ok, i tried the UniversalIsomorphismTester and used the getSubgraphAtomsMaps() method, however it seems to contain null rMaps while getSubgraphMaps() returns the bond no. correctly, so m i using it wrongly?
Rajarshi Guha-3 wrote: > > > On Jul 8, 2007, at 11:28 AM, RzmmDX wrote: > >> >> i been using the fragmenter class made by Rajarshi Guha. >> >> i parse this smiles string "C(CC(C(=O)O)N)CNC(=NO)N" it has 2 hydroxyl >> groups, >> how do i break the bond that bonds the hydroxyl group to the molecule? > > The trick will be to identify the -OH group (either by SMARTS or by > hand). Once you have the hydroxyl O atom, you can get all the bonds > connected to it (getConnectedBonds) and then choose that bond whose > other atom is a C. You can then remove that bond. > > Of course, this will result in 3 disconnected components. If just > want to remove the -OH's then make sure to remove the O's as well > > ------------------------------------------------------------------- > Rajarshi Guha <[EMAIL PROTECTED]> > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > ------------------------------------------------------------------- > Does Ramanujan know Polish? > -- E.B. Ross > > > > ------------------------------------------------------------------------- > 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 > > -- View this message in context: http://www.nabble.com/cutting-a-functional-group-from-a-molecule-tf4044824.html#a11762038 Sent from the cdk-user mailing list archive at Nabble.com. ------------------------------------------------------------------------- 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
