Omega TK 2.8.0¶
New features (Preliminary API)¶
The following new preliminary APIs have been added for macrocycle functionality in the Omega TK:
- OEMacrocycleOmega and OEMacrocycleOmegaOptions classes to generate a macrocycle molecule conformer ensemble
- OEMacrocycleBuilder and OEMacrocycleBuilderOptions classes to generate a single conformer structure of a macrocycle molecule
- OEConfGen::OEDuplicateScanner and OEConfGen::OEDuplicateScanOptions classes to enable fast scanning and removal of duplicate conformers from a conformer ensemble
- OEIsMacrocycle function to detect if a molecule contains a macrocycle
The following new preliminary APIs have been added to enhance small molecule conformer generation functionality in the Omega TK:
- OEMakeFragLib class to generate a fragment library
- OEMolBuilder and OEMolBuilderOptions classes to generate small molecule conformers using a fragment library
- OEConformerBuilder class to generate a single conformer structure of a small molecule
- OEFragBuilder and OEFragBuilderOptions classes to generate fragment conformers using distance geometry. The OEFragBuilderOptions class combines multiple options related to building a fragment library for both OEMakeFragLib and OEMolBuilder.
- OETorDriver and OETorDriveOptions classes to generate small molecule conformer ensembles from torsion driving
- OEFragOptions class to store options related to generating a single fragment structure
- OERingFragOptions class to store options related to generating a single ring fragment structure
- OEConfFixOptions class to store options related to fixing part of the structure of small molecules during a conformational search
- OESliceEnsembleOptions class to store options for ensemble pruning during a small molecule conformational search
- OEFragBuilderMode namespace to set up OEFragBuilderOptions for specific uses
New additions and modifications have been made to existing APIs to enhance small molecule conformer generation functionality in Omega TK:
- Three new modes, OEOmegaSampling_Pose, OEOmegaSampling_ROCS, and OEOmegaSampling_FastROCS, have been added to the OEOmegaSampling namespace.
- A new torsion library based on the work of Wolfgang Guba has been added. A new namespace, OETorLibType, has been introduced to provide options for the choice of torsion library. Additionally, the OETorLib constructor now takes a torsion type value from the OETorLibType namespace. Also, a new overload of the OETorLib.SetTorsionLibrary method has been added to allow setting the desired torsion library from the above-mentioned namespace.
- The OEOmegaForceFieldType namespace has been replaced by the OEMMFFSheffieldFFType namespace. The new namespace adds 4 new options for the force field used in the OEOmega class. These new options are based on a modified variation of the OEMMFF94sParams parameters that prefers the appropriate axial/equatorial conformers for many molecules in OEOmega.
Major bug fixes¶
- The SMILES string hash in the internal fragment library in the OEOmega class has been updated to reflect the proper canonicalization of the fragments. This ensures that OEOmega will always find the fragment in the library if it exists.
- The default search force field in the OEOmega class has been changed to the newly introduced OEMMFFSheffieldFFType_MMFF94Smod_NOESTAT type to generate more appropriate axial/equatorial conformers.
- An issue that caused the OEOmega class to not honor the parity bits on relative stereo marked rings has been fixed.
Minor bug fixes¶
- An issue that caused the OEOmega class to report the same warning about atoms multiple times has been fixed.
The following C++ and Python examples have been added to demonstrate using the new preliminary APIs:
- New examples have been added to the Macrocycle Examples section that generate a macrocycle conformer ensemble or a single macrocycle conformer.
- A new example has been added to the Fragment Library generation Examples section that generates fragment libraries.
- A new example has been added to the Generating Torsion Driven Conformation Examples section that generates a conformer ensemble by torsion driving from a given 3D structure.