Omega TK 2.5.1

New features

  • An option has been added to allow hydrogen atoms in -OH, -SH, and amines to take part in conformational sampling. New methods have been added for accessing this option: GetSampleHydrogens and SetSampleHydrogens. By default, hydrogen atoms are not sampled.

  • A warts option has been added to OEFlipper. Enabling this option will number the output molecules with an @ symbol.

  • The parameterless version of OEOmega.AddFragLib will now load the built-in fraglib immediately. By default, the built-in fraglib does not load until operator() is called for the first time.

Major bug fixes

  • Now using SetFixSmarts without SetFixMol will rematch for every input structure. Previously, this would only match the first input structure and reuse that match for the rest of the calculation. Using both SetFixSmarts and SetFixMol will continue to match against the fixmol and use that match for the entire calculation.

  • Partial ring matching with SetFixSmarts or SetFixMol could cause a crash. Now only full ring systems may be specified and any attempt at matching a partial ring system will fail gracefully.

  • The default value for max matches with SetFixSmarts or SetFixMol has been changed from 10 to 1. This value can be adjusted with SetFixMaxMatch.

  • A bug has been fixed where multiple threads using OEOmega could cause a license failure.

  • Planar molecules could have problems sprouting hydrogens when disabling SetFromCT because OMEGA was treating them as 2D. Now OMEGA will assume that planar molecules are properly defined 3D coordinates in this situation.

  • Stereochemistry at the attachment points of rings with four or less atoms could be lost. Now stereochemistry is saved for rings of all sizes.

  • A bug has been fixed where exceptionally long torsion rules could get cutoff early.

Minor bug fixes

  • Only 3D coordinates were being cleared in FLIPPER. Now 2D coordinates are cleared as well.

  • Fragment generation during an OMEGA calculation with SetStrictFrags enabled could yield slightly different fragments than the MakeFraglib app. This has been corrected for consistency.

Documentation fixes

  • The Omega TK documentation was showing the incorrect version number.