/// <summary>
/// Calculate effective atom polarizability.
/// </summary>
/// <param name="atomContainer">IAtomContainer</param>
/// <param name="atom">atom for which effective atom polarizability should be calculated</param>
/// <param name="influenceSphereCutOff">cut off for spheres which should taken into account for calculation</param>
/// <param name="addExplicitH">if set to true, then explicit H's will be added, otherwise it assumes that they have
/// been added to the molecule before being called</param>
/// <returns>polarizabilitiy</returns>
public static double CalculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer, IAtom atom, int influenceSphereCutOff, bool addExplicitH)
{
double polarizabilitiy = 0;
IAtomContainer acH;
if (addExplicitH)
{
acH = atomContainer.Builder.NewAtomContainer(atomContainer);
AddExplicitHydrogens(acH);
}
else
{
acH = atomContainer;
}
var startAtom = new List <IAtom>(1);
startAtom.Insert(0, atom);
double bond;
polarizabilitiy += GetKJPolarizabilityFactor(acH, atom);
for (int i = 0; i < acH.Atoms.Count; i++)
{
if (!acH.Atoms[i].Equals(atom))
{
bond = PathTools.BreadthFirstTargetSearch(acH, startAtom, acH.Atoms[i], 0, influenceSphereCutOff);
if (bond == 1)
{
polarizabilitiy += GetKJPolarizabilityFactor(acH, acH.Atoms[i]);
}
else
{
polarizabilitiy += (Math.Pow(0.5, bond - 1) * GetKJPolarizabilityFactor(acH, acH.Atoms[i]));
} //if bond==0
} //if !=atom
} //for
return(polarizabilitiy);
}
