CDKRender1.4.java

StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.setMolecule(mol, false);
sdg.generateCoordinates();

AtomContainerRenderer renderer =
        new AtomContainerRenderer(Arrays.asList(new BasicSceneGenerator(),
                                                new BasicBondGenerator(),
                                                new ExtendedAtomGenerator()),
                                  new AWTFontManager());
BufferedImage img = new BufferedImage(256, 256, BufferedImage.TYPE_4BYTE_ABGR);
Graphics2D g2 = img.createGraphics();

g2.setBackground(Color.WHITE);
g2.clearRect(0, 0, 256, 256);

IDrawVisitor visitor = new AWTDrawVisitor(g2);
Rectangle2D bounds = new Rectangle2D.Double(0, 0, 256, 256);

renderer.paint(mol, visitor, bounds, true);
g2.dispose();

ImageIO.write(img, "PNG", new File("myoutput.png"));