OEFlexProteinLigandOptimizer

class OEFlexProteinLigandOptimizer

This class provides an interface to optimize a ligand in a protein active site, where the protein can be treated a partially flexible. The protein active site can be defined either by using a OEDesignUnit or by simple passing in a protein molecule.

The OEFlexProteinLigandOptimizer class defines the following public methods:

Constructor

OEFlexProteinLigandOptimizer();
OEFlexProteinLigandOptimizer(const OEProteinLogandOptOptions&);
OEFlexProteinLigandOptimizer(const OEFlexProteinLigandOptimizer &)

Default and copy constructors.

operator=

OEFlexProteinLigandOptimizer &operator=(const OEFlexProteinLigandOptimizer &)

Energy

unsigned Energy(OEFF::OEComplexEnergies& res, const OEBio::OEDesignUnit& du,
               const unsigned proteinMask, const unsigned ligandMask,
               const OESystem::OEUnaryPredicate<OEChem::OEAtomBase>& protFlexPred) const;
unsigned Energy(OEFF::OEComplexEnergies& res, const OEChem::OEMolBase& protein, const OEChem::OEMolBase& ligand,
               const OESystem::OEUnaryPredicate<OEChem::OEAtomBase>& protFlexPred) const;
unsigned Energy(OEFF::OEComplexEnergies& res, const OEBio::OEDesignUnit& du,
               const unsigned proteinMask, const unsigned ligandMask, const OEProteinFlexOptions& flexOpts) const;
unsigned Energy(OEFF::OEComplexEnergies& res, const OEChem::OEMolBase& protein, const OEChem::OEMolBase& ligand,
               const OEProteinFlexOptions& flexOpts) const;

Calculate the single point energy of the protein ligand complex. Only the flexible portion of the intra-molecular protein energy components are considered by this method. The methods return a value from the OESzybkiReturnType namespace reporting the success or failure of the calculation.

Optimize

unsigned Optimize(OESz::OEProteinLigandOptResults& res, OEBio::OEDesignUnit& du,
                  const unsigned proteinMask, const unsigned ligandMask,
                  const OESystem::OEUnaryPredicate<OEChem::OEAtomBase>& protFlexPred) const;
unsigned Optimize(OESz::OEProteinLigandOptResults& res, OEChem::OEMolBase& protein, OEChem::OEMolBase& ligand,
                  const OESystem::OEUnaryPredicate<OEChem::OEAtomBase>& protFlexPred) const;
unsigned Optimize(OESz::OEProteinLigandOptResults& res, OEBio::OEDesignUnit& du,
                  const unsigned proteinMask, const unsigned ligandMask, const OEProteinFlexOptions& flexOpts) const;
unsigned Optimize(OESz::OEProteinLigandOptResults& res, OEChem::OEMolBase& protein, OEChem::OEMolBase& ligand,
                  const OEProteinFlexOptions& flexOpts) const;

Optimize the protein ligand complex. Only the flexible portion of the intra-molecular protein energy components are considered by this method. The methods return a value from the OESzybkiReturnType namespace reporting the success or failure of the calculation.