Dear Adel, On Thu, Nov 13, 2008 at 3:13 PM, Adel Golovin <[EMAIL PROTECTED]> wrote: > 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); > org.openscience.cdk.renderer.SimpleRenderer2D renderer = new > org.openscience.cdk.renderer.SimpleRenderer2D(); > Rectangle2D bounds = new Rectangle2D.Double(0, 0, 180, 180); > BufferedImage bufferedImage = new BufferedImage( 180, > 180,BufferedImage.TYPE_INT_RGB ); > Graphics2D graphics = bufferedImage.createGraphics(); > renderer.paintMolecule(mol, graphics, bounds); > javax.imageio.ImageIO.write(bufferedImage, "png", out);
In this code you do not create 2D coordinates, and... <snip> > the mdl file is as follows: > > 3D_NCI753 > 3D_NCI > > 9 10 0 0 0 0 0 0 0 0 1 V2000 > -0.0170 1.4060 0.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0020 -0.0040 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.2560 2.0480 0.0300 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.0610 0.7840 -0.0130 C 0 0 0 0 0 0 0 0 0 0 0 0 > -2.2920 -0.0100 0.0250 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.2730 1.8200 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 1.3260 -0.3630 -0.0130 N 0 0 0 0 0 0 0 0 0 0 0 0 > -1.1490 -0.6630 0.0100 N 0 0 0 0 0 0 0 0 0 0 0 0 > -2.3520 1.3100 0.0410 N 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 4 0 0 0 0 > 1 3 4 0 0 0 0 > 1 6 4 0 0 0 0 > 2 7 4 0 0 0 0 > 2 8 4 0 0 0 0 > 3 9 4 0 0 0 0 > 4 6 4 0 0 0 0 > 4 7 4 0 0 0 0 > 5 8 4 0 0 0 0 > 5 9 4 0 0 0 0 > M END This file only has 3D coordinates... I think you can solve your problem by using the StructureDiagramGenerator... Hope that helps, Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
