Omega TK 2.9.1

New features

• The following new methods have been added to the OESliceEnsembleOptions class to make it more efficient with large macrocycles and energy-optimized structures:

  • SetEnergyThreshold

  • GetEnergyThreshold

  • OESliceEnsembleOptions::SetMaxTerminalHeavy

  • OESliceEnsembleOptions::GetMaxTerminalHeavy

  • SetSliceByEnergy

  • GetSliceByEnergy

• A new class, OEConfSlicer, has been added that complements the OESliceEnsemble method. In addition, a new overload has been added to OESliceEnsemble that provides broader functionality by working with an OESliceEnsembleOptions object.

• Deduplication of conformer ensembles in OEMacrocycleOmega has been improved by replacing two preliminary API methods, OEConfGen::OEMacrocycleOmegaOptions::SetDeduplicateScanOptions and OEConfGen::OEMacrocycleOmegaOptions::GetDeduplicateScanOptions, with OEMacrocycleOmegaOptions::SetSliceEnsembleOptions and OEMacrocycleOmegaOptions::GetSliceEnsembleOptions, respectively.

Major bug fixes

• OEMacrocycleOmega::Build now generates conformer ensembles that are centered and aligned to each other, and with better deduplication.

• An issue that occasionally caused knotted conformations of some complex molecules generated with OEOmega::Build has been fixed.

Minor bug fixes

• OEOmega::Build now properly adds hydrogens to single heavy atom molecules.

• Two preliminary API classes, OEConfGen::OEDuplicateScanner and OEConfGen::OEDuplicateScanOptions, have been removed.

• Two preliminary API methods, OEConfGen::OETorDriveOptions::SetIncludeInput and OEConfGen::OETorDriveOptions::GetIncludeInput, have been removed.

• Defaults for OEMolBuilderOptions::SetEnumNitrogen and SetSampleHydrogens in the OEOmegaSampling::Dense mode have been changed from OENitrogenEnumeration::Unspecified and false to OENitrogenEnumeration::All and true, respectively.

• An issue regarding the OEOmegaOptions::SetEnergyWindow not being properly honored for some molecules with OEOmega::Build has been fixed.

• Fragment conformations for CCN and CN have been updated in the built-in fragments library to properly reflect the tetrahedral geometry.

• Occasional failure to generate conformations for molecules containing chiral N=N or C=N bonds has been fixed.