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: