Biotite 0.19.1

Changelog

Additions

• FASTA files can be downloaded from RCSB PDB via database.rcsb
• Added structure.rotate_about_axis() and structure.align_vectors()
• Added shape property and copy() method to structure.Atom
• All array-like objects can be used to set an annotation array in an atom array (stack)
• Added structure.info.residue() for getting the standard atoms and their coordinates for a given residue name
• Added structure.graphics.plot_atoms() for interactive molecular visualization
• Added exclusive_stop parameter to structure.get_residue_starts and structure.get_chain_starts
• Added connect_via_residue_names() and connect_via_distances() for calculating a structure.BondList for a structure.AtomArray

Changes

• structure.rotate() does not rotate the box of an atom array (stack) anymore
• structure.BondList equality is not order dependent

Fixes

• structure.BondList accepts all dtypes for integer arrays
• structure.BondList accepts negative integers as indices
• sequence.io.fasta.FastaFile: Tests for invalid or empty files
• structure.io.pdb.PDBFile: Exception is raised if an invalid field in extra_fields is given
• structure.rotate(): Fixed rotation direction

Biotite 0.18.0

Changelog

Additions

• Added shape property to structure.AtomArray() and
  structure.AtomArrayStack()
• structure.Atom() has default values for annotation arrays
• The functions structure.rmsf(), structure.rmsd() and structure.average()
  accept directly coordinates
• Added use_author_fields parameter to structure.io.pdbx.get_structure(),
  that allows to decide between the usage of label_xxx and auth_xxx fields
• Added chunk_size parameter to read() method of trajectory files to
  resolve memory issues
• Added density() function for calculating atom densities.
• Added sequence.align.get_pairwise_sequence_identity()
• API reference shows source files of Cython modules

Changes

• The module name (__module__ attribute) of functions/classes are
  changed to the name of the respective Biotite subpackage
  (e.g. biotite.structure.atoms to biotite.structure)
• Changed handling of PDB insertion codes:
  • Atoms with insertion codes are not filtered out
  • Removed insertion_code parameter in
    biotite.structure.io.xxx.get_structure()
  • New mandatory annotation category ins_code
  • Changed structure.filter_inscode_and_altloc() to
    structure.filter_altloc()

Fixes

• The step parameter in the read() method of trajectory files does not
  increase the stop frame
• Negative residue IDs are handled correctly by structure file readers/writers
• Fixed issues with indexing behavior in sequence.align.Alignment class
• structure.remove_pbc() raises proper error message when box is missing
  in the given atom array (stack)
• sequence.align.align_multiple() raises proper error message, if
  pairwise distance cannot be calculated due to great sequence dissimilarity
• In sequence.io.genbank.get_annotation() qualifier keys without values
  (e.g. /pseudo) are handled properly
• Added pyproject.toml specifying build dependencies for setup.py

Biotite 0.17.0

Changelog

Additions

• Support for hybrid-36 encoding in structure.io.pdb.PDBFile
• Added get_coord() method in structure.io.pdb.PDBFile for efficiently reading only the coordinates from a file
• structure.CellList can be configured to put only a subset of atoms into the cells via the selection parameter
• Improved functionalities in database subpackage.
  • A lot of new query types in database.rcsb
  • The min and max parameter of some database.rcsb queries are now optional
  • database.rcsb.fetch() and database.entrez.fetch() are able to write the downloaded files into a file-like object instead of writing the file to hard drive
  • database.entrez.fetch() properly checks for invalid responses from server based on https://github.com/kblin/ncbi-entrez-error-messages
  • database.entrez.fetch() also supports common database names
  • database.entrez.SimpleQuery also supports abbreviated field names
• structure.io.load_structure() and structure.io.save_structure() support keyword arguments that are forwarded to the respective read() or get_structure() method.

Changes

• database subpackage raises database.RequestError objects when the server gives an invalid response

Fixes

• Fixed cross references in the API reference
• sequence.io.genbank.GenBankFile raises a warning instead of an exception if the feature's location identifier is not understood and skips the feature
• structure.io.pdb.PDBFile properly checks whether all models have the same amount of atoms, when building a structure.AtomArrayStack

Biotite 0.16.0

Changelog

Additions

• New alignment color schemes
  • Color schemes for protein sequence alignments created with Gecos software
    • Including a color scheme adapted for red-green blindness
  • Color scheme for protein block sequence alignments created with Gecos software
  • Color schemes for protein sequence alignments adapted from JalView
• More functionalities for external MSA software (application.MSAApp subclasses)
  • Additional CLI options can be set via add_additional_options()
  • The executed command of application.LocalApp can be optained via get_coomand()
  • Most MSA software interfaces allow setting and getting the distance matrix and the guide tree
    • The corresponding method are get_guide_tree(), set_guide_tree(), get_distance_matrix() and set_distance_matrix()
  • MSA software supporting cutom substitution matrices can be used to align almost any type of sequence, even if the type is not directly supported by the underlying software
• Added euality operator for sequence.align.Alignment objects
• sequence.phylo.Tree supports non-binary trees
  • sequence.phylo.TreeNode can handle more than two child nodes
  • len() gives amount of leaves in sequence.phylo.Tree
  • sequence.phylo.Tree and sequence.phylo.TreeNode support hash and equality operator
  • sequence.phylo.as_binary() function converts non-binary tree into binary tree, as required for guide trees
• Added sequence.phylo.neighbor_joining() for hierarchical clustering

Changes

• Removed X as symbol for ambiguous nucleotides, use N instead
• Removed protected method get_default_bin_path() from application.MSAApp
• Renamed protected method set_options() to set_arguments() application.LocalApp
• Renamed set_matrix() to set_substitution_matrix() application.muscle.MuscleApp
• Removed protected method get_cli_arguments() in application.LocalApp
• Adapted constructor of sequence.phylo.TreeNode for variable amount of child nodes
• application.MSAApp subclasses must implement abstract static methods describing which sequence types they support and whether they support custom substitution matrices

Fixes

• U is automatically converted to T when loading nulceotide sequences from FASTA files
• Score matrix in sequence.align.SubstitutionMatrix is now truly read-only via ndarray flag
• application.Application subclasses (all external software interfaces) now properly check whether the corresponding objects are in the correct application.AppState
• Error in evaluation step of application.Application now leaves application in application.AppState.CANCELLED state
• Fixed InvalidFileError not being exposed to user
• Symmetry checks in sequence.phylo.upgma() allow for small rounding errors

Biotite 0.15.1

Changelog

Additions

• Increased performance of sequence.NucleotideSequence.translate() method
  • Added map_codon_codes() method to sequence.CodonTable for efficient codon to amino acid mapping

Biotite 0.15.0

Changelog

Additions

• Highly increased performance of encoding/decoding of sequence to sequence code and vice versa
  • sequence.Alphabet.decode_multiple() accepts any array-like object as sequence code
• Added read/write support for GFF3 files
  • Added sequence.io.gff subpackage
  • Contains sequence.io.gff.GFFFile as low level interface to GFF3 files
  • Contains get_annotation() and set_annotation() functions as high level interface to GFF3 files

Biotite 0.14.0

Changelog

Additions

• Added convenience functions for chains, similar to the functions for residues
  • Added get_chain_starts()
  • Added get_chains()
  • Added get_chain_count()
  • Added chain_iter()
• Revamped interface for GenBank files
  • sequence.io.genbank.GenBankFile provides a low-level API for obtaining field names and the corresponding lines and subfields
  • sequence.io.genbank.GenBankFile is now used for both GenBank and GenPept files
  • High level objects are obtained via module-level functions
    • get_locus(), get_definition(), get_accession(), get_version(), get_gi(), get_source(), get_db_link(), get_annotation(), get_sequence() and get_annotated_sequence() are now functions sequence.io.genbank
  • Added set_locus(), set_annotation(), set_sequence(), set_annotated_sequence(), to sequence.io.genbank for creating and editing GenBank files

Changes

• structure.dihedral_backbone() does not require a chain ID anymore
  • The dihedrals are automatically calculated over all chains
  • Dihedrals at the transition of one chain to the next one are NaN
• Completely changed usage of sequence.io.genbank.GenBankFile (see above)

Fixes

• Atom IDs above 99999 and residue IDs above 9999 do not break writing structure.io.gro.GROFile
  • In case of overflow, the ID restarts at 1
• Dummy boxes in .gro files are not converted into a real box attribute of a structure.AtomArray anymore
• When creating a sequence.Alignment from strings, it is checked whether at least to strings (sequences) are given
• Fixed annotation equality checks when setting an structure.AtomArrayStack element with an structure.AtomArray
• Fixed indexing a sequence.AnnotatedSequence with a sequence.Feature containing multiple locations
  • Previously the locations were merged in a random order resulting in wrong sequence.Sequence objects

Biotite 0.13.1

Changelog

Fixes

• structure.io.gro.GROFile appends a newline at the end of file
  • This allows PyMOL to open .gro files
• structure.io.pdb.PDBFile raises an exception when coordinates contain NaN values
• structure.io.pdb.PDBFile works properly for residue IDs greater than 9999
• structure.io.pdb.PDBFile works properly for atom array lengths greater than 199998

Biotite 0.13.0

Changelog

Additions

• structure.hbond() supports periodic boundary conditions
• Added structure.remove_pbc() and structure.remove_pbc_coord(), that sanitize structures that are segmented due to periodic boundaries
• Write support for trajectory files
  • This includes structure.io.save_structure()
• Support for DCD and NetCDF trajectory formats (structure.io.dcd and structure.io.netcdf)

Changes

• The coord and box attribute in structure.AtomArray and structure.AtomArrayStack are stored as float32 arrays
  • File readers are changed accordingly
  • Previously, both float64 and float32 were allowed, which made type conversions necessary for some functions
  • If an atom array (stack) is provided with an float64 array, the type is implicitly converted.
• Faster encoding and decoding in sequence.LetterAlphabet
  • Internally uses bytes instead of str for symbols
  • sequence.LetterAlphabet does only accept ASCII characters
• Discontinued support for Python type annotations
  • May be re-enabled when official type annotations for NumPy arrive
• Changed protected abstract methods in structure.io.TrajectoryFile
• structure.filter_solvent() regards only the res_name and ignores the hetero field

Fixes

• structure.io.mmtf.MMTFFile fields can be set with ndarray objects for non-encoded fields
  • The ndarray objects are implicitly converted into list objects
• The box attribute of structure.AtomArrayStack objects are correctly sliced when slicing the atom array stack
• structure.displacement(), structure.distance(), structure.angle() and structure.dihedral() accept structure.Atom instances as parameter

Biotite 0.12.0

Changelog

Additions

• Added new structure.info subpackage that contains all kinds of basic structure-related data
  • structure.info.mass() function provides weight for elements, residue name and enitre structures
  • structure.info.vdw_radius_single() and structure.info.vdw_radius_protor() function provides Van-der-Waals radii for single elements or atoms with bonded hydrogens, respectively
  • structure.info.bond_order() and structure.info.bonds_in_residue() provide information about bonded atoms
  • structure.full_name() provides the full name of an up to 3-letter residue/compound name
  • structure.link_type() provides the link type for a residue name
• Added structure.rdf() function for calculation of the radial distribution function of positions in an AtomArray or AtomArrayStack
• Added structure.residue_iter() function, that yields each residue in an AtomArray or AtomArrayStack as an subarray (stack)

Changes

• Removed structure.mass_of_element() and structure.atom_masses()
• When writing MMTF files, the chemCompType in groupList is determined via structure.link_type()

Fixes

• PDB files can be written for structures with more than 100,000 atoms
  • When the amount of 99,999 atoms is exceeded, the atom ID starts over again
• dir() function gives proper results for AtomArray and AtomArrayStack
• Fixed ProtOr radii in structure.sasa()
• structure.stack() includes the box attribute when stacking AtomArray objects