Hi Guillaume, please use the cdk-jchempaint or cdk-user mailing list next time.
On Mon, Aug 31, 2009 at 3:24 PM, Guillaume Durieu<gdur...@...> wrote: > I have trouble with a peculiar molecule that I cannot render well using > CDK (tried all versions...) > For instance, the smile C(=O)c1cnn2ccccc12 should be rendered with > double bonds in both cycles. Instead, only single bonds are shown. CDK readers read what you pass them. The above indicates (at least by the OpenSMILES definition) aromatic bonds, but they do not include bond order information for the bonds, so that is not read and not displayed. Surely it is possible to deduce those missing double bond orders (the location of them, that is), which can be done with the DeduceBondSystemTool... it is not perfect, but does a good fairly good job. Make sure you have turned on the JChemPaint option to show aromatic rings, and you should be set. Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
