Biotite 0.23.0

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)