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.
The respective line in SmilesGenerator.java to generate lower case aromatic atom symbols is: if (a.getHybridization() == CDKConstants.HYBRIDIZATION_SP2) I did a full text search on the cdk source code but it seems that CDKConstants.HYBRIDIZATION_SP2 is never set in any class. Any suggestions? -Andreas P.S.: On another note: would it be possible to preferably omit constructs like "C=1" as in the example above and preferably use the alternative form: C1=CC=CC=C1? -- Andreas Schüller PhD student in the research group of Prof. Dr. Gisbert Schneider Johann Wolfgang Goethe University Beilstein-endowed Chair for Chemoinformatics Building B - 3rd floor Siesmayerstr. 70 60323 Frankfurt am Main Germany Tel.: +49 69 798 24879 Fax: +49 69 798 24880 http://www.modlab.de/ ------------------------------------------------------------------------- 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
