OpenStructure 2.10

Release Notes

• Fixed a bug in Molck where atoms in unknown residues would not be cleaned up with rm_unk_atoms=True.
• Changed default MolckSettings so that rm_unk_atoms defaults to True.
• Chain mapping updates:
  • In a first step, groups of identical chains need to be indentified in the reference structure. The default is sequence based clustering. Now this can be set explicitely and the compare-structures/compare-ligand-structures actions extract this information from the mmCIF entity record if the structure is provided as mmCIF file.
  • Model chains need to be assigned to any of these groups which is done by maximum sequence identity upon alignment. Previous behavior: use max sequence identity to force an assignment. New behavior: specify a minimum sequence identity below which a model chain is considered unassigned. The comparison actions use 70%.
  • Add chain mapping method described by AF2-Multimer (https://doi.org/10.1101/2021.10.04.463034). Available as ChainMapper.GetAFMMapping.
  • Remove "greedy_fast" strategies in ChainMapper.GetlDDTMappingChainMapper.GetQSScoreMapping
• OMF updates:
  • Construct assemblies
  • Getters for residue numbers, backbone traces and occupancies
  • OMF support in mmCIF writer
• Added details in documentation for Molck.
• add lDDTScorer.DRMSD - Distance RMSD that operates on distance differences.
• Remove custom boost configuration code . Use preferred way of boost provided configuration files for newer cmake/boost versions.
• Silence CMake warnings
• Several bug fixes and improvements.