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Added progress monitor and handle fixAromaticBondORder timeout.
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fix for bug 3067
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@goglepox
goglepox committed Feb 16, 2012
1 parent b3c8152 commit 831e683
Showing 1 changed file with 87 additions and 37 deletions.
124 changes: 87 additions & 37 deletions plugins/net.bioclipse.cdk.ui/src/net/bioclipse/cdk/ui/wizards/NewFromSMILESWizard.java
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Expand Up @@ -10,25 +10,39 @@
******************************************************************************/
package net.bioclipse.cdk.ui.wizards;

import static org.openscience.cdk.graph.ConnectivityChecker.partitionIntoMolecules;

import java.lang.reflect.InvocationTargetException;
import java.util.concurrent.Callable;
import java.util.concurrent.Executor;
import java.util.concurrent.Executors;
import java.util.concurrent.FutureTask;

import net.bioclipse.cdk.business.ICDKManager;
import net.bioclipse.cdk.domain.CDKMolecule;
import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.cdk.ui.Activator;
import net.bioclipse.core.util.LogUtils;

import org.apache.log4j.Logger;
import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.core.runtime.OperationCanceledException;
import org.eclipse.core.runtime.SubMonitor;
import org.eclipse.jface.operation.IRunnableWithProgress;
import org.eclipse.jface.viewers.IStructuredSelection;
import org.eclipse.ui.IWorkbench;
import org.eclipse.ui.wizards.newresource.BasicNewResourceWizard;
import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
import org.openscience.cdk.graph.ConnectivityChecker;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
import org.openscience.cdk.smiles.DeduceBondSystemTool;

import com.sun.javadoc.ThrowsTag;

public class NewFromSMILESWizard extends BasicNewResourceWizard {

private static final Logger logger =
Expand Down Expand Up @@ -68,44 +82,80 @@ public void init(IWorkbench workbench, IStructuredSelection currentSelection) {

public boolean performFinish() {
//Open editor with content (String) as content
ICDKManager cdk = net.bioclipse.cdk.business.Activator.getDefault().getJavaCDKManager();
try {
ICDKMolecule mol = cdk.fromSMILES(getSMILES());
IMoleculeSet containers =
ConnectivityChecker.partitionIntoMolecules(mol.getAtomContainer()
);
for (IAtomContainer container : containers.molecules()) {
// ok, try to do something smart (tm) with SMILES input:
// try to resolve bond orders
DeduceBondSystemTool tool = new DeduceBondSystemTool();
org.openscience.cdk.interfaces.IMolecule cdkMol =
asCDKMolecule(container);
cdkMol = tool.fixAromaticBondOrders(cdkMol);
mol = new CDKMolecule(cdkMol);

mol = cdk.generate2dCoordinates(mol);
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(
NoNotificationChemObjectBuilder.getInstance()
);
IAtomType[] types = matcher.findMatchingAtomType(
IRunnableWithProgress job = new IRunnableWithProgress() {
public void run(IProgressMonitor monitor) {
SubMonitor progress = SubMonitor.convert(monitor);
progress.beginTask("Creating molecule from SMILES", 200);
Executor executor = Executors.newSingleThreadExecutor();
try {
ICDKManager cdk = net.bioclipse.cdk.business.Activator.getDefault().getJavaCDKManager();
progress.subTask("Generating molecule");
ICDKMolecule mol = cdk.fromSMILES(getSMILES());
IMoleculeSet containers =partitionIntoMolecules(mol.getAtomContainer());
progress.worked(50);
for (IAtomContainer container : containers.molecules()) {
// ok, try to do something smart (tm) with SMILES input:
// try to resolve bond orders
final DeduceBondSystemTool tool = new DeduceBondSystemTool();
final org.openscience.cdk.interfaces.IMolecule cdkMol =
asCDKMolecule(container);
try{
progress.setWorkRemaining(150);
FutureTask<IMolecule> future =
new FutureTask<IMolecule>(new Callable<IMolecule>() {
public IMolecule call() throws CDKException{
return tool.fixAromaticBondOrders(cdkMol);
}});
progress.subTask("Deducing aromaticity");
executor.execute(future);
while(!future.isDone()) {
progress.worked(1);
if(progress.isCanceled()) {
future.cancel(true);
throw new OperationCanceledException();
}
Thread.sleep(1000);
}
} catch(Exception e) {
logger.warn("Aromaticity detection failed du to "+e.getMessage());
}
mol = new CDKMolecule(cdkMol);
progress.setWorkRemaining(50);
progress.subTask("Generating coordinates");
progress.worked(25);
mol = cdk.generate2dCoordinates(mol);
progress.subTask("Preforming atom type matching");
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(
NoNotificationChemObjectBuilder.getInstance()
);
IAtomType[] types = matcher.findMatchingAtomType(
mol.getAtomContainer()
);
for (int i=0; i<types.length; i++) {
if (types[i] != null) {
mol.getAtomContainer().getAtom(i).setAtomTypeName(
);
progress.setWorkRemaining(types.length);
for (int i=0; i<types.length; i++) {
progress.worked(1);
if (types[i] != null) {
mol.getAtomContainer().getAtom(i).setAtomTypeName(
types[i].getAtomTypeName()
);
}
}
net.bioclipse.ui.business.Activator.getDefault().getUIManager()
.open(mol, "net.bioclipse.cdk.ui.editors.jchempaint.cml");
}
} catch (Exception e) {
LogUtils.handleException(
e, logger,
Activator.PLUGIN_ID
);
}
);
}
}
net.bioclipse.ui.business.Activator.getDefault().getUIManager()
.open(mol, "net.bioclipse.cdk.ui.editors.jchempaint.cml");
}
} catch (Exception e) {
LogUtils.handleException( e, logger, Activator.PLUGIN_ID );
}
progress.done();
}
};
try {
getContainer().run(true, true,job);
} catch (InvocationTargetException e) {
LogUtils.handleException( e, logger, Activator.PLUGIN_ID );
} catch (InterruptedException e) {
LogUtils.handleException( e, logger, Activator.PLUGIN_ID );
}
return true;
}

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