Biotite 0.22.0

Changelog

Additions

• Added structure.filter_nucleotides()
• structure.io.pdbx.get_sequence() is able to parse a
  sequence.NucleotideSequence from a PDBx file in addition to
  sequence.ProteinSequence
• Added structure.base_pairs() for determining base pairs in nucleic acid
  structures
• Added structure.get_residue_starts_for()
• Added structure.check_atom_id_continuity()
• Added structure.renumber_atom_ids() and structure.renumber_res_ids()
  to fix structures with discontinuous atom/residue IDs
• Added get_model_count() to structure.io.pdb, structure.io.pdbx,
  structure.io.mmtf and structure.io.gro to obtain the total number
  of models
• The model parameter in get_structure() in structure.io.pdb,
  structure.io.pdbx, structure.io.mmtf and structure.io.gro supports
  negative values to start indexing beginning from the last model
• Increased performance of residue and chain-related functions
  (e.g. structure.get_residue.starts())

Changes

• Revamped altloc ID handling (#194)
  • Instead of choosing each alternate location individually there are three
    options:
  • 'first' choses always chooses the atoms with the first altloc ID
    for each residue
  • 'occupancy' choses always chooses the atoms with the highest occupancy
    for each residue
  • 'all' does not filter any altloc IDs and adds the altloc_id
    annotation to the resulting structure.AtomArray or
    structure.AtomArrayStack
• Renamed structure.check_id_continuity() into
  structure.check_res_id_continuity(); structure.check_id_continuity()
  is still available, but is deprecated

Fixes

• Fixed structure.BondList being iterable, yielding nonsense values
• Improved element guesses in structure.io.pdb.PDBFile when the
  element column is missing (#188)
• Fixed parsing of single models from structure.io.mmtf.MMTFFile (#205)
• Fixed missing unit cell values in structure.io.pdbx.get_structure()
  raising an error; the box attribute is set to None instead