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:
Constructors¶
OEOverlapPrep()
OEOverlapPrep(const OEOverlapPrepOptions&)
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 atoms 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 hydrogen 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 atoms 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)
Sets the color force field to be used. By default, the ImplicitMillsDean color force field is used.