OEChem TK 4.1.1

New features

  • Support has been implemented for OEGroup information for OEMiniMol to support the return of enhanced stereogroup information from OEFastFPDatabase hits. Previously, enhanced stereogroup information on the indexed structures would be ignored during indexing and thus missed from returned hits.

  • LINK records in the PDB metadata are now parsed to improve perception of covalently bound heterogens. The equivalent _struct_conn metadata is also parsed from mmCIF files. The distance between the listed atoms is confirmed before applying the bond.

Minor bug fixes

  • If any parse error results from parsing a OEFormat::CXSMILES appendix specifically, the full appendix plus the molecule title are now returned in the molecule title to allow user inspection and corrective action.

  • OEFormat::SDF data parsing has been modified to ensure that >-prefixed data is properly captured. Since SDF data field name lines are >-prefixed as well, the new behavior explicitly requires a blank line delimiter to be present between data entries, including null data items, per the SDF file format specification. This allows unambiguous identification of data field name header lines versus data entry lines.

  • An issue has been fixed to avoid generating duplicate data tags from generic data that can result in invalid JSON output.

  • Titles returned from OEMolDatabase::GetTitle when OEFormat::CXSMILES files are indexed no longer contain the CXSMILES appendix unless there is a parse error with the appendix information itself.

  • An error has been fixed that sometimes resulted in missing atom parity information in output SDF format files when a nondefault oemolistream::SetConfTest was provided.

  • A line ending parse error has been fixed for OEFormat::FASTA files affecting windows files.

  • Propagation of perceived query aromaticity has been added for alternating single/double Kekulé forms so that alternate and equivalent s/d bond patterns are treated consistently.

  • Null pointer protections have been added to some internal search matching code that could cause a crash.

  • OEFileStringTypeFlavor::Default has been augmented to exclude file types that are not suggested for use. Accordingly, a new constant, OEFileStringTypeFlavor::Pretty, has been defined and is part of the new definition of OEFileStringTypeFlavor::Default. Removing OEFileStringTypeFlavor::Pretty from OEFileStringTypeFlavor::Default would provide the file types that include everything.

  • A new type, OEMMFFType::CION, has been added to define a generic type for counterions.

OEPlatform TK 4.1.1

New features

  • The ZSTD library has been updated from version 1.5.2 to 1.5.6.

OEBio TK 4.1.1

Major bug fixes

  • In the Iridium categorization of a design unit, a properly perceived, covalently bound ligand no longer triggers an HT to MT category transition. The rule flags atoms that are within what is considered a covalent bond distance, where a bond is not properly perceived.

  • An issue has been fixed so that ClearComponent can be used to clear user-defined components.