OEFixedProteinLigandOptimizer

class OEFixedProteinLigandOptimizer

This class provides an interface to optimize a ligand in a protein active site, where the protein is kept fixed during the optimization. The protein active site can be defined either by using a OEDesignUnit or by simple passing in a protein molecule.

The OEFixedProteinLigandOptimizer class defines the following public methods:

Energy
Optimize
SetProtein

Constructor

OEFixedProteinLigandOptimizer(opts: OEProteinLigandOptOptions = OEProteinLigandOptOptions()) -> OEFixedProteinLigandOptimizer
OEFixedProteinLigandOptimizer(arg2: OEFixedProteinLigandOptimizer) -> OEFixedProteinLigandOptimizer

Default and copy constructors.

Assignment operator.
Energy
Energy(mol: OEMol) -> Iterable[OEComplexEnergies]
Energy(res: OEComplexEnergies, mol: Union[OEGraphMol,OEMol,OEQMol]) -> int
Calculate the single point energy of the ligand interacting with the protein. The intra-molecular protein energy components are ignored by this method. The second overload returns a value from the OESzybkiReturnCode namespace reporting the success or failure of the calculation.

Optimize
Optimize(mol: OEMol) -> Iterable[OEProteinLigandOptResults]
Optimize(res: OEProteinLigandOptResults,
         mol: Union[OEGraphMol,OEMol,OEQMol]) -> int
Optimize the ligand in the protein active site. The intra-molecular protein energy components are ignored by this method. The second overload returns a value from the OESzybkiReturnCode namespace reporting the success or failure of the optimization. The return code for each conformer in the first overload can be obtained from the corresponding results object.

SetProtein
SetProtein(du: OEDesignUnit, proteinMask: int,
           proteinPred: OEUnaryAtomPred = OEIsTrueAtom()) -> int
SetProtein(mol: Union[OEGraphMol,OEMol,OEQMol]) -> int
Set the protein molecule for the calculation. In the first two overload, the proteinMask define the portion of the OEDesignUnit that should be used as the target protein active site. An optional proteinPred can be also provided along with the mask, to define additional residue components to be part of the target. Method returns a value from the OESzybkiReturnCode namespace reporting the success or failure.