code: public static List<IAtomContainer> getAllAtomContainers(IChemFile file) {
          List<IAtomContainer> acList = new ArrayList<IAtomContainer>();
          for (IChemSequence sequence : file.chemSequences()) {
              acList.addAll(ChemSequenceManipulator.getAllAtomContainers(sequence));
          }
          return acList;
      }
docs: Returns all the AtomContainer's of a ChemFile.