Either is valid for benzene according to OpenSmiles (http://opensmiles.org/spec/open-smiles-3-input.html#3.5). I don't know if CDK conforms though...
- Noel 2009/5/26 gilleain torrance <gilleain.torra...@gmail.com>: > Hi, > > As far as I understand, the molecule 'c1ccccc1' has 6 aromatic bonds, > while 'C1=CC=CC=C1' has three double bonds, and three single bonds. I > know that they are the same in some sense, but as far as the CDK is > concerned, they are different. > > That said, both will be drawn with a circle in the center if the > renderer model has setShowAromaticity=true. I don't think there is a > way to show aromatic circles AND the double bonds in aromatic > systems... > > gilleain > > On Tue, May 26, 2009 at 3:53 PM, sebi <sebastian.kl...@hispeed.ch> wrote: >> 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 >> > > ------------------------------------------------------------------------------ > 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
