private static double[] Listpolarizability(IAtomContainer container, int[][] dmat)
{
int natom = container.Atoms.Count;
double[] polars = new double[natom];
for (int i = 0; i < natom; i++)
{
IAtom atom = container.Atoms[i];
try
{
polars[i] = Polarizability.CalculateGHEffectiveAtomPolarizability(container, atom, false, dmat);
}
catch (Exception ex1)
{
throw new CDKException("Problems with assign Polarizability due to " + ex1.ToString(), ex1);
}
}
return(polars);
}
/// <summary>
/// The method calculates the Effective Atom Polarizability of a given atom
/// It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
/// </summary>
/// <param name="atom">The <see cref="IAtom"/> for which the <see cref="Result"/> is requested</param>
/// <returns>return the effective polarizability</returns>
public Result Calculate(IAtom atom)
{
// FIXME: for now I'll cache a few modified atomic properties, and restore them at the end of this method
var originalAtomtypeName = atom.AtomTypeName;
var originalNeighborCount = atom.FormalNeighbourCount;
var originalHCount = atom.ImplicitHydrogenCount;
var originalValency = atom.Valency;
var originalHybridization = atom.Hybridization;
var originalFlag = atom.IsVisited;
var originalBondOrderSum = atom.BondOrderSum;
var originalMaxBondOrder = atom.MaxBondOrder;
var polarizability = Polarizability.CalculateGHEffectiveAtomPolarizability(container, atom, 100, true);
// restore original props
atom.AtomTypeName = originalAtomtypeName;
atom.FormalNeighbourCount = originalNeighborCount;
atom.Valency = originalValency;
atom.ImplicitHydrogenCount = originalHCount;
atom.IsVisited = originalFlag;
atom.Hybridization = originalHybridization;
atom.MaxBondOrder = originalMaxBondOrder;
atom.BondOrderSum = originalBondOrderSum;
return(new Result(polarizability));
}
private static Result CalculateMain(IAtomContainer container, int nhigh, int nlow)
{
var iso = CDK.IsotopeFactory;
int nheavy = 0;
// find number of heavy atoms
nheavy += container.Atoms.Count(atom => !atom.AtomicNumber.Equals(AtomicNumbers.H));
if (nheavy == 0)
{
throw new CDKException("No heavy atoms in the container");
}
var diagvalue = new double[nheavy];
// get atomic mass weighted BCUT
try
{
var counter = 0;
foreach (var atom in container.Atoms.Where(atom => !atom.AtomicNumber.Equals(AtomicNumbers.H)))
{
diagvalue[counter] = iso.GetMajorIsotope(atom.AtomicNumber).ExactMass.Value;
counter++;
}
}
catch (Exception e)
{
throw new CDKException($"Could not calculate weight: {e.Message}", e);
}
double[] eval1, eval2, eval3;
{
var burdenMatrix = BurdenMatrix.EvalMatrix(container, diagvalue);
if (HasUndefined(burdenMatrix))
{
throw new CDKException("Burden matrix has undefined values");
}
var matrix = Matrix <double> .Build.DenseOfColumnArrays(burdenMatrix);
var eigenDecomposition = matrix.Evd().EigenValues;
eval1 = eigenDecomposition.Select(n => n.Real).ToArray();
}
try
{
// get charge weighted BCUT
CDK.LonePairElectronChecker.Saturate(container);
var charges = new double[container.Atoms.Count];
var peoe = new GasteigerMarsiliPartialCharges();
peoe.AssignGasteigerMarsiliSigmaPartialCharges(container, true);
for (int i = 0; i < container.Atoms.Count; i++)
{
charges[i] += container.Atoms[i].Charge.Value;
}
for (int i = 0; i < container.Atoms.Count; i++)
{
container.Atoms[i].Charge = charges[i];
}
}
catch (Exception e)
{
throw new CDKException("Could not calculate partial charges: " + e.Message, e);
}
{
var counter = 0;
foreach (var atom in container.Atoms.Where(atom => !atom.AtomicNumber.Equals(AtomicNumbers.H)))
{
diagvalue[counter++] = atom.Charge.Value;
}
}
{
var burdenMatrix = BurdenMatrix.EvalMatrix(container, diagvalue);
if (HasUndefined(burdenMatrix))
{
throw new CDKException("Burden matrix has undefined values");
}
var matrix = Matrix <double> .Build.DenseOfColumnArrays(burdenMatrix);
var eigenDecomposition = matrix.Evd().EigenValues;
eval2 = eigenDecomposition.Select(n => n.Real).ToArray();
}
var topoDistance = PathTools.ComputeFloydAPSP(AdjacencyMatrix.GetMatrix(container));
// get polarizability weighted BCUT
{
var counter = 0;
foreach (var atom in container.Atoms.Where(atom => !atom.AtomicNumber.Equals(AtomicNumbers.H)))
{
diagvalue[counter++] = Polarizability.CalculateGHEffectiveAtomPolarizability(container, atom, false, topoDistance);
}
}
{
var burdenMatrix = BurdenMatrix.EvalMatrix(container, diagvalue);
if (HasUndefined(burdenMatrix))
{
throw new CDKException("Burden matrix has undefined values");
}
var matrix = Matrix <double> .Build.DenseOfColumnArrays(burdenMatrix);
var eigenDecomposition = matrix.Evd().EigenValues;
eval3 = eigenDecomposition.Select(n => n.Real).ToArray();
}
// return only the n highest & lowest eigenvalues
int lnlow, lnhigh, enlow, enhigh;
if (nlow > nheavy)
{
lnlow = nheavy;
enlow = nlow - nheavy;
}
else
{
lnlow = nlow;
enlow = 0;
}
if (nhigh > nheavy)
{
lnhigh = nheavy;
enhigh = nhigh - nheavy;
}
else
{
lnhigh = nhigh;
enhigh = 0;
}
var retval = new List <double>((lnlow + enlow + lnhigh + enhigh) * 3);
for (int i = 0; i < lnlow; i++)
{
retval.Add(eval1[i]);
}
for (int i = 0; i < enlow; i++)
{
retval.Add(double.NaN);
}
for (int i = 0; i < lnhigh; i++)
{
retval.Add(eval1[eval1.Length - i - 1]);
}
for (int i = 0; i < enhigh; i++)
{
retval.Add(double.NaN);
}
for (int i = 0; i < lnlow; i++)
{
retval.Add(eval2[i]);
}
for (int i = 0; i < enlow; i++)
{
retval.Add(double.NaN);
}
for (int i = 0; i < lnhigh; i++)
{
retval.Add(eval2[eval2.Length - i - 1]);
}
for (int i = 0; i < enhigh; i++)
{
retval.Add(double.NaN);
}
for (int i = 0; i < lnlow; i++)
{
retval.Add(eval3[i]);
}
for (int i = 0; i < enlow; i++)
{
retval.Add(double.NaN);
}
for (int i = 0; i < lnhigh; i++)
{
retval.Add(eval3[eval3.Length - i - 1]);
}
for (int i = 0; i < enhigh; i++)
{
retval.Add(double.NaN);
}
return(new Result(retval, nhigh, nlow));
}
