/// <param name="maxIterations">Number of maximum iterations</param>
/// <param name="checkLonePairElectron">Checking lone pair electrons. Default <see langword="true"/></param>
/// <param name="maxResonanceStructures">Number of maximum resonance structures to be searched</param>
public PartialPiChargeDescriptor(IAtomContainer container,
int maxIterations = int.MaxValue,
bool checkLonePairElectron = true,
int maxResonanceStructures = int.MaxValue)
{
clonedContainer = (IAtomContainer)container.Clone();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(clonedContainer);
var pepe = new GasteigerPEPEPartialCharges();
if (checkLonePairElectron)
{
CDK.LonePairElectronChecker.Saturate(clonedContainer);
}
if (maxIterations != int.MaxValue)
{
pepe.MaxGasteigerIterations = maxIterations;
}
if (maxResonanceStructures != int.MaxValue)
{
pepe.MaxResonanceStructures = maxResonanceStructures;
}
foreach (var catom in clonedContainer.Atoms)
{
catom.Charge = 0;
}
pepe.AssignGasteigerPiPartialCharges(clonedContainer, true);
this.container = container;
}
/// <param name="maxIterations">Number of maximum iterations</param>
/// <param name="checkLonePairElectron">Checking lone pair electrons. Default <see langword="true"/></param>
/// <param name="maxResonanceStructures">Number of maximum resonance structures to be searched</param>
public PartialTChargePEOEDescriptor(IAtomContainer container,
int maxIterations = int.MaxValue,
bool checkLonePairElectron = true,
int maxResonanceStructures = int.MaxValue)
{
clonedContainer = (IAtomContainer)container.Clone();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(clonedContainer);
var pepe = new GasteigerPEPEPartialCharges();
if (checkLonePairElectron)
{
CDK.LonePairElectronChecker.Saturate(clonedContainer);
}
if (maxIterations != int.MaxValue)
{
pepe.MaxGasteigerIterations = maxIterations;
}
if (maxResonanceStructures != int.MaxValue)
{
pepe.MaxResonanceStructures = maxResonanceStructures;
}
var peoe = new GasteigerMarsiliPartialCharges();
peoe.AssignGasteigerMarsiliSigmaPartialCharges(clonedContainer, true);
var peoeAtom = clonedContainer.Atoms.Select(n => n.Charge.Value).ToList();
foreach (var aatom in clonedContainer.Atoms)
{
aatom.Charge = 0;
}
pepe.AssignGasteigerPiPartialCharges(clonedContainer, true);
for (int i = 0; i < clonedContainer.Atoms.Count; i++)
{
var aatom = clonedContainer.Atoms[i];
aatom.Charge = aatom.Charge.Value + peoeAtom[i];
}
this.container = container;
}