code: public PermutationGroup getAutomorphismGroup(IAtomContainer atomContainer) {
          setup(atomContainer);
          super.refine(refinable.getInitialPartition());
          return super.getAutomorphismGroup();
      }
docs: Gets the automorphism group of the atom container. By default it uses an
  initial partition based on the element symbols (so all the carbons are in
  one cell, all the nitrogens in another, etc). If this behaviour is not
  desired, then use the {@link #ignoreElements} flag in the constructor.
  
  @param atomContainer the atom container to use
  @return the automorphism group of the atom container