/**
* Get the summed exact mass of all isotopes from an MolecularFormula. It assumes isotope masses
* to be preset, and returns 0.0 if not.
*
* @param formula The IMolecularFormula to calculate
* @return The summed exact mass of all atoms in this MolecularFormula
*/
public static double getTotalExactMass(IMolecularFormula formula) {
Double mass = 0.0;
for (IIsotope isotope : formula.isotopes()) {
if (isotope.getExactMass() == CDKConstants.UNSET) {
try {
IIsotope majorIsotope = Isotopes.getInstance().getMajorIsotope(isotope.getSymbol());
if (majorIsotope != null) {
mass += majorIsotope.getExactMass() * formula.getIsotopeCount(isotope);
}
} catch (IOException e) {
throw new RuntimeException("Could not instantiate the IsotopeFactory.");
}
} else mass += isotope.getExactMass() * formula.getIsotopeCount(isotope);
}
if (formula.getCharge() != null) mass = correctMass(mass, formula.getCharge());
return mass;
}
/**
* 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;
}
