OMEGA 4.1.0.0¶

Fall 2020

New Features¶

The defaults for the -warts and -flipper_warts in OMEGA have been changed from false to true.
The Boolean flag -mmff has been added to the Filter application to allow filtering of atoms that cannot be atom-typed with MMFF. It is false by default.
Six new flags have been added to Flipper to allow more control when selecting stereo centers as well as improving usability of the program:
- -enumEZ
- -enumRS
- -enumBridgehead
- -molNames
- -prefix
- -progress
The built-in default filter for the Filter application is now in sync with the provided filter_frag.txt file.
GPU-OMEGA now requires a minimum NVIDIA Driver version of 450.x and a minimum GPU compute capability of 3.5. See NVIDIA Drivers and Supported GPUs for more details.
Conformer generation using dense mode will now default to running on the CPU instead of the GPU. The other torsion driving sampling modes (classic, rocs, fastrocs and pose) will still run on a GPU by default if one is available on a Linux platform. For details on how to run with dense mode sampling on a GPU see the Usage section of the GPU-OMEGA docs.

Documentation for the -erange, -maxConfRange, and -rmsrange for OMEGA has been improved for clarification.

Fall 2020

GPU-Omega now requires a minimum NVIDIA Driver version of 450.x and a minimum GPU compute capability of 3.5. See NVIDIA Drivers and Supported GPUs for more details.
Conformer generation using dense mode now defaults to running on the CPU instead of the GPU. The other torsion-driving sampling modes (sparse, rocs, fastrocs, and pose) will still run on a GPU by default if one is available on a Linux platform. For details on how to run with dense mode sampling on a GPU, see the Usage section of the GPU-Omega docs.
A new class, OEFlipperOptions, has been added that defines parameters for specifying stereo centers and other options.
OEFlipper has been updated to take a molecule and an OEFlipperOptions value. The old version of OEFlipper that takes five parameters has been deprecated.
A new function, OEFlipperStereoCenters, has been added that returns a number of undefined stereo centers in a molecule as interpreted by OEFlipper.

A memory leak in GPU-Omega has been fixed.
An issue with generating conformers on the CPU using child processes with the same OEOmega object has been fixed.
GPU-Omega no longer throws an error when attempting to generate conformers with the same OEOmega object in child processes. Instead, it falls back to the CPU. To use GPU-Omega with child processes, each child must construct a new OEOmega object.

OEConfGen now clears all fragment libraries. Previous releases did not clear the internal shared fragment library (a shared memory library of fragments accrued while generating conformers with the same OEOmega object).

Fall 2020