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:
OEPositOptions(); OEPositOptions(const OEPositOptions &)
Default and copy constructors.
OEPositOptions &operator=(const OEPositOptions &)
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
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 relexation of the pose would be carried out when
SetPoseRelaxModeis set to
OEPoseRelaxMode.CLASHED. Default is
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.
SetFullConformationSearch¶bool SetFullConformationSearch(const bool)
Sets flag to perform full conformation search. Setting this option to
falsedisables internal rotamer conformer searching during the flexible searching algorithm. If this option is set to
falseand a 3D input is not given, this setting is ignored and a full conformation search is automatically performed. Default:
SetIgnoreNitrogenStereo¶bool SetIgnoreNitrogenStereo(const bool)
Sets flag to ignore Nitrogen stereo specifications in input molecule. Setting this option to
falseignores Nitrogen stereo specifications in the input molecule, and a value to
trueensures 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
truewould respect those stereo specifications. Default:
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
SetPoseRelaxMode¶bool SetPoseRelaxMode(const unsigned)
Sets the trigger to perform relexation of the generated pose. The relexation is performed by allowing flexibility to the ligand and parts of the receptor. Turning on relexation can significantly slow down the calculations. Pose relexation modes are defined in the
OEPoseRelaxModenamespace. Default is
SetBestReceptorPoseOnly¶bool SetBestReceptorPoseOnly(const bool)
Sets flag if only the best receptor should be considered for pose prediction. If this flag set to
falsethe 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
truepose prediction is only performed on the
best receptorfor any given ligand. Note that, setting the flag to
falsecould increse the runtime significantly depending on the number of receptors used for the calculation.