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Added method that uses multiple threads to calculate 3d coordinates f…
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…or sd-file.

Molecules need to be sent to balloon one by one because we might get more than one conformation even if only one is asked for.
Solves bug 3190
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@goglepox
goglepox committed Apr 19, 2012
1 parent 16e45cb commit b342901
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Showing 3 changed files with 260 additions and 3 deletions.
4 changes: 3 additions & 1 deletion plugins/net.bioclipse.balloon.business/META-INF/MANIFEST.MF
View file
Expand Up @@ -11,7 +11,9 @@ Require-Bundle: org.eclipse.ui,
org.eclipse.core.resources,
net.bioclipse.ui.business,
net.bioclipse.cdk.business,
org.openscience.cdk.interfaces
org.openscience.cdk.interfaces,
org.openscience.cdk.io;bundle-version="1.4.6",
org.openscience.cdk.core;bundle-version="1.4.6"
Bundle-RequiredExecutionEnvironment: J2SE-1.5
Bundle-ActivationPolicy: lazy
Export-Package: net.bioclipse.balloon.business
Expand Down
252 changes: 252 additions & 0 deletions ...ins/net.bioclipse.balloon.business/src/net/bioclipse/balloon/business/BalloonManager.java
View file
Expand Up @@ -14,8 +14,13 @@
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.concurrent.ArrayBlockingQueue;
import java.util.concurrent.BlockingQueue;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.TimeoutException;

Expand All @@ -37,6 +42,7 @@
import org.eclipse.core.runtime.Platform;
import org.eclipse.core.runtime.content.IContentDescription;
import org.eclipse.core.runtime.content.IContentType;
import org.openscience.cdk.io.SDFWriter;

/**
* A Bioclipse Manager for invoking Balloon
Expand Down Expand Up @@ -475,5 +481,251 @@ private String getAFilename(String pathname, String ext, int cnt) {

}

/**
* Thread safe method for calling balloon with one mdl-file
*
* @param infile
* @param numConformations
* @return
* @throws BioclipseException
*/
private String calculateWithBalloon( String infile, int numConformations )
throws BioclipseException {

String outfile = constructOutputFilename( infile, numConformations );
try {

//Read timeout from prefs
int timeout = net.bioclipse.balloon.business.Activator
.getDefault().getPreferenceStore()
.getInt( net.bioclipse.balloon.business.Activator
.BALLOON_TIMEOUT );

//Just to be sure...
if (timeout<=0)
timeout = net.bioclipse.balloon.business
.Activator.DEFAULT_BALLOON_TIMEOUT;

//Seconds -> ms
Long msTimout=new Long(timeout*1000);

//Create a native runner and execute Balloon with it for a
//certain timeout writing from inputfile to outputfile with
//desired number of conformations
BalloonRunner runner=new BalloonRunner(msTimout);
boolean failed =
!runner.runBalloon( infile, outfile,
numConformations );
if ( failed ) {
throw new BioclipseException(
"Balloon execution failed. Native " +
"BalloonRunner returned false." );
}
} catch ( ExecutionException e ) {
throw new BioclipseException( "Balloon execution failed. Reason: "
+ e.getMessage(), e );
} catch ( InterruptedException e ) {
throw new BioclipseException( "Balloon Was interrupted. Reason: "
+ e.getMessage(), e );
} catch ( TimeoutException e ) {
throw new BioclipseException( "Balloon timed out. Reason: "
+ e.getMessage(), e );
} catch ( IOException e ) {
throw new BioclipseException( "Balloon I/O error. Reason: "
+ e.getMessage(), e );
}

return outfile;

}

public IFile generate3Dcoordinates( final IFile input,
final IProgressMonitor monitor )
throws BioclipseException,
CoreException,
IOException {
final ICDKManager cdk = net.bioclipse.cdk.business.Activator.getDefault().getJavaCDKManager();
final int numOfMolcules = cdk.numberOfEntriesInSDF( input, monitor );
monitor.beginTask( "Generating 3D coordinates", numOfMolcules );

final String file =
constructOutputFilename( input.getRawLocation()
.toOSString(), 1 );

final BlockingQueue<MolPos> inputMoleculesQueue =
new ArrayBlockingQueue<MolPos>( 10 );
final BlockingQueue<MolPos> outputMoleculesQueue =
new ArrayBlockingQueue<MolPos>( 10 );
final Boolean[] fileIsParsed = { Boolean.FALSE};
final MolPos POISION =
new MolPos( -1, Collections.emptyMap(),
"This is the end of the line" );
// @new thread
Runnable parse = new Runnable() {
public void run() {

try {
Iterator<? extends ICDKMolecule> parserIterator =
cdk.createMoleculeIterator( input );
long pos = 0;
while ( parserIterator.hasNext() ) {
ICDKMolecule molecule = parserIterator.next();
++pos;
// save to temp file
String tempFile =
serializeMoleculeToTempFile( molecule );
MolPos mp =
new MolPos( pos, molecule
.getAtomContainer()
.getProperties(),
tempFile );
inputMoleculesQueue.put( mp );
if ( monitor.isCanceled() )
break;
}
} catch ( Exception e ) {
e.printStackTrace();// TODO handel exception
}
fileIsParsed[0] = Boolean.TRUE;
}
};

Runnable generator = new Runnable() {
public void run() {

while ( !fileIsParsed[0] || !inputMoleculesQueue.isEmpty() ) {
try {
MolPos input = inputMoleculesQueue.take();
String output = calculateWithBalloon( input.file, 1 );

MolPos out = input.newOutput( output );
outputMoleculesQueue.put( out );
if ( monitor.isCanceled() )
break;
} catch (InterruptedException e) {
e.printStackTrace();
} catch (BioclipseException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}

}
try {
outputMoleculesQueue.put(POISION);
} catch (InterruptedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
};
final int numThreads = Runtime.getRuntime().availableProcessors();
Runnable writer = new Runnable() {
int numberOfThreads = numThreads;
public void run() {

SDFWriter mdlwriter;
try {
mdlwriter = new SDFWriter(
new FileWriter( new File( file ) ) );
} catch ( IOException e) {
logger.error( e.getMessage(), e );
return;
}
long pos = 1;
LinkedList<MolPos> buffer = new LinkedList<MolPos>();
int foundPoinsions = 0;
while ( !buffer.isEmpty() || foundPoinsions < numberOfThreads ) {
try {
MolPos input = null;
if ( !buffer.isEmpty()
&& outputMoleculesQueue.isEmpty() )
input = buffer.pop();
else
input = outputMoleculesQueue.take();

if ( input == POISION ) {
foundPoinsions++;
continue;
}
// Buffer if not in order
if ( pos != input.pos ) {
// check in buffer
MolPos newInput = null;
Iterator<MolPos> bufferIterator = buffer.iterator();
while ( bufferIterator.hasNext() ) {
MolPos p = bufferIterator.next();
if ( pos == p.pos ) {
bufferIterator.remove();
newInput = p;
break;
}
}
buffer.add( input );
if ( newInput == null ) {
continue;
} else
input = newInput;
}
++pos;
monitor.worked( 1 );
monitor.subTask( "Done " + pos + "/" + numOfMolcules );
List<ICDKMolecule> molecules =
cdk.loadMolecules( input.file );
ICDKMolecule molecule = molecules.get(0);
molecule.getAtomContainer()
.setProperties( input.properties );
mdlwriter.write(molecule.getAtomContainer());
if ( monitor.isCanceled() )
break;
} catch ( Exception e ) {
logger.error( e.getMessage(), e );
}
}
try {
mdlwriter.close();
} catch (IOException e) {
logger.error( e.getMessage(), e );
}
}
};

Thread parserThread = new Thread( parse );
parserThread.start();

for ( int i = 0; i < numThreads; i++ )
new Thread( generator ).start();

Thread writerThread = new Thread( writer );
writerThread.start();
while ( true ) {
try {
writerThread.join();
break;
} catch ( InterruptedException e ) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
return ResourcePathTransformer.getInstance()
.transform( file );
}

}

class MolPos {

final long pos;
final Map<Object, Object> properties;
final String file;

public MolPos(long pos, Map<Object, Object> properties, String file) {
this.pos = pos;
this.properties = properties;
this.file = file;
}

public MolPos newOutput( String outputFile ) {

return new MolPos( pos, properties, outputFile );
}
}
7 changes: 5 additions & 2 deletions ...ns/net.bioclipse.balloon.business/src/net/bioclipse/balloon/business/IBalloonManager.java
View file
Expand Up @@ -12,16 +12,18 @@

import java.util.List;

import org.eclipse.core.runtime.IProgressMonitor;

import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.PublishedClass;
import net.bioclipse.core.PublishedMethod;
import net.bioclipse.core.Recorded;
import net.bioclipse.core.business.BioclipseException;
import net.bioclipse.core.domain.IMolecule;
import net.bioclipse.jobs.BioclipseUIJob;
import net.bioclipse.managers.business.IBioclipseManager;

import org.eclipse.core.resources.IFile;
import org.eclipse.core.runtime.IProgressMonitor;


@PublishedClass( "Contains methods related to Balloon")
/**
Expand Down Expand Up @@ -191,4 +193,5 @@ public List<ICDKMolecule> generateMultiple3Dconformations(
IProgressMonitor monitor)
throws BioclipseException;

public void generate3Dcoordinates( IFile input, BioclipseUIJob<IFile> uiJob );
}

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