code: public PermutationGroup getAutomorphismGroup(IAtomContainer atomContainer, Partition initialPartition) {
          setup(atomContainer);
          super.refine(initialPartition);
          return super.getAutomorphismGroup();
      }
docs: Get the automorphism group of the molecule given an initial partition.
  
  @param atomContainer the atom container to use
  @param initialPartition an initial partition of the atoms
  @return the automorphism group starting with this partition