biotite-dev/biotite v0.5.0

Biotite 0.5.0

on GitHub

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