On Jan 11, 2008 9:43 AM, Thorsten Meinl <[EMAIL PROTECTED]> wrote: > One of KNIME's users has found a strange effect with some of the CDK > nodes. Parsing molecules with explicit hydrogens and generating 2D > coordinates for structure diagrams works fine. But after he added > explicit hydrogen atoms to the molecules and again generated 2D > coordinates for the changed molecules, in the structure diagrams almost > all hetero atoms are display as carbon (there are very few exception, > without any regularity).
That sounds like the hydrogens having the same coordinates as the hetero atoms... did you check that? > However, if the internal CDK representation is > translated back into a textual format the molecules look just fine. So I > suspect it has something to do with the Renderer2D having problems > drawing molecules with explicit hydrogens. Any ideas? No, that should normally not be a problem... can you disclose the molecules, the data they started with, and maybe the workflow? So, that we may attempt to reproduce it... just those one or two molecules that give trouble... Oh, pointers to the source code of the nodes would be useful... do you have a viewcvs or so installed? Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- 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
