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 (1) adding or removing explicit hydrogens; (2) adding color atoms; and (3) assigning Bondi radii to all the atoms. When color atoms are added to molecules for overlap calculations, it is often required that those are removed 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:

Constructors

OEOverlapPrep()
OEOverlapPrep(const OEOverlapPrep&)

Default and copy constructors.

operator=

OEOverlapPrep &operator=(const OEOverlapPrep &)

GetAssignBondiRadii

bool GetAssignBondiRadii() const

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

GetAssignColor

bool GetAssignColor() const

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

GetColorForceField

const OEColorForceField& GetColorForceField() const

Gets the instance of OEColorForceField currently associated with the OEOverlapPrep.

GetUseHydrogens

bool GetUseHydrogens() const

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

Prep

bool Prep(OEChem::OEMCMolBase&);
bool Prep(OEChem::OEMolBase&);

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

SetAssignBondiRadii

void SetAssignBondiRadii(const bool)

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

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.

SetColorForceField

bool SetColorForceField(const OEColorForceField &cff)

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

SetUseHydrogens

void SetUseHydrogens(const bool)

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