CDK Highlight

gistfile1.java

    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");

    }