Sorry not my field! But I would first give NAUTY[1] a try before trying more exotic, structure-exploiting stuff.<p>[1] <a href="http:&#x2F;&#x2F;www3.cs.stonybrook.edu&#x2F;~algorith&#x2F;implement&#x2F;nauty&#x2F;implement.shtml" rel="nofollow">http:&#x2F;&#x2F;www3.cs.stonybrook.edu&#x2F;~algorith&#x2F;implement&#x2F;nauty&#x2F;impl...</a>