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;
}