Package org.openscience.cdk.io

Examples of org.openscience.cdk.io.MDLReader

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        return results;       
      } else if("text/plain".equals(type) && "Name did not parse!".equals(new BufferedReader(new InputStreamReader(conn.getInputStream())).readLine())) {
        // Failure from SimpleOPSINServlet
        return null;
      } else if("chemical/x-mdl-molfile".equals(type)) {
        MDLReader mdlr = new MDLReader(conn.getInputStream());
        IMolecule outputMol = (IMolecule)mdlr.read(new Molecule());
        StructureConverter.configureMolecule(outputMol);
        String smiles = generator.createSMILES(outputMol);
        String inchi = ConverterToInChI.getInChI(outputMol);
        Results results = new Results(smiles, inchi, null);
        return results; 
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      //proc.waitFor();
      /* This loop seems to work better under windows than proc.waitFor(), which hangs */
     
      //System.out.println(tmpMolFile.getAbsolutePath());
     
      IMolecule mol = (IMolecule)new MDLReader(new InputStreamReader(new FileInputStream(tmpMolFile), "UTF-8")).read(new Molecule());
     
      //System.out.println(FileTools.readTextFile(tmpMolFile));
     
      tmpMolFile.delete();
      tmpInChIAuxFile.delete();
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    super(new ChemModel(), 0, 0, true, false, null);

    // Load the structure
    StringReader reader = new StringReader(structure);

    MDLReader molReader = new MDLReader(reader);
    ChemModel chemModel = new ChemModel();
    chemModel = (ChemModel) molReader.read(chemModel);

    setChemModel(chemModel);

  }
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                int x;
                    while((x=sbis.read())!=-1){
                        sb.append((char)x);
                    }
                    reader = new MDLReader(new StringReader(sb.toString()));
        } catch (UnsupportedFlavorException e1) {
          e1.printStackTrace();
        } catch (IOException e1) {
          e1.printStackTrace();
              } catch (Exception e1) {
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        JTextComponentFixture text = dialog.textBox();
        text.setText(file.toString());
        JButtonFixture okbutton = new JButtonFixture(dialog.robot, dialog.robot.finder().find(new ButtonTextComponentMatcher("Save")));
        okbutton.click();
        //not the bug, but still worth testing
        MDLReader reader = new MDLReader(new FileInputStream(file));
        IAtomContainer mol = (IAtomContainer)reader.read(DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class));
        Assert.assertEquals(panel.getChemModel().getMoleculeSet().getAtomContainer(0).getAtomCount(), mol.getAtomCount());
        Assert.assertEquals(panel.getChemModel().getMoleculeSet().getAtomContainer(0).getBondCount(), mol.getBondCount());
        applet.menuItem("new").click();
        applet.button("hexagon").click();
        applet.click();
        applet.button("bondTool").click();
        Point2d moveto=getAtomPoint(panel,0);   
        applet.panel("renderpanel").robot.click(applet.panel("renderpanel").component(), new Point((int)moveto.x,(int)moveto.y), MouseButton.LEFT_BUTTON,1);
        applet.menuItem("saveAs").click();
        dialog = applet.dialog();
        combobox = dialog.robot.finder().find(new ComboBoxTextComponentMatcher("org.openscience.jchempaint.io.JCPFileFilter"));
        combobox.setSelectedItem(combobox.getItemAt(SAVE_AS_MOL_COMBOBOX_POS));
        text = dialog.textBox();
        file=new File(System.getProperty("java.io.tmpdir")+File.separator+"test2.mol");
        if(file.exists())
            file.delete();
        text.setText(file.toString());
        okbutton = new JButtonFixture(dialog.robot, dialog.robot.finder().find(new ButtonTextComponentMatcher("Save")));
        okbutton.click();
        //not the bug, but still worth testing
        reader = new MDLReader(new FileInputStream(file));
        mol = (IAtomContainer)reader.read(DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class));
        Assert.assertEquals(panel.getChemModel().getMoleculeSet().getAtomContainer(0).getAtomCount(), mol.getAtomCount());
        Assert.assertEquals(panel.getChemModel().getMoleculeSet().getAtomContainer(0).getBondCount(), mol.getBondCount());
        //ok, now the critical bits - open mol1
        file=new File(System.getProperty("java.io.tmpdir")+File.separator+"test1.mol");
        applet.menuItem("open").click();
        dialog = applet.dialog();
        text = dialog.textBox();
        text.setText(file.toString());
        okbutton = new JButtonFixture(dialog.robot, dialog.robot.finder().find(new ButtonTextComponentMatcher("Open")));
        okbutton.click();
        //"save as" mol1
        file.delete();
        applet.menuItem("saveAs").click();
        dialog = applet.dialog();
        combobox = dialog.robot.finder().find(new ComboBoxTextComponentMatcher("org.openscience.jchempaint.io.JCPFileFilter"));
        combobox.setSelectedItem(combobox.getItemAt(SAVE_AS_MOL_COMBOBOX_POS));
        text = dialog.textBox();
        text.setText(file.toString());
        okbutton = new JButtonFixture(dialog.robot, dialog.robot.finder().find(new ButtonTextComponentMatcher("Save")));
        okbutton.click();
        //open mol2
        file=new File(System.getProperty("java.io.tmpdir")+File.separator+"test2.mol");
        applet.menuItem("open").click();
        dialog = applet.dialog();
        text = dialog.textBox();
        text.setText(file.toString());
        okbutton = new JButtonFixture(dialog.robot, dialog.robot.finder().find(new ButtonTextComponentMatcher("Open")));
        okbutton.click();
        //save should write to mol2, ie mol1=6 atoms, mol2=7atoms
        applet.menuItem("save").click();
        file=new File(System.getProperty("java.io.tmpdir")+File.separator+"test1.mol");
        reader = new MDLReader(new FileInputStream(file));
        mol = (IAtomContainer)reader.read(DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class));
        Assert.assertEquals(6, mol.getAtomCount());
        file=new File(System.getProperty("java.io.tmpdir")+File.separator+"test2.mol");
        reader = new MDLReader(new FileInputStream(file));
        mol = (IAtomContainer)reader.read(DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class));
        Assert.assertEquals(7, mol.getAtomCount());
        restoreModelToEmpty();
  }
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        combobox.setSelectedItem(combobox.getItemAt(SAVE_AS_MOL_COMBOBOX_POS));
        JTextComponentFixture text = dialog.textBox();
        text.setText(file.toString());
        JButtonFixture savebutton = new JButtonFixture(dialog.robot, dialog.robot.finder().find(new ButtonTextComponentMatcher("Save")));
        savebutton.click();
        MDLReader reader = new MDLReader(new FileInputStream(file));
        IAtomContainer mol = (IAtomContainer)reader.read(DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class));
        Assert.assertEquals("aaa",(String)mol.getProperty(CDKConstants.TITLE));
  }
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              combobox.setSelectedIndex(index);
        JTextComponentFixture text = dialog.textBox();
        text.setText(file.toString());
        JButtonFixture okbutton = new JButtonFixture(dialog.robot, dialog.robot.finder().find(new ButtonTextComponentMatcher("Save")));
        okbutton.click();
        MDLReader reader = null;
        try {
          reader = new MDLReader(new FileInputStream(file));
        } catch (Exception e) {
          // TODO Auto-generated catch block
          Assert.fail("File not found.");
          return;
        }
        IAtomContainer mol = (IAtomContainer)reader.read(DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class));
        JPanelFixture jcppanel=applet.panel("appletframe");
        JChemPaintPanel panel = (JChemPaintPanel)jcppanel.target;
        Assert.assertEquals(panel.getChemModel().getMoleculeSet().getAtomContainer(0).getAtomCount(), mol.getAtomCount());
        Assert.assertEquals(panel.getChemModel().getMoleculeSet().getAtomContainer(0).getBondCount(), mol.getBondCount());
    }
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