OESzybkiGeneralOptions

class OESzybkiGeneralOptions : public OESystem::OEOptions

This class represents general options for szybki.

Constructors

OESzybkiGeneralOptions()
OESzybkiGeneralOptions(const OESzybkiGeneralOptions &)

Default and copy constructors.

operator=

OESzybkiGeneralOptions &operator=(const OESzybkiGeneralOptions &)

GetCalculateGradients

bool GetCalculateGradients() const

Returns the state of the calculate gradients flag. If true, OESzybki will calculate and report gradients.

GetForceField

const OEMolPotential::OEForceField* GetForceField() const

Returns the pointer to the OEForceField object which was used in the method OESzybkiGeneralOptions::SetForceField.

GetForceFieldType

unsigned int GetForceFieldType() const

Returns the force field type to be used for OESzybki calculations, as unsigned int from the OEForceFieldType namespace.

GetIEFFCluster

bool GetIEFFCluster() const

Returns the state of the IEFF cluster flag. If true, OESzybki will optimize a cluster of molecules with the MMFF94-IEFF or MMFF94S-IEFF force field.

GetIntramolecularVdWCutoff

double GetIntramolecularVdWCutoff() const

Returns the value of the intramolecular vdW interactions cutoff. The intramolecular VdW interactions are considered to be zero between atoms that are separated by distances larger than the cutoff.

GetLigandRMSDHeavy

bool GetLigandRMSDHeavy() const

Returns the state of the Ligand RMSD heavy flag. If true, OESzybki reports RMSD for the optimized molecular systems based on heavy atoms only.

GetRemoveAttractiveVdWForces

bool GetRemoveAttractiveVdWForces() const

Returns the state of the Remove Attractive VdW Forces terms flag. If true, OESzybki removes the attractive part of the VdW interaction terms from the force field for calculations.

GetRemoveCoulombTerms

bool GetRemoveCoulombTerms() const

Returns the state of the Remove Coloumb terms flag. If true, OESzybki removes the Coulomb terms from the force field for calculations.

GetSoluteDielectric

float GetSoluteDielectric() const

Returns the value of ligand dielectric constant used for the optimization of ligand in solution.

GetTemperature

double GetTemperature() const

Returns the value of temperature to be used for entropy calculation, in units of kelvins.

GetVerbose

bool GetVerbose() const

Returns the state of the verbose flag. If true, OESzybki is set for reporting optimization progress.

SetCalculateGradients

bool SetCalculateGradients(const bool)

Sets the state of the calculate gradients flag. If true is passed, OESzybki will calculate and report gradients.

SetForceField

bool SetForceField(OEMolPotential::OEForceField&)

Sets the force field to be used for OESzybki calculations, using an instance of OEForceField. This method provids an alternative to setting force field by a predefined type with OESzybkiGeneralOptions::SetForceFieldType. Method returns true when the setting is successful, false otherwise.

SetForceFieldType

bool SetForceFieldType(const unsigned int)

Sets the force field to be used for OESzybki calculations, using constants defined in the OEForceFieldType namespace. This method provids an alternative to setting force field by a force field instance with OESzybkiGeneralOptions::SetForceField. Method returns true when the setting is successful, false otherwise.

SetIEFFCluster

bool SetIEFFCluster(const bool)

Sets the state of the IEFF cluster flag. If true is passed, OESzybki will optimize a cluster of molecules with the MMFF94-IEFF or MMFF94S-IEFF force field.

SetIntramolecularVdWCutoff

bool SetIntramolecularVdWCutoff(const double)

Sets the value of the intramolecular vdW interactions. The intramolecular VdW interactions are considered to be zero between atoms that are separated by distances larger than the cutoff. By default no cutoff is used.

SetLigandRMSDHeavy

bool SetLigandRMSDHeavy(const bool)

Sets the state of the Ligand RMSD heavy flag. If true is passed, OESzybki reports RMSD for the optimized molecular systems based on heavy atoms only. By default, RMSD is calculated based on all atoms.

SetRemoveAttractiveVdWForces

bool SetRemoveAttractiveVdWForces(const bool) const

Sets the state of the Remove Attractive VdW Forces terms flag. If true, OESzybki removes the attractive part of the VdW interaction terms from the force field for calculations.

SetRemoveCoulombTerms

bool SetRemoveCoulombTerms(const bool)

Sets the state of the Remove Coloumb terms flag. If true is passed, OESzybki removes the Coulomb terms from the force field for calculations.

SetSoluteDielectric

bool SetSoluteDielectric(const double)

Sets the value of ligand dielectric constant used for the optimization of ligand in solution.

SetTemperature

bool SetTemperature(const double)

Returns the value of temperature to be used for entropy calculation, in units of kelvins. The default temperature is set to 298.15K.

SetVerbose

bool SetVerbose(const bool)

Sets the state of the verbose flag. If true is passed, OESzybki is set for reporting optimization progress.