OEFreeFormConfAdvanced¶

class OEFreeFormConfAdvanced

This class represents OEFreeFormConfAdvanced.

The following methods are publicly inherited from OEFreeFormConf:

Constructors¶

OEFreeFormConfAdvanced()
OEFreeFormConfAdvanced(const OEFreeFormConfOptions&)
OEFreeFormConfAdvanced(const OEFreeFormConfAdvanced&)

Default and copy constructors.

operator=¶

OEFreeFormConfAdvanced& operator=(const OEFreeFormConfAdvanced&)

EstimateEnergies¶

unsigned int EstimateEnergies(OEChem::OEMCMolBase& mol) const

Estimates the Gibbs free energy to convert an ensemble of solution conformations into a state where only a single specific conformation is present. This method assumes that a duplicate free solution ensemble is provided as input. Function returns a success or failure code as unsigned int from the OEFreeFormReturnCode namespace. The molecule conformers contain the estimated free energy components on return.

EstimateRestrictionEnergy¶

unsigned int EstimateRestrictionEnergy(OEChem::OEMCMolBase& freeMol, const OEChem::OEMCMolBase& restrictedMol) const

Estimates the restriction energies on the restricted conformers. Function returns a success or failure code as unsigned int from the OEFreeFormReturnCode namespace.

freeMol: Molecule with unrestricted conformers identified from the set of solution ensemble, corresponding to the restricted conformers. The estimated restriction energies are tagged on conformers on return.
restrictedMol: Molecule with the restricted conformers for which to estimate the restriction energies.

IdentifyConformer¶

unsigned int IdentifyConformer(OEChem::OEMCMolBase& mol, const OEChem::OEMCMolBase& ensemble) const

Identifies the given conformers from the solution ensemble. Function returns a success or failure code as unsigned int from the OEFreeFormReturnCode namespace.

mol: Molecule with conformers to be identified from the set of solution ensemble. Conformer free energies from identified conformers are tagged on these conformers on return.
ensemble: Molecule with the solution ensemble with corresponding conformer free energies.

Optimize¶

unsigned int Optimize(OEChem::OEMCMolBase& mol) const

Optimize the molecule conformers using the optimization options. Function returns a success or failure code as unsigned int from the OEFreeFormReturnCode namespace. The molecule conformers contain optimized geometry and are tagged with estimated energies on return.

OptimizeRestraint¶

unsigned int OptimizeRestraint(OEChem::OEMCMolBase& mol) const

Perform restraint optimization of the molecule conformers using the optimization options. A harmonic restraint is applied to retain the shape of the given conformers. Function returns a success or failure code as unsigned int from the OEFreeFormReturnCode namespace. The molecule conformers contain optimized geometry and are tagged with estimated energies on return.

PreOptimizeEnsemble¶

unsigned int PreOptimizeEnsemble(OEChem::OEMCMolBase& mol) const

Optimize the molecule conformers using the pre-optimization options. Function returns a success or failure code as unsigned int from the OEFreeFormReturnCode namespace. The molecule conformers contain optimized geometry and are tagged with estimated energies on return.

PrepareEnsemble¶

unsigned int PrepareEnsemble(OEChem::OEMCMolBase& mol) const
unsigned int PrepareEnsemble(OEChem::OEMCMolBase& mol, OEChem::OEMCMolBase& restrictionMol, OEChem::OEMCMolBase& freeMol) const

Generates a comprehensive set of conformer ensemble when desired, using OEOmega. Function returns a success or failure code as unsigned int from the OEFreeFormReturnCode namespace. The input molecule is filled with the generated ensemble on return.

Prepares the conformer ensemble for subsequent FreeForm calculations, this includes generation of a comprehensive set of conformers using OEOmega as desired, validation of the structures and charge assignment. The second overload is provided for preparing an ensemble that would include un-restricted (free) conformers corresponding to a set of given restriction ensemble of conformers. Charges are also assigned on the given restriction ensemble of conformers. Function returns a success or failure code as unsigned int from the OEFreeFormReturnCode namespace.

mol: Molecule with the solution ensemble prepared for FreeFormConf calculations.
restrictionMol: Molecule with the restricted conformers.
freeMol: Molecule with the un-restricted conformers, corresponding to the restricted conformers.

RemoveDuplicates¶

unsigned int RemoveDuplicates(OEChem::OEMCMolBase& mol) const

Removes duplicates from the given ensemble of molecule conformers. Function returns a success or failure code as unsigned int from the OEFreeFormReturnCode namespace.