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
andOEMacrocycleOmegaOptions
classes to generate a macrocycle molecule conformer ensembleOEMacrocycleBuilder
andOEMacrocycleBuilderOptions
classes to generate a single conformer structure of a macrocycle moleculeOEConfGen::OEDuplicateScanner
andOEConfGen::OEDuplicateScanOptions
classes to enable fast scanning and removal of duplicate conformers from a conformer ensembleOEIsMacrocycle
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 libraryOEMolBuilder
andOEMolBuilderOptions
classes to generate small molecule conformers using a fragment libraryOEConformerBuilder
class to generate a single conformer structure of a small moleculeOEFragBuilder
andOEFragBuilderOptions
classes to generate fragment conformers using distance geometry. TheOEFragBuilderOptions
class combines multiple options related to building a fragment library for bothOEMakeFragLib
andOEMolBuilder
.OETorDriver
andOETorDriveOptions
classes to generate small molecule conformer ensembles from torsion drivingOEFragOptions
class to store options related to generating a single fragment structureOERingFragOptions
class to store options related to generating a single ring fragment structureOEConfFixOptions
class to store options related to fixing part of the structure of small molecules during a conformational searchOESliceEnsembleOptions
class to store options for ensemble pruning during a small molecule conformational searchOEFragBuilderMode
namespace to set upOEFragBuilderOptions
for specific uses
New features¶
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
, andOEOmegaSampling_FastROCS
, have been added to theOEOmegaSampling
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, theOETorLib
constructor now takes a torsion type value from theOETorLibType
namespace. Also, a new overload of theOETorLib.SetTorsionLibrary
method has been added to allow setting the desired torsion library from the above-mentioned namespace.The
OEOmegaForceFieldType
namespace has been replaced by theOEMMFFSheffieldFFType
namespace. The new namespace adds 4 new options for the force field used in theOEOmega
class. These new options are based on a modified variation of theOEMMFF94sParams
parameters that prefers the appropriate axial/equatorial conformers for many molecules inOEOmega
.
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 thatOEOmega
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 introducedOEMMFFSheffieldFFType_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.
Documentation changes¶
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.