On Aug 17, 2007, at 12:22 PM, Peter Maas wrote: > Hi all, > > Just curious if any of you got any further on this?
I got a chance to run the test file you had sent me (using the CDKDescUI program) and the Path and Path-Cluster descriptors do appear a little slow - on my machine (OS X 10.4.1, JDK 1.5, 2.16GHz dual core, 1GB RAM) the Path descriptors complete in about 15 to 20 sec. Of course this is still too slow. Now, for the Path descriptor which just looks for contiguous chains of N atoms (such as CCC or CCCC) we can replace the graph isomorphism approach with a simple BFS approach. This will be faster and in addition one could just do a search for upto N atom paths which would imply paths of 2, 3, ... N-1. On the other hand, the Path-Cluster descriptors involve looking for branched fragments - and I can't see how one could identify such fragments via a BFS approach (at least in a relatively simple manner). So I think Path-Cluster descriptors are going to stay slow. But I'm open to ideas ------------------------------------------------------------------- Rajarshi Guha <[EMAIL PROTECTED]> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- "whois awk?", sed Grep. ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
