Omega TK 2.9.0

New features

• A new method, OEOmega::Build, has been introduced that provides a proper return code on failure, unlike the operator(). Operator() was then deprecated.

• A new namespace, OEOmegaReturnCode, has been introduced that defines return codes for various API methods.

• A new function, OEGetOmegaError, has been introduced that returns error descriptions corresponding to various Omega return codes.

• A new method, OETorLib::GetTorRule, has been introduced that returns the torsion rule corresponding to a rotatable bond.

• A new method, OETorLib::HasTorRule, has been introduced that determines whether a torsion rule is defined for a rotatable bond.

• A new function, OEGetTorValues, has been introduced that provides torsion values from a torsion rule-defined OESubSearch object.

• The following preliminary APIs, which were introduced in Omega TK 2.8.0, have been modified to return an unsigned return code instead of a bool:

  • OEConformerBuilder::Build

  • OEFragBuilder::Build

  • OEMacrocycleBuilder::Build

  • OEMacrocycleOmega::Build

  • OEMolBuilder::Build

  • OETorDriver::GenerateConfs

  Note

  The change in the preliminary APIs mentioned above is a breaking change and needs to be addressed properly by scripts and code that use these APIs. Since bool and unsigned are mutually compatible, any scripts or code using these API methods may continue to function without a proper fix and may not give any runtime or compile-time error. However, the end results obtained from such scripts or codes could be incorrect.

• The following APIs have been modified to be const and some of their arguments have been modified to be const:

  • OEConformerBuilder::Build

  • OEFragBuilder::Build

  • OEMacrocycleBuilder::Build

  • OEMacrocycleOmega::Build

  • OEMakeFragLib::GenerateMissingFrags

  • OEMakeFragLib::GetMissingFrags

  • OEMolBuilder::Build

  • operator()

  • OEIsMacrocycle

  • OETorDriveOptions::ExceedsMaxRotors

  • OETorDriver::GenerateConfs

• The following APIs have been modified to return a bool instead of a void:

  • OEBuilderBase::AddFragLib

  • OETorLib::AddTorsionLibrary

  • OETorLib::SetTorsionLibrary

  • OETorLib::ResetTorsionLibrary

Major bug fixes

• An issue that caused an occasional Coulombic collapse for conformations of zwitterionic molecules generated with the Macrocycle algorithm has been fixed.

• An issue that caused Omega* to fail to produce conformations for molecules containing chiral nitrogen atom using macrocycle mode has been fixed.

Minor bug fixes

• OEConformerBuilder::Build no longer fails due to unspecified stereo in the input molecule.

• OEConformerBuilder::Build no longer generates more than one conformer in the output molecule.

• OEConformerBuilder::Build no longer writes anything in standard output.

• The default for EnumNitrogen in OEMolBuilderOptions has been changed from OENitrogenEnumeration::All to OENitrogenEnumeration::Unspecified so that any user-specified stereo information is not lost by default.

• OEMacrocycleOmega::Build has been fixed to generate conformers in cases when a MaxConfs of 1 is requested.

• operator() now generates a title in the output even when the input molecule has no OEMCMolBase title.

• operator() now produces a title in output conformers when OEOmegaOptions::GetWarts is false.

• operator() now produces correct conformer coordinates when both OEOmegaOptions::SetIncludeInput and OEMolBuilderOptions::SetCanonOrder are set to be true.

• Omega calculations no longer repeat an error message.

• OEMakeFragLib::GenerateMissingFrags no longer crashes with extreme energy window value.

• The torsion rule for [CH3:1][CX4H:2]([CH3])[CX4H2:3][!#1:4] in the default torsion library has been improved.