OMEGA 2.3.0

New features

  • The distribution and installation of OMEGA has been modified. The Windows distribution is now a standard .exe installer, and the OS X distribution is a dmg containing a standard pkg installer. The executables are now scripts that chose the correct version of the program at runtime. Please see the Installation and Platform Notes for details.
  • The defaults for MaxConfs and RMSThreshold are changed in this version. The default for MaxConfs is reduced from 400 to 200, while the value for RMSThreshold goes from 0.8 down to 0.5. These changes are based on maintaining good reproduction of the crystal structure test set, virtual screening tests with ROCS and FRED, and pose prediction tests with FRED.
  • The method OEConfGen::OEOmega::ClearFixFile is added to the OMEGA library. This allows an OEConfGen::OEOmega instance to be reused for an unrestrained search after it has previously been used for a fixed search.
  • Untitled molecules are given unique titles of omega_1, omega_2, and so on. Titles allow molecules to be located in the log files.

Bug fixes

  • Fixed a major bug where molecules that have missing torsion rules caused OMEGA to crash. Molecules with missing torsion rules are now sent to the omega2.fail file and are not processed. Missing torsion rules are typically caused by highly unusual molecules for which OEChem cannot properly assign valence to all atoms.
  • Fixed a bug in duplicate conformer removal that caused some conformers that should have been removed to pass through as unique. This bug also caused occurrences where a reduction in maxconfs led to an increase in the number of conformers returned.
  • Fixed a bug that caused SD data on single conformer molecules to be removed.
  • Fixed a bug in the flipper library that left 3D coordinates intact, which caused stereo chemistry to be ambiguous. The flipper library now replaces 3D coordinates with zeros.
  • Fixed a bug where the SyM tag from previous OMEGA calculations caused problems when those molecules where passed back in. Also, the O2MolId tag is now removed from molecules before they are sent to the output.
  • When the number of stereo centers exceeds the number of -maxcenters M, flipper now generates 2^{M} random non-repeating flips. Previous versions generated 2^{M} random flips, leading to molecules with the same stereochemistry being returned multiple times.

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