private void fixCarbonHCount(IAtomContainer mol) {
/*
* the following line are just a quick fix for this
* particluar carbon-only molecule until we have a proper
* hydrogen count configurator
*/
double bondCount = 0;
org.openscience.cdk.interfaces.IAtom atom;
for (int f = 0; f < mol.getAtomCount(); f++) {
atom = mol.getAtom(f);
bondCount = mol.getBondOrderSum(atom);
int correction =
(int) bondCount - (atom.getCharge() != null ? atom.getCharge().intValue() : 0);
if (atom.getSymbol().equals("C")) {
atom.setImplicitHydrogenCount(4 - correction);
} else if (atom.getSymbol().equals("N")) {
atom.setImplicitHydrogenCount(3 - correction);
}
if (standAlone) {
System.out.println("Hydrogen count for atom " + f + ": " + atom.getImplicitHydrogenCount());
}
}
}
public static boolean hasPartialCharges(IAtomContainer molecule) {
for (IAtom atom : molecule.atoms()) if (atom.getCharge() != 0.0000) return true;
return false;
}