- 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
- 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.
- 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 random non-repeating flips.
Previous versions generated random flips, leading to
molecules with the same stereochemistry being returned multiple