/**
* Returns the ring that is formed by the atoms in the given vector.
*
* @param vec The vector that contains the atoms of the ring
* @param mol The molecule this ring is a substructure of
* @return The ring formed by the given atoms
*/
private IRing prepareRing(List vec, IAtomContainer mol) {
// add the atoms in vec to the new ring
int atomCount = vec.size();
IRing ring = mol.getBuilder().newInstance(IRing.class, atomCount);
IAtom[] atoms = new IAtom[atomCount];
vec.toArray(atoms);
ring.setAtoms(atoms);
// add the bonds in mol to the new ring
try {
IBond b;
for (int i = 0; i < atomCount - 1; i++) {
b = mol.getBond(atoms[i], atoms[i + 1]);
if (b != null) {
ring.addBond(b);
} else {
logger.error("This should not happen.");
}
}
b = mol.getBond(atoms[0], atoms[atomCount - 1]);
if (b != null) {
ring.addBond(b);
} else {
logger.error("This should not happen either.");
}
} catch (Exception exc) {
logger.debug(exc);
}
logger.debug("found Ring ", ring);
return ring;
}
