OESzybkiResults¶

class OESzybkiResults


This class represents OESzybkiResults.

Constructors¶

OESzybkiResults()
OESzybkiResults(const OESzybkiResults &)


Default and copy constructors.

operator=¶

OESzybkiResults &operator=(const OESzybkiResults &)


Clear¶

void Clear()


Removes all data from the OESzybkiResults object.

GetCPUTime¶

float GetCPUTime() const


Returns CPU time in seconds for the optimization.

GetConfIdx¶

unsigned int GetConfIdx() const


Returns conformer id number.

GetEnergyTerm¶

double GetEnergyTerm(unsigned int) const


Returns the current energy value for a specified potential term. The integer values which determine potential terms are defined in the namespace OEPotentialTerms

double GetFinalRMSGradient() const


Returns final RMS of forces, $$\sqrt\frac{\bf{g} \cdot \bf{g}}{n_v}$$, where $$\bf{g}$$ is the gradient vector and $$n_v$$ the number of variables.

bool GetGradients(double* gradients, const OEChem::OEAtomBase* atom) const


Fills the passed double array with gradients for the atom passed as a second argument. Returns true if the gradients are successfully exported, false otherwise. Export of gradients is available only when the method OESzybkiGeneralOptions.SetCalculateGradients is called prior to the calculation performed with one of the OESzybki.operator() operators. Currently calculation of gradients is available only for single-point runs.

GetFinalTotalPotential¶

double GetFinalTotalPotential() const


Returns the value of the optimized potential for the molecular system.

GetIntramolecularLigandEnergy¶

double GetIntramolecularLigandEnergy() const


Returns the value of the value of intramolecular MMFF energy.

double GetInitialRMSGradient() const


Returns the initial RMS of forces, $$\sqrt\frac{\bf{g} \cdot \bf{g}}{n_v}$$, where $$\bf{g}$$ is the gradient vector and $$n_v$$ the number of variables.

GetInitialTotalPotential¶

double GetInitialTotalPotential() const


Returns the value of the initial potential for the molecular system to be optimized.

GetInterEnergy¶

double GetInterEnergy() const


Returns the interaction energy between protein (or DNA) and the ligand optimized inside the macromolecule. For ligands optimized in vacuum or in solution, this function returns 0.

GetMaxDisplacement¶

double GetMaxDisplacement() const


Returns the maximum atomic displacement for a single atom in Å during optimization.

GetNumCycles¶

unsigned int GetNumCycles() const


Returns the number of cycles performed by the optimizer.

GetNumFixAtoms¶

unsigned int GetNumFixAtoms() const


Returns the number of atoms which will be fixed during optimization.

GetNumRotors¶

unsigned int GetNumRotors() const


Returns the number of rotatable bonds in the molecule.

GetProteinRMSD¶

double GetProteinRMSD() const


In the case of a partially optimized protein (residues, side chains, polar hydrogens in proximity to the ligand) the function returns the RMS displacement of a protein from its initial structure.

GetRMSD¶

double GetRMSD() const


Returns the RMS displacement of the optimized structure with respect to the initial structure.

GetTotalEnergy¶

double GetTotalEnergy() const


Returns the total energy of the optimized system. That includes all intra and inter molecular MMFF terms, solvation energy (Sheffield or PB, if present) and protein-ligand interaction energy if a ligand is optimized inside the protein. Harmonic energy constraint energy is excluded.

GetTotalEnergyWithHarmConstraint¶

double GetTotalEnergyWithHarmConstraint() const


Returns total energy of the optimized system plus harmonic energy constraint.

IsActiveTerm¶

bool IsActiveTerm(unsigned int term) const


Returns true if the potential term specified by the parameter term is included in the potential function of the system. Possible parameters values are defined in the namespace OEPotentialTerms.

GetConfFreeEnergyFromEnsemble¶

double GetConfFreeEnergyFromEnsemble() const


Returns the free energy of selecting a conformation out of the ensemble calculated as: $$-RTln(q/Q)$$, where $$q$$ is the partition function of a ligand conformer and $$Q$$ is the partition function for the entire ensemble. The method will throw an error unless it is run following the call to OESzybki.GetEntropy method which takes the OESzybkiEnsembleResults instance as a second parameter, followed by the call to OESzybkiEnsembleResults.GetResultsForConformations on the returned OESzybkiEnsembleResults object.

GetVibEntropy¶

double GetVibEntropy() const


Returns the vibrational entropy of a conformation in e.u. (cal/(mol K)) when entropy has been calculated with one of the OESzybki.GetEntropy methods.

GetRotEntropy¶

double GetRotEntropy() const


Returns the rotational entropy of a conformation in e.u. (cal/(mol K)) when entropy has been calculated with one of the OESzybki.GetEntropy methods.

GetLnQvib¶

double GetLnQvib() const


Returns the natural logarithm of a vibrational partition function when entropy has been calculated with one of the OESzybki.GetEntropy methods.

GetLnQrot¶

double GetLnQrot() const


Returns the natural logarithm of a rotational partition function when entropy has been calculated with one of the OESzybki.GetEntropy methods.

IsUnique¶

bool IsUnique() const


Returns true if the conformation is unique in terms of the structure. Although the method OESzybki.GetEntropy which takes a non-const OEMCMolBase object is guaranteed to return an ensemble of unique conformations, the other methods in oeszybki library do not. The method might be therefore useful to make sure if the current conformation is unique or not.

Print¶

void Print(OEPlatform::oeostream &) const
void Print(OESystem::OEErrorHandler &) const


Both functions allow the generation of log information on the optimized system. The following information is reported:

• Conformer id
• Number of fixed atoms (if any)
• Number of torsions (if any and if optimization in torsion space is true)
• Initial energy