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(loadColorFF: bool = True) -> OEOverlapPrepOptions
OEOverlapPrepOptions(argOpts: OEOverlapPrepOptions) -> OEOverlapPrepOptions

Default and copy constructors.

Assignment operator.

GetAssignBondiRadii

GetAssignBondiRadii() -> bool

See SetAssignBondiRadii method.

GetAssignColor

GetAssignColor() -> bool

See SetAssignColor method.

GetRemoveColor

GetRemoveColor() -> bool

See SetRemoveColor method.

GetDuplicateDistance

GetDuplicateDistance() -> float

See SetDuplicateDistance method.

GetRemoveDuplicate

GetRemoveDuplicate() -> bool

See SetRemoveDuplicate method.

GetUseHydrogens

GetUseHydrogens() -> bool

See SetUseHydrogens method.

GetColorForceField

GetColorForceField() -> OEColorForceField

See SetColorForceField method.

SetAssignBondiRadii

SetAssignBondiRadii(value: bool) -> bool

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

SetAssignColor

SetAssignColor(value: bool) -> 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

SetRemoveColor(value: bool) -> bool

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

SetDuplicateDistance

SetDuplicateDistance(value: float) -> bool

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

SetRemoveDuplicate

SetRemoveDuplicate(value: bool) -> bool

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

SetUseHydrogens

SetUseHydrogens(value: bool) -> 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

SetColorForceField(value: OEColorForceField) -> bool

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

AddDuplicateSmarts

AddDuplicateSmarts(smarts: str) -> bool

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

GetDuplicateSmarts() -> OEStringVector

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

ClearDuplicateSmarts

ClearDuplicateSmarts() -> bool

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