/// <summary>
/// Constructor of the <see cref="IsotopeContainer"/> object setting a <see cref="IMolecularFormula"/> object and intensity value.
/// </summary>
/// <param name="formula">The formula of this container</param>
/// <param name="intensity">The intensity of this container</param>
public IsotopeContainer(IMolecularFormula formula, double intensity)
{
forms.Add(formula);
if (formula != null)
{
Mass = MolecularFormulaManipulator.GetTotalExactMass(formula);
}
Intensity = intensity;
}
/// <summary>
/// Validate the Tolerance Range of this IMolecularFormula.
/// </summary>
/// <param name="formula">Parameter is the IMolecularFormula</param>
/// <returns>A double value meaning 1.0 True, 0.0 False</returns>
public double Validate(IMolecularFormula formula)
{
Trace.TraceInformation("Start validation of ", formula);
double totalExactMass = MolecularFormulaManipulator.GetTotalExactMass(formula);
if (Math.Abs(totalExactMass - mass) > tolerance)
{
return(0.0);
}
else
{
return(1.0);
}
}
/// <summary>
/// Calculates the 3 MI's, 3 ration and the R_gyr value.
/// The molecule should have hydrogens.
/// </summary>
/// <returns>An <see cref="Result"/> containing 7 elements in the order described above</returns>
public Result Calculate(IAtomContainer container)
{
container = (IAtomContainer)container.Clone();
var factory = CDK.IsotopeFactory;
factory.ConfigureAtoms(container);
if (!GeometryUtil.Has3DCoordinates(container))
{
throw new ThreeDRequiredException("Molecule must have 3D coordinates");
}
var retval = new List <double>(7);
double ccf = 1.000138;
double eps = 1e-5;
var imat = Arrays.CreateJagged <double>(3, 3);
var centerOfMass = GeometryUtil.Get3DCentreOfMass(container).Value;
double xdif;
double ydif;
double zdif;
double xsq;
double ysq;
double zsq;
for (int i = 0; i < container.Atoms.Count; i++)
{
var currentAtom = container.Atoms[i];
var _mass = factory.GetMajorIsotope(currentAtom.Symbol).ExactMass;
var mass = _mass == null?factory.GetNaturalMass(currentAtom.Element) : _mass.Value;
var p = currentAtom.Point3D.Value;
xdif = p.X - centerOfMass.X;
ydif = p.Y - centerOfMass.Y;
zdif = p.Z - centerOfMass.Z;
xsq = xdif * xdif;
ysq = ydif * ydif;
zsq = zdif * zdif;
imat[0][0] += mass * (ysq + zsq);
imat[1][1] += mass * (xsq + zsq);
imat[2][2] += mass * (xsq + ysq);
imat[1][0] += -1 * mass * ydif * xdif;
imat[0][1] = imat[1][0];
imat[2][0] += -1 * mass * xdif * zdif;
imat[0][2] = imat[2][0];
imat[2][1] += -1 * mass * ydif * zdif;
imat[1][2] = imat[2][1];
}
// diagonalize the MI tensor
var tmp = Matrix <double> .Build.DenseOfColumnArrays(imat);
var eigenDecomp = tmp.Evd();
var eval = eigenDecomp.EigenValues.Select(n => n.Real).ToArray();
retval.Add(eval[2]);
retval.Add(eval[1]);
retval.Add(eval[0]);
var etmp = eval[0];
eval[0] = eval[2];
eval[2] = etmp;
if (Math.Abs(eval[1]) > 1e-3)
{
retval.Add(eval[0] / eval[1]);
}
else
{
retval.Add(1000);
}
if (Math.Abs(eval[2]) > 1e-3)
{
retval.Add(eval[0] / eval[2]);
retval.Add(eval[1] / eval[2]);
}
else
{
retval.Add(1000);
retval.Add(1000);
}
// finally get the radius of gyration
var formula = MolecularFormulaManipulator.GetMolecularFormula(container);
var pri = Math.Abs(eval[2]) > eps
? Math.Pow(eval[0] *eval[1] *eval[2], 1.0 / 3.0)
: Math.Sqrt(eval[0] * ccf / MolecularFormulaManipulator.GetTotalExactMass(formula));
retval.Add(Math.Sqrt(Math.PI * 2 * pri * ccf / MolecularFormulaManipulator.GetTotalExactMass(formula)));
return(new Result(retval));
}