Biotite

Changelog

Additions
- Support for unit cells and simulation boxes
- Added `box` attribute for `structure.AtomArray` and `structure.AtomArrayStack` that represents the three box vectors
- The `box` attribute is automatically read from and written into all supported structure file formats
- Added methods for handling boxes in `structure` package
- `vectors_from_unitcell()` and `unitcell_from_vectors()` faciliate the conversion between box vectors and lengths/angles
- `coord_to_fraction()` and `fraction_to_coord` allow expressing coordinates as fraction of box vectors
- `repeat_box()` and `repeat_box_coord()` create periodic copies of coordinates or an atom array (stack).
- `box_volume()` calculates the volume of a box
- `is_orthogonal()` is used to check whether a box is orthogonal
- `check_in_box()` checks whether atoms of a structure are outside the box
- Added `structure.index_xxx()` versions of functions for geometric measurements (e.g. `structure.index_distance()`)
- The functions take an atom array (stack) and referring indices, similar to *MDTraj*.
- Optionally use a minimum-image convention based on the `box` attribute
- `displacement()` and `index_displacement()` are used for calculation of displacement vectors
- `structure.CellList` optionally uses minimum-image convention for distance calculation based on the `box` attribute
- Added `structure.io.pdb.get_structure()` and `structure.io.pdb.set_structure()` as thin wrappers around the corresponding methods of `structure.io.pdb.PDBFile`

Changes
- `structure.io.mmtf.MMTFFile` and `structure.io.pdbx.PDBxFile` implement `MutableMapping`, offering a wider range of dictionary-like methods
- *Cython* language level is set to 3

Fixes
- A single model can now be read from a `structure.io.pdb.PDBFile`, if the models in the file have a different amount of atoms
- Clarified in the documentation that *Biotite* uses Å as base unit

Changelog

Fixes
- Fixed 'Conservation of *LexA* DNA-binding site' example in the gallery
- `application.blast.BlastWebApp` indicates, when URI is too large

v.0.10.0
Changelog

Additions
- `sequence.io.fastq.FastqFile` for reading and writing FASTQ files
- Dictionary-like usage
- Support for sequence and quality scores
- Different offsets for quality scores are available
- `database.entrez.fetch_single_file()` has `overwrite` parameter
- By default the file is not downloaded, if a file with the same name already exists
- `application.blast.BlastWebApp` have `set_entrez_query()` and `set_max_results()` methods for more customization
- `reverse_complement()` method for `sequence.AnnotatedSequence`
- Creates the reverse complement strand for both the sequence and the features

Changes
- `sequence.io.fastq.FastaFile` behaves properly like a dictionary
- Inherits `MutableMapping`
- Iteration yields keys (header strings) only, instead of a key-value tuple
- *SciPy* is required for building the documentation
- `sequence.Feature` and `sequence.Location` are immutable and hashable
- `sequence.Location` objects in `sequence.Feature` are stored as set
- `sequence.Feature` objects in `sequence.Annotation` are stored as set

Fixes
- Doctests as part of the unit tests
- Corrected erroneous docstrings
- Index checks for `sequence.Annotation` and `sequence.AnnotatedSequence`
- `sequence.io.fasta.get_sequence()` and `sequence.io.fasta.get_sequences()` can read lower case sequences
- `//` is correctly propagated to `sequence.io.genbank.GenBankFile` in `sequence.io.genbank.MultiFile`

Changelog

Additions
- Added support for phylogenetic trees
- Represented by `sequence.phylo.Tree` and `sequence.phylo.TreeNode` class
- Can be read from/ written into Newick format
- `sequence.phylo.upgma()` for `sequence.phylo.Tree` creation from distances
- Added `sequence.align.align_multiple()` for simple multiple sequence alignments
- Added customization methods in `application.muscle.MuscleApp`
- Revamped visualiazation system
- Usage of functions instead of `Visualizer` objects
- `sequence.graphics.SymbolPlotter` class for custom alignment visualizations
- `sequence.graphics.FeaturePlotter` class for custom feature visualizations
- Added `sequence.graphics.plot_dendrogram()` for `sequence.phylo.Tree` visualization
- Expanded the tutorial


Changes
- Revamped visualization system (see *Additions*)

Fixes
- Added `max_number` parameter in `sequence.align.align_optimal()` to avoid *branch explosion*
- Fixed rare scoring error in `sequence.align.align_optimal()`
- Fixed slicing `sequence.Annotation` objects with multi-location features

Changelog

Additions
- Added scripts to example gallery
- Added *Biotite* citation
- Added `len()` support for `sequence.Annotation` and `align.Alignment`

Changelog

Additions
- Added support for Python 3.7
- Discontinued support for Python 3.4 and 3.5
- Added type hints for public API via stub files (PEP 484)
- Revamped documentation
- New sidebar
- New main page
- Summaries in API documentation
- New layout of class attributes in API documentation
- Function signatues of C-extension functions are shown
- Documentation of decorated functions are correctly shown
- Cross references in tutorial
- Tutorial output is dynamically generated using `sphinx-gallery`
- Specified version number for dependencies
- Created `environment.yaml` for convenient creation of a development
environment in conda
- Improvements to `structure.CellList`
- Improved perfromance
- `get_atoms()` and `get_atoms_in_cells()` can be used in a vectorized
manner (replacing `efficient mode`)
- `get_atoms()` and `get_atoms_in_cells()` have optional `as_mask` parameter
- Added `create_adjacency_matrix()` method
- Added hydrogen bond detection (`structure.hbond()`)
- Missing element names in `structure.io.pdb.PDBFile` are automatically
inferred (Gromacs support)
- Added support for Gromacs' `.gro` file format (`structure.io.gro`).
- Color schemes can bes loaded from custom files
- `File` objects can read/write from/to a file object
- Temporary files automastically generate a file name
- STDOUT adn STDERR are accessible from `application.Application` runs

Changes
- Changes in `Enum` types
- `sequence.Location.Strand` is an `Enum`
- `sequence.Location.Defect` is a `Flag`
- `structure.BondType` is an `Enum`
- `application.AppState` is a `Flag`
- Usage of f-strings for exception messages (and some other places)
- `res_id` is read from `auth_seq_id` instead of `label_seq_id` in mmCIF files

Fixes
- Fixed custom color schemes in
`sequence.graphics.AlignmentSimilarityVisualizer`
- All integral types can be used as indices, instead of only `int`
- Installing Biotite from a `.whl` no longer requires `Cython` to be installed

Changelog

Additions
- Utility functions for `sequence.align.Alignment` objects
- Read/write functionality for alignments from FASTA files
- `get_codes()`, `get_symbols()`, `get_sequence_identity()`, `score()`

Changes
- Renamed `structure.AdjacencyMap` to `structure.CellList`
- Renamed `sequence.align.simple_score()` to `sequence.align.align_ungapped()`
- By default the new function returns an alignment, optionally only the score is returned
- Slightly increased performance of `structure.sasa()`
- Default `point_number` in `structure.sasa()` increased to 1000
- Boolean mask replaces the inflexible `ca_only` parameter in `structure.superimpose()`

Fixes
- Fixed occasional wrong alphabet when loading as protein seqence from FASTA file (29)
- Fixed deallocation issue in `structure.CellList` objects, when an exception is raised in the constructor
- Iteration over alignments is forbidden now, yielded empty generator before

Notes
Currently no wheels are provided for Python 3.5 on Windows due to issues with `openssl` in the install process.