
+type CHFL_CELL_TYPES = c_uint;
chemfiles_sys::CHFL_LOG_LEVEL
+
+ [−]
+
+ [src]
+type CHFL_LOG_LEVEL = c_uint;
chemfiles_sys::CHFL_STATUS
+
+ [−]
+
+ [src]
+type CHFL_STATUS = c_int;
chemfiles_sys::c_bool
+
+ [−]
+
+ [src]
+type c_bool = u8;
chemfiles_sys::chfl_logging_callback_t
+
+ [−]
+
+ [src]
+type chfl_logging_callback_t = extern "C" fn(CHFL_LOG_LEVEL, *const c_char);
chemfiles_sys::size_t
+
+ [−]
+
+ [src]
+type size_t = usize;
Crate lazy_static + + [−] + + [src]
+A macro for declaring lazily evaluated statics.
+ +Using this macro, it is possible to have statics that require code to be
+executed at runtime in order to be initialized.
+This includes anything requiring heap allocations, like vectors or hash maps,
+as well as anything that requires function calls to be computed.
Syntax
++lazy_static! { + [pub] static ref NAME_1: TYPE_1 = EXPR_1; + [pub] static ref NAME_2: TYPE_2 = EXPR_2; + ... + [pub] static ref NAME_N: TYPE_N = EXPR_N; +}+ +
Metadata (such as doc comments) is allowed on each ref.
+ +Semantic
+For a given static ref NAME: TYPE = EXPR;, the macro generates a unique type that
+implements Deref<TYPE> and stores it in a static with name NAME. (Metadata ends up
+attaching to this type.)
On first deref, EXPR gets evaluated and stored internally, such that all further derefs
+can return a reference to the same object.
Like regular static muts, this macro only works for types that fulfill the Sync
+trait.
Example
+Using the macro:
+ ++#[macro_use] +extern crate lazy_static; + +use std::collections::HashMap; + +lazy_static! { + static ref HASHMAP: HashMap<u32, &'static str> = { + let mut m = HashMap::new(); + m.insert(0, "foo"); + m.insert(1, "bar"); + m.insert(2, "baz"); + m + }; + static ref COUNT: usize = HASHMAP.len(); + static ref NUMBER: u32 = times_two(21); +} + +fn times_two(n: u32) -> u32 { n * 2 } + +fn main() { + println!("The map has {} entries.", *COUNT); + println!("The entry for `0` is \"{}\".", HASHMAP.get(&0).unwrap()); + println!("A expensive calculation on a static results in: {}.", *NUMBER); +}+ +
Implementation details
+The Deref implementation uses a hidden static variable that is guarded by a atomic check on each access. On stable Rust, the macro may need to allocate each static on the heap.
Modules
+| lazy | ++ + | +
Macros
+| __lazy_static_create! | ++ + | +
| lazy_static! | ++ + | +
Traits
+| __Deref | +
+ The |
+