Biotite

Changelog

Additions
- Extended functionalities for homology searches
- Added `application.tantan.TantanApp` for sequence repeat masking with
`Tantan`
- `sequence.align.KmerAlphabet` and `sequence.align.KmerTable` support spaced
*k-mers*
- Added `sequence.align.local_gapped()` and `sequence.align.local_ungapped()`
for aligning sequences locally with *X-drop* heuristic
- Added `EValueEstimator` for calculation of *expect values* (E-values)
from alignment scores
- Increased performance of `sequence.LetterAlphabet.extends()`
- Added `sequence.SequenceProfile` for representing sequence profiles by means
of a symbol frequency table
- `sequence.SequenceProfile.from_alignment()` creates a profile from an
alignment
- `sequence.SequenceProfile.to_consenus()` creates a consensus sequence
- Increased performance of `sequence.align.get_codes()` and
`sequence.align.get_symbols()`
- Bonds can be read from and written to `CONECT` records in
`structure.io.pdb.PDBFile` (329)


Changes
- Documentation now uses *sphinxcontrib-bibtex* for citations
- Citations include DOI with link to publication


Fixes
- Fixed protein color schemes for sequences containing `'X'` or `'*'` (322)
- `sequence.graphics,plot_nucleotide_secondary_structure()` is now able to set
the color of symbols (333)

Changelog

Additions
- Most classes support now the `repr()` function (290)
- Add equality comparison for `sequence.CodonTable`
- Added `structure.info.all_residues()`, that gives all residue names from the
*Chemical Component Dictionary*
- Updated resources from *Chemical Component Dictionary* in `structure.info`
- Add `structure.io.mol.MOLFile` to support *MOL* and *SDF* files for
small molecule structure data
- Add `database.uniprot` for *UniProt* database support
- `database.uniprot.search()` searches for *Uniprot* IDs that match a given
`database.uniprot.Query`
- `database.uniprot.fetch()` downloads the file corresponding to the given
*Uniprot* ID.
- Increase performance of `structure.pseudoknots()` by using *NetworkX*
to identify conflicting regions (289)


Changes
- Changed `structure.BondType` enum values for more precise description of
aromatic bonds
- `BondType.AROMATIC` is replaced by
`BondType.AROMATIC_SINGLE` and `BondType.AROMATIC_DOUBLE`
- New method `structure.BondList.remove_aromaticity()` converts
`BondType.AROMATIC_SINGLE` to `BondType.SINGLE` and
`BondType.AROMATIC_DOUBLE` to `BondType.DOUBLE` in-place


Fixes
- Fixed error, when reading a single model from a `structure.io.PDBFile`,
if the `MODEL` line is missing in the file
- Fixed the format of formal charges written to `structure.io.PDBFile`
- Previously it was e.g. `'+2'` instead of the correct `2+`
- Fixed `atom_i` parameter when reading a trajectory via
`structure.io.load_structure()` (308)
- Fixed performance issue of `structure.CellList`
- Previously the number of evaluated cells was too large, if the `radius`
parameter of `structure.CellList.get_atoms()` was equal to the
`cell_size` parameter of the constructor (311)
- Setting an existing annotation array in `structure.AtomArray` and
`structure.AtomArrayStack` preserves the *NumPy* `dtype`

Changelog

Additions
- Added interface to *AutoDock Vina*
- `application.autodock.VinaApp` uses `vina` executable to perform
docking of ligand to a receptor molecule
- Uses new `structure.io.pdbqt.PDBQTFile` class for writing input for
and reading output from `vina`
- An *MGLTools* installation is not necessary
- By default the receptor is handled as rigid structure, however,
flexible side chains can be defined
- Added modular system for fast *k-mer* based sequence searches/mappings
- `sequence.align.KmerAlphabet` encodes a `sequence.Sequence` into
*k-mers*
- `sequence.align.KmerTable` is able to find *k-mer* matches between
sequence in an efficient manner
- `sequence.align.SimilarityRule` allows matching *similar* instead of
*exact* *k-mer* matches via a `sequence.align.KmerTable`
- `sequence.align.align_banded()` performs a heuristic local or
semi-global sequence alignment within a defined diagonal band
- Added `sequence.align.remove_terminal_gaps()` function
- Added `application.sra.FastqDumpApp.get_file_paths()` method
- Increased performance of `sequence.Sequence.get_symbol_frequency()`
- Increased performance of `sequence.NucleotideSequence.complement()`
- `sequence.Sequence.reverse()` can optionally create an array view
instead of a copy

Changes
- `application.sra.FastqDumpApp.get_file_paths()` only parses
downloaded PDBQT files, if required
- Running *pytest* automatically recompiles changed *Cython* source code

Changelog

Additions
- Added interface to some programs of the *ViennaRNA* software package
- `application.viennarna.RNAfoldApp` uses `RNAfold` to predict the minimum
free energy secondary structure of an RNA sequence
- `application.viennarna.RNAplotApp` uses `RNAplot` to calculate the
2D coordinates for base symbols in a secondary structure plot
- Added `structure.graphics.plot_nucleotide_secondary_structure()` for
visualization of an RNA secondary structure via *Matplotlib*
- Internally uses `RNAplot`
- Optional visualization of pseudoknots
- Increased performance of `structure.find_connected()`
- Increased performance of `structure.partial_charges()`
- Added `structure.BondList.remove_bonds_to`
- Added molecule-level atom selections
- `structure.get_molecule_indices()`, `structure.get_molecule_masks()` and
`structure.molecule_iter` select atoms belong to a single molecule, i.e.
atoms that are connected via bonds
- Added interface to *NetworkX* package
- Added `as_graph()` method to `sequence.phylo.Tree` and `structure.BondList`
for conversion into a *NetworkX* `Graph`
- The `find_rotatable_bonds()` function uses *NetworkX* to identify
rotatable bonds, i.e. single bonds that are not part of a cycle,
in structures with a `structure.BondList()`

Changes
- Add support for Python 3.9, remove support for Python 3.6
- Add `networkx` package as dependency
- `structure.io.pdbx.set_structure()` does not convert the *residue ID* `-1`
to `"."` anymore

Fixes
- Fixed missing check for string length of *chain ID*, *residue name*
and *atom name* when setting a structure in a `structure.io.pdb.PDBFile`
- `structure.io.pdbx.set_structure()` supports now *atom IDs* larger than
one million
- Fixed `application.dssp.DsspApp` unable to work with multicharacter chain
identifiers (264)
- Fixed `application.muscle.MuscleApp` sometimes not finishing for long
alignments (273)
- Fixed the creation an AtomArray from atoms with optional annotations (279)
- Fixed deletion of annotation arrays in `structure.AtomArray
- Fixed `structure.BondList` potentially ending in a broken state after
indexing it with an unordered index array
- `structure.partial_charges()` uses bond order instead of number of bond
partners to calculate correct charges for atoms with positive or negative
formal charge

Changelog

Additions
- New analysis capabilities for nucleic acid base pairs
- Added `structure.info.nucleotide_names()`
- Increased performance of `structure.base_pairs()`
- Support for exotic nucleotides in `structure.base_pairs()` and
`structure.filter_nucleotides()`
- Added `structure.base_pairs_edge()` and
`structure.base_pairs_glycosidic_bond()` for further
characterization of base pairs
- Added `structure.base_stacking()` for identification of pi-stacking
of nucleobases
- Added `structure.pseudoknots()` for identification of pseudoknots
in a given list of base pairings
- Added `structure.dot_bracket()`,
`structure.dot_bracket_from_structure()` and
`structure.base_pairs_from_dot_bracket()` for conversion of
base pairs to *dot-bracket-letter* notation and vice versa
- New methods for `structure.BondList`:
- Added `get_all_bonds()` for obtaining the bonds atoms for each atom
in the structure
- Added `adjacency_matrix()` and `bond_type_matrix()`
- Added `structure.partial_charges()` for partial charge calculation
using the PEOE method
- Added `structure.info.standardize_order()`, that reorders atoms in
residues into the PDB standard atom order for the respective residue
- Added `structure.graphics.plot_ball_and_stick_model()`
- Increased performance of residue level utilities
- Added `structure.get_residue_positions()`
- Added `sequence.io.genbank.get_raw_sequence()` which returns the
sequence as string

Changes
- `structure.hbond()` raises a warning if an input structure without
hydrogen atoms is given (241)
- `get_sequence()` and `get_sequences()` of `biotite.sequence.io.fasta`
and `biotite.sequence.io.fastq` convert selenocysteine to cysteine (232)
- Changed order of sequence type `biotite.sequence.io.fasta.get_sequence()` and
`biotite.sequence.io.fasta.get_sequences()` try to create (232):
- First: `sequence.NucleotideSequence`
- If this fails: `sequence.ProteinSequence`
- Temporary files used by the `application` subpackage are removed via
`os.remove()` due to issues on Windows (243)

Fixes
- Fixed `structure.base_pairs()` for structures that contian residues,
that are not in the PDB standard order (237)
- Fixed slightly incorrect aspect ratio in molecular visualizations
created via `structure.graphics.plot_atoms()`
- Fixed bounds check for input bonds the `structure.BondList` constructor
(related to 252):
- Previously, the bond type value was not allowed to exceed the number
of atoms
- Fixed `structure.BondList` indexing with an unsorted index array (238)
- Fixed the ``charge`` annotation of molecules obtained via
`structure.info.residue()` (254)

Changelog

Additions
- Added `sequence.ProteinSequence.get_molecular_weight()` method
- Added `application.sra` subpackage as interface to *NCBI SRA tools*
- `FastqDumpApp` is used for fetching FASTQ files from the *NCBI SRA*
- Added `iter_read()` static method to `sequence.io.fasta.FastaFile`
and `sequence.io.fasta.FastqFile`
- This method is used to parse header-sequence-pairs from FASTA/FASTQ
files without the necessity to keep the entire file in memory.
- `set_sequence` and `set_sequences` in `sequence.io.fasta`
and `sequence.io.fasta` support writing RNA sequences with the new
`as_rna` parameter

Fixes
- Fixed missing whitespace at the end of `_loop` category labels in
*PDBx/mmCIF* files (224)
- Fixed inconsistent handling of model IDs over different file formats
for structures where the first model ID is greater than `1` (227)
- Removed warning in `structure.density()`
- `sequence.io.fastq.get_sequence()` and `sequence.io.fastq.get_sequences()`
properly handle RNA and ambiguous sequences now
- Fixed `start` parameter in `structure.renumber_atom_ids` and
`structure.renumber_res_ids`
- Updated fetch URL for FASTA files in `database.rcsb.fetch()`