OESzybkiSolventOptions

class OESzybkiSolventOptions

This class represents options related to solvent modeling in szybki.

Constructors

OESzybkiSolventOptions()
OESzybkiSolventOptions(const OESzybkiSolventOptions &)

Default and copy constructors.

operator=

OESzybkiSolventOptions &operator=(const OESzybkiSolventOptions &)

GetAtomicRadiiType

unsigned int GetAtomicRadiiType() const

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

GetCavitySolventParameter

double GetCavitySolventParameter() const

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

GetSaltConcentration

double GetSaltConcentration() const

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

GetSolventDielectric

double GetSolventDielectric() const

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

GetSolventModel

unsigned int GetSolventModel() const

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

SetAtomicRadiiType

void SetAtomicRadiiType(const unsigned int)

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

SetCavitySolventParameter

void SetCavitySolventParameter(const double)

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

void SetSaltConcentration(const double)

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

void SetSolventDielectric(const double)

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

bool SetSolventModel(const unsigned int)

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

SetChargeEngine

void SetChargeEngine(const OEProton::OEChargeEngineBase&)

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