OESzybkiProteinOptions¶

class OESzybkiProteinOptions : public OESystem::OEOptions

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 separated 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¶

bool SetExactVdWProteinLigand(const bool)

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

SetIntermolecularVdWCutoff¶

bool 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 separated 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¶

bool SetProteinDielectric(const double)

Sets the value of protein dielectric constant for 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¶

bool 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.