Hi Egon, > That sounds like the hydrogens having the same coordinates as the > hetero atoms... did you check that? That was a good hint! The 2D coordinate node only generates new coordinates if the molecules does not already have some 2D coordinates (unless you force it to generate some). It seems I used the wrong method in GeometryTools, has2DCoordinates, but that returns true if at least one molecule has 2D coordinates. has2DCoordinates seems to be better suited, judging from the javadoc. So the node did not generate any new coordinates, leaving the explicit hydrogens without any coordinates. And *that* seems to confuse the renderer. If you want to look into that, I can send you a small workflow.
> Oh, pointers to the source code of the nodes would be useful... do you > have a viewcvs or so installed? Unfortunately no (not yet?). But you can download the source plugins for each KNIME plugin in the Update Manager (KNIME Development category). Thorsten -- Thorsten Meinl room: Z815 Nycomed Chair for Bioinformatics fax: +49 (0)7531 88-5132 and Information Mining phone: +49 (0)7531 88-5016 Box M712, 78457 Konstanz, Germany ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
