Biotite 0.28.0

Changelog

Additions

• Most classes support now the repr() function (#290)
• Add equality comparison for sequence.CodonTable
• Added structure.info.all_residues(), that gives all residue names from the
  Chemical Component Dictionary
• Updated resources from Chemical Component Dictionary in structure.info
• Add structure.io.mol.MOLFile to support MOL and SDF files for
  small molecule structure data
• Add database.uniprot for UniProt database support
  • database.uniprot.search() searches for Uniprot IDs that match a given
    database.uniprot.Query
  • database.uniprot.fetch() downloads the file corresponding to the given
    Uniprot ID.
• Increase performance of structure.pseudoknots() by using NetworkX
  to identify conflicting regions (#289)

Changes

• Changed structure.BondType enum values for more precise description of
  aromatic bonds
  • BondType.AROMATIC is replaced by
    BondType.AROMATIC_SINGLE and BondType.AROMATIC_DOUBLE
  • New method structure.BondList.remove_aromaticity() converts
    BondType.AROMATIC_SINGLE to BondType.SINGLE and
    BondType.AROMATIC_DOUBLE to BondType.DOUBLE in-place

Fixes

• Fixed error, when reading a single model from a structure.io.PDBFile,
  if the MODEL line is missing in the file
• Fixed the format of formal charges written to structure.io.PDBFile
  • Previously it was e.g. '+2' instead of the correct 2+
• Fixed atom_i parameter when reading a trajectory via
  structure.io.load_structure() (#308)
• Fixed performance issue of structure.CellList
  • Previously the number of evaluated cells was too large, if the radius
    parameter of structure.CellList.get_atoms() was equal to the
    cell_size parameter of the constructor (#311)
• Setting an existing annotation array in structure.AtomArray and
  structure.AtomArrayStack preserves the NumPy dtype

Biotite 0.27.0

Changelog

Additions

• Added interface to AutoDock Vina
  • application.autodock.VinaApp uses vina executable to perform
    docking of ligand to a receptor molecule
  • Uses new structure.io.pdbqt.PDBQTFile class for writing input for
    and reading output from vina
    • An MGLTools installation is not necessary
  • By default the receptor is handled as rigid structure, however,
    flexible side chains can be defined
• Added modular system for fast k-mer based sequence searches/mappings
  • sequence.align.KmerAlphabet encodes a sequence.Sequence into
    k-mers
  • sequence.align.KmerTable is able to find k-mer matches between
    sequence in an efficient manner
  • sequence.align.SimilarityRule allows matching similar instead of
    exact k-mer matches via a sequence.align.KmerTable
  • sequence.align.align_banded() performs a heuristic local or
    semi-global sequence alignment within a defined diagonal band
• Added sequence.align.remove_terminal_gaps() function
• Added application.sra.FastqDumpApp.get_file_paths() method
• Increased performance of sequence.Sequence.get_symbol_frequency()
• Increased performance of sequence.NucleotideSequence.complement()
• sequence.Sequence.reverse() can optionally create an array view
  instead of a copy

Changes

• application.sra.FastqDumpApp.get_file_paths() only parses
  downloaded PDBQT files, if required
• Running pytest automatically recompiles changed Cython source code

Biotite 0.26.0

Changelog

Additions

• Added interface to some programs of the ViennaRNA software package
  • application.viennarna.RNAfoldApp uses RNAfold to predict the minimum
    free energy secondary structure of an RNA sequence
  • application.viennarna.RNAplotApp uses RNAplot to calculate the
    2D coordinates for base symbols in a secondary structure plot
• Added structure.graphics.plot_nucleotide_secondary_structure() for
  visualization of an RNA secondary structure via Matplotlib
  • Internally uses RNAplot
  • Optional visualization of pseudoknots
• Increased performance of structure.find_connected()
• Increased performance of structure.partial_charges()
• Added structure.BondList.remove_bonds_to
• Added molecule-level atom selections
  • structure.get_molecule_indices(), structure.get_molecule_masks() and
    structure.molecule_iter select atoms belong to a single molecule, i.e.
    atoms that are connected via bonds
• Added interface to NetworkX package
  • Added as_graph() method to sequence.phylo.Tree and structure.BondList
    for conversion into a NetworkX Graph
  • The find_rotatable_bonds() function uses NetworkX to identify
    rotatable bonds, i.e. single bonds that are not part of a cycle,
    in structures with a structure.BondList()

Changes

• Add support for Python 3.9, remove support for Python 3.6
• Add networkx package as dependency
• structure.io.pdbx.set_structure() does not convert the residue ID -1
  to "." anymore

Fixes

• Fixed missing check for string length of chain ID, residue name
  and atom name when setting a structure in a structure.io.pdb.PDBFile
• structure.io.pdbx.set_structure() supports now atom IDs larger than
  one million
• Fixed application.dssp.DsspApp unable to work with multicharacter chain
  identifiers (#264)
• Fixed application.muscle.MuscleApp sometimes not finishing for long
  alignments (#273)
• Fixed the creation an AtomArray from atoms with optional annotations (#279)
• Fixed deletion of annotation arrays in `structure.AtomArray
• Fixed structure.BondList potentially ending in a broken state after
  indexing it with an unordered index array
• structure.partial_charges() uses bond order instead of number of bond
  partners to calculate correct charges for atoms with positive or negative
  formal charge

Biotite 0.25.0

Changelog

Additions

• New analysis capabilities for nucleic acid base pairs
  • Added structure.info.nucleotide_names()
  • Increased performance of structure.base_pairs()
  • Support for exotic nucleotides in structure.base_pairs() and
    structure.filter_nucleotides()
  • Added structure.base_pairs_edge() and
    structure.base_pairs_glycosidic_bond() for further
    characterization of base pairs
  • Added structure.base_stacking() for identification of pi-stacking
    of nucleobases
  • Added structure.pseudoknots() for identification of pseudoknots
    in a given list of base pairings
  • Added structure.dot_bracket(),
    structure.dot_bracket_from_structure() and
    structure.base_pairs_from_dot_bracket() for conversion of
    base pairs to dot-bracket-letter notation and vice versa
• New methods for structure.BondList:
  • Added get_all_bonds() for obtaining the bonds atoms for each atom
    in the structure
  • Added adjacency_matrix() and bond_type_matrix()
• Added structure.partial_charges() for partial charge calculation
  using the PEOE method
• Added structure.info.standardize_order(), that reorders atoms in
  residues into the PDB standard atom order for the respective residue
• Added structure.graphics.plot_ball_and_stick_model()
• Increased performance of residue level utilities
• Added structure.get_residue_positions()
• Added sequence.io.genbank.get_raw_sequence() which returns the
  sequence as string

Changes

• structure.hbond() raises a warning if an input structure without
  hydrogen atoms is given (#241)
• get_sequence() and get_sequences() of biotite.sequence.io.fasta
  and biotite.sequence.io.fastq convert selenocysteine to cysteine (#232)
• Changed order of sequence type biotite.sequence.io.fasta.get_sequence() and
  biotite.sequence.io.fasta.get_sequences() try to create (#232):
  • First: sequence.NucleotideSequence
  • If this fails: sequence.ProteinSequence
• Temporary files used by the application subpackage are removed via
  os.remove() due to issues on Windows (#243)

Fixes

• Fixed structure.base_pairs() for structures that contian residues,
  that are not in the PDB standard order (#237)
• Fixed slightly incorrect aspect ratio in molecular visualizations
  created via structure.graphics.plot_atoms()
• Fixed bounds check for input bonds the structure.BondList constructor
  (related to #252):
  • Previously, the bond type value was not allowed to exceed the number
    of atoms
• Fixed structure.BondList indexing with an unsorted index array (#238)
• Fixed the charge annotation of molecules obtained via
  structure.info.residue() (#254)

Biotite 0.24.0

Changelog

Additions

• Added sequence.ProteinSequence.get_molecular_weight() method
• Added application.sra subpackage as interface to NCBI SRA tools
  • FastqDumpApp is used for fetching FASTQ files from the NCBI SRA
• Added iter_read() static method to sequence.io.fasta.FastaFile
  and sequence.io.fasta.FastqFile
  • This method is used to parse header-sequence-pairs from FASTA/FASTQ
    files without the necessity to keep the entire file in memory.
• set_sequence and set_sequences in sequence.io.fasta
  and sequence.io.fasta support writing RNA sequences with the new
  as_rna parameter

Fixes

• Fixed missing whitespace at the end of _loop category labels in
  PDBx/mmCIF files (#224)
• Fixed inconsistent handling of model IDs over different file formats
  for structures where the first model ID is greater than 1 (#227)
• Removed warning in structure.density()
• sequence.io.fastq.get_sequence() and sequence.io.fastq.get_sequences()
  properly handle RNA and ambiguous sequences now
• Fixed start parameter in structure.renumber_atom_ids and
  structure.renumber_res_ids
• Updated fetch URL for FASTA files in database.rcsb.fetch()

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)