code: public static List<IChemObject> getAllChemObjects(IAtomContainerSet set) {
          ArrayList<IChemObject> list = new ArrayList<IChemObject>();
          list.add(set);
          for (IAtomContainer atomContainer : set.atomContainers()) {
              list.add(atomContainer);
          }
          return list;
      }
docs: Does not recursively return the contents of the AtomContainer.
  
  @param set The collection of IAtomContainer objects
  @return a list of individual ChemObject's