OEPositOptions

class OEPositOptions : public OESystem::OEOptions

This class provides an interface to setup options required for performing pose prediction using POSIT.

The OEPositOptions class defines the following public methods:

• GetAllowedClashType and SetAllowedClashType

• GetBestReceptorPoseOnly and SetBestReceptorPoseOnly

• GetExcludeSelf and SetExcludeSelf

• GetFlexiOverlayOptions and SetFlexiOverlayOptions

• GetFullConformationSearch and SetFullConformationSearch

• GetIgnoreNitrogenStereo and SetIgnoreNitrogenStereo

• GetMinProbability and SetMinProbability

• GetPoserCacheCount and SetPoserCacheCount

• GetPoseRelaxMode and SetPoseRelaxMode

• GetPoseRelaxOptions and SetPoseRelaxOptions

• GetPositMethods and SetPositMethods

• GetTorLib and SetTorLib

Constructor

OEPositOptions(fullConformationalSearch: bool = True,
               ipositMethods: int) -> OEPositOptions
OEPositOptions(arg2: OEPositOptions) -> OEPositOptions

Constructors.

fullConformationalSearch

If true, a full flexible conformational search is performed during pose prediction. If false, only a rigid overlay is used. Default: true.

ipositMethods

Bit-mask of POSIT pose-prediction methods to enable. See OEPositMethod for valid values. Default: OEPositMethod_ALL.

Assignment operator.

GetAllowedClashType

GetAllowedClashType() -> int

See SetAllowedClashType method.

GetBestReceptorPoseOnly

GetBestReceptorPoseOnly() -> bool

See SetBestReceptorPoseOnly method.

GetExcludeSelf

GetExcludeSelf() -> bool

See SetExcludeSelf method.

GetFlexiOverlayOptions

GetFlexiOverlayOptions() -> OEShapeFitOptions

See SetFlexiOverlayOptions method.

GetFullConformationSearch

GetFullConformationSearch() -> bool

See SetFullConformationSearch method.

GetIgnoreNitrogenStereo

GetIgnoreNitrogenStereo() -> bool

See SetIgnoreNitrogenStereo method.

GetMinProbability

GetMinProbability() -> float

See SetMinProbability method.

GetPoserCacheCount

GetPoserCacheCount() -> int

See SetPoserCacheCount method.

GetPoseRelaxMode

GetPoseRelaxMode() -> int

See SetPoseRelaxMode method.

GetPoseRelaxOptions

GetPoseRelaxOptions() -> OEPoseOptimizerOptions

See SetPoseRelaxOptions method.

GetPositMethods

GetPositMethods() -> int

See SetPositMethods method.

GetTorLib

GetTorLib() -> OETorLib

See SetTorLib method.

SetAllowedClashType

SetAllowedClashType(value: int) -> bool

Sets the allowed clash type between the ligand pose and the protein, for pose generation. Allowed clash types are defined in the OEAllowedClashType namespace.

The allowed clash type defines if a generated pose contains a clash or not, as reported in a pose calculation result. The allowed clash type also determines if a relaxation of the pose would be carried out when SetPoseRelaxMode is set to OEPoseRelaxMode_CLASHED. Default is OEAllowedClashType_HYDROGEN.

SetBestReceptorPoseOnly

SetBestReceptorPoseOnly(value: bool) -> bool

Sets flag if only the best receptor should be considered for pose prediction. If this flag set to false the pose prediction is performed using all of the receptors and the best set of poses from all of the receptors combined is provided as the results. With the default setting of true pose prediction is only performed on the best receptor for any given ligand. Note that, setting the flag to false could increase the runtime significantly depending on the number of receptors used for the calculation.

SetExcludeSelf

SetExcludeSelf(value: bool) -> bool

Sets flag to exclude receptor that contains a given ligand as its bound ligand, when choosing the best receptor for a ligand during pose prediction. This option is meant to be used when running cross docking validation experiments, and allows the user to prevent docking a ligand to a receptor containing itself, without having to generate a number of leave one out receptor datasets. Default: False.

SetFlexiOverlayOptions

SetFlexiOverlayOptions(opts: OEShapeFitOptions) -> None

Sets options related to flexible optimization with shape, color, and forcefield, relevant for pose generation with OEPositMethod_SHAPEFIT.

SetFullConformationSearch

SetFullConformationSearch(value: bool) -> bool

Sets flag to perform full conformation search. Setting this option to false disables internal rotamer conformer searching during the flexible searching algorithm. If this option is set to false and a 3D input is not given, this setting is ignored and a full conformation search is automatically performed. Default: true.

SetIgnoreNitrogenStereo

SetIgnoreNitrogenStereo(value: bool) -> bool

Sets flag to ignore Nitrogen stereo specifications in input molecule. Setting this option to false ignores Nitrogen stereo specifications in the input molecule, and a value to true ensures that any specified Nitrogen stereo information is restored. A molecule would always be processed, irrespective of this setting. When Nitrogen stereo is specified in the incoming molecule, setting flag is set to true would respect those stereo specifications. Default: false.

SetMinProbability

SetMinProbability(value: float) -> bool

Sets the minimum pose probability, for poses to be of interest. Poses that has a probability below the minimum value are not relaxed even when the SetPoseRelaxMode is set to CLASHED or ALL`. Default is 0.33.

SetPoserCacheCount

SetPoserCacheCount(value: int) -> bool

Sets the maximum number of posers to be kept in memory cache during POSIT calculation. Each poser takes ~0.75GB of memory. Ability to keep more poser in the cache speeds up the calculation when working with multiple receptors. Default is 10.

SetPoseRelaxMode

SetPoseRelaxMode(value: int) -> bool

Sets the trigger to perform relaxation of the generated pose. The relaxation is performed by allowing flexibility to the ligand and parts of the receptor. Turning on relaxation can significantly slow down the calculations. Pose relaxation modes are defined in the OEPoseRelaxMode namespace. Default is OEPoseRelaxMode_NONE.

SetPoseRelaxOptions

SetPoseRelaxOptions(opts: OEPoseOptimizerOptions) -> None

Sets options related to post-optimization of the generated pose.

SetPositMethods

SetPositMethods(value: int) -> bool

Sets the posing methods to be used. Methods are set as bits in the supplied integer, see the OEPositMethod namespace for more details. Default is OEPositMethod_ALL.

SetTorLib

SetTorLib(value: int) -> bool
SetTorLib(value: str) -> bool
SetTorLib(value: oeistream) -> bool
SetTorLib(value: OETorLib) -> bool

Sets the torsion library that is used for torsion driving during conformer generation. The first overload takes an unsigned from the OETorlibType namespace, and the second overload takes the corresponding string values. Default: Original