sphinx-documentation.md

rdkit_to_params package

Submodules

rdkit_to_params.constraint module

This contains make_constraint which is creates a constraint file. It is completely independent and different in style because it was different. It is not integral to the conversion, it’s just a utility.

class rdkit_to_params.constraint.Constraints(smiles, names, ligand_res, target_res)

Bases: object

_init_(smiles, names, ligand_res, target_res)

Give smiles of the two sides (with \*) and the names, residue numbers convert. It requires 2 atoms on each side in addition to the attachment point. Note that the atom names are stored in a non-standard way out of laziness. in the Atom prop ‘_AtomName’. The instance has the following attributes

• smiles: stored input smiles string

• names: stored input list of names

• ligand_res: stored input liagnd residue

• target_res: stored input protein residue

• cov_template: Chem.Mol from first smiles.

• target_template: Chem.Mol from first smiles

• combo: combined templates

• atom_pair_constraint: AtomPair

• angle_constraint: Angle . NB. this is two lines.

• dihedral_constaint: dihedral

Class methods: * assign_names(mol, list) classmethods that assigns names to a mol in place. * join_by_dummy(molA, molB) classmethods that returns a joined molecule

• Parameters

  • smiles (Tuple[str, str]) – a tuple/list of two string. The first is the ligand, the second is the peptide.

  • names (List[str]) – a list of atom names. The ‘*’ will need a name -but will be ignored-, but not the H.

  • ligand_res (Union[str, int]) – ligand residue in pose or PDB format (12 vs. 12A)

  • target_res (Union[str, int]) – peptide residue in pose or PDB format (12 vs. 12A)

classmethod assign_names(mol, names)

Stores names of atoms as given in the list. totally non-standard way. PDBInfo is correct way. But too much effort.

• Return type

  None

get_atom(mol, name)

• Return type

  Atom

classmethod get_conn(mol)

Get connecting atom of mol.

• Return type

  Atom

classmethod join_by_dummy(a, b)

• Return type

  Mol

rdkit_to_params.entries module

The main class here is Entries`, which is a fancy list. It gets called for each uppercase attribute in the initialisation of Params (which happens in _ParamsInitMixin e.g. Entries.from_name('IO_STRING')).

class rdkit_to_params.entries.AAEntry(body='UNK')

Bases: rdkit_to_params.entries.GenericEntry

_init_(body='UNK')

Initialize self. See help(type(self)) for accurate signature.

class rdkit_to_params.entries.ACT_COORD_ATOMSEntry(*args)

Bases: rdkit_to_params.entries.GenericListEntry

_init_(*args)

Initialize self. See help(type(self)) for accurate signature.

class rdkit_to_params.entries.ADD_RINGEntry(body)

Bases: rdkit_to_params.entries.GenericEntry

_init_(body)

Initialize self. See help(type(self)) for accurate signature.

class rdkit_to_params.entries.ATOMEntry(name: str, rtype: str, mtype: str = 'X', partial: float = 0)

Bases: object

_init_(name: str, rtype: str, mtype: str = 'X', partial: float = 0)

• Return type

  None

classmethod from_str(text)

mtype(: str = 'X')

name(: str = None)

partial(: float = 0)

rtype(: str = None)

class rdkit_to_params.entries.ATOM_ALIASEntry(body)

Bases: rdkit_to_params.entries.GenericEntry

_init_(body)

Initialize self. See help(type(self)) for accurate signature.

class rdkit_to_params.entries.BONDEntry(first: str, second: str, order: int = 1)

Bases: object

dataclass class for both BOND and BOND_ENTRY. The __str__ method will know based on .order. The hash is the two atom names sorted. So BOND records with the same names will be equal.

_init_(first: str, second: str, order: int = 1)

• Return type

  None

_post_init_()

first(: str = None)

classmethod from_str(text)

order(: int = 1)

second(: str = None)

class rdkit_to_params.entries.CHIEntry(index: int, first: str, second: str, third: str, fourth: str)

Bases: object

_init_(index: int, first: str, second: str, third: str, fourth: str)

• Return type

  None

_post_init_()

first(: str = None)

fourth(: str = None)

classmethod from_str(text)

index(: int = None)

second(: str = None)

third(: str = None)

class rdkit_to_params.entries.CONNECTEntry(atom_name: str, index: int = 1, connect_type: str = '', connect_name: str = '')

Bases: object

This is a mess, but it guesses what you mean. Deals with UPPER, LOWER and CONNECT.

_init_(atom_name: str, index: int = 1, connect_type: str = '', connect_name: str = '')

• Return type

  None

_post_init_()

atom_name(: str = None)

connect_name(: str = '')

connect_type(: str = '')

classmethod from_str(text)

index(: int = 1)

class rdkit_to_params.entries.CUT_BONDEntry(first: str, second: str)

Bases: object

No idea what CUT_BOND is for.

_init_(first: str, second: str)

• Return type

  None

_post_init_()

first(: str = None)

classmethod from_str(text)

second(: str = None)

class rdkit_to_params.entries.CommentEntry(body)

Bases: rdkit_to_params.entries.GenericEntry

_init_(body)

Initialize self. See help(type(self)) for accurate signature.

class rdkit_to_params.entries.Entries(entry_cls, singleton=True)

Bases: collections.abc.MutableSequence

A fancy default list, where the elements are instances of whatver is in entry_cls. It can be initialised via the class method from_name which accepst a string that has to be present in the class attribute .choices. The .append method can work with str, list, dict or instance of the actual class it wants. Note that the string for the string way must be without the header to the line. The entry classes requires a from_str classmethod that returns an instance for this. They also require str method as this is how the entries are converted into string.

Entries.from_name('BOND')

_init_(entry_cls, singleton=True)

The entries class is a fancy constrained list. The data is actually stored in .data.

• Parameters

  • entry_cls – what is the allowed class of the entries

  • singleton (bool) – is only one entry allowed?

choices( = {'#': (<class 'rdkit_to_params.entries.CommentEntry'>, False), 'AA': (<class 'rdkit_to_params.entries.AAEntry'>, True), 'ACT_COORD_ATOMS': (<class 'rdkit_to_params.entries.ACT_COORD_ATOMSEntry'>, True), 'ADD_RING': (<class 'rdkit_to_params.entries.ADD_RINGEntry'>, False), 'ATOM': (<class 'rdkit_to_params.entries.ATOMEntry'>, False), 'ATOM_ALIAS': (<class 'rdkit_to_params.entries.ATOM_ALIASEntry'>, False), 'BOND': (<class 'rdkit_to_params.entries.BONDEntry'>, False), 'CHI': (<class 'rdkit_to_params.entries.CHIEntry'>, False), 'CONNECT': (<class 'rdkit_to_params.entries.CONNECTEntry'>, False), 'CUT_BOND': (<class 'rdkit_to_params.entries.CUT_BONDEntry'>, False), 'FIRST_SIDECHAIN_ATOM': (<class 'rdkit_to_params.entries.FIRST_SIDECHAIN_ATOMEntry'>, True), 'ICOOR_INTERNAL': (<class 'rdkit_to_params.entries.ICOOR_INTERNALEntry'>, False), 'IO_STRING': (<class 'rdkit_to_params.entries.IO_STRINGEntry'>, True), 'METAL_BINDING_ATOMS': (<class 'rdkit_to_params.entries.METAL_BINDING_ATOMSEntry'>, True), 'NBR_ATOM': (<class 'rdkit_to_params.entries.NBR_ATOMEntry'>, True), 'NBR_RADIUS': (<class 'rdkit_to_params.entries.NBR_RADIUSEntry'>, True), 'PDB_ROTAMERS': (<class 'rdkit_to_params.entries.PDB_ROTAMERSEntry'>, True), 'PROPERTIES': (<class 'rdkit_to_params.entries.PROPERTIESEntry'>, False), 'RAMA_PREPRO_FILENAME': (<class 'rdkit_to_params.entries.RAMA_PREPRO_FILENAMEEntry'>, True), 'ROTAMER_AA': (<class 'rdkit_to_params.entries.ROTAMER_AAEntry'>, True), 'TYPE': (<class 'rdkit_to_params.entries.TYPEEntry'>, True), 'comment': (<class 'rdkit_to_params.entries.CommentEntry'>, False)})

classmethod from_name(name)

insert(index, value)

S.insert(index, value) – insert value before index

class rdkit_to_params.entries.FIRST_SIDECHAIN_ATOMEntry(body)

Bases: rdkit_to_params.entries.GenericEntry

_init_(body)

Initialize self. See help(type(self)) for accurate signature.

class rdkit_to_params.entries.GenericEntry(header, body)

Bases: object

This is meant to be inherited. header is the entry type. body is a string.

_init_(header, body)

Initialize self. See help(type(self)) for accurate signature.

classmethod from_str(text)

class rdkit_to_params.entries.GenericListEntry(header, *args)

Bases: object

This is meant to be inherited. header is the entry type. values is a list of strings.

_init_(header, *args)

Initialize self. See help(type(self)) for accurate signature.

classmethod from_str(text)

class rdkit_to_params.entries.ICOOR_INTERNALEntry(child: str, phi: float, theta: float, distance: float, parent: str, second_parent: str, third_parent: str)

Bases: object

Lines stolen from Rosetta documentation

                Child  Phi Angle    Theta        Distance   Parent  Angle  Torsion

ICOOR_INTERNAL C14 167.536810 59.880644 1.473042 N2 C11 C12

• Child atom (A4)

• phi angle (torsion angle between A1, A2, A3, A4)

• theta angle (improper angle = (180 - (angle between A4, A3, A2)))

• distance (between A4 and A3)

• parent atom (A3)

• angle atom (A2)

• torsion atom (A4)

_init_(child: str, phi: float, theta: float, distance: float, parent: str, second_parent: str, third_parent: str)

• Return type

  None

_post_init_()

child(: str = None)

distance(: float = None)

classmethod from_str(text)

parent(: str = None)

phi(: float = None)

second_parent(: str = None)

theta(: float = None)

third_parent(: str = None)

class rdkit_to_params.entries.IO_STRINGEntry(name3: str = 'LIG', name1: str = 'Z')

Bases: object

• .name3 is three letter name. Params().NAME is actually a dynamic attribute that uses this.

• .name1 is a one letter name.

These get checked for length.

_init_(name3: str = 'LIG', name1: str = 'Z')

• Return type

  None

_post_init_()

classmethod from_str(text)

name1(: str = 'Z')

name3(: str = 'LIG')

class rdkit_to_params.entries.METAL_BINDING_ATOMSEntry(*args)

Bases: rdkit_to_params.entries.GenericListEntry

_init_(*args)

Initialize self. See help(type(self)) for accurate signature.

class rdkit_to_params.entries.NBR_ATOMEntry(body)

Bases: rdkit_to_params.entries.GenericEntry

_init_(body)

Initialize self. See help(type(self)) for accurate signature.

class rdkit_to_params.entries.NBR_RADIUSEntry(body)

Bases: rdkit_to_params.entries.GenericEntry

_init_(body)

Initialize self. See help(type(self)) for accurate signature.

class rdkit_to_params.entries.PDB_ROTAMERSEntry(body)

Bases: rdkit_to_params.entries.GenericEntry

This does zero checks for fine existance.

_init_(body)

Initialize self. See help(type(self)) for accurate signature.

class rdkit_to_params.entries.PROPERTIESEntry(*args)

Bases: rdkit_to_params.entries.GenericListEntry

_init_(*args)

Initialize self. See help(type(self)) for accurate signature.

class rdkit_to_params.entries.RAMA_PREPRO_FILENAMEEntry(body)

Bases: rdkit_to_params.entries.GenericEntry

_init_(body)

Initialize self. See help(type(self)) for accurate signature.

class rdkit_to_params.entries.ROTAMER_AAEntry(body)

Bases: rdkit_to_params.entries.GenericEntry

_init_(body)

Initialize self. See help(type(self)) for accurate signature.

class rdkit_to_params.entries.TYPEEntry(body='LIGAND')

Bases: rdkit_to_params.entries.GenericEntry

LIGAND or POLYMER. No exceptions.

_init_(body='LIGAND')

Initialize self. See help(type(self)) for accurate signature.

Module contents

The main class here is Params. All underscore base classes are not meant to be used standalone. Entries is the class for an list of entries of the same kind.

class rdkit_to_params.Params()

Bases: rdkit_to_params._io_mixin._ParamsIoMixin, rdkit_to_params._rdkit_convert._RDKitCovertMixin, rdkit_to_params._pyrosetta_mixin._PoserMixin

Params creates and manipulates params files. It can handles several types of params operations, such as “atom name surgery” and rdkit.Chem.Mol to a params file.

Key methods

• Params.load(filename) will instantiate from file.

• Params.from_mol(mol) will instantiate from Chem.Mol

• p.dump(filename) will save a file.

• loads and

``

dumps``for strings.

• p.fields will return all header fields.

• p.test tests the params file in PyRosetta.

• p.rename_atom(old, new) changes an atom name

Attributes

The attributes are generally the uppercase line headers, with a few exceptions.

• .comments is for # lines

• “BOND_TYPE” and “BOND” are merged into .BOND.

• “UPPER”, “LOWER” and “CONNECT” are merged into .CONNECT

With the exception of .NAME which depends on .IO_STRING basically all the header type attributes are actually instances of the class Entries, which holds a sequence of specific entries. see entry.py for the properties of each. These can be a singleton, such as .IO_STRING which when a new line is added it gets overwritten instead, or not like say .ATOM. That is to say that .ATOM[0] will give the first atom as expected, but this has to be done for .IO_STRING[0] too.

Atomnames…

• p.get_correct_atomname will return the 4 letter name of the atom with nice spacing as present in the entries

• p.rename_atom will change one atomname to a new one across all entries.

• BOND, CHI, CUT_BOND entries store 4 char atomnames as .first, .second, .third, .fourth.

• ICOOR_INTERNAL entries store 5 char atomnames as .child,``.parent``,``.second_parent``,``.third_parent``.

• ATOM_ALIAS, NBR_ATOM, FIRST_SIDECHAIN_ATOM, ADD_RING are just entries.GenericEntries instances, where .body is a string which will contain the atomname.

• METAL_BINDING_ATOMS, ACT_COORD_ATOMS are entries.GenericListEntries instances where .values is a list of string with maybe atomnames.

Inheritance

It inherits several class, which are not not mean to be used standalone, except for testing.

The pyrosetta and rdkit functionality are dependent on these being installed.

• _ParamsIoMixin adds read write, and inherits

• _ParamsInitMixin which adds the basics.

• _PoserMixin is a base that adds pyrosetta functionality if avaliable.

• _RDKitCovertMixin, which adds rdkit from_mol conversion functionality, the class is split in two, the other part being

• _RDKitParamsPrepMixin, which prepares the molecule for _RDKitCovertMixin.from_mol`.

property NAME()

rename_atom(oldname, newname)

Change the atom name from oldname to newname and returns the 4 char newname.

• Parameters

  • oldname (str) – atom name, preferably 4 char long.

  • newname (str) – atom name, preferably 4 char long.

• Return type

  str

• Returns

  4 char newname

get_correct_atomname(name)

Given a name, gets the correctly spaced out one. This has nothing to do with ._get_PDBInfo_atomname which just returns the atom name from a Chem.Atom.

• Parameters

  name (str) – dirty name

• Return type

  str

• Returns

  correct name

validate()