Hi Paul, the problem you hit is, it seems, that certain properties only work in combination. More specifically: - The implicit Hs are only shown on atoms where some other property switches on labels. If you have e. g. a benzene ring, no atom labels are shown anyway and therefore no implicit Hs. If you also switch on explicit carbons, it works. You also need to have implicit Hs set in the structure you display. The renderer does not do calculations or so, setHydrogen count must be used to set hydrogens beforehand. - The showAromaticity can only work if aromaticity has been detected before. Again, no calculation done. If it has been detected (or aromaticity flag set otherwise), it should work. Stefan
On Wednesday 17 March 2010 18:13:12 Paul Dwinnell wrote: > I'm using JCP version 3.0.1 for rendering structures. I've tried to modify > some of the rendering properties and they don't seem to have any affect. > For example the following properties do not modify the rendered structure > (renderer is an instance of org.openscience.jchempaint.renderer.Renderer). > renderer.getRenderer2DModel().setShowImplicitHydrogens(true); > renderer.getRenderer2DModel().setShowExplicitHydrogens(true); > renderer.getRenderer2DModel().setShowAromaticity(true); > > But some properties do seem to work. For example this will turn off the > Atom Coloring: renderer.getRenderer2DModel().setColorAtomsByType(false); > > Is there some other setting I need to make in order for those three > properties to work? -- Stefan Kuhn B. Sc. M. A. Software Engineer in the Chemoinformatics and Metabolism Team European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK Phone +44 1223 49 2657 Fax +44 (0)1223 494 468 ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
