OESzybkiGeneralOptions

class OESzybkiGeneralOptions : public OESystem::OEOptions

This class represents general options for szybki.

Constructors

OESzybkiGeneralOptions() -> OESzybkiGeneralOptions
OESzybkiGeneralOptions(arg2: OESzybkiGeneralOptions) -> OESzybkiGeneralOptions

Default and copy constructors.

GetCalculateGradients

GetCalculateGradients() -> bool

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

GetForceField

GetForceField() -> OEForceField

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

GetForceFieldType

GetForceFieldType() -> int

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

GetIEFFCluster

GetIEFFCluster() -> bool

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

GetIntramolecularVdWCutoff() -> float

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

GetLigandRMSDHeavy() -> bool

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

GetRemoveAttractiveVdWForces() -> bool

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

GetRemoveCoulombTerms() -> bool

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

GetSoluteDielectric

GetSoluteDielectric() -> float

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

GetTemperature

GetTemperature() -> float

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

GetVerbose

GetVerbose() -> bool

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

SetCalculateGradients

SetCalculateGradients(value: bool) -> bool

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

SetForceField

SetForceField(value: OEForceField) -> bool

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

SetForceFieldType(value: int) -> bool

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

SetIEFFCluster(value: bool) -> 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

SetIntramolecularVdWCutoff(value: float) -> bool

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

SetLigandRMSDHeavy(value: bool) -> 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

SetRemoveAttractiveVdWForces(value: bool) -> bool

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

SetRemoveCoulombTerms(value: bool) -> 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

SetSoluteDielectric(value: float) -> bool

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

SetTemperature

SetTemperature(value: float) -> bool

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

SetVerbose

SetVerbose(value: bool) -> bool

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