Ejemplo n.º 1
0
  /*
   * Creates a structure image based on a MOL string. The image rendering is
   * done with CDK.
   */
  public final Image getImage4MOL(IAtomContainer molAC) throws Exception {

    // creates CDK Molecule object and get the renderer
    // Molecule   mol      = prepareMolecule(molfile);
    IMolecule molSource = new Molecule(molAC);
    StructureDiagramGenerator sdg = new StructureDiagramGenerator();
    sdg.setMolecule(molSource);
    sdg.generateCoordinates();
    IMolecule mol = sdg.getMolecule();

    Java2DRenderer renderer = prepareRenderer(mol);

    BufferedImage bimage = null;
    try {

      // paint molecule to java.awt.BufferedImage
      bimage = new BufferedImage(vRenderSizeX, vRenderSizeY, BufferedImage.TYPE_BYTE_INDEXED);
      Graphics2D g = bimage.createGraphics();
      g.setBackground(Color.WHITE);
      g.setColor(Color.WHITE);
      g.fillRect(0, 0, vRenderSizeX, vRenderSizeY);
      renderer.paintMolecule(mol, g, new Rectangle(0, 0, vRenderSizeX, vRenderSizeY));

    } catch (Exception e) {
      e.printStackTrace();
      throw new Exception("Rendering of structure(s) failed");
    }

    return bimage;
  }
Ejemplo n.º 2
0
  /*
   * Creates a structure PDF based on a MOL string
   */
  public final void writeMOL2PDFFile(IMolecule molSource, File epsFile) throws Exception {

    // creates CDK Molecule object and get the renderer
    // Molecule   mol      = prepareMolecule(MOLString);

    StructureDiagramGenerator sdg = new StructureDiagramGenerator();
    sdg.setMolecule(molSource);
    sdg.generateCoordinates();
    IMolecule mol = sdg.getMolecule();

    Java2DRenderer renderer = prepareRenderer(mol);

    try {

      // paint molecule to java.awt.BufferedImage
      VectorGraphics vg = new PDFGraphics2D(epsFile, new Dimension(vRenderSizeX, vRenderSizeY));

      Properties p = new Properties();
      p.setProperty("PageSize", "A5");
      vg.setProperties(p);
      vg.startExport();
      renderer.paintMolecule(mol, vg, new Rectangle(vRenderSizeX, vRenderSizeY));
      vg.endExport();
    } catch (Exception e) {
      e.printStackTrace();
      throw new Exception("PDF rendering of structure(s) failed");
    }
  }
Ejemplo n.º 3
0
  /*
   * Creates a structure gif on a MOL string
   */
  public final void writeMOL2GIFFile(IAtomContainer mol, String pngFile) throws Exception {

    BufferedImage bimage = null;

    try {
      bimage = (BufferedImage) getImage4MOL(mol);
      ImageIO.write(bimage, "gif", new File(this.folder + pngFile));

    } catch (Exception e) {
      e.printStackTrace();
      // throw new Exception("EPS rendering of structure(s) failed");
    }
  }
Ejemplo n.º 4
0
  private Java2DRenderer prepareRenderer(IMolecule mol) throws Exception {

    Renderer2DModel r2dm;
    Java2DRenderer renderer;
    Dimension imgSize;

    try {
      CDKHueckelAromaticityDetector.detectAromaticity(mol);
    } catch (CDKException cdke) {
      cdke.printStackTrace();
    }

    try {

      imgSize = new Dimension(vRenderSizeX, vRenderSizeY);

      r2dm = new Renderer2DModel();
      r2dm.setDrawNumbers(false);
      r2dm.showAtomTypeNames();
      r2dm.setBackgroundDimension(imgSize);
      r2dm.setBackColor(Color.WHITE);
      r2dm.setDrawNumbers(false);
      r2dm.setUseAntiAliasing(true);
      r2dm.setColorAtomsByType(true);
      r2dm.setShowImplicitHydrogens(true);
      r2dm.setShowExplicitHydrogens(this.showHydrogen);
      r2dm.setIsCompact(this.isCompact);
      r2dm.setShowReactionBoxes(false);
      r2dm.setKekuleStructure(false);
      r2dm.setBondWidth(3);

      // r2dm.setFont(new java.awt.Font("SansSerif", java.awt.Font.PLAIN, 14));

      renderer = new Java2DRenderer(r2dm);

      // 1200,900
      // create renderer to render MOLString into an java.awt.Image
      // renders 2D structures

    } catch (Exception e) {
      e.printStackTrace();
      throw new Exception("Creation of renderer failed");
    }

    return renderer;
  }
Ejemplo n.º 5
0
  public static void main(final String[] args) {

    //        String mf;
    //        String molfile;

    try {
      //            BufferedReader reader = new BufferedReader(new FileReader("renderTest.mol"));
      //            StringBuffer   sbuff  = new StringBuffer();
      //            String         line;
      //
      //            while ( (line = reader.readLine()) != null ) {
      //                sbuff.append(line + "\n");
      //            }
      //            reader.close();
      //            molfile = sbuff.toString();
      //            System.out.println(molfile);

      // the graph
      SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
      PubChemWebService pw = new PubChemWebService();
      String PCID = "1148";
      IAtomContainer container = pw.getSingleMol(PCID);
      container = AtomContainerManipulator.removeHydrogens(container);
      //            IAtomContainer container = sp.parseSmiles("OC1C(O)=COC(CO)C1(O)");

      // Render.Draw(container, "test");

      IMolecule test = new Molecule(container);
      StructureDiagramGenerator sdg = new StructureDiagramGenerator();
      sdg.setMolecule(test);
      sdg.generateCoordinates();
      IMolecule mol = sdg.getMolecule();

      // adds implicit H atoms to molecule
      //    		CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(mol.getBuilder());
      //    		for (IAtom atom : mol.atoms()) {
      //    			IAtomType type = matcher.findMatchingAtomType(mol, atom);
      //	    		AtomTypeManipulator.configure(atom, type);
      //			}
      //
      //    		CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(mol.getBuilder());
      //    		adder.addImplicitHydrogens(mol);
      //    		AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol);

      // detects aromaticity; used to display aromatic ring systems correctly
      CDKHueckelAromaticityDetector.detectAromaticity(mol);

      Render.Draw(mol, "test");

      DisplayStructureVector test12 =
          new DisplayStructureVector(200, 200, "/home/swolf/", true, true);
      // test12.writeMOL2PNGFile(mol, "test_cdk12.png");
      //    		test12.writeMOL2PDFFile(mol, new File("/home/swolf/test_cdk12.pdf"));
      test12.writeMOL2SVGFile(mol, new File("/home/swolf/" + PCID + ".svg"));

      // ChemRenderer crender = new ChemRenderer();
      // crender.writeMOL2PNGFile(mol, new File("/home/swolf/test_new.png"));
      // crender.writeMOL2EPSFile(mol, new File("/home/swolf/test_new.eps"));
      // crender.writeMOL2PDFFile(mol, new File("/home/swolf/test_new.pdf"));

      // crender.writeMOL2SVGFile(molfile,new File("Output.svg"));

    } catch (Exception e) {
      System.out.println("Error: " + e.getMessage() + ".");
      e.printStackTrace();
    }
  }