code: private List<Integer[]> getRingSystem(IAtomContainer mol, IRingSet ringSet) {
          List<Integer[]> bondsArray;
          bondsArray = new ArrayList<Integer[]>();
          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));
              }
              bondsArray.add(bondNumbers);
          }
          return bondsArray;
      }
docs: Stores an {@link IRingSet} corresponding to a molecule using the bond numbers.
  
  @param mol The IAtomContainer for which to store the IRingSet.
  @param ringSet The IRingSet to store
  @return The List of Integer arrays for the bond numbers of each ringSet