On Nov 14, 2007, at 2:15 PM, Javi Muriel Zafra wrote: > > noComun.removeAtomAndConnectedElectronContainers(noComun.getAtom( > ((Integer)i.next()).intValue() ));
In this step I'm not sure that you want to remove atoms and associated bonds by serial number. When you remove atom 0, what was atom 1 will become atom 0. So in the second round, if you try to remove atom 1 it won't work. That's why in my code I get the actual atom objects based on serials and then delete them I ran my code with the SMILES corresponding to your images C1=CC(CCCC)CC=C1S(=O)ON (Molecula 1) C1=CC(C(=O)OCCC)CC=C1S(=O)ON (Molecula 2) The uncommon part from the first case should be CCC and is shown correctly. For the second case there will be two parts: a single O (corresponding to the carbonyl oxygen - obviously since it is a single atom, there is no bond) and a CCCO fragment. My code brings up the correct images -I don't know why your example is showing a CO - it should either be O or CCCO ------------------------------------------------------------------- Rajarshi Guha <[EMAIL PROTECTED]> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- All the evidence concerning the universe has not yet been collected, so there's still hope. ------------------------------------------------------------------------- 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
