code: private void checkAndStore(int bondToStore, IBond.Order bondOrder, ArrayList<Integer> singleVec,
              ArrayList<Integer> doubleVec, ArrayList<Integer> cycloexVec, int a1, ArrayList<Integer> atomVec,
              int sphere, boolean isBondInCycloex) {
          if (!atomVec.contains(Integer.valueOf(a1))) {
              if (sphere < 6) atomVec.add(Integer.valueOf(a1));
          }
          if (!cycloexVec.contains(Integer.valueOf(bondToStore))) {
              if (isBondInCycloex) {
                  cycloexVec.add(bondToStore);
              }
          }
          if (bondOrder == IBond.Order.DOUBLE) {
              if (!doubleVec.contains(bondToStore)) doubleVec.add(bondToStore);
          }
          if (bondOrder == IBond.Order.SINGLE) {
              if (!singleVec.contains(Integer.valueOf(bondToStore))) singleVec.add(bondToStore);
          }
      }
docs: this method store atoms and bonds in proper lists: