Biotite 1.0.1

Changelog

Fixes

• Fixed structure.AtomArray.chain_id having the chain ID restricted to 4 characters. (#643)
• Fixed corrupted category parsing in structure.io.pdbx.CIFFile, when a multiline value contains a quote character. (#651)
• Fixed duplicate bonds written to chem_comp_bond category, when include_bonds=True is set in structure.io.pdbx.set_structure(). (#653)
• Fixed non-deterministic altloc atom selection by occupancy, if two altlocs have the same occupancy. (#649)
• Fixed the version switcher in the documentation showing the latest version twice. (#646)

Biotite 1.0.0

Changelog

Additions

• Support for Numpy 2.0 (#529)
  • 1.x versions are still compatible.
• Trajectory file interfaces in structure.io do not require mdtraj as extra dependency anymore (#627).
  • Instead the much smaller biotraj package is now a mandatory dependency of Biotite.
• New documentation website (#552).
• Improved performance of multiple auxiliary methods in sequence.Alphabet.

Changes

• sequence.graphics uses flower color scheme as default instead of rainbow. (#617).
  • It represents similarity of amino acids better.
• structure.io.pdbx.get_sequence() returns dict mapping chain IDs to sequences (#611).
• Previously deprecated functionality was removed. (#624)
  • read() instance method of File classes: Use read() class method instead.
  • temp_file() and temp_dir(): Use corresponding functionality from tempfile instead.
  • application.viennarna.RNAfoldApp.get_mfe(): Use application.viennarna.RNAfoldApp.get_free_energy() instead.
  • atom_mask parameter of structure.connect_via_distances() and structure.connect_via_residue_names(): Filter the atoms before instead.
  • Support for Alignment objects as input to sequence.graphics.plot_sequence_logo(): Input a Profile instead.
  • sequence.io.fastq.FastqFile.get_sequence(): Use sequence.io.fastq.FastqFile.get_seq_string() or sequence.io.fastq.get_sequence() instead.
  • structure.filter_backbone(): Use structure.filter_peptide_backbone() instead.
  • structure.check_id_continuity(): Use structure.check_res_id_continuity() instead.
  • structure.check_bond_continuity(): Use structure.check_backbone_continuity() instead.
  • structure.renumber_atom_ids(): Set the atom_id annotation with numpy.arange() instead.
  • structure.renumber_res_ids(): Use structure.create_continuous_res_ids() instead.
  • chain_id parameter of structure.annotate_sse(): Filter the AtomArray before instead.
  • structure.superimpose_apply(): Use structure.AffineTransformation.apply() instead.
  • structure.io.read_structure_from_ctab() and structure.io.write_structure_to_ctab(): Use corresponding functions from structure.io.mol.
  • structure.io.mol.MolFile.get_header() and structure.io.mol.MolFile.set_header(): Use the header attribute instead.
  • structure.io.npz: Internal .npz format is not used anymore.
  • structure.io.pdbx.PDBxFile: Use structure.io.pdbx.CIFFile instead.
  • structure.io.mmtf: .mmtf was superseded by .bcif accessible with structure.io.pdbx.BinaryCIFFile.

Fixes

• Fixed compilation warnings about deprecated NumPy API. (#626)
• Fixed structure.BondList sometime discarding bonds after merging to bond lists (#618).
• Fixed incorrect handling of quotes when reading and writing a structure.io.pdbx.CIFFile (#619).

Biotite 0.41.2

Changelog

Fixes

• Updated platform and tooling versions in CI. The previous configuration caused wheels to not be available for MacOS-ARM. (#603)
• Fix Atom __repr__() (#602)
• Fix artifact name for source distribution (#608)
• Fix indexing with inverse slices(#610)
• Fix mdtraj 1.10 incompatibility (#612)

Biotite 0.41.1

Changelog

Fixes

• NumPy version is now properly restricted (#601)

Biotite 0.41.0

Changelog

Additions

• Improved MOL/SDF file support in biotite.structure.mol
  • CTAB V3000 blocks can be read and written in addition to V2000 in MOLFile (#575)
  • M CHG lines in CTAB V2000 block can can be read and written in MOLFile (#589)
  • Added biotite.structure.SDFile for full support of SD files (#589)
    • SD files with multiple records (i.e. multiple molecules) ca be read and written
    • Metadata in SD files can be read and written
• Intra-residue bonds can now be read/written to CIF/BinaryCIF files in biotite.structure.io.pdbx (#567)
  The bonds are written to the chem_comp_bond category, if include_bonds=True in set_structure()
  • Previously Intra-residue bonds were obtained from the Chemical Component Dictionary which only works for residues in the PDB
• Added repair functions for AtomArray objects with missing or irregular annotations
  • structure.create_continuous_res_ids() renumbers residue IDs to make them continuous for each chain (#576)
  • structure.infer_elements() guesses chemical elements from atom names in case the element annotation is missing (#576)
  • structure.create_atom_names() names atoms based on their element in case the atom_name annotation is missing (#581)
• Canonical amino acids/nucleotides can be found for arbitrary residues
  • structure.info.one_letter_code() obtains the most appropriate one-letter code (if existing) for a residue name, based on information from the Chemical Component Dictionary (#572)
  • structure.to_sequence() converts an AtomArray into a Sequence based on codes obtained via structure.info.one_letter_code() (#587)
• Added new superimposition functions (#587)
  • structure.superimpose_without_outliers() allows superimposition with iterative conformational outlier removal to decrease the RMSD of the remaining atoms
  • structure.superimpose_homologs() finds corresponding atoms via sequence alignment and optional outlier removal
    • This function is quite robust for simply superimposing homologous proteins/nucleic acids without the need of atom filtering
  • structure.AffineTransform can be converted into a 4x4 transformation matrix containing both, translation and rotation (#576)
• sequence.align.write_alignment_to_cigar() now includes terminal gaps in the segment sequence (usually the shorter sequence) in the CIGAR string, if include_terminal_gaps is set to True (#563)
  • The default behavior is unchanged

Changes

• Deprecated get_header() and set_header() in biotite.structure.io.mol.MOLFile
  • MOLFile.header attribute should be used instead (#589)
• Deprecated structure.renumber_atom_ids() and structure.renumber_res_ids()
  • renumber_res_ids() can be substituted with create_continuous_res_ids()

Fixes

• Fixed parsing multi-line values in PDBx NextGen files in structure.io.pdbx.CIFFile (#555)
• Fixed parsing of some operation expressions in structure.io.pdbx.get_assembly() (#555)
• structure.io.pdb.PDBFile.set_structure() checks if input annotations exceed the fixed number of columns, preventing writing malformed PDB files (#588)
• Trying to write malformed CIF files with categories containing no rows now raises an exception (#586)
• Added more descriptive error message, if structure.residue() cannot find the requested residue (#580)
• sequence.io.fasta.get_sequence() converts pyrrolyine (O) into lysine (K) when creating the Sequence object (#587)
• Fixed indexing with an Annotation in sequence.AnnotatedSequence if annotation is on the minus strand (#577)
• Fixed exception in biotite.structure.base_pairs() and biotite.structure.dot_bracket_from_structure() if no base paris were found (#573)

Biotite 0.40.0

Changelog

Additions

• Refactored struc.superimpose() (#526)
  • Multiple fixed models are allowed
  • Increased performance for multiple models
• Support for BinaryCIF file format (#531)
  • Added 'bcif' format to database.rcsb.fetch()
  • Added structure.io.pdbx.BinaryCIFFile to parse BinaryCIF files
  • Added structure.io.pdbx.CIFFile to parse CIF files with analogous API to BinaryCIFFile
  • High-level PDBx API (get_structure(), get_assembly(), etc.) supports these new file classes
  • Added include_bondsparameter to structure.io.pdbx.get_structure() and structure.io.pdbx.get_assembly() to parse bond information from file
• Refactored structure.info subpackage (#540)
  • Decreased initial loading time when package is imported
  • The component dataset is now stored as compressed BinaryCIF decreasing the Biotite package size
  • The component dataset is updated to the current version, i.e. the latest chemical components from the wwPDB are included
  • The project now contains the setup_ccd.py script, enabling the user to get an up-to-date version of the component dataset

Changes

• Removed structure.info.bond_order() and structure.info.bond_dataset (#540)
• struc.superimpose returns now an AffineTransformation object instead of a transformation tuple (#526)
  • superimpose_apply() is deprecated in favor of AffineTransformation.apply()
• structure.io.pdbx.PDBxFile is deprecated and superseded by CIFFile (#531)
• structure.io.mmtf is deprecated and superseded by BinaryCIFFile (#531)
  • This is reflected by the RCSB announcement to deprecate MMTF

Fixes

• Handle invalid CRYST1 records in PDB files correctly (#523)
• Ensure that NumPy 1.x is used (#537)
  • Support for 2.x will be added in the future

Biotite 0.39.0

Changelog

Additions

• Add build for Python 3.12 (#513)
• Added modern fast k-mer subsetting methods to sequence.align (#510)
  • These include:
    • MinimizerSelector
    • SyncmerSelector
    • CachedSyncmerSelector
    • MincodeSelector
  • The following k-mer ordering methods are available:
    • RandomPermutation
    • FrequencyPermutation
  • Added BucketKmerTable to support indexing of long k-mers with reasonable memory consumption
• Support conversion of biotite.sequence.align.Alignment from/to CIGAR strings (#516)
  • read_alignment_from_cigar()
  • write_alignment_to_cigar()
• Added sequence.graphics.plot_alignment_array() (#485)
• Support new 5-character residue names in structures from PDB (#512)
• Support NCBI API keys in database.entrez to increase download limits (#514)
• Increased performance of application.sra(#504).
  • prefetch is called before fasterq_dump, as suggested here
  • FastaDumpApp is added, which decreases computation time by writing as FASTA instead of a FASTQ file, which omits the scores

Changes

• application.sra.FastaDumpApp.get_sequences() now only returns sequence (#504) strings and not scores anymore (#504)
  • Use get_sequences_and_scores() instead

Fixes

• Fixed memory leak in sequence.align.KmerTable.from_tables() (#510)
• Fixed problems of plotting functionalities with recent Matplotlib versions (#518)

Biotite 0.38.0

Changelog

Additions

• Faster k-mer decomposition in sequence.align.KmerAlphabet.create_kmers() (#475)
• Sequence type can be set when reading sequences and alignments using sequence.io.fasta ( #478)

Fixes

• Fixed error that appeared when indexing an sequence.AnnotatedSequence with a slice (#479)
• Fixed reading MOL/SDF files with more than 100 bonds (#480)
• Fixed compilation of Biotite with Cython 3.x (#493)
• Fixed usage of box parameter in structure.rdf() (#494)

Biotite 0.37.0

Changelog

Additions

• Added PubChem database interface with database.pubchem (#472)
  • Analogous to the other database subpackages, it supports, search() and fetch()
  • fetch_property() can be used to quickly obtain a wide range of properties for a given list of compound IDs
  • Automatic throttle control ensures that the PubChem usage control is obeyed
• Extended functionality for database.rcsb.search() and database.rcsb.count() (#466):
  • Added support for computational structures (e.g. from Alphafold DB) via the content_types parameter
  • Added support for grouping via the new group_by and return_groups parameters
    • the type of grouping is selected via Grouping subclasses
  • Added support for ascending sorting with the Sorting class
• database.entrez.search() now also accepts the common database name in addition to the E-utility database name (#471)
  • This is now consistent with the behavior in database.entrez.fetch()
• Added structure.io.pdb.PDBFile.get_b_factor() analogous to structure.io.pdb.PDBFile.get_coord() (#469)
• Added structure.io.pdbx.get_component() and set_component() (#468)
  • Allows getting/setting chemical components from/to PDBx files via their chem_comp group of categories instead of atom_site

Changes

• Deprecate atom_mask parameter in structure.connect_via_residue_names() and structure.connect_via_distances() (#474)
  • It has no effect anymore
• In structure.BondList.merge() the BondList given as parameter takes precedence, if both BondLists contain the same bond with different BondType (#473)
  • Previously it was the other way round
• The BondList returned by structure.io.pdb.PDBFile.get_structure() (if include_bonds is True) gives appropriate BondTypes, if they can be determined using the CCD (#473)
  • Otherwise the BondType is BondType.ANY
  • Previously it was BondType.ANY for all bonds
• Refactored structure.remove_pbc()(#460)
  • PCB removal is conducted for each molecule separately
  • Not the first atom but the centroid of a molecule is placed within the box
  • The selection can only be a boolean matrix

Fixes

• Fixed a bug in structure.connect_via_distances() and structure.connect_via_residue_names() that allowed unexpected bonds between polymer and non-polymer residues (#473)

Biotite 0.36.1

Changelog

Fixes

• Fixed parsing of remarks < 100 in structure.io.PDBFile (#457)
• Bonds can now be read and written using hybrid-36 encoding in structure.io.PDBFile (#456)