/**
* Get the summed major isotopic mass of all elements from an MolecularFormula.
*
* @param formula The IMolecularFormula to calculate
* @return The summed exact major isotope masses of all atoms in this MolecularFormula
*/
public static double getMajorIsotopeMass(IMolecularFormula formula) {
double mass = 0.0;
IsotopeFactory factory;
try {
factory = Isotopes.getInstance();
} catch (IOException e) {
throw new RuntimeException("Could not instantiate the IsotopeFactory.");
}
for (IIsotope isotope : formula.isotopes()) {
IIsotope major = factory.getMajorIsotope(isotope.getSymbol());
if (major != null) {
mass += major.getExactMass() * formula.getIsotopeCount(isotope);
}
}
return mass;
}
/**
* Calculates the 3 MI's, 3 ration and the R_gyr value.
*
* <p>The molecule should have hydrogens
*
* @param container Parameter is the atom container.
* @return An ArrayList containing 7 elements in the order described above
*/
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer container) {
if (!GeometryTools.has3DCoordinates(container))
return getDummyDescriptorValue(new CDKException("Molecule must have 3D coordinates"));
IAtomContainer clone;
IsotopeFactory factory;
try {
clone = (IAtomContainer) container.clone();
factory = IsotopeFactory.getInstance(container.getBuilder());
factory.configureAtoms(clone);
} catch (Exception e) {
logger.debug(e);
return getDummyDescriptorValue(e);
}
DoubleArrayResult retval = new DoubleArrayResult(7);
double ccf = 1.000138;
double eps = 1e-5;
double[][] imat = new double[3][3];
Point3d centerOfMass = GeometryTools.get3DCentreOfMass(clone);
double xdif;
double ydif;
double zdif;
double xsq;
double ysq;
double zsq;
for (int i = 0; i < clone.getAtomCount(); i++) {
IAtom currentAtom = clone.getAtom(i);
double mass = factory.getMajorIsotope(currentAtom.getSymbol()).getExactMass();
xdif = currentAtom.getPoint3d().x - centerOfMass.x;
ydif = currentAtom.getPoint3d().y - centerOfMass.y;
zdif = currentAtom.getPoint3d().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
Matrix tmp = new Matrix(imat);
EigenvalueDecomposition eigenDecomp = tmp.eig();
double[] eval = eigenDecomp.getRealEigenvalues();
retval.add(eval[2]);
retval.add(eval[1]);
retval.add(eval[0]);
double 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
double pri;
IMolecularFormula formula = MolecularFormulaManipulator.getMolecularFormula(clone);
if (Math.abs(eval[2]) > eps) pri = Math.pow(eval[0] * eval[1] * eval[2], 1.0 / 3.0);
else pri = Math.sqrt(eval[0] * ccf / MolecularFormulaManipulator.getTotalExactMass(formula));
retval.add(
Math.sqrt(
Math.PI * 2 * pri * ccf / MolecularFormulaManipulator.getTotalExactMass(formula)));
return new DescriptorValue(
getSpecification(), getParameterNames(), getParameters(), retval, getDescriptorNames());
}
