Thanks for the quick reply Stefan. The only reason I needed the different smiles string is to distinguish between the strings when converted to lower case. I know they are not legal smiles, but I am storing all of them in lower case. In that case, the difference between benzene and cyclohexane are lost, unless I can generate the alternating single/double bonds OR explicitly represent the aromatic bonds.
SmilesGenerator will always output c1ccccc1 with setUseAromaticityFlag(true) (even if the ring has alternating single and double bonds with bond orders 1 and 2). But I did find the DeAromatizationTool class, so if I use that and then call SmilesGenerator with setUseAromaticityFlag(false), I get C1C=CC=CC=1. Thanks, Bala. On Mon, Jul 7, 2008 at 3:45 PM, Stefan Kuhn <[EMAIL PROTECTED]> wrote: > The C1C=CC=CC=1 version should result if you remove the aromaticity flag > before writing from all atoms and bonds (and have the molecule properly > saturated). Not sure if c:1c:c:c:c:c:1 can be result somehow. Not sure about > why this is needed right now anyway. Isn't it sort of redundant? > Stefan > > > >> -----Ursprüngliche Nachricht----- >> Von: "Bala B K" <[EMAIL PROTECTED]> >> Gesendet: 07.07.08 21:31:33 >> An: [email protected] >> Betreff: [Cdk-user] SmilesGenerator question > > >> Hi all, >> >> I am using SmilesGenerator in CDK 1.0.3 with >> setUseAromatiticyFlag(true). For aromatic molecules such as benzene, >> it always generates c1ccccc1 . This happens if I create my molecule >> with the input smiles being C1C=CC=CC=1 or c1ccccc1 or c1c=cc=cc=1. Is >> there a way to generate C1C=CC=CC=1 or c1c=cc=cc=1 or c:1c:c:c:c:c:1 >> instead? >> >> Thanks, >> Bala. >> >> ------------------------------------------------------------------------- >> Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! >> Studies have shown that voting for your favorite open source project, >> along with a healthy diet, reduces your potential for chronic lameness >> and boredom. Vote Now at http://www.sourceforge.net/community/cca08 >> _______________________________________________ >> Cdk-user mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/cdk-user >> > > > _______________________________________________________________________ > Jetzt neu! Schützen Sie Ihren PC mit McAfee und WEB.DE. 30 Tage > kostenlos testen. http://www.pc-sicherheit.web.de/startseite/?mc=022220 > > > ------------------------------------------------------------------------- > Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! > Studies have shown that voting for your favorite open source project, > along with a healthy diet, reduces your potential for chronic lameness > and boredom. Vote Now at http://www.sourceforge.net/community/cca08 > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user > ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
