- FILTER is now bundled with the OMEGA distribution and will run with a valid OMEGA license.
- OMEGA and makefraglib may now be run with MPI using the oempirun script. (Not available on all platforms)
- The default for OMEGA has been changed to require all stereocenters to be specified. Molecules with unspecified stereo will fail, except for unspecified invertible nitrogens which are allowed and will not cause the molecule to 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.
- By default, FLIPPER will no longer flip invertible nitrogens. The default path is for FLIPPER to leave them unspecified and allow OMEGA to enumerate them. Flipping invertible nitrogens in both FLIPPER and then OMEGA will lead to duplication. These options can be changed with the -enumNitrogen flag available in both applications.
- 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.
- Improper formatting of the -erange, -maxConfRange, and -rmsrange parameters will cause OMEGA to exit immediately. Previously the application would throw a warning but continue the calculation without using the parameters.
- 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.
- A bug was fixed in makefraglib where the setting -fromCT false could give nonsense fragments.
- 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.