OEFreeFormSolvOptions

class OEFreeFormSolvOptions : public OESystem::OEOptions

This class represents OEFreeFormSolvOptions.

Constructors

OEFreeFormSolvOptions()
OEFreeFormSolvOptions(const OEFreeFormSolvOptions&)

Default and copy constructors.

operator=

OEFreeFormSolvOptions& operator=(const OEFreeFormSolvOptions&)

GetAtomicRadiiType

unsigned int GetAtomicRadiiType() const = 0

Returns the type of atomic radii used for PB calculations. Possible values passed to the method are defined in OEAtomicRadii namespace.

GetChargeType

unsigned int GetChargeType() const = 0

Returns the type of partial charges used for Sheffield and PB calculations.

GetConfGenRMS

double GetConfGenRMS() const = 0

Returns the value of RMSD used by the conformation generator for conformation deduplication. The default values are 0.6 Å for solvation free energy estimation and 0.3 Å for conformation free energy estimation.

GetIonicState

unsigned int GetIonicState() const = 0

Returns the type of charge state. Possible values are defined in the OEFreeFormIonicState namespace. The default value is OEFreeFormIonicState::PH74.

GetMaxConfGen

unsigned int GetMaxConfGen() const = 0

Returns the maximum conformations number used by the conformation generator.

GetUseInput3D

  bool GetUseInput3D() const = 0

Determines if the calculations are set to use 3D coordinates of the input molecule.

GetUseInputEnsemble

bool GetUseInputEnsemble() const = 0

Determines if the calculations are set to use the input ensemble of conformations rather than generate the ensemble internally.

SetAtomicRadiiType

bool SetAtomicRadiiType(unsigned int radii_type) = 0

Sets the atomic radii type for all PB calculations. Possible values passed to the method are defined in OEAtomicRadii namespace.

SetChargeType

bool SetChargeType(unsigned int charge_type) = 0

Sets the partial charges type. Possible values to pass to the method are defined in a subset of the `OEProton::OECharges` namespace (please look at the documentation of The Quacpac TK.) The allowed types are: OECharges::NoOp (to use existing partial charges), OECharges::AM1BCCSym, OECharges::AM1BCCNoSym, OECharges::AM1BCCSymSPt, OECharges::AM1BCCNoSymSPt and OECharges::MMFF94. The default values are OECharges::AM1BCCNoSymSPt and OECharges::AM1BCCSym for solvation free energy estimation and conformation free energy estimation respectively.

SetConfGenRMS

bool SetConfGenRMS(double rms) = 0

Sets the value of RMSD used by the conformation generator for conformation deduplication. The default values are 0.6 Å for solvation free energy estimation and 0.3 Å for conformation free energy estimation.

SetIonicState

bool SetIonicState(unsigned int ionic_state) = 0

Sets the charge state of the molecule. Possible values are defined in the OEFreeFormIonicState namespace. The default value is OEFreeFormIonicState::PH74.

SetMaxConfGen

bool SetMaxConfGen(unsigned int nmax) = 0

Sets the maximum number of conformations generated by the conformation generator. The default values are 200 for solvation free energy estimation and 20000 for conformation free energy estimation.

SetUseInput3D

bool SetUseInput3D(bool use3D) = 0

When parameter use3D is set to true, solvation free energy is calculated just for the input structure representing specific conformation. This option allows to find what is the difference in solvation energy between different conformations.

SetUseInputEnsemble

bool SetUseInputEnsemble(bool use_ensemble) = 0

Sets the usage of the input ensemble rather than generating it internally when the parameter use_ensemble is set to true.

Note

The value set by the OEFreeFormSolvOptions::SetUseInput3D method takes precedence over OEFreeFormSolvOptions::SetUseInputEnsemble. In other words when the first of those methods passes boolean value true, solvation code is looking for a single 3D structure (conformation) provided by the user and determines its solvation free energy. When the value passed by this method is false or when it is not used, solvation code is selecting the lowest force field energy conformation either from the user ensemble (when medthod OEFreeFormSolvOptions::SetUseInputEnsemble passes boolean true) or from the ensemble generated internally and determines its solvation free energy.