Omega TK 2.4.1

New features

  • 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 was available. 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.

Bug fixes

  • Crashes have been fixed that could occur when the -fixfile could not find a valid match or did not have enough atoms to match against in a ring system.
  • Program no longer crashes if there is not enough memory for duplicate removal. If there is not enough memory available for allocation then the application will exit immediately.