OMEGA 4.2.0

Spring 2022

New features

OMEGA torsion driving (that is, in the classic, rocs, fastrocs, dense, and pose modes) now generates outputs that are consistent with outputs generated in the macrocycle mode. The following outputs are generated by default:
- oeomega_mode_conformers.oeb.gz: Output molecule conformers
- oeomega_mode_log.txt: Output run log
- oeomega_mode_param.txt: Parameters file for re-running the job
- oeomega_mode_rpt.csv: Output Report
OMEGA now supports cxsmiles file format with enhanced stereo information as input.
A new command line parameter, -flipper_enhstereo, has been added to provide enhanced stereo support for stereo enumeration when -flipper is set to true.
OMEGA no longer supports writing outputs in non-3D file formats (e.g. smi).
OMEGA now provides a detailed description of available modes when an invalid mode is presented in the command line.
OMEGA torsion driving (i.e., in the classic, rocs, fastrocs, dense, and pose modes) now reports correct defaults for parameters in the command line help.

oeomega classic --help now returns a list of simple command line parameters. A list of all parameters can be viewed by typing oeomega classic --help all
Inputs for OMEGA command line range parameters (i.e., -erange, -maxConfRange, and -rmsrange) have been simplified and now accept list-like parameters (e.g., -maxConfRange 10 20 30 is a valid input).
An issue has been fixed to enable OMEGA to generate an appropriate set of conformers when run with -fixfile and a -maxmatch value greater than 1.
An issue has been fixed related to GPU-OMEGA occasionally writing to standard out stream.
An issue has been fixed to enable Flipper to support piped input.

Support for consideration of MDL enhanced stereo collection information during isomer generation has been added. The OEFlipperOptions class adds a new SetEnhancedStereo option to control consideration of explicit enhanced stereo groups defined by OEGroupBase information that may have been read from V3000 the OEFormat values indicating SDF structures or CXSMILES files.
A new method, SetFragBuilderMode, has been added that allows setting fragment building mode in the corresponding OEFragBuilderOptions.

Internal generic data tags applied to the flip-ee used for performance during the flipping activity are now stripped from the structures returned by OEFlipper as this information is no longer relevant.

The ability to filter based on aromatic ring count and fraction of CSP3 carbons has been added.