pypi biotite 0.23.0
Biotite 0.23.0

latest releases: 1.0.1, 1.0.0, 0.41.2...
4 years ago

Changelog

Additions

  • Improved example gallery
    • Added minigalleries in the API reference to get tangible examples for the
      respective function/class
    • Added support for animated Matplotlib plots
    • Using Ammolite for rendering
      PyMOL images
  • Added support for new RCSB search API
    • New database.rcsb.Query classes, that reflect the entirety of the new
      search API, including sequence, sequence motif and structure searches
      • Multiple database.rcsb.Query objects can be combined/negated using the
        operators |, & and ~
    • Added the return_type, sort_by and range parameter to
      database.rcsb.search()
    • Added database.rcsb.count() function to count the number of results a
      database.rcsb.Query would yield in a less costly way than
      database.rcsb.search()
  • Increased indexing speed in biotite.structure.BondList
  • Added attribute sequence.Sequence.alphabet property, that is equivalent to
    sequence.Sequence.get_alphabet()
  • Added convenience functions fastq.get_sequence(), fastq.get_sequences(),
    fastq.set_sequence() and fastq.set_sequences()
  • Drastically increased writing speed of sequence.io.fasta.FastaFile
  • Increased mapping speed of sequence.AlphabetMapper
  • Added sequence.Alphabet.is_letter_alphabet() method
  • Added general sequence I/O convenience functions
    sequence.io.load_sequence(), sequence.io.load_sequences(),
    sequence.io.save_sequence() and sequence.io.save_sequences() that derive
    the appropriate File class from the suffix of the file name.

Changes

  • The omit_chain parameter has been removed from database.rcsb.search()
  • The old database.rcsb.Query classes have been removed
  • Removed python setup.py test and python setup.py build_sphinx commands,
    please use pytest and sphinx-build directly instead
  • Renamed sequence.NucleotideSequence.alphabet to
    sequence.NucleotideSequence.alphabet_unamb
  • sequence.io.fastq.FastqFile returns its entries only as str instead of
    sequence.NucleotideSequence for consistency with
    sequence.io.fastq.FastaFile
    • The method sequence.io.fastq.FastqFile.get_sequence() is deprecated
    • The method sequence.io.fastq.FastqFile.get_seq_string() returns the
      sequence as a str instead of a sequence.NucleotideSequence

Fixes

  • Fixed expect_looped parameter in
    structure.io.pdbx.PDBxFile.get_category()
  • Fixed error in structure.io.pdbx.PDBxFile, that was raised, if a PDBx
    field and its single-line value are in separate lines
  • Added check for boolean mask length, when a boolean mask is given as index
    to biotite.structure.BondList
  • Changed chain_id dtype from 'U3' to 'U4' (#215)

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