You could take a look at http://cheminfo.informatics.indiana.edu/~rguha/code/java/#depict
On Nov 21, 2008, at 10:47 AM, Adel Golovin wrote: > 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 ------------------------------------------------------------------- Rajarshi Guha <[EMAIL PROTECTED]> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 ------------------------------------------------------------------- "whois awk?", sed Grep. ------------------------------------------------------------------------- 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
