I agree with that. Anyhow I think it would be nice to have an option to set this behaviour in the SmilesGenerator. If we then would add a method to the SMILESWriter to set a custom SmilesGenerator, those lower case SMILES could also be written to disk.
But still the problem remains, that the hybridization of an atom is never set in CDK. -Andreas Rajarshi Guha wrote: > > On Aug 10, 2007, at 1:23 PM, Andreas Schüller wrote: > >> Hello all, >> >> I noticed that for aromatic rings cdk-1.0.1 no longer creates SMILES >> with lower case atom symbols, e.g. c1ccccc1 is written as C=1C=CC=CC=1. > > I think that this is not such a bad idea - basically it allows one to > use ones own aromaticity algorithm to detect the aromaticity, rather > than forcing the generators model (CDK in this case) of aromaticity onto > the output SMILES > > ------------------------------------------------------------------- > Rajarshi Guha <[EMAIL PROTECTED]> > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > ------------------------------------------------------------------- > "355/113 -- Not the famous irrational number PI, > but an incredible simulation!" > > > ------------------------------------------------------------------------- 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
