public Object execute(ExecutionEvent event) throws ExecutionException {
ISelection sel =
PlatformUI.getWorkbench().getActiveWorkbenchWindow().getSelectionService().getSelection();
if (!sel.isEmpty() && sel instanceof IStructuredSelection) {
IStructuredSelection ssel = (IStructuredSelection) sel;
ICDKManager cdk = Activator.getDefault().getJavaCDKManager();
IUIManager ui = net.bioclipse.ui.business.Activator.getDefault().getUIManager();
List<IMolecule> molecules = new ArrayList<IMolecule>(ssel.size());
for (Object file : ssel.toList()) molecules.add(cdk.loadMolecule((IFile) file));
String path = "/Virtual/matrix.csv";
while (ui.fileExists(path)) path = "/Virtual/matrix" + UUID.randomUUID() + ".csv";
try {
String matrix = cdk.calculateTanimoto(molecules, path);
ui.open(matrix, "net.bioclipse.editors.MatrixGridEditor");
} catch (BioclipseException cause) {
throw new ExecutionException("Error while calculating Tanimoto matrix...", cause);
}
}
return null;
}
@Override
public Object execute(ExecutionEvent event) throws ExecutionException {
ISelection sel = HandlerUtil.getCurrentSelection(event);
if (!(sel instanceof IStructuredSelection))
throw new ExecutionException("Selection is not a SMILES file");
IStructuredSelection ssel = (IStructuredSelection) sel;
// We onlu operate on a single file currently
Object obj = ssel.getFirstElement();
if (!(obj instanceof IFile)) throw new ExecutionException("Selection is not a SMILES file");
final IFile input = (IFile) obj;
IPath outPath = input.getFullPath().removeFileExtension().addFileExtension("sdf");
final IFile output = ResourcesPlugin.getWorkspace().getRoot().getFile(outPath);
if (ui.fileExists(output)) {
if (!MessageDialog.openConfirm(
PlatformUI.getWorkbench().getActiveWorkbenchWindow().getShell(),
"SD-file already exists, confirm overwrite",
"A file with the same name but the sdf file ending "
+ "already exists. Okey to overwrite it?")) {
return null;
}
}
Job job =
new Job("Converting " + input.getFullPath().toPortableString() + " to SDF") {
@Override
protected IStatus run(IProgressMonitor monitor) {
monitor.beginTask("Converting SMILES", 100);
ICDKManager cdk = Activator.getDefault().getJavaCDKManager();
int count = 0;
Scanner s;
try {
s = new Scanner(input.getContents());
} catch (CoreException e) {
LogUtils.handleException(e, logger, "net.bioclipse.cdk.ui");
return new Status(
IStatus.ERROR,
net.bioclipse.cdk.ui.Activator.PLUGIN_ID,
"Error, failed to read file.");
}
while (s.hasNextLine()) {
s.nextLine();
count++;
}
Iterator<ICDKMolecule> iterator = null;
try {
iterator = cdk.createMoleculeIterator(input);
} catch (Exception e) {
LogUtils.handleException(e, logger, "net.bioclipse.cdk.ui");
return new Status(
IStatus.ERROR,
net.bioclipse.cdk.ui.Activator.PLUGIN_ID,
"Error, failed to read file.");
}
if (ui.fileExists(output)) {
ui.remove(output);
}
monitor.beginTask("Converting file", count);
AtomTypeAwareSaturationChecker ataSatChecker = new AtomTypeAwareSaturationChecker();
// FixBondOrdersTool bondOrderTool = new FixBondOrdersTool();
long timestamp = System.currentTimeMillis();
long before = timestamp;
int current = 0;
int last = 0;
int failedCount = 0;
while (iterator.hasNext()) {
try {
ICDKMolecule mol = iterator.next();
boolean filterout = false;
for (IAtom atom : mol.getAtomContainer().atoms()) {
if (atom.getAtomTypeName() == null || atom.getAtomTypeName().equals("X")) {
filterout = true;
}
}
if (!filterout) {
// IMolecule newAC =
// bondOrderTool.kekuliseAromaticRings((IMolecule)
// mol.getAtomContainer());
IAtomContainer newAC = mol.getAtomContainer();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(newAC);
ataSatChecker.decideBondOrder(newAC);
mol = new CDKMolecule(newAC);
cdk.appendToSDF(output, mol);
} else {
++failedCount;
}
} catch (BioclipseException e) {
++failedCount;
logger.error(e.getMessage(), e);
} catch (CDKException e) {
++failedCount;
logger.warn("Could not deduce bond orders");
}
current++;
if (System.currentTimeMillis() - timestamp > 1000) {
monitor.subTask(
"Done: "
+ current
+ "/"
+ count
+ " ("
+ TimeCalculator.generateTimeRemainEst(before, current, count)
+ " )");
monitor.worked(current - last);
last = current;
synchronized (monitor) {
if (monitor.isCanceled()) {
return Status.CANCEL_STATUS;
}
}
timestamp = System.currentTimeMillis();
}
}
monitor.done();
logger.debug("Wrote file" + output);
if (failedCount != 0) {
setProperty(IProgressConstants.KEEP_PROPERTY, true);
}
return new Status(
IStatus.OK,
net.bioclipse.cdk.ui.Activator.PLUGIN_ID,
"Failed to convert " + failedCount + " molecules");
}
};
job.setUser(true);
job.schedule();
return null;
}