New functionality has been added for generating a densely sampled set of conformers, as required during conformer free energy calculations using OEFreeFormConf.
Omega has used random coordinate embedding with distance-geometry refinement to generate initial 3D fragment and ring conformers for more than a decade. The pseudo-random number generator used has been upgraded to an implementation of the Mersenne Twister adapted from the work of Kohei Takeda.
Omega now recognizes and adjusts ring sampling for macrocycles. This improves reproduction of small and medium-sized macrocycle structures without increasing maximum ensemble sizes.
A new class, OEOmegaOptions, has been added that sets all options of the OEOmega object during its construction. All the OEOmega methods with the same name as their OEOmegaOptions counterparts are now deprecated except for the options for fraglib, which are still maintained through the OEOmega interface.
The following table shows the older, deprecated functions and their new option replacements:
| Deprecated Method | New option Method |
| OEConfGen::OEOmega::SetCommentEnergy | OEOmegaOptions::SetCommentEnergy |
| OEConfGen::OEOmega::GetCommentEnergy | OEOmegaOptions::GetCommentEnergy |
| OEConfGen::OEOmega::SetIncludeInput | OEOmegaOptions::SetIncludeInput |
| OEConfGen::OEOmega::GetIncludeInput | OEOmegaOptions::GetIncludeInput |
| OEConfGen::OEOmega::SetRotorOffset | OEOmegaOptions::SetRotorOffset |
| OEConfGen::OEOmega::GetRotorOffset | OEOmegaOptions::GetRotorOffset |
| OEConfGen::OEOmega::SetSDEnergy | OEOmegaOptions::SetSDEnergy |
| OEConfGen::OEOmega::GetSDEnergy | OEOmegaOptions::GetSDEnergy |
| OEConfGen::OEOmega::SetWarts | OEOmegaOptions::SetWarts |
| OEConfGen::OEOmega::GetWarts | OEOmegaOptions::GetWarts |
| OEConfGen::OEOmega::SetBuildForceField | OEOmegaOptions::SetBuildForceField |
| OEConfGen::OEOmega::GetBuildForceField | OEOmegaOptions::GetBuildForceField |
| OEConfGen::OEOmega::SetCanonOrder | OEOmegaOptions::SetCanonOrder |
| OEConfGen::OEOmega::GetCanonOrder | OEOmegaOptions::GetCanonOrder |
| OEConfGen::OEOmega::SetFromCT | OEOmegaOptions::SetFromCT |
| OEConfGen::OEOmega::GetFromCT | OEOmegaOptions::GetFromCT |
| OEConfGen::OEOmega::SetFixRMS | OEOmegaOptions::SetFixRMS |
| OEConfGen::OEOmega::GetFixRMS | OEOmegaOptions::GetFixRMS |
| OEConfGen::OEOmega::SetFixDeleteH | OEOmegaOptions::SetFixDeleteH |
| OEConfGen::OEOmega::GetFixDeleteH | OEOmegaOptions::GetFixDeleteH |
| OEConfGen::OEOmega::SetFixUniqueMatch | OEOmegaOptions::SetFixUniqueMatch |
| OEConfGen::OEOmega::GetFixUniqueMatch | OEOmegaOptions::GetFixUniqueMatch |
| OEConfGen::OEOmega::SetFixMaxMatch | OEOmegaOptions::SetFixMaxMatch |
| OEConfGen::OEOmega::GetFixMaxMatch | OEOmegaOptions::GetFixMaxMatch |
| OEConfGen::OEOmega::SetStrictAtomTypes | OEOmegaOptions::SetStrictAtomTypes |
| OEConfGen::OEOmega::GetStrictAtomTypes | OEOmegaOptions::GetStrictAtomTypes |
| OEConfGen::OEOmega::SetStrictStereo | OEOmegaOptions::SetStrictStereo |
| OEConfGen::OEOmega::GetStrictStereo | OEOmegaOptions::GetStrictStereo |
| OEConfGen::OEOmega::SetEnumNitrogen | OEOmegaOptions::SetEnumNitrogen |
| OEConfGen::OEOmega::GetEnumNitrogen | OEOmegaOptions::GetEnumNitrogen |
| OEConfGen::OEOmega::SetEnumRing | OEOmegaOptions::SetEnumRing |
| OEConfGen::OEOmega::GetEnumRing | OEOmegaOptions::GetEnumRing |
| OEConfGen::OEOmega::SetSampleHydrogens | OEOmegaOptions::SetSampleHydrogens |
| OEConfGen::OEOmega::GetSampleHydrogens | OEOmegaOptions::GetSampleHydrogens |
| OEConfGen::OEOmega::SetEnergyWindow | OEOmegaOptions::SetEnergyWindow |
| OEConfGen::OEOmega::GetEnergyWindow | OEOmegaOptions::GetEnergyWindow |
| OEConfGen::OEOmega::SetEnergyRange | OEOmegaOptions::SetEnergyRange |
| OEConfGen::OEOmega::GetEnergyRange | OEOmegaOptions::GetEnergyRange |
| OEConfGen::OEOmega::SetMaxConfs | OEOmegaOptions::SetMaxConfs |
| OEConfGen::OEOmega::GetMaxConfs | OEOmegaOptions::GetMaxConfs |
| OEConfGen::OEOmega::SetMaxConfRange | OEOmegaOptions::SetMaxConfRange |
| OEConfGen::OEOmega::GetMaxConfRange | OEOmegaOptions::GetMaxConfRange |
| OEConfGen::OEOmega::SetMaxRotors | OEOmegaOptions::SetMaxRotors |
| OEConfGen::OEOmega::GetMaxRotors | OEOmegaOptions::GetMaxRotors |
| OEConfGen::OEOmega::SetMaxSearchTime | OEOmegaOptions::SetMaxSearchTime |
| OEConfGen::OEOmega::GetMaxSearchTime | OEOmegaOptions::GetMaxSearchTime |
| OEConfGen::OEOmega::SetRangeIncrement | OEOmegaOptions::SetRangeIncrement |
| OEConfGen::OEOmega::GetRangeIncrement | OEOmegaOptions::GetRangeIncrement |
| OEConfGen::OEOmega::SetRMSRange | OEOmegaOptions::SetRMSRange |
| OEConfGen::OEOmega::GetRMSRange | OEOmegaOptions::GetRMSRange |
| OEConfGen::OEOmega::SetRMSThreshold | OEOmegaOptions::SetRMSThreshold |
| OEConfGen::OEOmega::GetRMSThreshold | OEOmegaOptions::GetRMSThreshold |
| OEConfGen::OEOmega::SetSearchForceField | OEOmegaOptions::SetSearchForceField |
| OEConfGen::OEOmega::GetSearchForceField | OEOmegaOptions::GetSearchForceField |
| OEConfGen::OEOmega::SetTorsionDrive | OEOmegaOptions::SetTorsionDrive |
| OEConfGen::OEOmega::GetTorsionDrive | OEOmegaOptions::GetTorsionDrive |
| OEConfGen::OEOmega::SetDielectric | OEOmegaOptions::SetDielectric |
| OEConfGen::OEOmega::GetDielectric | OEOmegaOptions::GetDielectric |
| OEConfGen::OEOmega::SetExponent | OEOmegaOptions::SetExponent |
| OEConfGen::OEOmega::GetExponent | OEOmegaOptions::GetExponent |
| OEConfGen::OEOmega::SetFixMol | OEOmegaOptions::SetFixMol |
| OEConfGen::OEOmega::GetFixMol | OEOmegaOptions::GetFixMol |
| OEConfGen::OEOmega::SetFixFile | OEOmegaOptions::SetFixFile |
| OEConfGen::OEOmega::ClearFixFile | OEOmegaOptions::ClearFixFile |
| OEConfGen::OEOmega::SetFixQuery | OEOmegaOptions::SetFixQuery |
| OEConfGen::OEOmega::SetFixSmarts | OEOmegaOptions::SetFixSmarts |
| OEConfGen::OEOmega::GetFixSubSearch | OEOmegaOptions::GetFixSubSearch |
| OEConfGen::OEOmega::SetTorLib | OEOmegaOptions::SetTorLib |
| OEConfGen::OEOmega::GetTorLib | OEOmegaOptions::GetTorLib |