FILTER is now completely bundled into the OMEGA package. The manuals have been consolidated into this single manual
and FILTER has taken on the OMEGA version number.
An option has been added to allow hydrogen atoms in -OH, -SH, and amines to take part in conformational sampling. This
new option can be enabled via the -sampleHydrogens parameter.
By default, hydrogen atoms are not sampled.
Now using -fixsmarts without -fixfile 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 -fixsmarts and
-fixfile will continue to match against the fixfile and use that match for the
Partial ring matching with -fixsmarts or -fixfile could
cause a crash. Now only full ring systems may be specified and any attempt at matching a partial ring system will fail
Planar molecules could have problems sprouting hydrogens when using -fromCT false
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.
A bug has been fixed where older TK licenses in the license file could cause the OMEGA application to fail. [Case #13466]
PVM (parallel virtual machine) is no longer supported. OpenMPI version 1.6 is supported
on all platforms. The -mpi_np and -mpi_hostfile flags are now used to run OMEGA and makefraglib in MPI mode.
These new flags replace the oempirun script.