jchempaintabstractapplet.java

化学图形处理软件

	
	/**
	 * loads a molecule from url or smiles
	 */
	protected void loadModelFromParam() {
		URL fileURL = null;
		String smiles=null;
		try {
			URL documentBase = getDocumentBase();
			String load = getParameter("load");
			if (load != null)
				fileURL = new URL(documentBase, load);
			smiles = getParameter("smiles");
			} catch (Exception exception) {
			System.out.println("Cannot load model: " + exception.toString());
			exception.printStackTrace();
		}
		loadModelFromUrl(fileURL);
		if(smiles!=null)
			loadModelFromSmiles(smiles);
	}
	
	/**
	 * Loads a molecule from a smiles into jcp
	 * 
	 * @param fileURL
	 */
	public void loadModelFromSmiles(String smiles) {
		if (smiles != null) {
			try {
				SmilesParser sp=new SmilesParser(DefaultChemObjectBuilder.getInstance());
				IMolecule mol = sp.parseSmiles(smiles);
				StructureDiagramGenerator sdg = new StructureDiagramGenerator();
				sdg.setMolecule(mol);
				sdg.generateCoordinates(new Vector2d(0, 1));
				mol=sdg.getMolecule();
				IChemModel chemModel = DefaultChemObjectBuilder.getInstance().newChemModel();
				chemModel.setMoleculeSet(DefaultChemObjectBuilder.getInstance().newMoleculeSet());
				chemModel.getMoleculeSet().addAtomContainer(mol);
				theModel = new JChemPaintModel(chemModel);
			} catch (Exception exception) {
				System.out.println("Cannot parse model: " + exception.toString());
				exception.printStackTrace();
			}
		}else{
			theModel=new JChemPaintModel();
		}
		initPanelAndModel(theJcpp);
	}

	/**
	 * Loads a molecule from a url into jcp
	 * 
	 * @param fileURL
	 */
	public void loadModelFromUrl(URL fileURL) {
		if (fileURL != null) {
			try {
				InputStreamReader isReader = new InputStreamReader(fileURL.openStream());
				IChemObjectReader reader = new ReaderFactory().createReader(isReader);
				ChemModel chemModel = (ChemModel) reader.read(new ChemModel());
        
				int count=0;
				for(int i=0;i<chemModel.getMoleculeSet().getMoleculeCount();i++){
					for(int k=0;k<chemModel.getMoleculeSet().getMolecule(i).getAtomCount();k++){
						chemModel.getMoleculeSet().getMolecule(i).getAtom(k).setProperty("OriginalNumber", new Integer(count));
						count++;
					}
				}
				theModel = new JChemPaintModel(chemModel);
			} catch (Exception exception) {
				System.out.println("Cannot parse model: " + exception.toString());
				exception.printStackTrace();
			}
		}else{
			theModel=new JChemPaintModel();
		}
		initPanelAndModel(theJcpp);
	}
	
	public void start() {
		//Parameter parsing goes here
		loadModelFromParam();
		String atomNumbers=getParameter("atomNumbersVisible");
		if(atomNumbers!=null){
			if(atomNumbers.equals("true"))
				theJcpp.getJChemPaintModel().getRendererModel().setDrawNumbers(true);
		}
		String background = getParameter("background");
		if(background!=null){
			theJcpp.getJChemPaintModel().getRendererModel().setBackColor(new Color(Integer.parseInt(background)));
		}
	}
	
	public void init(){
		prepareExternalFrame();
	}

	public void stop() {
	}
	/**
	 * @return Returns the theJcpp.
	 */
	public JChemPaintPanel getTheJcpp() {
		return theJcpp;
	}
	/**
	 * @param theJcpp The theJcpp to set.
	 */
	public void setTheJcpp(JChemPaintPanel theJcpp) {
		this.theJcpp = theJcpp;
	}
  
  public void setTheModel(JChemPaintModel theModel){
    this.theModel=theModel;
  }
  
  public String getMolFile() throws Exception{
    StringWriter sw = new StringWriter();
    MDLWriter mdlwriter = new MDLWriter(sw);
    mdlwriter.dontWriteAromatic();
    mdlwriter.write(theJcpp.getJChemPaintModel().getChemModel());
    return(sw.toString());
  }
  
  
  public String getSmiles(){
		ChemModel model = (ChemModel) theJcpp.getJChemPaintModel().getChemModel();
        SmilesGenerator generator = new SmilesGenerator();
		Iterator containers = ChemModelManipulator.getAllAtomContainers(model).iterator();
		String SMILES = "";
		while (containers.hasNext()) {
			IMolecule molecule = model.getBuilder().newMolecule((IAtomContainer)containers.next());
			SMILES += generator.createSMILES(molecule);
			if (containers.hasNext()) SMILES += ".";
		}
		return SMILES;
  }

  
  public String getSmilesChiral() throws Exception{
		ChemModel model = (ChemModel) theJcpp.getJChemPaintModel().getChemModel();
        Iterator containers = ChemModelManipulator.getAllAtomContainers(model).iterator();
		String SMILES = "";
		while (containers.hasNext()) {
			IAtomContainer container = (IAtomContainer)containers.next();
			IMolecule moleculewithh = model.getBuilder().newMolecule(container);
			new HydrogenAdder().addExplicitHydrogensToSatisfyValency(moleculewithh);
			double bondLength = GeometryTools.getBondLengthAverage(container,theJcpp.getJChemPaintModel().getRendererModel().getRenderingCoordinates());
			new HydrogenPlacer().placeHydrogens2D(moleculewithh, bondLength);
			boolean[] bool=new boolean[moleculewithh.getBondCount()];
			SmilesGenerator sg = new SmilesGenerator();
			for(int i=0;i<bool.length;i++){
				if (sg.isValidDoubleBondConfiguration(moleculewithh, moleculewithh.getBond(i)))
					bool[i]=true;
			}
			SMILES += sg.createSMILES(moleculewithh);
			if (containers.hasNext()) SMILES += ".";
		}
		return SMILES;
  }

  /**
   * This method sets a structure in the editor and leaves the old one.
   * This method replaces all \n characters with the system line separator. This can be used when setting a mol file in an applet
   * without knowing which platform the applet is running on.
   * 
   * @param mol The mol file to set (V2000)
   * @throws Exception
   */
  public void addMolFileWithReplace(String mol) throws Exception{
	StringBuffer newmol=new StringBuffer();
    int s = 0;
    int e = 0;
    while ((e = mol.indexOf("\\n", s)) >= 0) {
      newmol.append(mol.substring(s, e));
      newmol.append(System.getProperty("file.separator"));
      s = e + 1;
    }
    newmol.append(mol.substring(s));
    MDLV2000Reader reader=new MDLV2000Reader(new StringReader(newmol.toString()));
    IMolecule cdkmol=(IMolecule)reader.read(DefaultChemObjectBuilder.getInstance().newMolecule());
    new InsertTextPanel(theJcpp,null).generateModel(cdkmol);
    repaint();
  }


  /**
   * This method sets a new structure in the editor and removes the old one.
   * This method replaces all \n characters with the system line separator. This can be used when setting a mol file in an applet
   * without knowing which platform the applet is running on.
   * 
   * @param mol The mol file to set
   * @throws Exception
   */
  public void setMolFileWithReplace(String mol) throws Exception{
	StringBuffer newmol=new StringBuffer();
    int s = 0;
    int e = 0;
    while ((e = mol.indexOf("\\n", s)) >= 0) {
      newmol.append(mol.substring(s, e));
      newmol.append(System.getProperty("file.separator"));
      s = e + 1;
    }
    newmol.append(mol.substring(s));
    theJcpp.showChemFile(new StringReader(newmol.toString()));
    repaint();
  }
  
  public void setMolFile(String mol) throws Exception{
    theJcpp.showChemFile(new StringReader(mol));
    repaint();
  }

  
  public void clear() throws Exception{
	  theModel.getChemModel().setMoleculeSet(new MoleculeSet());
	  repaint();
  }

  public void selectAtom(int atom){
    theJcpp.getJChemPaintModel().getRendererModel().setExternalHighlightColor(Color.RED);
    IAtomContainer ac=theJcpp.getJChemPaintModel().getChemModel().getMoleculeSet().getBuilder().newAtomContainer();
    ac.addAtom(theJcpp.getJChemPaintModel().getChemModel().getMoleculeSet().getMolecule(0).getAtom(atom));
    theJcpp.getJChemPaintModel().getRendererModel().setExternalSelectedPart(ac);
    getTheJcpp().repaint();
  }

	/**
	 * @return Returns the jexf.
	 */
	private JExternalFrame getJexf() {
		if (jexf == null)
			jexf = new JExternalFrame();
		return jexf;
	}

	/**
	 * sets title for external frame
	 * adds listener for double clicks in order to open external frame
	 */
	private void prepareExternalFrame() { 
		if (this.getParameter("name") != null)
			getJexf().setTitle(this.getParameter("name"));
		getTheJcpp().getDrawingPanel().addMouseListener(new MouseAdapter() {
			public void mousePressed(MouseEvent e) {
				if (e.getButton() == 1 && e.getClickCount() == 2)
					if (!getJexf().isShowing()) {
						getJexf().show(getTheJcpp());
				}	
			}
		});
	}
}