OEChargeEngineBase

class OEChargeEngineBase

This is the abstract base class for all charge engines, containing methods used by the function OEAssignCharges.

The following charge engine classes derive from this base class:

• OEAM1BCCCharges

• OEAM1BCCELF10Charges

• OEAM1Charges

• OEAmberFF94Charges

• OEChargeEngineNoOp

• OEClearCharges

• OECombineChargeEngines

• OEDesignUnitCharges

• OEELFCharges

• OEFormalToPartialCharges

• OEGasteigerCharges

• OEInitialCharges

• OEMMFF94Charges

ApplyCharges

ApplyCharges(du: OEDesignUnit) -> bool

Assigns partial charges to the atoms of the molecule. The OEMCMolBase overload assigns charges using all conformers where applicable. The OEDesignUnit overload charges the small-molecule component of the design unit.

CheckCharges

CheckCharges(mol: Union[OEGraphMol,OEQMol]) -> bool
CheckCharges(mcMol: OEMol) -> bool
CheckCharges(du: OEDesignUnit) -> bool

Used by OEAssignCharges to determine if the charges on the molecule are as expected.

CreateCopy

CreateCopy() -> OEChargeEngineBase

Deep copy of the charge engine.

GetExpectValidMol

GetExpectValidMol() -> bool

Returns true if an input molecule must be valid before OEAssignCharges attempts to assign charges.

GetName

GetName() -> str

Returns the name of the charge engine.

GetRepairRequestedHint

GetRepairRequestedHint() -> bool

Returns true if OEAssignCharges is requested to repair the input molecule before assigning charges. Examples of repairing a molecule include adding explicit hydrogens and perceiving residues.

GetRequirements

GetRequirements() -> int

Returns a bit mask used by OEAssignCharges describing aspects of the input molecule required for this charging method. Examples include 3D coordinates, explicit hydrogens, and PDB order.

IsValid

IsValid(mol: Union[OEGraphMol,OEQMol]) -> bool
IsValid(mcMol: OEMol) -> bool
IsValid(du: OEDesignUnit) -> bool

Returns true if the input molecule appears to be valid for use with this method.

SetExpectValidMol

SetExpectValidMol(expect: bool = True) -> None

Defines whether an input molecule must be valid before OEAssignCharges attempts to assign charges. If set to false and the molecule is not valid, then OEAssignCharges attempt to charge the molecule anyway.

SetRepairRequestedHint

SetRepairRequestedHint(repair: bool = True) -> None

Define whether OEAssignCharges is requested to repair the input molecule before assigning charges. Examples of repairing a molecule include adding explicit hydrogens and perceiving residues. If set to false and the molecule requires repairs, then OEAssignCharges will fail and return false.

TransferCharge

TransferCharge(dstAtom: OEAtomBase, srcAtom: OEAtomBase) -> bool

If OEAssignCharges must make a copy of the input molecule before charges can be applied, this method is used to transfer charges back to the input molecule.