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
AddDuplicateSmarts, GetDuplicateSmarts, and ClearDuplicateSmarts
GetRemoveColor and SetRemoveColor
GetRemoveDuplicate and SetRemoveDuplicate
GetUseHydrogens and SetUseHydrogens
GetColorForceField and SetColorForceField

Constructor

OEOverlapPrepOptions(const bool loadColorFF = true)
OEOverlapPrepOptions(const OEOverlapPrepOptions&)

Default and copy constructors.

Assignment operator.

GetAssignBondiRadii

bool GetAssignBondiRadii() const

See SetAssignBondiRadii method.

GetAssignColor

bool GetAssignColor() const

See SetAssignColor method.

GetRemoveColor

bool GetRemoveColor() const

See SetRemoveColor method.

GetDuplicateDistance

float GetDuplicateDistance() const

See SetDuplicateDistance method.

GetRemoveDuplicate

bool GetRemoveDuplicate() const

See SetRemoveDuplicate method.

GetUseHydrogens

bool GetUseHydrogens() const

See SetUseHydrogens method.

GetColorForceField

const OEColorForceField& GetColorForceField() const

See SetColorForceField method.

SetAssignBondiRadii

void SetAssignBondiRadii(const bool)

Sets if Bondi Radii should be assigned. If true, Bondi radii would be assigned to all atoms during the Prep. Default: False.

SetAssignColor

void SetAssignColor(const bool)

Sets if color atoms should be assigned. If true, color atoms would be assigned during the Prep. Color atoms are only assigned to molecules that currently do not have any color atoms. To re-assign color atoms to all molecules, use SetRemoveColor to True. Default: True.

SetRemoveColor

bool SetRemoveColor(const bool)

Sets if existing color atoms should be removed. If true, existing color atoms are removed during Prep. Default: False.

SetDuplicateDistance

bool SetDuplicateDistance(const float)

Sets the threshold distance for duplicate removal of color atoms. The acceptable range is between 0.0 and 1.0. Default 0.0.

SetRemoveDuplicate

bool SetRemoveDuplicate(const bool)

Sets if duplicate color atoms should be removed. Default True.

SetUseHydrogens

bool SetUseHydrogens(const bool)

Sets if explicit hydrogen atoms should be used. If true, explicit hydrogen atoms would be created during the Prep. If false, all hydrogen atoms would be removed. Default False.

SetColorForceField

bool SetColorForceField(const OEColorForceField&)

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

AddDuplicateSmarts

bool AddDuplicateSmarts(const std::string& smarts)

Adds a SMARTS pattern used to identify duplicate color atoms. Returns false if the SMARTS pattern already exists in the list, true otherwise. By default, SMARTS patterns for Cubane and Adamantane are included.

GetDuplicateSmarts

const std::vector<std::string>& GetDuplicateSmarts() const

Returns the list of SMARTS patterns used for identifying duplicate color atoms. See AddDuplicateSmarts method.

ClearDuplicateSmarts

bool ClearDuplicateSmarts()

Removes all SMARTS patterns from the duplicate detection list. See AddDuplicateSmarts method.