Biotite 0.18.0

Changelog

Additions

• Added shape property to structure.AtomArray() and
  structure.AtomArrayStack()
• structure.Atom() has default values for annotation arrays
• The functions structure.rmsf(), structure.rmsd() and structure.average()
  accept directly coordinates
• Added use_author_fields parameter to structure.io.pdbx.get_structure(),
  that allows to decide between the usage of label_xxx and auth_xxx fields
• Added chunk_size parameter to read() method of trajectory files to
  resolve memory issues
• Added density() function for calculating atom densities.
• Added sequence.align.get_pairwise_sequence_identity()
• API reference shows source files of Cython modules

Changes

• The module name (__module__ attribute) of functions/classes are
  changed to the name of the respective Biotite subpackage
  (e.g. biotite.structure.atoms to biotite.structure)
• Changed handling of PDB insertion codes:
  • Atoms with insertion codes are not filtered out
  • Removed insertion_code parameter in
    biotite.structure.io.xxx.get_structure()
  • New mandatory annotation category ins_code
  • Changed structure.filter_inscode_and_altloc() to
    structure.filter_altloc()

Fixes

• The step parameter in the read() method of trajectory files does not
  increase the stop frame
• Negative residue IDs are handled correctly by structure file readers/writers
• Fixed issues with indexing behavior in sequence.align.Alignment class
• structure.remove_pbc() raises proper error message when box is missing
  in the given atom array (stack)
• sequence.align.align_multiple() raises proper error message, if
  pairwise distance cannot be calculated due to great sequence dissimilarity
• In sequence.io.genbank.get_annotation() qualifier keys without values
  (e.g. /pseudo) are handled properly
• Added pyproject.toml specifying build dependencies for setup.py