Biotite

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`