Biotite 0.5.3

Changelog

• Slightly higher performance of sasa()
• Fixed issue with sasa() in combination with Windows x64 version

Biotite 0.5.2

Changelog

• matplotlib is now an optional requirement
• Added mass_of_element(), atom_masses(), mass_center() and gyration_radius() to structure subpackage
• Increased performance of AdjacencyMap and sasa()

Note

Currently the build fails for the Windows x64 wheels, due to an error in the unit tests for the new SASA implementation. This will (hopefully) be fixed in the next version.

Biotite 0.5.1

Changelog

• Added get_residue_count() in structure subpackage
• Added get_symbol_frequency() method to Sequence
• Added terminal_penalty parameter to align_optimal()
  • If set to false, terminal gaps are not penalized
• Fixed parser for trajectory files

Biotite 0.5.0

Changelog

• Removed pure Python implementation
• Added wheels for Windows
• Added support for sequence features
  • Added GenBank and GenPept parser
  • A Feature describes a functional part of a sequence
  • An Annotation is a collection of Feature objects corresponding to one sequence
  • An AnnotatedSequence combines an Annotationwith a Sequence
• More indexing options for Sequence objects
• Moved static method Sequence.encode() and Sequence.decode()
  to alphabet member functions encode_multiple() and decode_multiple()
• Added Alphabet subclass LetterAlphabet
  • LetterAlphabet has massively improved performance for encoding and decoding
  • Removed is_letter_alphabet() method from Alphabet
• Improved performance of sequence.align.simple_score()
• SubstitutionMatrix.score_matrix() does not copy the internal ndarray
• Added 'MSE' and 'SEC' as 3-letter amino acids in ProteinSequence
• ProteinSequence accepts lower case strings in constructor
• Improved PDB file support
  • Ability to choose insertion codes and alternative locations
  • Added model parameter
• Added MMTF file parser
  • MMTFFile instances efficiently decode MMTF file contents
  • biotite.structure.io.mmtf.get_structure() constructs AtomArray and AtomArrayStack
    instances from MMTFFile
  • biotite.structure.io.get_model_from() accepts MMTF files
• Added DSSPApp to interface DSSP for secondary structure annotation
• Added MafftApp and ClustalOmegaApp for multiple sequence alignments

Biotite 0.4.1

Changelog

• Fixed bug in coordinate superimposition that occured when the rotation matrix contained a reflection

Biotite 0.4.0

Changelog

• Python 3.4 and 3.5 compatibility
• Wheels for MacOS X
• Changed enum type of AppState from Flag to IntEnum
• Added class sequence.CodonTable
  • CodonTable can load NCBI codon tables
  • Removed codon table functionality from ProteinSequence
  • NucleotideSequence.translate() takes a CodonTable as optional parameter
• Removed structure.simple_view()
• Drastic performance increase in sequence.align.align_optimal() for affine gap penalty when using C-extensions
• Added structure.check_duplicate_atoms()
• Added structure.spread_residue_wise()
• Improved performance and atom array stack acceptance in structure.dihedral_backbone()

Biotite 0.3.3

Changelog

• Added get_gapped_sequences() method in Alignment class
• Documentation now contains examples and logo page

Biotite 0.3.2

v0.3.2

Added download URL, fixes (hopefully) twine upload issue