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())

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

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