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

• 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

• GetBestReceptorPoseOnly and SetBestReceptorPoseOnly

Constructor

OEPositOptions();
OEPositOptions(const OEPositOptions &)

Default and copy constructors.

operator=

OEPositOptions &operator=(const OEPositOptions &)

GetAllowedClashType

unsigned GetAllowedClashType() const

See SetAllowedClashType method.

GetExcludeSelf

unsigned GetExcludeSelf() const

See SetExcludeSelf method.

GetFlexiOverlayOptions

OEFlexiOverlayOptions& GetFlexiOverlayOptions()
const OEFlexiOverlayOptions& GetFlexiOverlayOptions() const

See SetFlexiOverlayOptions method.

GetFullConformationSearch

bool GetFullConformationSearch() const

See SetFullConformationSearch method.

GetIgnoreNitrogenStereo

bool GetIgnoreNitrogenStereo() const

See SetIgnoreNitrogenStereo method.

GetMinProbability

double GetMinProbability() const

See SetMinProbability method.

GetPoserCacheCount

bool GetPoserCacheCount() const

See SetPoserCacheCount method.

GetPoseRelaxMode

unsigned GetPoseRelaxMode() const

See SetPoseRelaxMode method.

GetPoseRelaxOptions

OEPoseOptimizerOptions& GetPoseRelaxOptions()
const OEPoseOptimizerOptions& GetPoseRelaxOptions() const

See SetPoseRelaxOptions method.

GetPositMethods

unsigned int GetPositMethods() const

See SetPositMethods method.

GetBestReceptorPoseOnly

bool GetBestReceptorPoseOnly() const

See SetBestReceptorPoseOnly method.

SetAllowedClashType

bool SetAllowedClashType(const unsigned)

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.

SetExcludeSelf

bool SetExcludeSelf(const 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

void SetFlexiOverlayOptions(const OEShapeFitOptions&)

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

SetFullConformationSearch

bool SetFullConformationSearch(const 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

bool SetIgnoreNitrogenStereo(const 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

bool SetMinProbability(const double)

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

bool SetPoserCacheCount(const unsigned)

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

bool SetPoseRelaxMode(const unsigned)

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

void SetPoseRelaxOptions(const OEPoseOptimizerOptions&)

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

SetPositMethods

bool SetPositMethods(const unsigned)

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.

SetBestReceptorPoseOnly

bool SetBestReceptorPoseOnly(const 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.