Package org.openscience.cdk.interfaces

Examples of org.openscience.cdk.interfaces.IChemObject


        Clipboard sysClip = jcpPanel.getToolkit().getSystemClipboard();

        if ("copy".equals(type)) {
            handleSystemClipboard(sysClip);
            IAtom atomInRange = null;
            IChemObject object = getSource(e);
            logger.debug("Source of call: ", object);
            if (object instanceof IAtom) {
                atomInRange = (IAtom) object;
            } else {
                atomInRange = renderModel.getHighlightedAtom();
            }
            if (atomInRange != null) {
                IAtomContainer tocopyclone =
                    atomInRange.getBuilder().newInstance(IAtomContainer.class);
                try {
          tocopyclone.addAtom((IAtom) atomInRange.clone());
        } catch (CloneNotSupportedException e1) {
          // TODO Auto-generated catch block
          e1.printStackTrace();
        }
                addToClipboard(sysClip, tocopyclone);
            }
            else if(renderModel.getHighlightedBond()!=null){
                IBond bond = renderModel.getHighlightedBond();
                if (bond != null) {
                    IAtomContainer tocopyclone =
                        bond.getBuilder().newInstance(IAtomContainer.class);
                    try {
                        tocopyclone.addAtom((IAtom) bond.getAtom(0).clone());
                        tocopyclone.addAtom((IAtom) bond.getAtom(1).clone());
                    } catch (CloneNotSupportedException e1) {
                        e1.printStackTrace();
                    }
                    tocopyclone.addBond(bond.getBuilder().newInstance(IBond.class,tocopyclone.getAtom(0), tocopyclone.getAtom(1), bond.getOrder()));
                    addToClipboard(sysClip, tocopyclone);
                }
            }else if(renderModel.getSelection().getConnectedAtomContainer()!=null){
              addToClipboard(sysClip,
                  renderModel.getSelection().getConnectedAtomContainer());
            }else{
        addToClipboard(sysClip, JChemPaintPanel.getAllAtomContainersInOne(chemModel));
            }
        } else if ("copyAsSmiles".equals(type)) {
            handleSystemClipboard(sysClip);
            try {
               
                final IAtomContainer selection = renderModel.getSelection().getConnectedAtomContainer();
               
                if(selection!=null){
                    final IChemObjectBuilder bldr = selection.getBuilder();
                    IChemModel selectionModel = bldr.newInstance(IChemModel.class);
                    selectionModel.setMoleculeSet(bldr.newInstance(IAtomContainerSet.class));
                    selectionModel.getMoleculeSet().addAtomContainer(selection);
                    sysClip.setContents(new SmilesSelection(CreateSmilesAction.getSmiles(selectionModel)), null);
                }else{
                    sysClip.setContents(new SmilesSelection(CreateSmilesAction.getSmiles(chemModel)),null);
                }
            } catch (Exception e1) {
                e1.printStackTrace();
            }
        } else if ("eraser".equals(type)) {
            RemoveModule newActiveModule = new RemoveModule(jcpPanel.get2DHub());
            newActiveModule.setID(type);
            jcpPanel.get2DHub().setActiveDrawModule(newActiveModule);
            IAtom atomInRange = null;
            IBond bondInRange = null;
            IChemObject object = getSource(e);
            logger.debug("Source of call: ", object);
            if (object instanceof IAtom) {
                atomInRange = (IAtom) object;
            } else {
                atomInRange = renderModel.getHighlightedAtom();
            }
            if (object instanceof IBond) {
                bondInRange = (IBond) object;
            } else {
                bondInRange = renderModel.getHighlightedBond();
            }
            if (atomInRange != null) {
                jcpPanel.get2DHub().removeAtom(atomInRange);
                renderModel.setHighlightedAtom(null);
            } else if (bondInRange != null) {
                jcpPanel.get2DHub().removeBond(bondInRange);
            } else if(renderModel.getSelection()!=null && renderModel.getSelection().getConnectedAtomContainer()!=null){
                IChemObjectSelection selection = renderModel.getSelection();
                IAtomContainer selected = selection.getConnectedAtomContainer();
                jcpPanel.get2DHub().deleteFragment(selected);
                renderModel.setSelection(new LogicalSelection(
                        LogicalSelection.Type.NONE));
                jcpPanel.get2DHub().updateView();
            }
        } else if(type.indexOf("pasteTemplate")>-1){
            //if templates are shown, we extract the tab to show if any
            String templatetab="";
            if(type.indexOf("_")>-1){
                templatetab=type.substring(type.indexOf("_")+1);
            }
            TemplateBrowser templateBrowser = new TemplateBrowser(templatetab);
            if(templateBrowser.getChosenmolecule()!=null){
                scaleStructure(templateBrowser.getChosenmolecule());
                insertStructure(templateBrowser.getChosenmolecule(), renderModel);
                jcpPanel.getRenderPanel().setZoomWide(true);
                jcpPanel.get2DHub().getRenderer().getRenderer2DModel().setZoomFactor(1);
            }
        } else if ("paste".equals(type)) {
            handleSystemClipboard(sysClip);
            Transferable transfer = sysClip.getContents( null );
            ISimpleChemObjectReader reader = null;
            String content=null;
           
            if (supported(transfer, molFlavor) ) {
                StringBuffer sb = new StringBuffer();
              try {
                    //StringBufferInputStream sbis=null;
          //sbis = (StringBufferInputStream) transfer.getTransferData(molFlavor);

                    StringReader sbis=null;
          sbis = (StringReader) transfer.getTransferData(molFlavor);

               
                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) {
                  reader = new RGroupQueryReader(new StringReader(sb.toString()));
                }

            } else if (supported(transfer, DataFlavor.stringFlavor) ) {
                try {
                    content = (String) transfer.getTransferData(DataFlavor.stringFlavor);
                    reader = new ReaderFactory().createReader(new StringReader(content));
                    //System.out.println(reader.getClass());
                } catch (Exception e1) {
                    e1.printStackTrace();
                }
            }

            // if looks like CML - InputStream required. Reader throws error.
            if(content!=null && content.indexOf("cml")>-1) {
                reader = new CMLReader(new ByteArrayInputStream(content.getBytes()));
            }

            IAtomContainer toPaste = null;
            boolean rgrpQuery=false;
            if (reader != null) {
                IAtomContainer readMolecule =
                    chemModel.getBuilder().newInstance(IAtomContainer.class);
                try {
                    if (reader.accepts(IAtomContainer.class)) {
                        toPaste = (IAtomContainer) reader.read(readMolecule);
                    } else if (reader.accepts(ChemFile.class)) {
                        toPaste = readMolecule;
                        IChemFile file = (IChemFile) reader.read(new ChemFile());
                        for (IAtomContainer ac :
                            ChemFileManipulator.getAllAtomContainers(file)) {
                            toPaste.add(ac);

                        }
                  } else if (reader.accepts(RGroupQuery.class)) {
                rgrpQuery=true;
                    IRGroupQuery rgroupQuery = (RGroupQuery) reader.read(new RGroupQuery(DefaultChemObjectBuilder.getInstance()));
                chemModel = new ChemModel();
                RGroupHandler rgHandler =  new RGroupHandler(rgroupQuery, this.jcpPanel);
                this.jcpPanel.get2DHub().setRGroupHandler(rgHandler);
                chemModel.setMoleculeSet(rgHandler.getMoleculeSet(chemModel));
                rgHandler.layoutRgroup();
               
                  }

                } catch (CDKException e1) {
                    e1.printStackTrace();
                }
            }

            //Attempt SMILES or InChI if no reader is found for content.
            if(rgrpQuery!=true && toPaste == null &&
                    supported(transfer, DataFlavor.stringFlavor)) {
                try{
                    if (content.toLowerCase().indexOf("inchi")>-1 ) {
                        toPaste = InChITool.parseInChI(content);
                    }
                    else {   
                        SmilesParser sp = new SmilesParser(
                                DefaultChemObjectBuilder.getInstance());
                        toPaste = sp.parseSmiles(
                                ((String) transfer.getTransferData(
                                        DataFlavor.stringFlavor)).trim());
                        toPaste = new FixBondOrdersTool().kekuliseAromaticRings(toPaste);

                        IAtomContainerSet mols = ConnectivityChecker.partitionIntoMolecules(toPaste);
                        for(int i=0;i<mols.getAtomContainerCount();i++)
                        {
                            StructureDiagramGenerator sdg =
                                new StructureDiagramGenerator((IAtomContainer)mols.getAtomContainer(i));

                            sdg.setTemplateHandler(
                                    new TemplateHandler(toPaste.getBuilder())
                            );
                            sdg.generateCoordinates();
                        }
                        //SMILES parser sets valencies, unset
                        for(int i=0;i<toPaste.getAtomCount();i++){
                            toPaste.getAtom(i).setValency(null);
                        }
                    }
                } catch (Exception ex) {
                    jcpPanel.announceError(ex);
                    ex.printStackTrace();
                }
            }
           
            if (toPaste != null || rgrpQuery==true) {
                jcpPanel.getRenderPanel().setZoomWide(true);
                jcpPanel.get2DHub().getRenderer().getRenderer2DModel().setZoomFactor(1);
                if ( rgrpQuery==true) {
                  this.jcpPanel.setChemModel(chemModel);
                }
                else {
                  scaleStructure(toPaste);
                  insertStructure(toPaste, renderModel);
                }
            }
            else{
                JOptionPane.showMessageDialog(jcpPanel, GT.get("The content you tried to copy could not be read to any known format"), GT.get("Could not process content"), JOptionPane.WARNING_MESSAGE);
            }

        } else if (type.equals("cut")) {
            handleSystemClipboard(sysClip);
            IAtom atomInRange = null;
            IBond bondInRange = null;
            IChemObject object = getSource(e);
            logger.debug("Source of call: ", object);
            if (object instanceof IAtom) {
                atomInRange = (IAtom) object;
            } else {
                atomInRange = renderModel.getHighlightedAtom();
            }
            if (object instanceof IBond) {
                bondInRange = (IBond) object;
            } else {
                bondInRange = renderModel.getHighlightedBond();
            }
            IAtomContainer tocopyclone =
                jcpPanel.getChemModel().getBuilder().newInstance(IAtomContainer.class);
            if (atomInRange != null) {
                tocopyclone.addAtom(atomInRange);
                jcpPanel.get2DHub().removeAtom(atomInRange);
                renderModel.setHighlightedAtom(null);
            } else if (bondInRange != null) {
                tocopyclone.addBond(bondInRange);
                jcpPanel.get2DHub().removeBond(bondInRange);
            }else if(renderModel.getSelection()!=null && renderModel.getSelection().getConnectedAtomContainer()!=null){
                IChemObjectSelection selection = renderModel.getSelection();
                IAtomContainer selected = selection.getConnectedAtomContainer();
                tocopyclone.add(selected);
                jcpPanel.get2DHub().deleteFragment(selected);
                renderModel.setSelection(new LogicalSelection(
                        LogicalSelection.Type.NONE));
                jcpPanel.get2DHub().updateView();
            }
      if(tocopyclone.getAtomCount()>0 || tocopyclone.getBondCount()>0)
          addToClipboard(sysClip, tocopyclone);
     
        }else if (type.equals("selectAll")) {
            ControllerHub hub = jcpPanel.get2DHub();
            IChemObjectSelection allSelection =
                new LogicalSelection(LogicalSelection.Type.ALL);

            allSelection.select(hub.getIChemModel());
            renderModel.setSelection(allSelection);
            SelectSquareModule succusorModule = new SelectSquareModule(hub);
            succusorModule.setID("select");
            MoveModule newActiveModule = new MoveModule(hub, succusorModule);
            newActiveModule.setID("move");
            hub.setActiveDrawModule(newActiveModule);

        } else if (type.equals("selectFromChemObject")) {

          // FIXME: implement for others than Reaction, Atom, Bond
          IChemObject object = getSource(e);
            if (object instanceof IAtom) {
                SingleSelection<IAtom> container = new SingleSelection<IAtom>((IAtom)object);
                renderModel.setSelection(container);
            }
            else if (object instanceof IBond) {
                SingleSelection<IBond> container = new SingleSelection<IBond>((IBond)object);
                renderModel.setSelection(container);
            }
            else if (object instanceof IReaction) {
                IAtomContainer wholeModel =
                    jcpPanel.getChemModel().getBuilder().newInstance(IAtomContainer.class);
                for (IAtomContainer container :
                    ReactionManipulator.getAllAtomContainers(
                            (IReaction)object)) {
                    wholeModel.add(container);
                }
                ShapeSelection container = new RectangleSelection();
                for (IAtom atom : wholeModel.atoms()) {
                    container.atoms.add(atom);
                }
                for (IBond bond : wholeModel.bonds()) {
                    container.bonds.add(bond);
                }
                renderModel.setSelection(container);
            }
            else {
                logger.warn("Cannot select everything in : ", object);
            }
        } else if (type.equals("selectReactionReactants")) {
            IChemObject object = getSource(e);
            if (object instanceof IReaction) {
                IReaction reaction = (IReaction) object;
                IAtomContainer wholeModel =
                    jcpPanel.getChemModel().getBuilder().newInstance(IAtomContainer.class);
                for (IAtomContainer container :
                    MoleculeSetManipulator.getAllAtomContainers(
                            reaction.getReactants())) {
                        wholeModel.add(container);
                }
                ShapeSelection container = new RectangleSelection();
                for (IAtom atom : wholeModel.atoms()) {
                    container.atoms.add(atom);
                }
                for (IBond bond : wholeModel.bonds()) {
                    container.bonds.add(bond);
                }
                renderModel.setSelection(container);
            }
            else {
                logger.warn("Cannot select reactants from : ", object);
            }
        } else if (type.equals("selectReactionProducts")) {
            IChemObject object = getSource(e);
            if (object instanceof IReaction) {
                    IReaction reaction = (IReaction) object;
                    IAtomContainer wholeModel =
                        jcpPanel.getChemModel().getBuilder().newInstance(IAtomContainer.class);
                for (IAtomContainer container :
View Full Code Here


  private static final long serialVersionUID = -598284013998335002L;

  public void actionPerformed(ActionEvent event) {
        logger.debug("Converting to: ", type);
        IChemObject object = getSource(event);
        Iterator<IAtom> atomsInRange = null;
    if (object == null){
      //this means the main menu was used
      if(jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().isFilled())
        atomsInRange=jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().getConnectedAtomContainer().atoms().iterator();
View Full Code Here

  }

  private void popupMenuForNearestChemObject(Point2d mouseCoords) {
      Renderer renderer = rendererPanel.getRenderer();
      JChemPaintRendererModel rendererModel = renderer.getRenderer2DModel();
    IChemObject objectInRange = rendererModel.getHighlightedAtom();
   
    if (objectInRange == null)
      objectInRange = rendererModel.getHighlightedBond();
   
    //look if we are in a reaction box
    IReactionSet reactionSet =
        rendererPanel.getChemModel().getReactionSet();
   
    if (objectInRange == null && reactionSet != null
                && reactionSet.getReactionCount() > 0) {
     
      for(int i=0;i<reactionSet.getReactionCount();i++){
        Rectangle reactionbounds =
            renderer.calculateDiagramBounds(reactionSet.getReaction(i));
        if (reactionbounds.contains(mouseCoords.x, mouseCoords.y))
          objectInRange = reactionSet.getReaction(i);
      }
    }
   
    if (objectInRange == null)
      objectInRange = chemModelRelay.getIChemModel();
    if (objectInRange instanceof IAtom)
        lastAtomPopupedFor = (IAtom)objectInRange;
   
    JChemPaintPopupMenu popupMenu = getPopupMenu(objectInRange.getClass(), objectInRange);
    if (popupMenu != null) {
      popupMenu.setSource(objectInRange);
      logger.debug("Set popup menu source to: ", objectInRange);
      popupMenu.show(rendererPanel, (int)mouseCoords.x, (int)mouseCoords.y);
    } else {
View Full Code Here

   * @see org.openscience.jchempaint.action.JCPAction#actionPerformed(java.awt.event.ActionEvent)
   */
  public void actionPerformed(ActionEvent event)
  {
    System.out.println("action iz "+type);
    IChemObject eventSource = getSource(event);

    IChemObjectSelection selection = jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection();
    if(selection ==null || !selection.isFilled()
        &&(type.equals("setRoot")||type.equals("setSubstitute")) ) {
      JOptionPane.showMessageDialog(jcpPanel, GT.get("You have not selected any atoms or bonds."));
View Full Code Here

            if(jcpPanel.isAlreadyAFile()!=null)
                chooser.setSelectedFile(jcpPanel.isAlreadyAFile());

            int returnVal = chooser.showSaveDialog(jcpPanel);

            IChemObject object = getSource(event);
            FileFilter currentFilter = chooser.getFileFilter();
            if(returnVal==JFileChooser.CANCEL_OPTION){
                ready=0;
                wasCancelled = true;
            }
View Full Code Here

  private static final long serialVersionUID = -8502905723573311893L;
 
  public void actionPerformed(ActionEvent event)
  {
    logger.debug("About to change valence of relevant atom!");
    IChemObject object = getSource(event);
    logger.debug("Source of call: ", object);
        Iterator<IAtom> atomsInRange = null;
    if (object == null){
      //this means the main menu was used
      if(jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().isFilled())
View Full Code Here

  private static final long serialVersionUID = 1898335761308427006L;
 
  public void actionPerformed(ActionEvent event) {
        logger.debug("Converting to radical: ", type);
        IChemObject object = getSource(event);
        Iterator<IAtom> atomsInRange = null;
    if (object == null){
      //this means the main menu was used
      if(jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().isFilled())
        atomsInRange=jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().getConnectedAtomContainer().atoms().iterator();
View Full Code Here

        ChangeFormalChargeModule newActiveModule = new ChangeFormalChargeModule(jcpPanel.get2DHub(), charge);
        newActiveModule.setID(action);
        jcpPanel.get2DHub().setActiveDrawModule(newActiveModule);
    logger.debug("About to change atom type of relevant atom!");
    Iterator<IAtom> atomsInRange = null;
    IChemObject object = getSource(event);
    logger.debug("Source of call: ", object);
    if (object == null){
      //this means the main menu was used
      if(jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection()!=null && jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().isFilled())
        atomsInRange=jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().getConnectedAtomContainer().atoms().iterator();
View Full Code Here

public class EditChemObjectPropsAction extends JCPAction {

  private static final long serialVersionUID = 7123137508085454087L;

  public void actionPerformed(ActionEvent event) {
    IChemObject object = getSource(event);
    logger.debug("Showing object properties for: ", object);
    ChemObjectEditor editor = null;
    if (object instanceof IPseudoAtom) {
      editor = new PseudoAtomEditor();
    }
View Full Code Here

  private static final long serialVersionUID = -7625810885316702776L;

  public void actionPerformed(ActionEvent event)
  {
    IChemObject object = getSource(event);

    logger.debug("CreateReaction action");
    IChemModel model = jcpPanel.getChemModel();
    IReactionSet reactionSet = model.getReactionSet();
    if (reactionSet == null)
    {
      reactionSet = model.getBuilder().newInstance(IReactionSet.class);
    }
    IAtomContainer container = null;
    if (object instanceof IAtom)
    {
      container = ChemModelManipulator.getRelevantAtomContainer(model, (IAtom) object);
    } else if(object instanceof IBond)
    {
      container = ChemModelManipulator.getRelevantAtomContainer(model, (IBond) object);
    } else
    {
      logger.error("Cannot add to reaction object of type: " + object.getClass().getName());
    }
    if (container == null)
    {
      logger.error("Cannot find container to add object to!");
    } else
View Full Code Here

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