OMEGA 5.0.0¶

New Features¶

The default fragment library in OMEGA has been updated in Linux and OSX platforms. The new fragment library consists of over 580 K fragments, replacing the previous library of ~80 K fragments. OMEGA in Windows still uses the previous library as default, but the modified library, omega_fragment_lib_2023.oeb.gz, is available through the -addfraglib on the database downloads page.
A new parameter, -failed, has been added to OMEGA to allow reporting the failed molecules into a separate file.

Running OMEGA with -fixfile and -mpi_np now appropriately picks up the file for fixing part of molecule.
Output rpt.csv file from OMEGA now contains SMILES strings for most molecules. The entry is still blank for extremely large molecules that are beyond 400 atoms.

Running OMEGA with one molecule in the classic/pose/dense/rocs/fastrocs modes and using -progress percent no longer causes the input molecule to be read twice.

The default fragment library for OEOmega and OEMolBuilder has been updated. The new fragment library consists of over 580 K fragments, replacing the previous library with ~80 K fragments.
Three new force fields have been added and can be used with OEMolBuilder and OETorDriver in OEOmega:
The behavior of OEFlipperOptions has changed. New flags have been added to OEFlipperOptions, facilitating more complete decoupling of individual flags and more selective enumeration of specific stereocenter classes and environments than was previously possible.
A new option class, OEFlipperClassicOptions, has been added to allow a detailed comparison of the new flag behaviors with the previous OEFlipper enumeration behavior. This class will be deprecated in a future toolkit release.
The internal algorithm for storage and usage of torsion rules in OETorLib has been modified to improve performance when working with a library containing a large set of rules.
A new return code FailedCharges has been added to OEOmegaReturnCode to indicate failures due to partial charge assignment.

The order of torsion rules in the default OETorLib has been changed to ensure that a specific rule is not ignored due to the presence of a more generic rule.

Minor internal improvements have been made.