Created
June 12, 2011 20:46
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A method to draw molecules with CDK
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public void drawMolecule(IMolecule molecule, String name) throws Exception { | |
// layout the molecule | |
StructureDiagramGenerator sdg = new StructureDiagramGenerator(); | |
sdg.setMolecule(molecule, false); | |
sdg.generateCoordinates(); | |
// make generators | |
List<IGenerator<IAtomContainer>> generators = new ArrayList<IGenerator<IAtomContainer>>(); | |
generators.add(new BasicSceneGenerator()); | |
generators.add(new BasicBondGenerator()); | |
generators.add(new RingPlateGenerator()); | |
generators.add(new BasicAtomGenerator()); | |
// setup the renderer | |
AtomContainerRenderer renderer = new AtomContainerRenderer(generators, new AWTFontManager()); | |
RendererModel model = renderer.getRenderer2DModel(); | |
model.set(BasicAtomGenerator.CompactAtom.class, true); | |
model.set(BasicAtomGenerator.AtomRadius.class, 6.0); | |
model.set(BasicAtomGenerator.CompactShape.class, BasicAtomGenerator.Shape.OVAL); | |
model.set(BasicAtomGenerator.KekuleStructure.class, true); | |
model.set(BasicBondGenerator.BondWidth.class, 5.0); | |
// get the image | |
Image image = new BufferedImage(400, 400, BufferedImage.TYPE_4BYTE_ABGR); | |
Graphics2D g = (Graphics2D)image.getGraphics(); | |
g.setColor(Color.WHITE); | |
g.fill(new Rectangle2D.Double(0, 0, 400, 400)); | |
// paint | |
// renderer.paint(molecule, new AWTDrawVisitor(g)); | |
renderer.paint(molecule, new AWTDrawVisitor(g), | |
new Rectangle2D.Double(0, 0, 400, 400), true); | |
g.dispose(); | |
// write to file | |
File file = new File(OUTPUT_DIR, name + ".png"); | |
ImageIO.write((RenderedImage)image, "PNG", file); | |
} |
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