OEOverlapPrepOptions

class OEOverlapPrepOptions : public OESystem::OEOptions

This class provides an interface to set up options required for OEOverlapPrep. In addition to preparing options available in OEOverlapPrep, this option class provides two more additional options to control the Prep process regarding the removal of color atoms which are closer than a threshold distance.

The OEOverlapPrepOptions class defines the following public methods:

GetAssignBondiRadii and SetAssignBondiRadii

GetAssignColor and SetAssignColor

GetDuplicateDistance and SetDuplicateDistance

GetRemoveDuplicate and SetRemoveDuplicate

GetUseHydrogens and SetUseHydrogens

GetColorForceField and SetColorForceField

Constructor

OEOverlapPrepOptions();
OEOverlapPrepOptions(const OEOverlapPrepOptions&)

Default and copy constructors.

operator=

OEOverlapPrepOptions &operator=(const OEOverlapPrepOptions&)

GetAssignBondiRadii

unsigned GetAssignBondiRadii() const

Returns the state of the assign Bondi radii flag. If true, Bondi radii would be assigned to all atoms during the Prep.

GetAssignColor

unsigned GetAssignColor() const

Returns the state of the assign color flag. If true, color atoms would be assigned during the Prep.

GetDuplicateDistance

float GetDuplicateDistance() const

Returns the threshold distance for duplicate removal of color atoms.

GetRemoveDuplicate

bool GetRemoveDuplicate() const

Returns the state of the remove duplicate flag. If true, color atoms would be removed if their distance is less than the threshold distance for duplicate removal during the Prep.

GetUseHydrogens

bool GetUseHydrogens() const

Returns the state of the use hydrogens flag. If true, explicit hydrogen atoms would be created during the Prep. If false, all hydrogen atoms would be removed.

GetColorForceField

const OEColorForceField& GetColorForceField() const

Gets the instance of OEColorForceField currently associated with the OEOverlapPrep.

SetAssignBondiRadii

void SetAssignBondiRadii(const bool)

Sets the state of the assign Bondi radii flag. If true, Bondi radii would be assigned to all atoms during the Prep. Default False.

SetAssignColor

void SetAssignColor(const bool)

Sets the state of the assign color flag. If true, color atoms would be assigned during the Prep. Color atoms from molecules can be removed using the OERemoveColorAtoms function for further modeling work involving a molecule. Default True.

SetDuplicateDistance

void SetDuplicateDistance(const float)

Sets the threshold distance for duplicate removal of color atoms. The acceptable range is between 0 and 1. Default 0.001.

SetRemoveDuplicate

void SetRemoveDuplicate(const bool)

Sets the state of the remove duplicate flag. Default False.

SetUseHydrogens

void SetUseHydrogens(const bool)

Sets the state of the use hydrogens flag. If true, explicit hydrogen atoms would be created during the Prep. If false, all hydrogen atoms would be removed. Default False.

SetColorForceField

void SetColorForceField(const OEColorForceField&)

Sets the color force field to be used. By default, the ImplicitMillsDean color force field is used.