On Aug 29, 2007, at 1:05 AM, sushil ronghe wrote: > Thanks for the change. > > > But since it does involve recursively fragmenting the initial set of > fragments, if your molecule has long chains, it can take a long time > to complete > > for a straight and branch chain of length upto 8 it is doing very > fast. > that is fine.. > But one problem is there, it is generating a same fragments. > say for (pentane) fragmenter is generating 5 fragments > all of the population is consisting of only 2 Unique fragments.
The web page notes that the resultant fragment list may contain topologically equivalent fragments since we only check for fragments that involve the same atoms in the parent molecule. So in pentane, you can have three CCC fragments - which involve different atoms of pentane, but are all topologically equivalent. To take topological equivalence into account, you'd have to do a graph isomorphism or else convert all fragments to canonical SMILES and do string comparisons etc ------------------------------------------------------------------- Rajarshi Guha <[EMAIL PROTECTED]> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Got Mole problems? Call Avogadro at 6.02 x 10^23. ------------------------------------------------------------------------- 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
