Changelog

Additions

• Added support for Python 3.14. (#830)
• Added structure.dihedral_side_chain() analogous to dihedral_backbone(). (#827)
• Added structure.get_all_residue_positions() and structure.get_atom_name_indices() to residue level functionalities. (#827)
• Expanded list of 'water' residue names in structure.filter_solvent(). (#832)

Changes

• structure.io.pdbx.get_structure(use_author_fields=False) assigns an incrementing res_id for hetero residues instead of -1. (#823)
  • Previously in edge cases assigning -1 to hetero residues lead to missing distinction of subsequent residues. (#553)
• A different res_name is not used anymore to distinct two subsequent residues in the residue-level functionalities. (#825)
  • Previously, if two altlocs of the same residue had a different res_name, both would be incorrectly kept. (#824)

Fixes

• Fixed reading BCIF files written by py-mmcif in structure.io.pdbx.BinaryCIFFile. (#833)
• structure.io.pdbx.BinaryCIFData.array is now writable if it was encoded only with ByteEncoding. (#833)
• Fixed issue where for some invalid UniProt IDs database.rcsb.fetch() would still downloaded another entry. (#833)
  • For example instead of the invalid A0A12345, A0A123 would have been downloaded.
• structure.io.pdb.get_structure() now only infers bonds from CCD for proteins and nucleic acids, not for other ligands. (#820)
  • This allows using residue names for compounds that clash with the compound names in the CCD without getting wrong bonds.

Changelog

Additions

• Added structure.find_pi_cation_interactions() to identify pi-cation interactions in a structure. (#810)
• Added more convenient bond type conversion methods for structure.BondList objects. (#808)
  • remove_kekulization() changes AROMATIC_<order> bonds to generic AROMATIC bonds.
  • convert_bond_type() maps the given bond type to a new bond type.

Changes

• Deprecated include_bonds parameter in structure.io.pdbx.set_structure(). (#804)
  • Intra-residue bonds are now always written to chem_comp_bond category.
• interface.rdkit.from_mol() writes the altloc into the altloc_id annotation instead of label_alt_id. (#807)

Fixes

• Fixed altloc filtering in structure.io.pdbx.set_structure() for PDBx files where each atom has an altloc. (#806)
• Fixed warning in structure.lddt() that was raised, if no contact exists. (#811)
• Fixed selection parameter interface.pymol.PyMOLObject methods that errored if a slice index was passed. (#801)
• Fixed the amount parameter in structure.repeat_box_coord() not being used. (#800)
• Fixed spurious bonds added to the structure returned by structure.io.pdb.PDBFile.get_structure(). (#810)
  • Appeared when an altloc atom that participated in a non-canonical bond, was removed during parsing.
• Fixed exception in structure.io.pdb.PDBFile.get_assembly(), if the file contains multiple assemblies. (#810)

Changelog

Additions

• Added support for parsing unit cells. (#778)
  • Added structure.space_group_transforms() to get transformations for a given space group.
  • Added structure.io.pdbx.get_unit_cell() to get AtomArray/AtomArrayStack that represents the entire unit cell.
  • Renamed structure.io.pdb.get_symmetry_mates() to structure.io.pdb.get_unit_cell().
  • The sym_id annotation array is also considered when determining chain starts. (#786)

Changes

• structure.io.pdb.PDBFile.get_symmetry_mates() and structure.io.pdb.get_symmetry_mates() are now deprecated in favor of get_unit_cell(). (#778)
• Removed support for Python 3.10.

Fixes

• Fixed integer overflows/underflows leading to potentially corrupted BinaryCIF files. (#783, #796)
  • Only affects cases where the Encoding is either manually set or it is set by structure.io.pdbx.compress() before writing the file.
  • Now structure.io.pdbx.Encoding.encode() always checks if the target data type is compatible with the values.
  • structure.io.pdbx.compress() will fallback to direct ByteArrayEncoding if the data type is incompatible with FixedPointEncoding.
• Fixed occasionally missing bonds in structure.io.pdbx.get_structure(altloc='occupancy'). (#781)
• Fixed missing support for PDBx files containing multiple operation expression per assembly in structure.io.pdbx.get_assembly(). (#792)

Changelog

Additions

• Added interfaces to other packages in the bioinformatics ecosystem via the new interface subpackage. (#762)
  • interface.rdkit allows conversion between AtomArray and Mol objects from the RDKit package. (#736, #741, #742)
  • interface.pymol allows conversion between AtomArray and PyMOL objects, supporting NumPy-style indices as atom selections. (#749)
  • interface.openmm allows conversion between AtomArray and OpenMM Toplology, System and State objects. (#750)
• Added database.alphafold subpackage for accessing structures from AlphaFold DB. (#492)
  • The IDs of computational models obtained via database.rcsb.search() can be passed directly to database.alphafold.fetch().
• Added new metrics for measuring similarity of two structures.
  • structure.lddt() computes the Local Distance Difference Test and can be highly customized with filtering and binning options. (#699)
  • structure.tm_score() computes the TM-score. Curresponding structure alignments can be performed with superimpose_structural_homologs(). (#705)
• Added functions related to aromatic rings. (#751)
  • structure.find_aromatic_rings() finds atom indices of aromatic rings in a structure.
  • structure.find_stacking_interactions() finds pi-stacking interactions between aromatic rings.
• Added structure.BondType.AROMATIC bond type, for bonds where the kekulized form is unknown. (#738)
• structure.info.residue() and structure.io.pdbx.get_component() now support chemical components without valid coordinates. (#730)
• label_entity_id annotation can now be written to PDBx files via structure.io.pdbx.set_structure(). (#732)
• structure.info.vdw_radius_single() now supports more elements. (#745)
• Improved performance of structure.spread_residue_wise() and structure.spread_chain_wise(). (#770)

Fixes

• Now only finite coordinates can be given to structure.CellList() (#733).
• Fixed structure.array() truncating string annotations. (#755)
• structure.io.pdbx.get_structure() with include_bonds=True is now much faster and more memory efficient for very large structures. (#765)
• Fixed serialization (and string representation) of structure.io.pdbx.CIFBlock objects raising an exception. (#767)
• Now structure.io.mol.set_structure() checks if the input coordinates fit into the fixed number of columns in MOL/SDF files. (#772)
• The height of letters in sequence.graphics.plot_feature_map.plot_sequence_logo() is now more accurate. (#769)

Changelog

Additions

• Support for Python 3.13 (#661).
• Support for structural alphabets that encodes geometric information from structure.AtomArray objects in sequence.Sequence objects.
  • structure.alphabet.to_3di converts a structure into a 3Di sequence from Foldseek. (#665)
  • structure.alphabet.to_protein_blocks() converts a structure into a Protein Blocks sequence. (#676)
  • Added color schemes and defailt sequence.align.SubstitutionMatrix for these structural alphabets. (#682)
• Support for positional substitution matrices. (#655)
  • sequence.PositionalSequence acts as a placeholder sequence for a sequence profile in alignment functions from sequence.align.
  • sequence.align.SubstitutionMatrix.as_positional() expands a substitution matrix into a positional substitution matrix.
• New functionalities for structure.io.pdbx:
  • Custom annotations can be written with set_structure() with extra_fields=True. (#669)
  • Missing columns in atom_site category are now handled by using sensible default annotations. (#670)
  • Added compress() function that automatically finds optimal encodings for BinaryCIFFile, decreasing the file size by a factor of approx 8x. (#674)
  • get_assembly() now adds a sym_id annotation to better distinguish copies of the asymmetric unit. (#700)
• Added PDBFile.get_space_group() and PDBFile.set_space_group() to read and write the space group information. (#707)
• Added structure.concatenate(), which supports concatenating more than AtomArrayStack objects. (#712)
• Performance improvements:
  • Doubled speed to parsing CIF files with structure.io.pdbx.CIFFile (#722).
  • Tripled speed of pickling sequence.align.KmerTable objects. (#664)
    • Speed of transferring sequence.align.KmerTable between processes improves likewise.

Changes

• structure.io.pdbx.set_structure() does not write 'canonical' bonds to struct_conn category anymore. (#678)
• The internal Chemical Component Dictionary is not version controlled anymore. (#687, #716)
  • For installations from local repository clones, it must be built with python -m biotite.setup_ccd.

Fixes

• structure.io.pdbx can now handle atom_site categories with quoted values containing whitespaces. (#673)
• nan values in structure.AtomArray now count as equal when comparing AtomArray objects. (#714)
• Fixed wrong band calculation in sequence.align.align_banded() that occurred when the given band was outside the sequence bounds. (#723)
  • This lead to premature traceback termination in rare cases.

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)

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).

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)

Changelog

Fixes

• NumPy version is now properly restricted (#601)

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)

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

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)

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)

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)

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)

Changelog

Additions

• Added Python 3.11 build
• Better support for macromolecular assemblies and symmetry mates (#450)
  • biotite.structure.io.pdb and biotite.structure.io.mmtf now support parsing of assemblies via list_assemblies() and get_assembly()
  • biotite.structure.io.pdb is able to parse all atoms within a single unit cell via get_symmetry_mates()
• Added structure.rmspd() to compute the root-mean-square-pairwise-deviation
  • This is a method to determine deviations between to models without the need of prior structure superimposition
• Refactored structure.annotate_sse() (#448)
  • Higher performance due to more vectorization
  • Multiple chains can be processed at once
• More granular macromolecule filters in structure subpackage (#436)
  • Added filter_peptide_backbone() and filter_phosphate_backbone() to filter backbone atoms of proteins and nucleotides, respectively
  • Added filter_linear_bond_continuity() that filters atoms that are within distance boundaries to the next atom
  • Added filter_polymer() that filters biomacromolecules of the given type (peptide, nucleotide, carbohydrate) and minimum length
• More integrity checks in structure subpackage (#436)
  • check_linear_continuity() gives positions in a structure where atoms are not within distance boundaries to the next atom
  • check_backbone_continuity() does the same exclusively for peptide/nucleotide backbone atoms
• Added sequence.common_alphabet() to determine the Alphabet from a list of alphabets that extends all other alphabets from this list (#446)
• sequence.phylo.Tree.to_newick() and sequence.phylo.TreeNode.to_newick() allow rounding of distance labels (#439)
• application.TantanApp is able to process multiple sequences in a single call (#446)
  • This significantly improves the performance especially for short sequences

Changes

• structure.filter_backbone() is deprecated and replaced by filter_peptide_backbone() (#436)
• structure.check_bond_continuity() is deprecated and replaced by check_backbone_continuity() (#436)
• Deprecated chain_id parameter in structure.annotate_sse(), multiple chains can now be processed at once (#448)

Fixes

• structure.CellList accepts empty query coordinates in get_atoms() and get_atoms_in_cells() (#448)
• Fixed padding of CRYST1 records to 80 instead of 70 characters (#453)
• Fixed issue, where application.dssp.DSSPApp did not give correct number of secondary structure elements for multi-chain structures (#444)
• Resolved MemoryError in structure.repeat_box() (#450)

Changelog

Additions

• Support stack-wise iteration over trajectory files (#420)
• Support Path objects in File.read()
• Improved filters for different types of residues in structure subpackage (#425)
  • filter_amino_acids() now also filters for non-canonical amino acids
  • filter_nucleotides() uses an updated list of nucleotides
  • New filter_carbohydrates() filters for saccharides
  • filter_canonical_amino_acids() and filter_canonical_nucleotides() filter the respective canonical residues
  • New structure.info.carbohydrate_names() and structure.info.amino_acid_names() give a list of residue names considered as carbohydrates and amino acids, respectively
• application.LocalApp now supports input to STDIN
• Improved ViennaRNA interfaces (#435)
  • Added application.viennarna.RNAalifoldApp interface to RNAalifold
  • Secondary structure constraints can be given to application.viennarna.RNAfoldApp and application.viennarna.RNAalifoldApp

Changes

• The residues that are recognized by structure.filter_amino_acids() have changed (see above)
• Deprecated application.viennarna.RNAfoldApp.get_mfe() and replaced it by application.viennarna.RNAfoldApp.get_free_energy()

Fixes

• Support PDB format dialect with inverted charge column (X+ instead of +X) in structure.io.PDBFile(#421)
• Fixed erroneous atom parsing in strutcure.io.mmtf.MMTFFile, if an MMTF file has multiple different groupType entries for the same residue name and the same number of atoms (#426)
• Fixed angle condition in structure.base_stacking() (#432)
• Fixed TypeError in database.muscle.Muscle5App
• Fixed bond_line_style parameter in structure.graphics.plot_secondary_structure()
• Fixed error in pseudoknots() and base_pairs_from_dot_bracket() in cases the secondary structure had no base pairs
• Update identification of error messages from server in database.entrez.fetch()

Fixes

• Support for new UniProt REST API (#409)
• Preserve lower-case chain IDs when an AtomArray is read from PDB and PDBQT files (#413)
• application.vina.VinaApp supports now docking of molecules containing certain metal elements

Changelog

Additions

• Support for new RCSB search API (#408)
  • Added case_sensitive parameter in database.rcsb.FieldQuery
• structure.info.mass() support deuterium
• structure.connect_via_distances() can connect atoms over periodic boundaries
• Added more chain-level utilities consistent with residue-level utilities
  • structure.apply_chain_wise()
  • structure.spread_chain_wise()
  • structure.get_chain_masks()
  • structure.get_chain_starts_for()
  • structure.get_chain_positions()
• structure.superimpose() supports also pure coordinates

Changes

• structure.hbond() uses an associated structure.BondList to find hydrogen atoms to potential hydrogen bond donors
• Lines depicting bonds in structure.graphics.plot_atoms() and structure.graphics.plot_ball_and_stick_model() use rounded tips

Fixes

• Fixed structure.io.pdbx.get_assembly missing chains in some structures (#387)
• Added a more meaningful error, if Matplotlib is required, but not installed (#302)
• Added more descriptive error, if a structure.io.pdb.PDBFile has erroneous atom IDs (#379)
• structure.io.pdb.PDBFile pads lines always to 80 characters
• Allow empty attribute string in sequence.io.GFFFile
• Fixed wrong similarity scores, if a sequence.align.SubstitutionMatrix with two different alphabets is read from string or file
• Fixed application.mafft.MafftApp runs for more than 10 sequences.

Changelog

Additions

• Added application.muscle.Muscle5App to support the changed CLI of Muscle 5
• Added structure.orient_principal_components() to orient atom coordinates to the given axes
• biotite.structure.io.pdbx.get_structure() uses label_xxx or auth_xxx field as fallback, if the respective other one is not available
• Added default_bond_type parameter to biotite.structure.io.write_structure_to_ctab() and biotite.structure.connect_via_distances to allow the user to change the BondType in the generated BondList

Fixes

• sequence.io.gff.GFFFile.read() is now able to read GFF records with trailing tabs
• Fixed DeprecationWarning in structure.align_vectors() (#295)
• Fixed alignment in atom name column in structure.io.pdb.PDBFile.write()
• Fixed error handling in structure.index_xxx() functions, if invalid input shape is given
• Ensured quoted values in looped categories will not be truncated in structure.io.pdbx.PDBxFile.set_category()

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)

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

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

Changelog

Fixes

• Fixed support for msgpack 1.0

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)