OEOverlapPrep

class OEOverlapPrep

This class provides facilities to prepare molecules for overlap calculations. Preparing a molecule for overlap calculation consists of any or all of the following: adding or removing explicit hydrogens; adding color atoms; and assigning Bondi radii to all the atoms. When color atoms are added to molecules for overlap calculations, it is often required to remove them before further modeling work involving those molecules. Color atoms from molecules can be removed using the OERemoveColorAtoms function.

The OEOverlapPrep class defines the following public methods:

• GetAssignBondiRadii

• GetAssignColor

• GetColorForceField

• GetUseHydrogens

• Prep

• SetAssignBondiRadii

• SetAssignColor

• SetColorForceField

• SetUseHydrogens

Constructors

OEOverlapPrep(opts: OEOverlapPrepOptions = OEOverlapPrepOptions()) -> OEOverlapPrep
OEOverlapPrep(arg2: OEOverlapPrep) -> OEOverlapPrep

Default and copy constructors.

Assignment operator.

GetAssignBondiRadii

GetAssignBondiRadii() -> bool

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

GetAssignColor

GetAssignColor() -> bool

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

GetColorForceField

GetColorForceField() -> OEColorForceField

Gets the instance of OEColorForceField currently associated with the OEOverlapPrep.

GetUseHydrogens

GetUseHydrogens() -> bool

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.

Prep

Prep(argMol: OEMol) -> bool
Prep(argMol: Union[OEGraphMol,OEQMol]) -> bool

Prepares the specified molecule for overlap calculation based on the current set of options set on Prep.

SetAssignBondiRadii

SetAssignBondiRadii(argValue: bool) -> None

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

SetAssignColor

SetAssignColor(argValue: bool) -> None

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.

SetColorForceField

SetColorForceField(argCff: OEColorForceField) -> bool

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

SetUseHydrogens

SetUseHydrogens(argValue: bool) -> None

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.