> Is it the SMARTS parsing that is the bottleneck? Or the actual > isomorphism step? if the latter then switch from the UIT to one Syed's > isomorphism implementations would likely speed things up
It's been a little while since I last looked at it. The UIT plays a part in the performance, and VF2 should speed things up. Other than that, for matching against a relatively large and complex compound, the ring and aromaticity perception done for such a target can also be quite expensive, considering it's done run-time as part of a (database) query. Mark ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
