Hi all, I am using CDK to generate SMILES strings and for some molecules it takes a very long time. I would like to know if there is a way to set a timeout (just like AllRingsFinder) for SmilesGenerator as well. In particular, for the Pubchem molecule with CID 24763 [1] SmilesGenerator takes over an hour!
Also, to generate the SMILES string for this molecule, I had to add more prime numbers to the math.Primes class (I added all primes less than 19,697) [2]. System details: Red Hat Enterprise Linux 3 Intel Xeon 2.8GHz processor 4GB RAM CDK version 1.0.1 (cdk-1.0.1.jar) Java version 1.5 Thanks, Bala. [1] http://cobweb.ecn.purdue.edu/~bkrishna/24763.sdf [2] http://cobweb.ecn.purdue.edu/~bkrishna/Primes.java ------------------------------------------------------------------------- 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
