Biotite

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_bonds`parameter 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- `structure.io.pdbx.PDBxFile` is deprecated and superseded by `CIFFile` (531)
- `structure.io.mmtf` is deprecated and superseded by `BinaryCIFFile` (531)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](https://www.rcsb.org/news/feature/65a1af31c76ca3abcc925d0c) 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](https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump)
- `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 `BondList`s 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 `BondType`s, 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)