code: private static Map<IAtom, Integer> indexAtoms(IAtomContainer container) {
          Map<IAtom, Integer> map = Maps.newHashMapWithExpectedSize(container.getAtomCount());
          for (int i = 0; i < container.getAtomCount(); i++)
              map.put(container.getAtom(i), i);
          return map;
      }
docs: Create an index of atoms for the provided {@code container}.
  
  @param container the container to index the atoms of
  @return the index/lookup of atoms to the index they appear