OESzybkiSolventOptions

class OESzybkiSolventOptions : public OESystem::OEOptions

This class represents options related to solvent modeling in szybki.

Constructors

OESzybkiSolventOptions() -> OESzybkiSolventOptions
OESzybkiSolventOptions(argOpts: OESzybkiSolventOptions) -> OESzybkiSolventOptions

Default and copy constructors.

Assignment operator.

GetAtomicRadiiType

GetAtomicRadiiType() -> int

Returns the type of atomic radii used for PB calculations, as an unsigned int from the OEAtomicRadii namespace.

GetCavitySolventParameter

GetCavitySolventParameter() -> float

Returns the microscopic surface tension coefficient (in kcal/(mol A**2)) used in hydrophobic ligand solvation model.

GetSaltConcentration

GetSaltConcentration() -> float

Returns the value of salt concentration in moles/liter (M).

GetSolventDielectric

GetSolventDielectric() -> float

Returns the value of solvent dielectric constant for the protein-ligand system.

GetSolventModel

GetSolventModel() -> int

Returns the type of solvent model used for the calculations of solution ligands, as an unsigned int from the OESolventModel namespace.

SetAtomicRadiiType

SetAtomicRadiiType(value: int) -> bool

Sets the type of atomic radii to be used for PB calculations, as an unsigned int from the OEAtomicRadii namespace.

SetCavitySolventParameter

SetCavitySolventParameter(value: float) -> bool

Sets the microscopic surface tension coefficient (in kcal/(mol A**2)) used in hydrophobic ligand solvation model. The default value is set to be 0.025 kcal/(mol A**2). Smaller values usually in the range 0-10 kcal/(mol A**2) usually reflects a combined hydrophobic solvation effect of cavitation and solute-solvent vdW interactions.

SetSaltConcentration

SetSaltConcentration(value: float) -> bool

Sets the value of salt concentration in moles/liter (M). By default a zero salt concentration is assumed. Values higher than 0.08 should not be used and are not supported.

SetSolventDielectric

SetSolventDielectric(value: float) -> bool

Sets the value of solvent dielectric constant for the protein-ligand systems in PB calculations. The default value of solvent dielectric constant is set to 80.0.

SetSolventModel

SetSolventModel(value: int) -> bool

Sets the type of solvent model used for the calculations of solution ligands, as an unsigned int from the OESolventModel namespace. Method returns false when the invalid selection is chosen, true otherwise.

SetChargeEngine

SetChargeEngine(argChargeEngine: OEChargeEngineBase) -> None

Sets the charging engine to obtain partial charges used for solvation calculation by passing in an OEChargeEngineBase instance.

SetUseCurrentCharges

SetUseCurrentCharges() -> None

Sets the charging engine to work with the existing charges. This command is equivalent to using the OESzybkiSolventOptions.SetChargeEngine method with an OEChargeEngineNoOp instance as input.