public void TestAssignrPiMarsilliFactors_IAtomContainerSet()
{
GasteigerPEPEPartialCharges peoe = new GasteigerPEPEPartialCharges();
IAtomContainer molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms.Add(builder.NewAtom("F"));
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;
}
var set = builder.NewAtomContainerSet();
set.Add(molecule);
set.Add(molecule);
AddExplicitHydrogens(molecule);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
CDK.LonePairElectronChecker.Saturate(molecule);
Assert.IsNotNull(peoe.AssignrPiMarsilliFactors(set));
}
/// <summary>
/// Calculate the electronegativity of orbitals pi.
/// </summary>
/// <param name="ac"></param>
/// <param name="atom">atom for which effective atom electronegativity should be calculated</param>
/// <param name="maxIterations">The maximal number of Iteration</param>
/// <param name="maxResonStruc">The maximal number of Resonance Structures</param>
/// <returns>Electronegativity of orbitals pi.</returns>
public double CalculatePiElectronegativity(IAtomContainer ac, IAtom atom, int maxIterations, int maxResonStruc)
{
MaxIterations = maxIterations;
MaxResonanceStructures = maxResonStruc;
double electronegativity = 0;
try
{
if (!ac.Equals(acOldP))
{
molPi = ac.Builder.NewAtomContainer(ac);
peoe = new GasteigerMarsiliPartialCharges();
peoe.AssignGasteigerMarsiliSigmaPartialCharges(molPi, true);
var iSet = ac.Builder.NewAtomContainerSet();
iSet.Add(molPi);
iSet.Add(molPi);
gasteigerFactors = pepe.AssignrPiMarsilliFactors(iSet);
acOldP = ac;
}
IAtom atomi = molPi.Atoms[ac.Atoms.IndexOf(atom)];
int atomPosition = molPi.Atoms.IndexOf(atomi);
int stepSize = pepe.StepSize;
int start = (stepSize * (atomPosition) + atomPosition);
double q = atomi.Charge.Value;
if (molPi.GetConnectedLonePairs(molPi.Atoms[atomPosition]).Any() ||
molPi.GetMaximumBondOrder(atomi) != BondOrder.Single || atomi.FormalCharge != 0)
{
return((gasteigerFactors[1][start]) + (q * gasteigerFactors[1][start + 1]) + (gasteigerFactors[1][start + 2] * (q * q)));
}
}
catch (Exception e)
{
Trace.TraceError(e.StackTrace);
}
return(electronegativity);
}