OEChem TK 4.2.0

New Features

  • If an mmCIF file with long residue names is written to PDB, it will first check whether the three-character version is unused and will use that if it is.

  • A new option parameter has been added to OEUniMolecularRxnOptions that enables hydrogen count conversions and perceptions of the target(s) required for the specified transformation (default: true).

Major Bug Fixes

  • An issue has been fixed that caused mmCIF files with long residue names to break the long residue names into multiple residues.

Minor Bug Fixes

  • An issue has been fixed that ensures that missing mmCIF metadata relevant for Iridium classification of a structure does not cause problems.

  • An issue has been fixed which ensures that LINK records are parsed only if formatted correctly.

  • A new option parameter in OEUniMolecularRxnOptions enables calling OEPrepareSearch for the query and target. This call suppresses the warning messages about unsynchronized explicit or implicit hydrogens between the internal query and the target that were unable to be remedied by any user action.

  • The function OEPrepareSearch is now called as part of the initialization in OELibraryGen to eliminate warning messages about explicit or implicit hydrogens and stereo perceptions on the provided starting materials.

Python-Specific Changes

  • A couple of issues have been fixed that caused crashes using Python 3.12, related to using OEResidue objects in a dictionary and setting an OEBitVector (or classes derived from it) or an OEHalfFloat as generic data on a molecule.

OEBio TK 4.2.0

Minor Bug Fixes