Thanks Egon, Still there are problems: The following code has the same coordinates of initial molecule (mol) and of the output molecule (layedOutMol)
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(); Even when I explicitly set all coordinates to 0: javax.vecmath.Point3d point3d = new javax.vecmath.Point3d(); Iterator<org.openscience.cdk.interfaces.IAtom> itatoms = mol.atoms(); while (itatoms.hasNext()) itatoms.next().setPoint3d(point3d); basically it does not generate coordinates. any thoughts? On Friday 21 November 2008 08:15, Egon Willighagen wrote: > 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 -- Adel Golovin EMBL-EBI/PDBe 44 1223 492531 [EMAIL PROTECTED] ------------------------------------------------------------------------- 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
