code: public static List<IAtomContainer> getAllAtomContainers(IChemModel chemModel) {
          IAtomContainerSet moleculeSet = chemModel.getBuilder().newInstance(IAtomContainerSet.class);
          if (chemModel.getMoleculeSet() != null) {
              moleculeSet.add(chemModel.getMoleculeSet());
          }
          if (chemModel.getReactionSet() != null) {
              moleculeSet.add(ReactionSetManipulator.getAllMolecules(chemModel.getReactionSet()));
          }
          return MoleculeSetManipulator.getAllAtomContainers(moleculeSet);
      }
docs: Returns all the AtomContainer's of a ChemModel.