On Apr 30, 2009, at 4:22 PM, Loren Lenzen wrote: > > I have a list of parent molecules in SMILES form, and I was running > the SQT against a list of SMARTS queries, to make sure that all my > queries were valid. It works great until it hits Petrichloral. The > SMILES and SMARTS strings parse fine, but there is no more output > when the SQT runs into this query (currently 264/326), so I believe > there might be a possible recursivity problem. There was no > CDKException thrown even after an hour, even though the first 263 > queries ran in 15 seconds.
The problem is in the isomorphism code it seems. If one ignores the SMARTS, and just tries to match the SMILES against itself, UIT, VF2 and Ullman all run forever (or at least 30 seconds, after which I stopped the run). Some symmetry based optimization seems to be called for here ------------------------------------------------------------------- Rajarshi Guha <rg...@indiana.edu> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 ------------------------------------------------------------------- Q: What's polite and works for the phone company? A: A deferential operator. ------------------------------------------------------------------------------ Register Now & Save for Velocity, the Web Performance & Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance & Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
