OESzybkiProteinOptions

class OESzybkiProteinOptions

This class represents options related to proteins in szybki.

Constructors

OESzybkiProteinOptions()
OESzybkiProteinOptions(const OESzybkiProteinOptions &)

Default and copy constructors.

operator=

OESzybkiProteinOptions &operator=(const OESzybkiProteinOptions &)

AddFlexibleResidue

AddFlexibleResidue(const OEChem::OEResidue&)

Adds a single residue to the list of residues which will be optimized together with the ligand. Has to be called multiple times in order to make more than one residue flexible.

ClearFlexibleResidues

void ClearFlexibleResidues()

Clears all of the currently set flexible residues.

GetExactVdWProteinLigand

bool GetExactVdWProteinLigand() const

Returns the state of the exact VdW protein-ligand flag. If true, OESzybki will be using analytical vdW protein-ligand interaction.

GetIntermolecularVdWCutoff

double GetIntermolecularVdWCutoff() const

Returns the value of the intermolecular vdW interactions cutoff in Å. The intermolecular VdW interactions are considered to be zero between atoms that are seperated by distances larger than the cutoff.

GetProteinDielectric

double GetProteinDielectric() const

Returns the value of protein dielectric constant.

GetProteinElectrostaticModel

unsigned int GetProteinElectrostaticModel() const

Returns the protein electrostatics model to be used for OESzybki calculations, as unsigned int from the OEProteinElectrostatics namespace.

GetProteinFlexibilityRange

double GetProteinFlexibilityRange() const

Returns the value of partial protein flexibility distance from the ligand.

GetProteinFlexibilityType

unsigned int GetProteinFlexibilityType() const

Returns the type of partial protein flexibility to be used for OESzybki calculations, as unsigned int from the OEProtFlex namespace.

HasFlexibleResidues

bool HasFlexibleResidues() const

Returns the state of flexible residues. If true, some flexible residues are currently set.

SetExactVdWProteinLigand

void SetExactVdWProteinLigand(const bool)

Sets the state of the exact VdW protein-ligand flag. If true, OESzybki will be using analytical vdW protein-ligand interaction.

SetIntermolecularVdWCutoff

void SetIntermolecularVdWCutoff(const double)

Sets the value of the intermolecular vdW interactions cutoff in Å. The intermolecular VdW interactions are considered to be zero between atoms that are seperated by distances larger than the cutoff. The default value is 18 Å, however when Newton-Raphson optimization is used (see method OESzybkiOptOptions.SetOptimizerType) the default cutoff of 50 Å is used.

SetProteinDielectric

void SetProteinDielectric(const double)

Sets the value of protein dielectric constantfor the calculation of protein-ligand interaction. The default value of the protein dielectric constant is 1.0.

SetProteinElectrostaticModel

bool SetProteinElectrostaticModel(unsigned int)

Sets the protein electrostatics model to be used for OESzybki calculations, as unsigned int from the OEProteinElectrostatics namespace. Method returns false when the invalid selection is chosen, true otherwise.

SetProteinFlexibilityRange

void SetProteinFlexibilityRange(const double)

Sets the value of partial protein flexibility distance from the ligand.

SetProteinFlexibilityType

bool SetProteinFlexibilityType(const unsigned int)

Sets the type of partial protein flexibility to be used for OESzybki calculations, as unsigned int from the OEProtFlex namespace. Method returns false when the invalid selection is chosen, true otherwise.