/// <summary>
/// Calculates 11 directional and 6 non-directional WHIM descriptors for.
/// the specified weighting scheme
/// </summary>
/// <returns>An ArrayList containing the descriptors in the order described above.</returns>
public Result Calculate(IAtomContainer container, AtomWeightingType type = AtomWeightingType.Unity)
{
if (!GeometryUtil.Has3DCoordinates(container))
{
throw new ThreeDRequiredException("Molecule must have 3D coordinates");
}
double sum = 0.0;
var ac = (IAtomContainer)container.Clone();
// do aromaticity detecttion for calculating polarizability later on
//HueckelAromaticityDetector had = new HueckelAromaticityDetector();
//had.DetectAromaticity(ac);
// get the coordinate matrix
var cmat = Arrays.CreateJagged <double>(ac.Atoms.Count, 3);
for (int i = 0; i < ac.Atoms.Count; i++)
{
var coords = ac.Atoms[i].Point3D.Value;
cmat[i][0] = coords.X;
cmat[i][1] = coords.Y;
cmat[i][2] = coords.Z;
}
// set up the weight vector
var wt = new double[ac.Atoms.Count];
IReadOnlyDictionary <int, double> hash = null;
switch (type)
{
case AtomWeightingType.Mass:
hash = hashatwt;
break;
case AtomWeightingType.Volume:
hash = hashvdw;
break;
case AtomWeightingType.Electronegativity:
hash = hasheneg;
break;
case AtomWeightingType.Polarizability:
hash = hashpol;
break;
default:
break;
}
switch (type)
{
case AtomWeightingType.Unity:
for (int i = 0; i < ac.Atoms.Count; i++)
{
wt[i] = 1.0;
}
break;
default:
for (int i = 0; i < ac.Atoms.Count; i++)
{
wt[i] = hash[ac.Atoms[i].AtomicNumber];
}
break;
}
PCA pcaobject = null;
try
{
pcaobject = new PCA(cmat, wt);
}
catch (CDKException cdke)
{
Debug.WriteLine(cdke);
}
// directional WHIM's
var lambda = pcaobject.GetEigenvalues();
var gamma = new double[3];
var nu = new double[3];
var eta = new double[3];
for (int i = 0; i < 3; i++)
{
sum += lambda[i];
}
for (int i = 0; i < 3; i++)
{
nu[i] = lambda[i] / sum;
}
var scores = pcaobject.GetScores();
for (int i = 0; i < 3; i++)
{
sum = 0.0;
for (int j = 0; j < ac.Atoms.Count; j++)
{
sum += scores[j][i] * scores[j][i] * scores[j][i] * scores[j][i];
}
sum = sum / (lambda[i] * lambda[i] * ac.Atoms.Count);
eta[i] = 1.0 / sum;
}
// look for symmetric & asymmetric atoms for the gamma descriptor
for (int i = 0; i < 3; i++)
{
double ns = 0.0;
double na = 0.0;
for (int j = 0; j < ac.Atoms.Count; j++)
{
bool foundmatch = false;
for (int k = 0; k < ac.Atoms.Count; k++)
{
if (k == j)
{
continue;
}
if (scores[j][i] == -1 * scores[k][i])
{
ns++;
foundmatch = true;
break;
}
}
if (!foundmatch)
{
na++;
}
}
var n = (double)ac.Atoms.Count;
gamma[i] = -1.0 * ((ns / n) * Math.Log(ns / n) / Math.Log(2.0) + (na / n) * Math.Log(1.0 / n) / Math.Log(2.0));
gamma[i] = 1.0 / (1.0 + gamma[i]);
}
{
// non directional WHIMS's
var t = lambda[0] + lambda[1] + lambda[2];
var a = lambda[0] * lambda[1] + lambda[0] * lambda[2] + lambda[1] * lambda[2];
var v = t + a + lambda[0] * lambda[1] * lambda[2];
double k = 0.0;
sum = 0.0;
for (int i = 0; i < 3; i++)
{
sum += lambda[i];
}
for (int i = 0; i < 3; i++)
{
k = (lambda[i] / sum) - (1.0 / 3.0);
}
k = k / (4.0 / 3.0);
var g = Math.Pow(gamma[0] * gamma[1] * gamma[2], 1.0 / 3.0);
var d = eta[0] + eta[1] + eta[2];
// return all the stuff we calculated
return(new Result(
lambda[0],
lambda[1],
lambda[2],
nu[0],
nu[1],
gamma[0],
gamma[1],
gamma[2],
eta[0],
eta[1],
eta[2],
t,
a,
v,
k,
g,
d));
}
}