On Friday 21 November 2008 18:38, Egon Willighagen wrote:
> On Fri, Nov 21, 2008 at 5:51 PM, Adel Golovin <[EMAIL PROTECTED]> wrote:
> > With this code I try to zero coordinates so, the generator will be forced
> > to produce them.
>
> Well, you can better make them 'null', and, you should at least change
> the 2D coordinates:
>
> for (IAtom atom : mol.atoms()) atom.setPoint2d(null);
>
> Egon
Thanks,
Now it generates the 2D coordinates but still the image I get back is black
square.
The code is as follows:
// read molecule from MDL file
org.openscience.cdk.io.MDLReader cdkMDL = new
org.openscience.cdk.io.MDLReader(mdl);
org.openscience.cdk.Molecule mol = new org.openscience.cdk.Molecule();
cdkMDL.read(mol);
// null the coordinates
Iterator<org.openscience.cdk.interfaces.IAtom> itatoms = mol.atoms();
while (itatoms.hasNext()) {
org.openscience.cdk.interfaces.IAtom atom = itatoms.next();
atom.setPoint2d(null);
atom.setPoint3d(null);
}
// generate coordinates
org.openscience.cdk.layout.StructureDiagramGenerator sdg = new
org.openscience.cdk.layout.StructureDiagramGenerator();
sdg.setMolecule(mol);
sdg.generateCoordinates();
org.openscience.cdk.interfaces.IMolecule layedOutMol = sdg.getMolecule();
// render
org.openscience.cdk.renderer.SimpleRenderer2D renderer = new
org.openscience.cdk.renderer.SimpleRenderer2D();
org.openscience.cdk.renderer.Renderer2DModel r2dm = new
org.openscience.cdk.renderer.Renderer2DModel();
r2dm.setDrawNumbers(false);
r2dm.setUseAntiAliasing(true);
r2dm.setColorAtomsByType(true);
r2dm.setShowImplicitHydrogens(true);
r2dm.setShowAromaticity(true);
r2dm.setShowReactionBoxes(false);
r2dm.setKekuleStructure(false);
renderer.setRenderer2DModel(r2dm);
BufferedImage bufferedImage = new BufferedImage(width, height,
BufferedImage.TYPE_INT_RGB);
Graphics2D graphics = bufferedImage.createGraphics();
Rectangle2D bounds = new Rectangle2D.Double(0, 0, width, height);
renderer.paintMolecule(layedOutMol, graphics, bounds);
// write the image
javax.imageio.ImageIO.write(bufferedImage, "png", out);
--
Adel
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