Biotite

Changelog

Fixes
- Fixed examples in gallery

Changelog

Additions
- *FASTA* files can be downloaded from *RCSB PDB* via `database.rcsb`
- Added `structure.rotate_about_axis()` and `structure.align_vectors()`
- Added `shape` property and `copy()` method to `structure.Atom`
- All array-like objects can be used to set an annotation array in an atom array (stack)
- Added `structure.info.residue()` for getting the standard atoms and their coordinates for a given residue name
- Added `structure.graphics.plot_atoms()` for interactive molecular visualization
- Added `exclusive_stop` parameter to `structure.get_residue_starts` and `structure.get_chain_starts`
- Added `connect_via_residue_names()` and `connect_via_distances()` for calculating a `structure.BondList` for a `structure.AtomArray`


Changes
- `structure.rotate()` does not rotate the `box` of an atom array (stack) anymore
- `structure.BondList` equality is not order dependent


Fixes
- `structure.BondList` accepts all dtypes for integer arrays
- `structure.BondList` accepts negative integers as indices
- `sequence.io.fasta.FastaFile`: Tests for invalid or empty files
- `structure.io.pdb.PDBFile`: Exception is raised if an invalid field in `extra_fields` is given
- `structure.rotate()`: Fixed rotation direction

Changelog

Additions
- Added `shape` property to `structure.AtomArray()` and
`structure.AtomArrayStack()`
- `structure.Atom()` has default values for annotation arrays
- The functions `structure.rmsf()`, `structure.rmsd()` and `structure.average()`
accept directly coordinates
- Added `use_author_fields` parameter to `structure.io.pdbx.get_structure()`,
that allows to decide between the usage of `label_xxx` and `auth_xxx` fields
- Added `chunk_size` parameter to `read()` method of trajectory files to
resolve memory issues
- Added `density()` function for calculating atom densities.
- Added `sequence.align.get_pairwise_sequence_identity()`
- API reference shows source files of *Cython* modules

Changes
- The module name (`__module__` attribute) of functions/classes are
changed to the name of the respective *Biotite* subpackage
(e.g. `biotite.structure.atoms` to `biotite.structure`)
- Changed handling of PDB insertion codes:
- Atoms with insertion codes are not filtered out
- Removed `insertion_code` parameter in
`biotite.structure.io.xxx.get_structure()`
- New mandatory annotation category `ins_code`
- Changed `structure.filter_inscode_and_altloc()` to
`structure.filter_altloc()`


Fixes
- The `step` parameter in the `read()` method of trajectory files does not
increase the `stop` frame
- Negative residue IDs are handled correctly by structure file readers/writers
- Fixed issues with indexing behavior in `sequence.align.Alignment` class
- `structure.remove_pbc()` raises proper error message when `box` is missing
in the given atom array (stack)
- `sequence.align.align_multiple()` raises proper error message, if
pairwise distance cannot be calculated due to great sequence dissimilarity
- In `sequence.io.genbank.get_annotation()` qualifier keys without values
(e.g. `/pseudo`) are handled properly
- Added `pyproject.toml` specifying build dependencies for `setup.py`

Changelog

Additions
- Support for *hybrid-36* encoding in `structure.io.pdb.PDBFile`
- Added `get_coord()` method in `structure.io.pdb.PDBFile` for efficiently reading only the coordinates from a file
- `structure.CellList` can be configured to put only a subset of atoms into the cells via the `selection` parameter
- Improved functionalities in `database` subpackage.
- A lot of new query types in `database.rcsb`
- The `min` and `max` parameter of some `database.rcsb` queries are now optional
- `database.rcsb.fetch()` and `database.entrez.fetch()` are able to write the downloaded files into a file-like object instead of writing the file to hard drive
- `database.entrez.fetch()` properly checks for invalid responses from server based on https://github.com/kblin/ncbi-entrez-error-messages
- `database.entrez.fetch()` also supports common database names
- `database.entrez.SimpleQuery` also supports abbreviated field names
- `structure.io.load_structure()` and `structure.io.save_structure()` support keyword arguments that are forwarded to the respective `read()` or `get_structure()` method.

Changes
- `database` subpackage raises `database.RequestError` objects when the server gives an invalid response

Fixes
- Fixed cross references in the API reference
- `sequence.io.genbank.GenBankFile` raises a warning instead of an exception if the feature's location identifier is not understood and skips the feature
- `structure.io.pdb.PDBFile` properly checks whether all models have the same amount of atoms, when building a `structure.AtomArrayStack`

Changelog

Additions
- New alignment color schemes
- Color schemes for protein sequence alignments created with *Gecos* software
- Including a color scheme adapted for red-green blindness
- Color scheme for *protein block* sequence alignments created with *Gecos* software
- Color schemes for protein sequence alignments adapted from JalView
- More functionalities for external MSA software (`application.MSAApp` subclasses)
- Additional CLI options can be set via `add_additional_options()`
- The executed command of `application.LocalApp` can be optained via `get_coomand()`
- Most MSA software interfaces allow setting and getting the distance matrix and the guide tree
- The corresponding method are `get_guide_tree()`, `set_guide_tree()`, `get_distance_matrix()` and `set_distance_matrix()`
- MSA software supporting cutom substitution matrices can be used to align almost any type of sequence, even if the type is not directly supported by the underlying software
- Added euality operator for `sequence.align.Alignment` objects
- `sequence.phylo.Tree` supports non-binary trees
- `sequence.phylo.TreeNode` can handle more than two child nodes
- `len()` gives amount of leaves in `sequence.phylo.Tree`
- `sequence.phylo.Tree` and `sequence.phylo.TreeNode` support hash and equality operator
- `sequence.phylo.as_binary()` function converts non-binary tree into binary tree, as required for guide trees
- Added `sequence.phylo.neighbor_joining()` for hierarchical clustering

Changes
- Removed `X` as symbol for ambiguous nucleotides, use `N` instead
- Removed protected method `get_default_bin_path()` from `application.MSAApp`
- Renamed protected method `set_options()` to `set_arguments()` `application.LocalApp`
- Renamed `set_matrix()` to `set_substitution_matrix()` `application.muscle.MuscleApp`
- Removed protected method `get_cli_arguments()` in `application.LocalApp`
- Adapted constructor of `sequence.phylo.TreeNode` for variable amount of child nodes
- `application.MSAApp` subclasses must implement abstract static methods describing which sequence types they support and whether they support custom substitution matrices

Fixes
- `U` is automatically converted to `T` when loading nulceotide sequences from FASTA files
- Score matrix in `sequence.align.SubstitutionMatrix` is now truly read-only via `ndarray` flag
- `application.Application` subclasses (all external software interfaces) now properly check whether the corresponding objects are in the correct `application.AppState`
- Error in evaluation step of `application.Application` now leaves application in `application.AppState.CANCELLED` state
- Fixed `InvalidFileError` not being exposed to user
- Symmetry checks in `sequence.phylo.upgma()` allow for small rounding errors

Changelog

Additions
- Increased performance of `sequence.NucleotideSequence.translate()` method
- Added `map_codon_codes()` method to `sequence.CodonTable` for efficient codon to amino acid mapping