OMEGA and makefraglib may now be run with MPI using the oempirun script. (May not available on all platforms)
The default for OMEGA has been changed to require all stereocenters to be specified. Molecules with any unspecified
stereo will fail. The previous
behavior was for OMEGA to choose a random stereoisomer. This default can be changed back to the previous behavior
by setting -strictstereo to false.
The default for OMEGA has been changed to no longer use ‘close enough’ atom typing. If a proper MMFF atom type
cannot be found for
an atom then the molecule will fail. Previous versions would use a different atom type of the same element if it
The previous behavior for atom type substitution can be enabled by setting -strictatomtyping to false.
OMEGA now has the option to require on-the-fly generation of fragments to be the same as the makefraglib utility
by setting -strictfrags to true.
This fragment generation is more rigorous but also more time consuming.
The convenience flag -strict has been added to turn on or off all of the strict options. These include
-strictstereo, -strictatomtyping and -strictfrags.
On-screen progress has been enabled for OMEGA and makefraglib using the -progress flag.
The options are none, dots, log, and percent.
The -maxconfgen and -maxpoolsize flags have been removed. These options are set internally and adjusted automatically
subject to the user
defined variable of -maxconfs. Additionally, hard limits have been removed from
these variables and they are now only limited by available memory.
The flag -fixsmarts has been created to allow a smarts pattern to be used to fix
a portion of the molecule. This requires 3D coordinates to be available from either
a 3D input file with -fromCT set to false or from a molecule set using -fixfile.