OESzybkiProteinOptions

class OESzybkiProteinOptions : public OESystem::OEOptions

This class represents options related to proteins in szybki.

Constructors

OESzybkiProteinOptions() -> OESzybkiProteinOptions
OESzybkiProteinOptions(argOpts: OESzybkiProteinOptions) -> OESzybkiProteinOptions

Default and copy constructors.

AddFlexibleResidue

AddFlexibleResidue(argRes: OEResidue) -> bool

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

ClearFlexibleResidues() -> None

Clears all of the currently set flexible residues.

GetExactVdWProteinLigand

GetExactVdWProteinLigand() -> bool

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

GetIntermolecularVdWCutoff

GetIntermolecularVdWCutoff() -> float

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

GetProteinDielectric() -> float

Returns the value of protein dielectric constant.

GetProteinElectrostaticModel

GetProteinElectrostaticModel() -> int

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

GetProteinFlexibilityRange

GetProteinFlexibilityRange() -> float

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

GetProteinFlexibilityType

GetProteinFlexibilityType() -> int

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

HasFlexibleResidues

HasFlexibleResidues() -> bool

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

SetExactVdWProteinLigand

SetExactVdWProteinLigand(value: bool) -> 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

SetIntermolecularVdWCutoff(value: float) -> bool

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

SetProteinDielectric(value: float) -> bool

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

SetProteinElectrostaticModel(value: int) -> bool

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

SetProteinFlexibilityRange(value: float) -> bool

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

SetProteinFlexibilityType

SetProteinFlexibilityType(value: int) -> bool

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.