A new command line parameter,
-fixmcs, has been added to provide enhanced support to fix part of a molecule during conformer generation based on maximum common substructures (MCS).
Minor bug fixes¶
OMEGA now generates report files with appropriate content.
Log files from OMEGA now contain newly generated titles of molecules for untitled molecules.
Omega TK 4.2.1¶
The ability to fix a part of a molecule during conformer generation based on maximum common substructure (MCS) has been added. The following new methods have been added to the OEConfFixOptions to enable this functionality:
New methods SetIgnoreStereo and GetIgnoreStereo have been added to OEMolBuilderOptions to allow continuation of conformer generation when specified stereo signatures in a molecule could not be honored.
New methods SetMaxEnumConfs and GetMaxEnumConfs have been added to OEMolBuilderOptions to allow specifying the maximum number of conformers to be generated from ring enumeration, nitrogen enumeration, and/or hydrogen sampling.
Verbose mode logging now reports torsion angles sampled, along with the rules, during torsion driving.
Minor bug fixes¶
Conformer generation with OEOmega.Build or OEMolBuilder.Build now fails correctly when specified stereo signatures on a molecule cannot be honored. The existing behavior, to carry on even if stereo signatures could not be honored, can be obtained by setting IgnoreStereo to
Ring fragment building during OEOmega.Build, OEFragBuilder.Build, OEMolBuilder.Build, or GenerateMissingFrags now properly honors the SetFragKeep parameter regarding the maximum number of generated fragment conformers to be kept.