public void TestAssignGasteigerSigmaMarsiliFactors_IAtomContainer()
{
GasteigerMarsiliPartialCharges peoe = new GasteigerMarsiliPartialCharges();
IAtomContainer molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms[0].Charge = 0.0;
molecule.Atoms.Add(builder.NewAtom("F"));
molecule.Atoms[1].Charge = 0.0;
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Single);
AddExplicitHydrogens(molecule);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
CDK.LonePairElectronChecker.Saturate(molecule);
foreach (var atom in molecule.Atoms)
{
atom.Charge = 0.0;
}
Assert.IsNotNull(peoe.AssignGasteigerSigmaMarsiliFactors(molecule).Length);
}
/// <summary>
/// calculate the electronegativity of orbitals sigma.
/// </summary>
/// <param name="ac">IAtomContainer</param>
/// <param name="atom">atom for which effective atom electronegativity should be calculated</param>
/// <param name="maxIterations">The maximal number of Iterations</param>
/// <param name="maxResonStruc">The maximal number of Resonance Structures</param>
/// <returns>piElectronegativity</returns>
public double CalculateSigmaElectronegativity(IAtomContainer ac, IAtom atom, int maxIterations, int maxResonStruc)
{
MaxIterations = maxIterations;
MaxResonanceStructures = maxResonStruc;
double electronegativity = 0;
try
{
if (!ac.Equals(acOldS))
{
molSigma = ac.Builder.NewAtomContainer(ac);
peoe.MaxGasteigerIterations = MaxIterations;
peoe.AssignGasteigerMarsiliSigmaPartialCharges(molSigma, true);
marsiliFactors = peoe.AssignGasteigerSigmaMarsiliFactors(molSigma);
acOldS = ac;
}
int stepSize = peoe.StepSize;
int atomPosition = ac.Atoms.IndexOf(atom);
int start = (stepSize * (atomPosition) + atomPosition);
electronegativity =
marsiliFactors[start]
+ (molSigma.Atoms[atomPosition].Charge.Value * marsiliFactors[start + 1])
+ (marsiliFactors[start + 2]
* (molSigma.Atoms[atomPosition].Charge.Value * molSigma.Atoms[atomPosition].Charge.Value));
return(electronegativity);
}
catch (Exception e)
{
Trace.TraceError(e.ToString());
}
return(electronegativity);
}