Biotite 0.23.0

Changelog

Additions

• Improved example gallery
  • Added minigalleries in the API reference to get tangible examples for the
    respective function/class
  • Added support for animated Matplotlib plots
  • Using Ammolite for rendering
    PyMOL images
• Added support for new RCSB search API
  • New database.rcsb.Query classes, that reflect the entirety of the new
    search API, including sequence, sequence motif and structure searches
    • Multiple database.rcsb.Query objects can be combined/negated using the
      operators |, & and ~
  • Added the return_type, sort_by and range parameter to
    database.rcsb.search()
  • Added database.rcsb.count() function to count the number of results a
    database.rcsb.Query would yield in a less costly way than
    database.rcsb.search()
• Increased indexing speed in biotite.structure.BondList
• Added attribute sequence.Sequence.alphabet property, that is equivalent to
  sequence.Sequence.get_alphabet()
• Added convenience functions fastq.get_sequence(), fastq.get_sequences(),
  fastq.set_sequence() and fastq.set_sequences()
• Drastically increased writing speed of sequence.io.fasta.FastaFile
• Increased mapping speed of sequence.AlphabetMapper
• Added sequence.Alphabet.is_letter_alphabet() method
• Added general sequence I/O convenience functions
  sequence.io.load_sequence(), sequence.io.load_sequences(),
  sequence.io.save_sequence() and sequence.io.save_sequences() that derive
  the appropriate File class from the suffix of the file name.

Changes

• The omit_chain parameter has been removed from database.rcsb.search()
• The old database.rcsb.Query classes have been removed
• Removed python setup.py test and python setup.py build_sphinx commands,
  please use pytest and sphinx-build directly instead
• Renamed sequence.NucleotideSequence.alphabet to
  sequence.NucleotideSequence.alphabet_unamb
• sequence.io.fastq.FastqFile returns its entries only as str instead of
  sequence.NucleotideSequence for consistency with
  sequence.io.fastq.FastaFile
  • The method sequence.io.fastq.FastqFile.get_sequence() is deprecated
  • The method sequence.io.fastq.FastqFile.get_seq_string() returns the
    sequence as a str instead of a sequence.NucleotideSequence

Fixes

• Fixed expect_looped parameter in
  structure.io.pdbx.PDBxFile.get_category()
• Fixed error in structure.io.pdbx.PDBxFile, that was raised, if a PDBx
  field and its single-line value are in separate lines
• Added check for boolean mask length, when a boolean mask is given as index
  to biotite.structure.BondList
• Changed chain_id dtype from 'U3' to 'U4' (#215)

Biotite 0.22.0

Changelog

Additions

• Added structure.filter_nucleotides()
• structure.io.pdbx.get_sequence() is able to parse a
  sequence.NucleotideSequence from a PDBx file in addition to
  sequence.ProteinSequence
• Added structure.base_pairs() for determining base pairs in nucleic acid
  structures
• Added structure.get_residue_starts_for()
• Added structure.check_atom_id_continuity()
• Added structure.renumber_atom_ids() and structure.renumber_res_ids()
  to fix structures with discontinuous atom/residue IDs
• Added get_model_count() to structure.io.pdb, structure.io.pdbx,
  structure.io.mmtf and structure.io.gro to obtain the total number
  of models
• The model parameter in get_structure() in structure.io.pdb,
  structure.io.pdbx, structure.io.mmtf and structure.io.gro supports
  negative values to start indexing beginning from the last model
• Increased performance of residue and chain-related functions
  (e.g. structure.get_residue.starts())

Changes

• Revamped altloc ID handling (#194)
  • Instead of choosing each alternate location individually there are three
    options:
  • 'first' choses always chooses the atoms with the first altloc ID
    for each residue
  • 'occupancy' choses always chooses the atoms with the highest occupancy
    for each residue
  • 'all' does not filter any altloc IDs and adds the altloc_id
    annotation to the resulting structure.AtomArray or
    structure.AtomArrayStack
• Renamed structure.check_id_continuity() into
  structure.check_res_id_continuity(); structure.check_id_continuity()
  is still available, but is deprecated

Fixes

• Fixed structure.BondList being iterable, yielding nonsense values
• Improved element guesses in structure.io.pdb.PDBFile when the
  element column is missing (#188)
• Fixed parsing of single models from structure.io.mmtf.MMTFFile (#205)
• Fixed missing unit cell values in structure.io.pdbx.get_structure()
  raising an error; the box attribute is set to None instead

Biotite 0.21.0

Changelog

Additions

• More functionality for structure.BondList
  • __contains__() method to test whether a bond exists
  • find_connected() identifies systems of connected atoms (aka molecules)
• Added frame wise iteration of trajectory files for saving memory
  • structure.io.TrajectoryFile.read_iter() yields coordinates, box and time for each frame
  • structure.io.TrajectoryFile.read_iter_structure() yields an structure.AtomArray for each frame
• Added ability to read entire biological assemblies from mmCIF files
  • structure.io.pdbx.list_assemblies() lists the available assemblies
  • structure.io.pdbx.get_assembly() returns the given assembly as
    structure.AtomArray or structure.AtomArrayStack
• Added the expect_looped parameter to
  structure.io.pdbx.PDBxFile.get_category
• structure.info.vdw_radius_single() provides VdW radii also for more
  uncommon elements
• Added structure.get_residue_masks(), which masks all residues to which the
  given atoms belong
• Added structure.repeat() functions to repeat atoms multiple times in the
  same model with different coordinates
• Added a bunch of new examples to the gallery

Changes

• temp_file() and temp_dir() is deprecated, use the Python standard library
  module tempfile instead
• For all File classes, read() is now a class method,
  e.g. pdbx_file = PDBxFile.read(), the old instance method is deprecated
• database.rcsb.fetch() and database.enrez.fetch() overwrite an existing
  file if it is empty

Fixes

• A newline character is appended to the end of file, when writing text files
• Fixed structure.CellList when using the periodic parameter in combination
  with the selection parameter; before unallocated memory was potentially
  accessed

Biotite 0.20.1

Changelog

Fixes

• Fixed support for msgpack 1.0

Biotite 0.20.0

Changelog

Additions

• Added structure.from_template() to create a structure.AtomArrayStack from an existing atom array (or stack) and coordinates
• Added ignore parameter to sequence.io.genbank.get_annotation() to ignore the given feature keys
• Added sequence.graphics.plot_plasmid_map() for visualizing sequence.Annotation objects as plasmid
• Added a bunch of new examples to the gallery
• Added support for Python 3.8 on Windows

Changes

• The output of the score_matrix() method of sequence.align.SubstitutionMatrix is not writable anymore, rendering a SubstitutionMatrix truly immutable
• Renamed environment.yaml to environment.yml
• A sequence.Feature must have at least one location

Fixes

• Fixed incorrect centroid calculation in structure.superimpose(), when providing a boolean mask
• Fixed installation of PyPI source distributions
• Fixed issues when reading text files with \r\n line breaks (line breaks with carriage return, typical for Windows)

Biotite 0.19.2

Changelog

Fixes

• Fixed examples in gallery

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