Changelog

Additions

• Added support for parsing unit cells. (#778)
  • Added structure.space_group_transforms() to get transformations for a given space group.
  • Added structure.io.pdbx.get_unit_cell() to get AtomArray/AtomArrayStack that represents the entire unit cell.
  • Renamed structure.io.pdb.get_symmetry_mates() to structure.io.pdb.get_unit_cell().
  • The sym_id annotation array is also considered when determining chain starts. (#786)

Changes

• structure.io.pdb.PDBFile.get_symmetry_mates() and structure.io.pdb.get_symmetry_mates() are now deprecated in favor of get_unit_cell(). (#778)
• Removed support for Python 3.10.

Fixes

• Fixed integer overflows/underflows leading to potentially corrupted BinaryCIF files. (#783, #796)
  • Only affects cases where the Encoding is either manually set or it is set by structure.io.pdbx.compress() before writing the file.
  • Now structure.io.pdbx.Encoding.encode() always checks if the target data type is compatible with the values.
  • structure.io.pdbx.compress() will fallback to direct ByteArrayEncoding if the data type is incompatible with FixedPointEncoding.
• Fixed occasionally missing bonds in structure.io.pdbx.get_structure(altloc='occupancy'). (#781)
• Fixed missing support for PDBx files containing multiple operation expression per assembly in structure.io.pdbx.get_assembly(). (#792)