code: public static List<IAtomContainer> getAllAtomContainers(IChemSequence sequence) {
          List<IAtomContainer> acList = new ArrayList<IAtomContainer>();
          for (IChemModel model : sequence.chemModels()) {
              acList.addAll(ChemModelManipulator.getAllAtomContainers(model));
          }
          return acList;
      }
docs: Returns all the AtomContainer's of a ChemSequence.