Generalized graph generator constructs optimized graphs for a fixed set of vertices with a given set of constraints
This is skeletal code. The final code is now part of a product released by Schrodinger Software, NY. My work has been released under an open source license.
See: Liu S, Wu Y, Lin T, Abel R, Redmann JP, Summa CM, Jaber VR, Lim NM, Mobley DL (2013) Lead optimization mapper: automating free energy calculations for lead optimization. Journal of Computer-Aided Molecular Design 27(9): 755-770
for more information and access to the source code.