I have a patch for master that reduces this to 88s - by keeping track of fragments generated and avoiding processing of identical fragments in recursive calls. I check for duplicates by generating the SMILES for the fragments (and storing them in a HashSet) - and this causes an expected slowdown.
My question is - si there a faster way to check for existence of a molecule that does not involve SMILES generation?
(Also, where can I send a patch for review - I'm a little out of date with protocols these days :)
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science