Package org.openscience.jchempaint.controller

Examples of org.openscience.jchempaint.controller.IChemModelRelay


        &&(type.equals("setRoot")||type.equals("setSubstitute")) ) {
      JOptionPane.showMessageDialog(jcpPanel, GT.get("You have not selected any atoms or bonds."));
      return;
    }

    IChemModelRelay hub = jcpPanel.get2DHub();
    boolean isNewRgroup=false;
    RGroupHandler rGroupHandler=null;
    Map<IAtom,IAtomContainer> existingAtomDistr = new HashMap<IAtom,IAtomContainer>();
    Map<IBond,IAtomContainer> existingBondDistr= new HashMap<IBond,IAtomContainer>();
    IAtomContainer existingRoot=null;
    Map<IAtom, Map<Integer, IBond>> existingRootAttachmentPoints = null;
    Map<RGroup, Map<Integer,IAtom>> existingRGroupApo=null;
    Map<Integer,RGroupList> existingRgroupLists =null;

    IRGroupQuery rgrpQuery=null;
    IAtomContainer molecule=null;

    /* User action: generate possible configurations for the R-group */
    if(type.equals("rgpGenerate")) {
      if((jcpPanel.get2DHub().getRGroupHandler()==null)) {
        JOptionPane.showMessageDialog(jcpPanel, GT.get("Please define an R-group (root and substituents) first."));
        return;
      }
            try {
        JFileChooser chooser = new JFileChooser();
        chooser.setCurrentDirectory(jcpPanel.getCurrentWorkDirectory());
        chooser.setFileView(new JCPFileView());
        chooser.showSaveDialog(jcpPanel);
        File outFile = chooser.getSelectedFile();
        System.out.println(outFile);
        List<IAtomContainer> molecules= jcpPanel.get2DHub().getRGroupHandler().getrGroupQuery().getAllConfigurations();
        if (molecules.size() > 0) {
          IAtomContainerSet molSet = molecules.get(0).getBuilder().newInstance(IAtomContainerSet.class);
          for (IAtomContainer mol : molecules) {
            molSet.addAtomContainer(mol);
          }
          SDFWriter sdfWriter = new SDFWriter(new FileWriter(outFile));
          sdfWriter.write(molSet);
          sdfWriter.close();
        }
      } catch (Exception e) {
        e.printStackTrace();
        JOptionPane.showMessageDialog(jcpPanel, GT.get("There was an error generating the configurations {0}", e.getMessage()));
        return;
      }
   
    }
    /* User action: advanced R-group logic */
    else if(type.equals("rgpAdvanced")) {

      if((jcpPanel.get2DHub().getRGroupHandler()==null)) {
        JOptionPane.showMessageDialog(jcpPanel, GT.get("Please define an R-group (root and substituent) first."));
        return;
      }
      jcpPanel.get2DHub().getRGroupHandler().cleanUpRGroup(jcpPanel.get2DHub().getChemModel().getMoleculeSet());
      ChemObjectEditor editor = new RGroupEditor(hub);
      editor.setChemObject((org.openscience.cdk.ChemObject)hub.getRGroupHandler().getrGroupQuery());
      ChemObjectPropertyDialog frame = new ChemObjectPropertyDialog(JOptionPane.getFrameForComponent(editor), jcpPanel.get2DHub(),editor);
      frame.pack();
      frame.setVisible(true);
      jcpPanel.get2DHub().updateView();
    }


    //FOLLOWING actions involve undo/redo

    else
    {

      /* User action: generate possible configurations for the R-group */
      if(type.equals("clearRgroup")) {
        if((jcpPanel.get2DHub().getRGroupHandler()==null)) {
          JOptionPane.showMessageDialog(jcpPanel, GT.get("There is no R-group defined"));
          return;
        }
        rGroupHandler=hub.getRGroupHandler();
        hub.unsetRGroupHandler();
        jcpPanel.get2DHub().updateView();

      }

      /* User has indicated that a certain atom in a substituent needs to become attachment point 1 or 2 */
      else if (type.startsWith("setAtomApoAction")) {
        rGroupHandler=hub.getRGroupHandler();
        IAtom apoAtom = (IAtom) eventSource;
        apoLoop:
          for (Iterator<Integer> rnumItr=rGroupHandler.getrGroupQuery().getRGroupDefinitions().keySet().iterator(); rnumItr.hasNext();) {
            for (RGroup rgrp: rGroupHandler.getrGroupQuery().getRGroupDefinitions().get(rnumItr.next()).getRGroups()) {
              if(rgrp.getGroup().contains(apoAtom)) {
                existingRGroupApo= new HashMap <RGroup,Map<Integer,IAtom>>();
                HashMap<Integer,IAtom> map = new HashMap<Integer,IAtom>();
                map.put(1, rgrp.getFirstAttachmentPoint());
                map.put(2, rgrp.getSecondAttachmentPoint());
                existingRGroupApo.put(rgrp,map);

                boolean firstApo = type.endsWith("1");
                if (firstApo) {
                  rgrp.setFirstAttachmentPoint(apoAtom);
                }
                else {
                  rgrp.setSecondAttachmentPoint(apoAtom);
                }
                break apoLoop;
              }
            }
          }
      }

      /* User action : certain bond in the root needs to become attachment bond 1 or 2 */
      else if (type.startsWith("setBondApoAction")) {
        rGroupHandler=hub.getRGroupHandler();
        IBond apoBond = (IBond) eventSource;
        Map<Integer, IBond> apoBonds=null;

        //Undo/redo business______
        IAtom pseudo=null;
        if (apoBond.getAtom(0) instanceof IPseudoAtom)
          pseudo=apoBond.getAtom(0);
        else
          pseudo=apoBond.getAtom(1);
        Map<Integer, IBond> keepApoBonds = new HashMap<Integer, IBond>();
        if (rGroupHandler.getrGroupQuery().getRootAttachmentPoints()!=null &&
            rGroupHandler.getrGroupQuery().getRootAttachmentPoints().get(pseudo)!=null) {
          apoBonds= rGroupHandler.getrGroupQuery().getRootAttachmentPoints().get(pseudo);
          for (Iterator<Integer> apoItr =apoBonds.keySet().iterator(); apoItr.hasNext();) {
            int apoNum=apoItr.next();
            keepApoBonds.put(apoNum,apoBonds.get(apoNum));
          }
        }
        existingRootAttachmentPoints = new HashMap<IAtom, Map<Integer, IBond>>();
        existingRootAttachmentPoints.put(pseudo, keepApoBonds);
        //________________________


        //Set the new Root APO
        if (rGroupHandler.getrGroupQuery().getRootAttachmentPoints()==null) {
          rGroupHandler.getrGroupQuery().setRootAttachmentPoints(new HashMap<IAtom, Map<Integer, IBond>>());
        }
        Map<IAtom, Map<Integer, IBond>> rootApo=rGroupHandler.getrGroupQuery().getRootAttachmentPoints();
        if (rootApo.get(pseudo)==null) {
          apoBonds=new HashMap<Integer,IBond>();
          rootApo.put(pseudo, apoBonds);
        }
        else
          apoBonds=rGroupHandler.getrGroupQuery().getRootAttachmentPoints().get(pseudo);

        if (type.endsWith("1")) {
          apoBonds.put(1, apoBond);
          if (apoBonds.get(2)!=null && apoBonds.get(2).equals(apoBond))
            apoBonds.remove(2);
        }
        if (type.endsWith("2")) {
          apoBonds.put(2, apoBond);
          if (apoBonds.get(1)!=null && apoBonds.get(1).equals(apoBond))
            apoBonds.remove(1);
        }

      }


      /* User action: certain atom+bond selection is to be the root structure. */
      else if (type.equals("setRoot")) {

        IAtomContainer atc =selection.getConnectedAtomContainer();
        if (!isProperSelection(atc)) {
          JOptionPane.showMessageDialog(jcpPanel, GT.get("Please do not make a fragmented selection."));
          return;
        }

        molecule = createMolecule (atc,existingAtomDistr,existingBondDistr);
        hub.getChemModel().getMoleculeSet().addAtomContainer(molecule);

        if (hub.getRGroupHandler() == null) {
          isNewRgroup=true;
          rgrpQuery = newRGroupQuery(molecule.getBuilder());
          rGroupHandler = new RGroupHandler(rgrpQuery, this.jcpPanel);
          hub.setRGroupHandler(rGroupHandler);
        }
        else {
          rGroupHandler=hub.getRGroupHandler();
          rgrpQuery = hub.getRGroupHandler().getrGroupQuery();
          if(rgrpQuery.getRootStructure()!=null) {
            existingRoot=rgrpQuery.getRootStructure();
            rgrpQuery.getRootStructure().removeProperty(CDKConstants.TITLE);
          }
        }
        molecule.setProperty(CDKConstants.TITLE,RGroup.ROOT_LABEL);
        rgrpQuery.setRootStructure(molecule);

        //Remove old root apo's
        existingRootAttachmentPoints = rgrpQuery.getRootAttachmentPoints();
        rgrpQuery.setRootAttachmentPoints(null);

        //Define new root apo's
        Map<IAtom, Map<Integer, IBond>> apoBonds= new HashMap<IAtom, Map<Integer, IBond>>();
        for (IAtom atom : molecule.atoms()) {
          if (atom instanceof IPseudoAtom) {
            IPseudoAtom pseudo = (IPseudoAtom)atom;
            if (pseudo.getLabel()!=null && RGroupQuery.isValidRgroupQueryLabel(pseudo.getLabel())) {
              chooseRootAttachmentBonds(pseudo,molecule,apoBonds);
            }
          }
        }
        rgrpQuery.setRootAttachmentPoints(apoBonds);

      }

      /* User action: certain atom+bond selection is to be a substituent. */
      else if (type.equals("setSubstitute")) {

        if (hub.getRGroupHandler() == null || hub.getRGroupHandler().getrGroupQuery()==null ||
            hub.getRGroupHandler().getrGroupQuery().getRootStructure()==null) {
          JOptionPane.showMessageDialog(jcpPanel, GT.get("Please define a root structure first."));
          return;
        }

        IAtomContainer atc =selection.getConnectedAtomContainer();
        if (!isProperSelection(atc)) {
          JOptionPane.showMessageDialog(jcpPanel, GT.get("Please do not make a fragmented selection."));
          return;
        }

        // Check - are there any R-groups -> collect them so that user input can be validated
        Map<Integer,Integer> validRnumChoices=new HashMap<Integer,Integer>();
        for (IAtom atom : hub.getRGroupHandler().getrGroupQuery().getRootStructure().atoms()) {
          if (atom instanceof IPseudoAtom) {
            IPseudoAtom pseudo = (IPseudoAtom)atom;
            if (pseudo.getLabel()!=null && RGroupQuery.isValidRgroupQueryLabel(pseudo.getLabel())) {
              int bondCnt=0;
              int rNum=new Integer(pseudo.getLabel().substring(1));
              for (IBond b : hub.getRGroupHandler().getrGroupQuery().getRootStructure().bonds())
                if (b.contains(atom))
                  bondCnt++;

              if ((!validRnumChoices.containsKey(rNum))||
                  validRnumChoices.containsKey(rNum)&& validRnumChoices.get(rNum)<bondCnt)
                validRnumChoices.put(rNum,bondCnt);
            }
          }
        }
        // Here we test: the user wants to define a substitute, but are there any R1..R32 groups to begin with?
        if (validRnumChoices.size()==0) {
          JOptionPane.showMessageDialog(jcpPanel, GT.get("There are no numbered R-atoms in the root structure to refer to."));
          return;
        }

        //Now get user input to determine which R# atom to hook up with the substituent
        boolean inputOkay=false;
        String userInput=null;
        Integer rNum=0;
        do {
          userInput = JOptionPane.showInputDialog(GT.get("Enter an R-group number "),validRnumChoices.get(0));
          if (userInput == null)
            return;
          try {
            rNum = new Integer(userInput);
            if(!validRnumChoices.containsKey(rNum))
              JOptionPane.showMessageDialog(null, GT.get("The number you entered has no corresponding R-group in the root."));
            else
              inputOkay=true;
          } catch (NumberFormatException e) {
            JOptionPane.showMessageDialog(null, GT.get("This is not a valid R-group label.\nPlease label in range R1 .. R32"));
          }
        }
        while (!inputOkay);
        rGroupHandler=hub.getRGroupHandler();

        rgrpQuery = hub.getRGroupHandler().getrGroupQuery();
        if (rgrpQuery.getRGroupDefinitions()==null) {
          rgrpQuery.setRGroupDefinitions(new HashMap<Integer, RGroupList>());
        }

        if (rgrpQuery.getRGroupDefinitions().get(rNum)==null) {
          RGroupList rList = new RGroupList(rNum);
          rList.setRGroups(new ArrayList<RGroup>());
          rgrpQuery.getRGroupDefinitions().put(rNum, rList);
        }

        molecule = createMolecule (atc,existingAtomDistr,existingBondDistr);
        existingRgroupLists = new HashMap<Integer,RGroupList>();

        // Now see if the user's choice for a substituent has overlaps with already defined existing
        // substitutes. If so, these existing ones get thrown out (we can't have multiple substituents
        // defined for the same atoms.
        for(Iterator<Integer> itr=rgrpQuery.getRGroupDefinitions().keySet().iterator();itr.hasNext();) {
          int rgrpNum=itr.next();
          RGroupList rgrpList = rgrpQuery.getRGroupDefinitions().get(rgrpNum);
          if(rgrpList!=null) {
            existingRgroupLists.put(rgrpNum,  makeClone(rgrpList));
            List<RGroup> cleanList = new ArrayList<RGroup>();
            for (int j=0; j<rgrpList.getRGroups().size(); j++){
              RGroup subst= rgrpList.getRGroups().get(j);
              boolean remove=false;
              removeCheck:
                for(IAtom atom : molecule.atoms()) {
                  if (subst.getGroup().contains(atom)) {
                    remove=true;
                    break removeCheck;
                  }
                }
              if (!remove) {
                cleanList.add(subst);
              }
            }
            rgrpList.setRGroups(cleanList);
          }
        }

        hub.getChemModel().getMoleculeSet().addAtomContainer(molecule);
        molecule.setProperty(CDKConstants.TITLE,RGroup.makeLabel(rNum));

        RGroup rgrp = new RGroup();
        rgrp.setGroup(molecule);
        rgrpQuery.getRGroupDefinitions().get(rNum).getRGroups().add(rgrp);

        //Set default APO atoms (randomly picked) for the new substitute
        int apoCount=validRnumChoices.get(rNum);
        int apoSet=0;
        apoBreak:
          for(IAtom atom : molecule.atoms()) {
            if (apoSet==apoCount)
              break apoBreak;
            if (apoSet==0) {
              rgrp.setFirstAttachmentPoint(atom);
            }
            if (apoSet==1) {
              rgrp.setSecondAttachmentPoint(atom);
            }
            apoSet++;
          }
      }


      if (hub.getUndoRedoFactory() != null && jcpPanel.get2DHub().getUndoRedoHandler() != null) {
        IUndoRedoable undoredo = jcpPanel.get2DHub().getUndoRedoFactory().getRGroupEdit
        ( type, isNewRgroup, hub,rGroupHandler, existingAtomDistr, existingBondDistr,
            existingRoot, existingRootAttachmentPoints, existingRGroupApo, existingRgroupLists,molecule);
        jcpPanel.get2DHub().getUndoRedoHandler().postEdit(undoredo);
      }
View Full Code Here


     *            Description of the Parameter
     */
    public void actionPerformed(ActionEvent e) {
        logger.info("Going to perform a clean up...");
        WaitDialog.showDialog();
        IChemModelRelay hub = jcpPanel.get2DHub();
        hub.cleanup();
        jcpPanel.setIsNewChemModel(true);
        WaitDialog.hideDialog();
        hub.updateView();
    }
View Full Code Here

    if (container == null)
    {
      logger.error("Cannot find container to add object to!");
    } else
    {
      IChemModelRelay hub = jcpPanel.get2DHub();
      IAtomContainer newContainer;
      try {
        newContainer = (IAtomContainer) container.clone();
        if(container.getID()!=null)
          newContainer.setID(container.getID());
View Full Code Here

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