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Only do cdk.fromSMILES and ui.open in the New From SMILES Wizard
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Removed extra saturation check and only partition molecule if it contains disconnected structures.

Also removed generate2dCoordinates as this is done in the JChemPaint editor on open

solves bug 3170
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@goglepox
goglepox committed Nov 20, 2012
1 parent ad98f92 commit 44a5409
Showing 1 changed file with 89 additions and 65 deletions.
154 changes: 89 additions & 65 deletions plugins/net.bioclipse.cdk.ui/src/net/bioclipse/cdk/ui/wizards/NewFromSMILESWizard.java
View file
Expand Up @@ -10,19 +10,26 @@
******************************************************************************/
package net.bioclipse.cdk.ui.wizards;

import static org.openscience.cdk.graph.ConnectivityChecker.isConnected;
import static org.openscience.cdk.graph.ConnectivityChecker.partitionIntoMolecules;
import static org.openscience.cdk.tools.manipulator.AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms;

import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.Executor;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
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 net.bioclipse.ui.business.IUIManager;

import org.apache.log4j.Logger;
import org.eclipse.core.runtime.IProgressMonitor;
Expand All @@ -32,12 +39,10 @@
import org.eclipse.jface.viewers.IStructuredSelection;
import org.eclipse.ui.IWorkbench;
import org.eclipse.ui.wizards.newresource.BasicNewResourceWizard;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.tools.AtomTypeAwareSaturationChecker;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;

public class NewFromSMILESWizard extends BasicNewResourceWizard {

Expand Down Expand Up @@ -76,75 +81,94 @@ public void init(IWorkbench workbench, IStructuredSelection currentSelection) {
setNeedsProgressMonitor(true);
}

private void doFinish(SubMonitor progress) throws Exception{
ICDKManager cdk = net.bioclipse.cdk.business.Activator.getDefault()
.getJavaCDKManager();
IUIManager ui = net.bioclipse.ui.business.Activator.getDefault()
.getUIManager();
ICDKMolecule mol = cdk.fromSMILES( getSMILES() );
List<ICDKMolecule> molecules;
if ( !isConnected( mol.getAtomContainer() ) ) {
IMoleculeSet containers = partitionIntoMolecules( mol
.getAtomContainer() );
final AtomTypeAwareSaturationChecker ataSatChecker = new AtomTypeAwareSaturationChecker();
molecules = new ArrayList<ICDKMolecule>( containers.getAtomContainerCount() );
SubMonitor child = progress.newChild( containers.getAtomContainerCount() );
for ( IAtomContainer container : containers.molecules() ) {
final IMolecule betterMol = asCDKMolecule( container );
percieveAtomTypesAndConfigureAtoms( betterMol );
ataSatChecker.decideBondOrder( betterMol );
molecules.add( new CDKMolecule( betterMol ) );
child.worked( 1 );
}
} else {
molecules = new ArrayList<ICDKMolecule>( 1 );
molecules.add( mol );
}

progress.setWorkRemaining( molecules.size() );
for ( ICDKMolecule molecule : molecules ) {
// cdk.generate2dCoordinates(molecule);
progress.worked( 1 );
ui.open( molecule, "net.bioclipse.cdk.ui.editors.jchempaint.cml" );
}
}
public boolean performFinish() {
//Open editor with content (String) as content
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 AtomTypeAwareSaturationChecker ataSatChecker = new AtomTypeAwareSaturationChecker();
// final FixBondOrdersTool tool = new FixBondOrdersTool();
final IMolecule cdkMol = asCDKMolecule(container);
try{
progress.setWorkRemaining(150);
FutureTask<IMolecule> future =
new FutureTask<IMolecule>(new Callable<IMolecule>() {
public IMolecule call() throws CDKException{
// IMolecule betterMol = tool.kekuliseAromaticRings(cdkMol);
IMolecule betterMol = cdkMol;
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms( betterMol );
ataSatChecker.decideBondOrder( betterMol );
return betterMol;
}});
progress.subTask("Finding double bonds");
executor.execute(future);
while(!future.isDone()) {
progress.worked(1);
if(progress.isCanceled()) {
future.cancel(true);
// tool.setInterrupted( true );
throw new OperationCanceledException();
}
Thread.sleep(1000);
}
mol = new CDKMolecule( future.get() );
} catch(Exception e) {
logger.warn("Aromaticity detection failed due to "+e.getMessage());
mol = new CDKMolecule( cdkMol );
}
progress.setWorkRemaining(50);
progress.subTask("Generating coordinates");
progress.worked(25);
mol = cdk.generate2dCoordinates(mol);
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();
}

// Open editor with content (String) as content
IRunnableWithProgress job = new IRunnableWithProgress() {

public void run( IProgressMonitor monitor ) {

final SubMonitor progress = SubMonitor.convert( monitor );
progress.beginTask( "Creating molecule from SMILES", 200 );
Executor executor = Executors.newSingleThreadExecutor();

try {
progress.subTask( "Generating molecule" );
FutureTask<Void> future = new FutureTask<Void>(
new Callable<Void>() {

@Override
public Void call() throws Exception {
doFinish( progress );
return null;
}
} );
executor.execute( future );
waitForFuture( future, progress );
try {
future.get();
} catch (ExecutionException e) {
LogUtils.handleException( e, logger ,Activator.PLUGIN_ID);
}
} catch ( InterruptedException e ) {
LogUtils.handleException( e, logger, Activator.PLUGIN_ID );
} finally {
}
}
};
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 );
}
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;
}

private void waitForFuture( Future<Void> future, IProgressMonitor progress )
throws InterruptedException {
while ( !future.isDone() ) {
progress.worked( 1 );
if ( progress.isCanceled() ) {
future.cancel( true );
throw new OperationCanceledException();
}
Thread.sleep( 1000 );
}
}
/**
* Converts (if needed) a CDK {@link IAtomContainer} into a CDK
* {@link IMolecule}.
Expand Down

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