//preprocess molecule into a standardized state for heavy atom rmsd computation
static void processMol(OBMol& mol)
{
//isomorphismmapper wants isomorphic atoms to have the same aromatic and ring state,
//but these proporties aren't reliable enough to be trusted in evaluating molecules
//should be considered the same based solely on connectivity
mol.DeleteHydrogens(); //heavy atom rmsd
for(OBAtomIterator aitr = mol.BeginAtoms(); aitr != mol.EndAtoms(); aitr++)
{
OBAtom *a = *aitr;
a->UnsetAromatic();
a->SetInRing();
}
for(OBBondIterator bitr = mol.BeginBonds(); bitr != mol.EndBonds(); bitr++)
{
OBBond *b = *bitr;
b->UnsetAromatic();
b->SetBondOrder(1);
b->SetInRing();
}
//avoid recomputations
mol.SetHybridizationPerceived();
mol.SetRingAtomsAndBondsPerceived();
mol.SetAromaticPerceived();
}
