github biotite-dev/biotite v0.27.0
Biotite 0.27.0

latest releases: v1.0.1, v1.0.0, v0.41.2...
3 years ago

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

Don't miss a new biotite release

NewReleases is sending notifications on new releases.