[Cdk-devel] Rendering selected bonds using CDK

[kalai <kal...@gm...>]

Dear all, 

I am trying to render selected bonds in a molecule with different colour, using CDK. 
I use the latest nightly built of CDK and version 26 of CDK-jchempaint. I use CDK-jchempaint for 
ExternalHighlightGenerator class. 

Below is my method code. It renders image for adenine(attached) but not with bonds highlighted. 
Has anyone done different colouring for bonds while rendering ? 

Any help  will be much appreciated. 
-------------------------------------------------------------------------------------------------------
public void generateImageWithBondsHighlighted() throws Exception {
            IAtomContainer molecule = MoleculeFactory.makeAdenine();
            IAtomContainer selectionMolecule = molecule.getBuilder().newInstance(IAtomContainer.class);

            for (int i = 0; i < 3; i++) {
                  selectionMolecule.addBond(molecule.getBond(i));
            }
            AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
            StructureDiagramGenerator structureDiagramGenerator = new StructureDiagramGenerator();
            structureDiagramGenerator.setMolecule(molecule);
            structureDiagramGenerator.generateCoordinates();
            IAtomContainer moleculeWithCoordinates = structureDiagramGenerator.getMolecule();

            IRenderer chemicalMoleculeRenderer = new AtomContainerRenderer(Arrays.asList(new BasicSceneGenerator(), new ExternalHighlightGenerator(),
                    new BasicBondGenerator(), new BasicAtomGenerator()), new AWTFontManager());
            RendererModel renderer2DModel = chemicalMoleculeRenderer.getRenderer2DModel();
            renderer2DModel.set(ExternalHighlightGenerator.ExternalHighlightDistance.class, (double) 12);
            renderer2DModel.set(RendererModel.ExternalHighlightColor.class, Color.ORANGE);
            renderer2DModel.setExternalSelectedPart(selectionMolecule);

            BufferedImage image = new BufferedImage(186, 186, BufferedImage.TYPE_INT_ARGB);
            Rectangle2D bounds = new Rectangle2D.Double(0, 0,
                    image.getWidth(),
                    image.getHeight());
            Graphics2D g2 = (Graphics2D) image.createGraphics();
            g2.setBackground(Color.WHITE);
            g2.clearRect(0, 0, 186, 186);
            AWTDrawVisitor awtDrawVisitor = new AWTDrawVisitor(g2);
            System.out.println("Atom count - " + moleculeWithCoordinates.getAtomCount());
            chemicalMoleculeRenderer.paint(moleculeWithCoordinates, awtDrawVisitor, bounds, true);
            g2.dispose();
            ImageIO.write((RenderedImage) image, "PNG", new File("/Users/kalai/adenine.png"));
            System.out.println("Finished rendering");
           
      }
-------------------------------------------------------------------------------------------------------



Kind regards,
Kalai


----
Ms Kalai Vanii Jayaseelan (Bioinformatician)
Cheminformatics and Metabolism Group
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 4581