Hi Again, I have a question regarding the new renderer.
Is it possible to draw an aromatic ring from a smiles like "c1ccccc1" with double bonds in Kekule style? I can't get it to work, only when I explicit say "C1=CC=CC=C1". I use the SmilesParser to build the molecule and pass it to the renderer, code as in the earlier mail. When I use HueckelAromaticityDetector, it says true on both formula. Greetings Sebastian On Sam, 2009-05-23 at 12:32 +0200, sebi wrote: > Hi > > 1) It's not really important. But people (end-users) are used to a > convention how molecules are drawn. Just noticed that the old code was > 'ugly' too, compared to what PubChem does. Anyway.. > > 2) Your code works fine. I didn't see that method. I think I need some > coffee :) > > Thanks for the fast answer. > > Sebastian > > > On Sam, 2009-05-23 at 11:05 +0100, gilleain torrance wrote: > > Hi, > > > > 1) Yes, that's something that does have to be fixed - things like > > sterols and cyclopentane will look odd upside-down. > > 2) I hadn't thought of users accidentally using the Visitor > > setRendererModel method; that won't work. What happens in the code you > > post is that the renderer over-writes the model you are setting in the > > visitor, and your settings are lost. Better to do: > > > > model = renderer.getRenderer2DModel > > model.setAtomColorer Color::CPKAtomColors.new > > ... > > > > that way, you only use the model that the renderer has. > > > > gilleain > > > > On Sat, May 23, 2009 at 10:40 AM, sebi <sebastian.kl...@hispeed.ch> wrote: > > > Hi > > > > > > I switched to the jchempaint-primary branch and it works well now. But I > > > have two questions. > > > > > > 1) The pictures are flipped vertical compared to the old code and I > > > couldn't find a method to flip it back. Not so important, just > > > wondering. > > > > > > 2) I tried to make settings to the RendererModel, but without result. > > > I'd like to change the bond width and more important, I'd like to use > > > the CPKAtomColors. Not sure if I'm doing right, so here's my code. (It's > > > Ruby with Java classes) > > > > > > ------------------------------------------------------------------- > > > def self.draw( molecule, width, height ) > > > # prepare molecule > > > sdg = Layout::StructureDiagramGenerator.new > > > sdg.setMolecule molecule > > > sdg.generateCoordinates > > > mol = sdg.getMolecule > > > > > > # prepare image > > > area = Java::Awt::Rectangle.new width, height > > > img = Java::Awt::Image::BufferedImage.new width, height, > > > Java::Awt::Image::BufferedImage.TYPE_INT_RGB > > > g2d = img.createGraphics > > > g2d.setColor Java::Awt::Color.WHITE > > > g2d.fillRect 0, 0, width, height > > > > > > # prepare renderer > > > generators = Java::Util::ArrayList.new > > > generators.add Generators::BasicBondGenerator.new > > > generators.add Generators::BasicAtomGenerator.new > > > font = Font::AWTFontManager.new > > > renderer = Renderer.new generators, font > > > visitor = Visitor::AWTDrawVisitor.new g2d > > > > > > # the lines below have no effect ??? > > > model = RendererModel.new > > > model.setAtomColorer Color::CPKAtomColors.new > > > model.setForeColor Java::Awt::Color.GREEN > > > visitor.setRendererModel model > > > > > > # paint > > > renderer.paintMolecule mol, visitor, area, true > > > img > > > end > > > ------------------------------------------------------------- > > > > > > On Sam, 2009-05-23 at 09:33 +0200, Egon Willighagen wrote: > > >> Yes, I removed it, and the rendering code should have had to be > > >> removed from 1.2.0 already, but I forgot this. Release 1.2.3 'Don't > > >> use this Renderer' release will be made asap, but was slightly delayed > > >> by panic in the Bioclipse camp. > > >> > > >> Egon > > >> > > > > > > A note somewhere would have been useful, > > > but you guys are nice and quick with answers :) > > > > > > Sebastian > > > > > > > > > ------------------------------------------------------------------------------ > > > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT > > > is a gathering of tech-side developers & brand creativity professionals. > > > Meet > > > the minds behind Google Creative Lab, Visual Complexity, Processing, & > > > iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian > > > Group, R/GA, & Big Spaceship. http://www.creativitycat.com > > > _______________________________________________ > > > Cdk-user mailing list > > > Cdk-user@lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/cdk-user > > > > > > > ------------------------------------------------------------------------------ > > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT > > is a gathering of tech-side developers & brand creativity professionals. > > Meet > > the minds behind Google Creative Lab, Visual Complexity, Processing, & > > iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian > > Group, R/GA, & Big Spaceship. http://www.creativitycat.com > > _______________________________________________ > > Cdk-user mailing list > > Cdk-user@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/cdk-user > > > ------------------------------------------------------------------------------ > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT > is a gathering of tech-side developers & brand creativity professionals. Meet > the minds behind Google Creative Lab, Visual Complexity, Processing, & > iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian > Group, R/GA, & Big Spaceship. http://www.creativitycat.com > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://www.creativitycat.com _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
