Changelog

Additions

• Add Python 3.10 build
• Add writer_iter() to some File classes
  • Allows entry-wise writing into a file to reduce memory consumption, as there is no longer the need to keep the entire file content in memory
  • Implemented for sequence.io.FastaFile, sequence.io.FastqFile and all classes inheriting from structure.io.TrajectoryFile
• Add symbol_spacing parameter to sequence.graphics.plot_alignment
  • If the parameter is given, a small gap is introduced every n symbols in the alignment
  • Also added to sequence.graphics.plot_alignment_similarity_based and sequence.graphics.plot_alignment_types_based

Changes

• Python 3.7 builds are discontinued

Fixes

• Now the simulation time for each frame is returned in structure.io.NetCDFFile, previously it was always None

Changelog

Additions

• New functionalities for sequence.SequenceProfile
  • Added method probability_matrix() to compute the symbol probabilities from total frequencies
  • Added method log_odds_matrix() to calculate a position weight matrix
  • Added methods sequence_probability() and sequence_score() to assess the adherence of a given sequence to a profile
• New functionalities for structure.BondList
  • New bond type structure.BondType.AROMATIC_TRIPLE to support triple bonds in aromatic systems
  • Added structure.BondList.without_aromaticity() to convert bonds with structure.BondType.AROMATIC_<order> to structure.BondType.<order>
• Added structure.info.bond_order()
  • Used to get the structure.BondType of the bond between two atoms in a residue
  • Replaces structure.info.bond_order()
  • Initial loading of bond dataset is much faster

Changes

• Deprecated structure.info.bond_order()

Fixes

• Fixed structure.io.pdb.PDBFile.get_structure() raising an exception, if the PDB file contains an invalid CRYST1 record, now a warning is printed
• Fixed CONECT records written by structure.io.pdb.PDBFile.set_structure()
  • Previously, an empty second CONECT record was created, if a atom has 4 bond partners
• Fixed installation of Biotite source distribution with Python 3.10 (#356)
• Fixed running application.muscle.MuscleApp with nucleotide sequences

Changelog

Changes

• sequence.graphics.plot_sequence_logo() requires now a sequence.SequenceProfile, usage of sequence.align.Alignment still works, but is deprecated
• database.rcsb.FieldQuery has now an optional molecular_definition parameter to allow searches in molecule related fields.

Fixes

• The new RCSB search API is now supported (#347)
• More than two database.rcsb.Query objects can be combined with logical operators
• application.blast.BlastWebApp now also reports hit sequences containing selenocysteine without errors (#344)
• Atom, AtomArray and AtomArrayStack can be unpickled (#349)
• sequence.graphics.plot_sequence_logo() supports now all Matplotlib backends (#345)

Changelog

Additions

• Extended functionalities for homology searches
  • Added application.tantan.TantanApp for sequence repeat masking with Tantan
  • sequence.align.KmerAlphabet and sequence.align.KmerTable support spaced k-mers
  • Added sequence.align.local_gapped() and sequence.align.local_ungapped() for aligning sequences locally with X-drop heuristic
  • Added EValueEstimator for calculation of expect values (E-values) from alignment scores
  • Increased performance of sequence.LetterAlphabet.extends()
• Added sequence.SequenceProfile for representing sequence profiles by means of a symbol frequency table
  • sequence.SequenceProfile.from_alignment() creates a profile from an alignment
  • sequence.SequenceProfile.to_consenus() creates a consensus sequence
• Increased performance of sequence.align.get_codes() and sequence.align.get_symbols()
• Bonds can be read from and written to CONECT records in structure.io.pdb.PDBFile (#329)

Changes

• Documentation now uses sphinxcontrib-bibtex for citations
  • Citations include DOI with link to publication

Fixes

• Fixed protein color schemes for sequences containing 'X' or '*' (#322)
• sequence.graphics,plot_nucleotide_secondary_structure() is now able to set the color of symbols (#333)

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

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

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

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)

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()

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)