Biotite

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)

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()`