code: private void storeRingSystem(IAtomContainer mol, IRingSet ringSet) {
          listOfRings = new ArrayList<Integer[]>(); // this is a list of int arrays
          for (int r = 0; r < ringSet.getAtomContainerCount(); ++r) {
              IRing ring = (IRing) ringSet.getAtomContainer(r);
              Integer[] bondNumbers = new Integer[ring.getBondCount()];
              for (int i = 0; i < ring.getBondCount(); ++i)
                  bondNumbers[i] = mol.indexOf(ring.getBond(i));
              listOfRings.add(bondNumbers);
          }
      }
docs: Stores an IRingSet corresponding to a AtomContainer using the bond numbers.
  
  @param mol      The IAtomContainer for which to store the IRingSet.
  @param ringSet  The IRingSet to store