Author: scooter
Date: 2013-02-19 10:44:38 -0800 (Tue, 19 Feb 2013)
New Revision: 31126
Added:
csplugins/trunk/ucsf/scooter/chemViz/lib/cdk-1.5.1.git.jar
csplugins/trunk/ucsf/scooter/chemViz/lib/commons-math3-3.0.jar
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/Fragment.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/JobType.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/MCSS.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/MCSSThread.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/TaskUpdater.java
Removed:
csplugins/trunk/ucsf/scooter/chemViz/lib/cdk-1.4.15-1.jar
Modified:
csplugins/trunk/ucsf/scooter/chemViz/build.xml
csplugins/trunk/ucsf/scooter/chemViz/resources/plugin.props
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/similarity/CDKTanimotoScore.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/AbstractCompoundTask.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreateMCSSTask.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/SMARTSSearchTask.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ui/CompoundTable.java
Log:
Reimplementation of MCSS with help from Asad.
Modified: csplugins/trunk/ucsf/scooter/chemViz/build.xml
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/build.xml 2013-02-15 22:35:56 UTC
(rev 31125)
+++ csplugins/trunk/ucsf/scooter/chemViz/build.xml 2013-02-19 18:44:38 UTC
(rev 31126)
@@ -103,8 +103,8 @@
=====================================================================
-->
<target name="jar" depends="compile" description="makes a jar for Cytoscape
under development">
- <mkdir dir="${build.dir}/classes/lib"/>
- <unzip dest="${build.dir}/classes/lib/">
+ <mkdir dir="${build.dir}/lib"/>
+ <unzip dest="${build.dir}/lib/">
<fileset dir="${lib.dir}">
<include name="*.jar"/>
</fileset>
@@ -118,7 +118,7 @@
<attribute name="Cytoscape-Plugin" value="chemViz.ChemViz" />
</manifest>
<fileset dir="${build.dir}/classes" />
- <fileset dir="${build.dir}/classes/lib"/>
+ <fileset dir="${build.dir}/lib" />
</jar>
</target>
Deleted: csplugins/trunk/ucsf/scooter/chemViz/lib/cdk-1.4.15-1.jar
===================================================================
(Binary files differ)
Added: csplugins/trunk/ucsf/scooter/chemViz/lib/cdk-1.5.1.git.jar
===================================================================
(Binary files differ)
Property changes on: csplugins/trunk/ucsf/scooter/chemViz/lib/cdk-1.5.1.git.jar
___________________________________________________________________
Added: svn:mime-type
+ application/zip
Added: csplugins/trunk/ucsf/scooter/chemViz/lib/commons-math3-3.0.jar
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/ucsf/scooter/chemViz/lib/commons-math3-3.0.jar
___________________________________________________________________
Added: svn:mime-type
+ application/zip
Modified: csplugins/trunk/ucsf/scooter/chemViz/resources/plugin.props
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/resources/plugin.props 2013-02-15
22:35:56 UTC (rev 31125)
+++ csplugins/trunk/ucsf/scooter/chemViz/resources/plugin.props 2013-02-19
18:44:38 UTC (rev 31126)
@@ -31,4 +31,4 @@
pluginAuthorsIntsitutions=John "Scooter" Morris:UCSF;Dazhi Jiao:Indiana
University School of Informatics
# Date this plugin/plugin version was released
-releaseDate=December 1th, 2012
+releaseDate=March 1st, 2013
Modified: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2013-02-15 22:35:56 UTC (rev 31125)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2013-02-19 18:44:38 UTC (rev 31126)
@@ -73,10 +73,9 @@
import cytoscape.util.URLUtil;
import giny.view.NodeView;
+import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.ChemModel;
-import org.openscience.cdk.Molecule;
-import org.openscience.cdk.MoleculeSet;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
import org.openscience.cdk.config.IsotopeFactory;
@@ -91,13 +90,12 @@
import org.openscience.cdk.inchi.InChIToStructure;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IAtomType.Hybridization;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IIsotope;
import org.openscience.cdk.interfaces.IMolecularFormula;
-import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IRing;
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.layout.StructureDiagramGenerator;
@@ -135,7 +133,7 @@
* could have multiple Compounds, either by having multiple attributes that
contain compound descriptors or
* by having a single attribute that contains multiple descriptors (e.g.
comma-separated SMILES strings). The
* creation of a Compound results in the building of a cached 2D image for
that compound, as well as the creation
- * of the CDK IMolecule, which is used for conversion from InChI to SMILES,
for calculation of the molecular weight,
+ * of the CDK IAtomContainer, which is used for conversion from InChI to
SMILES, for calculation of the molecular weight,
* and for the calculation of Tanimoto coefficients.
*/
@@ -309,8 +307,8 @@
protected Image renderedImage;
protected boolean laidOut;
private AttriType attrType;
- private IMolecule iMolecule;
- private IMolecule iMolecule3D;
+ private IAtomContainer iMolecule;
+ private IAtomContainer iMolecule3D;
private BitSet fingerPrint;
private IFingerprinter fp;
private int lastImageWidth = -1;
@@ -336,7 +334,7 @@
}
/**
- * This alternative form of the constructor is called when we've
calculated an IMolecule internally and it
+ * This alternative form of the constructor is called when we've
calculated an IAtomContainer internally and it
* bypasses the creation.
*
* @param source the graph object that holds this compound
@@ -344,7 +342,7 @@
* @param mstring the compound descriptor itself
* @param attrType the type of the compound descriptor (inchi or smiles)
*/
- public Compound(GraphObject source, String attribute, String mstring,
IMolecule molecule,
+ public Compound(GraphObject source, String attribute, String mstring,
IAtomContainer molecule,
AttriType attrType) {
this.source = source;
this.attribute = attribute;
@@ -369,7 +367,7 @@
}
- public void createStructure(IMolecule molecule) {
+ public void createStructure(IAtomContainer molecule) {
long startTime = Calendar.getInstance().getTimeInMillis();
this.renderedImage = null;
@@ -412,7 +410,7 @@
long smilesTime = Calendar.getInstance().getTimeInMillis();
totalSMILESTime += smilesTime-fpTime;
- // At this point, we should have an IMolecule
+ // At this point, we should have an IAtomContainer
try {
CDKHueckelAromaticityDetector.detectAromaticity(iMolecule);
@@ -470,11 +468,11 @@
}
/**
- * Return the CDK IMolecule for this compound
+ * Return the CDK IAtomContainer for this compound
*
- * @return the IMolecule for this compound
+ * @return the IAtomContainer for this compound
*/
- public IMolecule getIMolecule() {
+ public IAtomContainer getIAtomContainer() {
return iMolecule;
}
@@ -487,7 +485,7 @@
if (fingerPrint == null) {
try {
synchronized (fp) {
- fingerPrint =
fp.getFingerprint(addh(iMolecule));
+ fingerPrint =
fp.getBitFingerprint(addh(iMolecule)).asBitSet();
}
} catch (Exception e) {
logger.warning("Error calculating fingerprint:
"+e);
@@ -881,11 +879,11 @@
// Is the structure connected?
if
(!ConnectivityChecker.isConnected(iMolecule)) {
// No, for now, find the largest
component and use that exclusively
- IMoleculeSet molSet =
ConnectivityChecker.partitionIntoMolecules(iMolecule);
- IMolecule largest =
molSet.getMolecule(0);
- for (int i = 0; i <
molSet.getMoleculeCount(); i++) {
- if
(molSet.getMolecule(i).getAtomCount() > largest.getAtomCount())
- largest =
molSet.getMolecule(i);
+ IAtomContainerSet molSet =
ConnectivityChecker.partitionIntoMolecules(iMolecule);
+ IAtomContainer largest =
molSet.getAtomContainer(0);
+ for (int i = 0; i <
molSet.getAtomContainerCount(); i++) {
+ if
(molSet.getAtomContainer(i).getAtomCount() > largest.getAtomCount())
+ largest =
molSet.getAtomContainer(i);
}
iMolecule = largest;
}
@@ -925,10 +923,10 @@
}
}
- private IMolecule addh(IMolecule mol) {
- IMolecule molH;
+ private IAtomContainer addh(IAtomContainer mol) {
+ IAtomContainer molH;
try {
- molH = (IMolecule)mol.clone();
+ molH = (IAtomContainer)mol.clone();
} catch (Exception e) {
return mol;
}
@@ -968,7 +966,7 @@
return null;
}
- IMolecule molecule = new
Molecule(intostruct.getAtomContainer());
+ IAtomContainer molecule = new
AtomContainer(intostruct.getAtomContainer());
// Use the molecule to create a SMILES string
SmilesGenerator sg = new SmilesGenerator();
return sg.createSMILES(molecule);
@@ -979,7 +977,7 @@
}
- private Image blankImage(IMolecule mol, int width, int height) {
+ private Image blankImage(IAtomContainer mol, int width, int height) {
final String noImage = "Image Unavailable";
if (width == 0 || height == 0)
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/similarity/CDKTanimotoScore.java
===================================================================
---
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/similarity/CDKTanimotoScore.java
2013-02-15 22:35:56 UTC (rev 31125)
+++
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/similarity/CDKTanimotoScore.java
2013-02-19 18:44:38 UTC (rev 31126)
@@ -5,7 +5,6 @@
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.exception.InvalidSmilesException;
import org.openscience.cdk.fingerprint.Fingerprinter;
-import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.similarity.Tanimoto;
import org.openscience.cdk.smiles.SmilesParser;
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/AbstractCompoundTask.java
===================================================================
---
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/AbstractCompoundTask.java
2013-02-15 22:35:56 UTC (rev 31125)
+++
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/AbstractCompoundTask.java
2013-02-19 18:44:38 UTC (rev 31126)
@@ -247,13 +247,13 @@
return cList;
}
- protected void updateMonitor() {
+ protected synchronized void updateMonitor() {
if (monitor == null || totalObjects == 0) return;
monitor.setPercentCompleted((int)(((double)objectCount/(double)totalObjects) *
100.0));
objectCount++;
}
- protected void setStatus(String status) {
+ protected synchronized void setStatus(String status) {
if (monitor != null) monitor.setStatus(status);
}
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreateMCSSTask.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreateMCSSTask.java
2013-02-15 22:35:56 UTC (rev 31125)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreateMCSSTask.java
2013-02-19 18:44:38 UTC (rev 31126)
@@ -46,6 +46,7 @@
import java.util.concurrent.Executors;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Future;
+import java.util.logging.Level;
import giny.model.GraphObject;
import giny.view.EdgeView;
@@ -65,31 +66,25 @@
import chemViz.ui.ChemInfoSettingsDialog;
import chemViz.ui.CompoundPopup;
-import org.openscience.cdk.Molecule;
-import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
-import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IMolecule;
-// import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
import org.openscience.cdk.smiles.SmilesGenerator;
-import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import org.openscience.cdk.smsd.Isomorphism;
-import org.openscience.cdk.smsd.interfaces.Algorithm;
+import tools.mcss.JobType;
+import tools.mcss.MCSS;
+import tools.mcss.TaskUpdater;
/**
* The CreateCompoundsTask fetches all of the compounds defined by the
* object passed in its constructor and provides some methods to allow
* the caller to fetch the compounds when the task is complete.
*/
-public class CreateMCSSTask extends AbstractCompoundTask {
+public class CreateMCSSTask extends AbstractCompoundTask implements
TaskUpdater {
List<GraphObject> objectList;
ChemInfoSettingsDialog dialog;
String type;
CyAttributes attributes;
List<Compound> compoundList;
- IMolecule mcss = null;
+ IAtomContainer mcss = null;
boolean showResult = false;
boolean createGroup = false;
boolean calculationComplete = false;
@@ -128,11 +123,41 @@
return g.createSMILES(mcss);
}
+ public void setTotalCount(int count) {
+ totalObjects = count;
+ objectCount = 0;
+ }
+
+ public synchronized void incrementCount() {
+ updateMonitor();
+ }
+
+ public synchronized void updateStatus(String status) {
+ setStatus(status);
+ }
+
+ public synchronized void logException(String className, Level level,
String message, Exception exception) {
+ if (message == null) message = exception.getMessage();
+
+ if (level == Level.SEVERE) {
+ monitor.setException(exception, "Fatal error in
"+className+": "+message);
+ }
+
+ if (level == Level.WARNING)
+ logger.warning("Error in "+className+": "+message);
+ else if(level == Level.INFO)
+ logger.info(className+": "+message);
+ else
+ logger.debug(className+": "+message);
+ }
+
/**
* Runs the task -- this will get all of the compounds, fetching the
images (if necessary) and creates the popup.
*/
public void run() {
+ long startTime = Calendar.getInstance().getTimeInMillis();
int maxThreads = dialog.getMaxThreads();
+ setStatus("Getting compounds");
compoundList = getCompounds(objectList, attributes,
dialog.getCompoundAttributes(type,AttriType.smiles),
dialog.getCompoundAttributes(type,AttriType.inchi), maxThreads);
@@ -142,19 +167,23 @@
List<IAtomContainer> mcssList =
Collections.synchronizedList(new
ArrayList<IAtomContainer>(compoundList.size()));
for (Compound c: compoundList) {
- mcssList.add(c.getIMolecule());
+ mcssList.add(c.getIAtomContainer());
}
int pass = 0;
while (mcssList.size() > 1) {
- mcssList = calculateMCSS(mcssList, nThreads);
- System.out.println("calculateMCSS returns
"+mcssList.size()+" structures");
+ MCSS mcssJob = new MCSS(mcssList, JobType.MCS, this,
nThreads);
+ mcssList = mcssJob.getCalculateMCSS();
+ // System.out.println("calculateMCSS returns
"+mcssList.size()+" structures");
pass++;
if (canceled) break;
}
if (mcssList.size() == 1)
- mcss = (IMolecule)mcssList.get(0);
+ mcss = (IAtomContainer)mcssList.get(0);
+ long endCalcTime = Calendar.getInstance().getTimeInMillis();
+ setStatus("Done. Total time: "+(endCalcTime-startTime)+"ms");
+
calculationComplete = true;
if (showResult) {
String mcssSmiles = getMCSSSmiles();
@@ -226,155 +255,4 @@
}
public List<Compound>getCompoundList() { return compoundList; }
-
-
- private List<IAtomContainer>
calculateMCSS(List<IAtomContainer>mcssList, int nThreads) {
- List<IAtomContainer> newMCSSList =
Collections.synchronizedList(new ArrayList<IAtomContainer>(nThreads));
- int taskNumber = 0;
-
- if (nThreads == 1) {
- GetMCSSTask task = new GetMCSSTask(mcssList,
newMCSSList, 1);
- task.call();
- return newMCSSList;
- } else {
- List<Future<IAtomContainer>> futureList = new
ArrayList<Future<IAtomContainer>>();
- ExecutorService threadPool =
Executors.newFixedThreadPool(nThreads);
- int step =
(int)Math.ceil((double)mcssList.size()/(double)nThreads);
- if (step < 2) step = 2; // Can't have a step size of
less than 2
- for (int i = 0; i < mcssList.size(); i=i+step) {
- int endPoint = i+step;
- if (endPoint > mcssList.size())
- endPoint = mcssList.size();
- List<IAtomContainer> subList = new
ArrayList<IAtomContainer>(mcssList.subList(i, endPoint));
- if (subList.size() > 1)
- futureList.add(threadPool.submit(new
GetMCSSTask(subList, null, taskNumber++)));
- else
- newMCSSList.add(subList.get(0));
- }
-
- for (Future<IAtomContainer> container: futureList) {
- if (container == null) continue;
- try {
- IAtomContainer f = container.get();
- if (f != null)
-
newMCSSList.add(container.get());
- } catch (Exception e) {
- logger.warning("Execution exception:
"+e);
- System.out.println("Execution
exception: "+e);
- e.printStackTrace();
- }
- }
-
- threadPool.shutdown();
-
-/*
- ExecutorService threadPool =
Executors.newFixedThreadPool(nThreads);
- try {
- threadPool.invokeAll(taskList);
- } catch (Exception e) {
- logger.warning("Execution exception: "+e);
- System.out.println("Execution exception: "+e);
- }
-*/
- }
- return newMCSSList;
- }
-
- private class GetMCSSTask implements Callable <IAtomContainer> {
- List<IAtomContainer> mcssList;
- List<IAtomContainer> resultsList;
- int taskNumber = 0;
- IAtomContainer innerMcss = null;
-
- public GetMCSSTask(List<IAtomContainer>mcssList,
List<IAtomContainer>resultsList, int taskNumber) {
- this.mcssList = mcssList;
- this.resultsList = resultsList;
- this.taskNumber = taskNumber;
- mcss = null;
- }
-
- public synchronized IAtomContainer call() {
- // System.out.println("Calling MCSSTask "+taskNumber+"
with "+mcssList.size()+" items");
- long startTime =
Calendar.getInstance().getTimeInMillis();
- innerMcss =
AtomContainerManipulator.removeHydrogens(mcssList.get(0));
-
- long calcTime = startTime;
- for (int index = 1; index < mcssList.size();
index++) {
- Isomorphism comparison = new
Isomorphism(Algorithm.DEFAULT, true);
-
comparison.setBondSensitiveTimeOut(0.5); // Increase timeout to 30 seconds
- IAtomContainer target =
AtomContainerManipulator.removeHydrogens(mcssList.get(index));
- try {
- // System.out.println("mcss for
task "+taskNumber+" has "+innerMcss.getAtomCount()+" atoms, and
"+innerMcss.getBondCount()+" bonds");
- // System.out.println("target
for task "+taskNumber+" has "+target.getAtomCount()+" atoms, and
"+target.getBondCount()+" bonds");
- //
System.out.println("comparison for task "+taskNumber+" is "+comparison);
- comparison.init(innerMcss,
target, true, true);
- //
comparison.setChemFilters(true, true, true);
- innerMcss = getMCSS(comparison);
- } catch (CDKException e) {
- logger.warning("CDKException:
"+e);
- } catch (Exception e) {
- logger.warning("Exception: "+e);
- }
-
- long endCalcTime =
Calendar.getInstance().getTimeInMillis();
- // System.out.println("Task
"+taskNumber+" index "+index+" took "+(endCalcTime-calcTime)+"ms");
- calcTime = endCalcTime;
- if (innerMcss == null || canceled)
break;
- }
- if (resultsList != null)
- resultsList.add(innerMcss);
- long endTime = Calendar.getInstance().getTimeInMillis();
- System.out.println("Done: task "+taskNumber+" took
"+(endTime-startTime)+"ms");
- return innerMcss;
- }
-
- private synchronized IMolecule getMCSS(Isomorphism comparison) {
- // if (comparison.getAllAtomMapping() == null) return
null;
- List<IAtomContainer> matchList = new
ArrayList<IAtomContainer>();
- IAtomContainer mol1 = comparison.getReactantMolecule();
- // IAtomContainer mol2 =
comparison.getProductMolecule();
- for (Map<IAtom,IAtom> mapping:
comparison.getAllAtomMapping()) {
- IAtomContainer match = getMatchedSubgraph(mol1,
mapping);
- matchList.add(match);
- }
- return maximumStructure(matchList);
- }
-
- private synchronized IAtomContainer
getMatchedSubgraph(IAtomContainer container, Map<IAtom, IAtom> matches) {
- IAtomContainer needle =
container.getBuilder().newInstance(IAtomContainer.class, container);
- // Every atom in our structure that *doesn't* have an
entry in the matches map should be removed
- List<IAtom> atomListToBeRemoved = new
ArrayList<IAtom>();
- for (IAtom containerAtom : container.atoms()) {
- if (!matches.containsKey(containerAtom)) {
- int index =
container.getAtomNumber(containerAtom);
-
atomListToBeRemoved.add(needle.getAtom(index));
- }
- }
- for (IAtom removeAtom : atomListToBeRemoved) {
-
needle.removeAtomAndConnectedElectronContainers(removeAtom);
- }
- return needle;
- }
-
- private synchronized IMolecule
maximumStructure(List<IAtomContainer> mcsslist) {
- int maxmcss = -99999999;
- IAtomContainer maxac = null;
- int fragment = 1;
- if (mcsslist == null || mcsslist.size() == 0) return
null;
- for (IAtomContainer a: mcsslist) {
- if (a.getAtomCount() > maxmcss) {
- maxmcss = a.getAtomCount();
- maxac = a;
- }
- }
- return new Molecule(maxac);
- }
-
- public IAtomContainer get() {
- if (innerMcss == null)
- return call();
- else
- return innerMcss;
- }
- }
}
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/SMARTSSearchTask.java
===================================================================
---
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/SMARTSSearchTask.java
2013-02-15 22:35:56 UTC (rev 31125)
+++
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/SMARTSSearchTask.java
2013-02-19 18:44:38 UTC (rev 31126)
@@ -118,7 +118,7 @@
try {
SMARTSQueryTool queryTool = new
SMARTSQueryTool(searchString);
for (Compound compound: cList) {
- boolean status =
queryTool.matches(compound.getIMolecule());
+ boolean status =
queryTool.matches(compound.getIAtomContainer());
if (status && queryTool.countMatches()
> 0)
matches.add(compound);
}
Added: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/Fragment.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/Fragment.java
(rev 0)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/Fragment.java
2013-02-19 18:44:38 UTC (rev 31126)
@@ -0,0 +1,110 @@
+
+/*
+ * Copyright (C) 2009-2013 Syed Asad Rahman <[email protected]>
+ *
+ * Contact: [email protected]
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ * All we ask is that proper credit is given for our work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may
distribute
+ * with programs based on this work.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package tools.mcss;
+
+import java.util.BitSet;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.fingerprint.ShortestPathFingerprinter;
+import org.openscience.cdk.interfaces.IAtomContainer;
+
+/**
+ *
+ * @author Syed Asad Rahman <[email protected]>
+ *
+ */
+final public class Fragment implements Comparable<Fragment> {
+
+ public synchronized IAtomContainer getContainer() {
+ return container;
+ }
+ private BitSet fingerprint;
+ private long fingerprintAsLong;
+ private final IAtomContainer container;
+
+ public Fragment(IAtomContainer container) throws CDKException {
+ if (container == null) {
+ throw new CDKException("NULL container not supported");
+ }
+ ShortestPathFingerprinter spf = new ShortestPathFingerprinter(1024);
+ this.container = container;
+ this.fingerprint = spf.getBitFingerprint(container).asBitSet();
+ this.fingerprintAsLong = convert(this.fingerprint);
+ }
+
+ @Override
+ public synchronized boolean equals(Object obj) {
+ if (obj == null) {
+ return false;
+ }
+ if (getClass() != obj.getClass()) {
+ return false;
+ }
+ final Fragment other = (Fragment) obj;
+
+ if (this.container != other.container && (this.container == null ||
(this.container.getAtomCount() != other.container.getAtomCount()))) {
+ return false;
+ }
+
+ if (this.fingerprint != other.fingerprint && (this.fingerprint == null
|| !this.fingerprint.equals(other.fingerprint))) {
+ return false;
+ }
+ if (this.fingerprintAsLong != other.fingerprintAsLong) {
+ return false;
+ }
+
+ return true;
+ }
+
+ @Override
+ public synchronized int hashCode() {
+ int hash = 3;
+ hash = 47 * hash + (this.fingerprint != null ?
this.fingerprint.hashCode() : 0);
+ hash = 47 * hash + (int) (this.fingerprintAsLong ^
(this.fingerprintAsLong >>> 32));
+ return hash;
+ }
+
+ @Override
+ public synchronized int compareTo(Fragment t) {
+
+ if (this.fingerprintAsLong == t.fingerprintAsLong) {
+ return 0;
+ } else if (this.fingerprintAsLong > t.fingerprintAsLong) {
+ return 1;
+ } else {
+ return -1;
+ }
+ }
+
+ private synchronized long convert(BitSet bits) {
+ long value = 0L;
+ if (bits == null || bits.isEmpty()) {
+ return value;
+ }
+ for (int i = 0; i < bits.length(); ++i) {
+ value += bits.get(i) ? (1L << i) : 0L;
+ }
+ return value;
+ }
+}
Added: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/JobType.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/JobType.java
(rev 0)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/JobType.java
2013-02-19 18:44:38 UTC (rev 31126)
@@ -0,0 +1,46 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package tools.mcss;
+
+/**
+ *
+ * @author Asad
+ */
+public enum JobType implements Comparable<JobType> {
+
+ /**
+ * Default MCS algorithm.
+ */
+ MCS(0, "MCS search"),
+ /**
+ * Substructure search algorithm.
+ */
+ Substructure(1, "Substructure search");
+ private final int type;
+ private final String description;
+
+ JobType(int aStatus, String desc) {
+ this.type = aStatus;
+ this.description = desc;
+ }
+
+ /**
+ * Returns type of algorithm.
+ *
+ * @return type of algorithm
+ */
+ public int type() {
+ return this.type;
+ }
+
+ /**
+ * Returns short description of the algorithm.
+ *
+ * @return description of the algorithm
+ */
+ public String description() {
+ return this.description;
+ }
+}
Added: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/MCSS.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/MCSS.java
(rev 0)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/MCSS.java
2013-02-19 18:44:38 UTC (rev 31126)
@@ -0,0 +1,141 @@
+/**
+ * Copyright (C) 2009-2013 Syed Asad Rahman <[email protected]>
+ *
+ * Contact: [email protected]
+ *
+ * This program is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General
+ * Public License as published by the Free Software Foundation; either version
2.1 of the License, or (at your option)
+ * any later version. All we ask is that proper credit is given for our work,
which includes - but is not limited to -
+ * adding the above copyright notice to the beginning of your source code
files, and to any copyright notice that you
+ * may distribute with programs based on this work.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied
+ * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
along with this program; if not, write to
+ * the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
02110-1301 USA.
+ */
+package tools.mcss;
+
+import cmd.AtomContainerComparator;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import org.openscience.cdk.interfaces.IAtomContainer;
+
+/**
+ *
+ * @author Syed Asad Rahman <[email protected]>
+ *
+ */
+final public class MCSS {
+
+ private final List<IAtomContainer> calculateMCSS;
+ private TaskUpdater updater;
+ private double percentDone = 0.01;
+
+ public MCSS(List<IAtomContainer> jobList, JobType jobType, TaskUpdater
updater, int numberOfThreads) {
+ this.updater = updater;
+ int threadsAvailable = Runtime.getRuntime().availableProcessors() - 1;
+ if (numberOfThreads > 0) {
+ threadsAvailable = numberOfThreads;
+ }
+ if (updater != null)
updater.updateStatus("Calculating MCSS using "+threadsAvailable+" threads");
+ Comparator<IAtomContainer> comparator = new AtomContainerComparator();
+ Collections.sort(jobList, comparator);
+ calculateMCSS = calculateMCSS(jobList, jobType, threadsAvailable);
+ }
+
+ private synchronized List<IAtomContainer>
calculateMCSS(List<IAtomContainer> mcssList, JobType jobType, int nThreads) {
+ if (updater != null) {
+ updater.setTotalCount(mcssList.size());
+ updater.incrementCount();
+ }
+
+ List<IAtomContainer> newMCSSList = Collections.synchronizedList(new
ArrayList<IAtomContainer>(nThreads));
+ if (nThreads == 1) {
+ MCSSThread task = new MCSSThread(mcssList, jobType, updater, 1);
+ List<IAtomContainer> results = task.call();
+ if (results != null) {
+ newMCSSList.addAll(results);
+ }
+ return newMCSSList;
+ } else {
+ /*
+ * Calling recursive MCS
+ */
+ newMCSSList = submitMultiThreadedJob(mcssList, jobType, updater,
nThreads);
+ while (newMCSSList.size() > 1) {
+ if (newMCSSList.size() > 2) {
+ newMCSSList = submitMultiThreadedJob(newMCSSList, jobType,
updater, nThreads);
+ } else {
+ newMCSSList = submitMultiThreadedJob(newMCSSList, jobType,
updater, 1);
+ }
+ }
+ }
+ return newMCSSList;
+ }
+
+ /**
+ * @return the calculateMCSS
+ */
+ public synchronized List<IAtomContainer> getCalculateMCSS() {
+ return Collections.unmodifiableList(calculateMCSS);
+ }
+
+ private synchronized List<IAtomContainer>
submitMultiThreadedJob(List<IAtomContainer> mcssList,
+ JobType
jobType, TaskUpdater updater, int nThreads) {
+ int taskNumber = 1;
+ List<IAtomContainer> newMCSSList = Collections.synchronizedList(new
ArrayList<IAtomContainer>(nThreads));
+ List<Future<List<IAtomContainer>>> futureList = new
ArrayList<Future<List<IAtomContainer>>>();
+ ExecutorService threadPool = Executors.newFixedThreadPool(nThreads);
+ int step = (int) Math.ceil((double) mcssList.size() / (double)
nThreads);
+ if (step < 2) {
+ step = 2; // Can't have a step size of less than 2
+ }
+ for (int i = 0; i < mcssList.size(); i += step) {
+ int endPoint = i + step;
+ if (endPoint > mcssList.size()) {
+ endPoint = mcssList.size();
+ }
+ List<IAtomContainer> subList = new
ArrayList<IAtomContainer>(mcssList.subList(i, endPoint));
+ if (subList.size() > 1) {
+ MCSSThread mcssJobThread = new MCSSThread(subList, jobType,
updater, taskNumber++);
+ Future<List<IAtomContainer>> callMCSSThread =
threadPool.submit(mcssJobThread);
+ futureList.add(callMCSSThread);
+ } else {
+ newMCSSList.add(subList.get(0));
+ }
+ }
+
+ for (Future<List<IAtomContainer>> results : futureList) {
+
+ if (results == null) {
+ continue;
+ }
+ try {
+ List<IAtomContainer> f = results.get();
+ if (f != null) {
+ newMCSSList.addAll(results.get());
+ }
+ } catch (Exception e) {
+
Logger.getLogger(MCSSThread.class.getName()).log(Level.WARNING, "Execution
exception: {0}", e);
+ }
+
+ }
+
+ threadPool.shutdown();
+ return newMCSSList;
+ }
+
+ public synchronized String getTitle() {
+ return "Calculating Maximum Commmon Substrutures (MCSS)";
+ }
+}
Added:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/MCSSThread.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/MCSSThread.java
(rev 0)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/MCSSThread.java
2013-02-19 18:44:38 UTC (rev 31126)
@@ -0,0 +1,149 @@
+/**
+ * Copyright (C) 2009-2013 Syed Asad Rahman <[email protected]>
+ *
+ * Contact: [email protected]
+ *
+ * This program is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General
+ * Public License as published by the Free Software Foundation; either version
2.1 of the License, or (at your option)
+ * any later version. All we ask is that proper credit is given for our work,
which includes - but is not limited to -
+ * adding the above copyright notice to the beginning of your source code
files, and to any copyright notice that you
+ * may distribute with programs based on this work.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied
+ * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
along with this program; if not, write to
+ * the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
02110-1301 USA.
+ */
+package tools.mcss;
+
+import java.util.*;
+import java.util.concurrent.Callable;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.smiles.SmilesGenerator;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
+import org.openscience.smsd.AtomAtomMapping;
+import org.openscience.smsd.BaseMapping;
+import org.openscience.smsd.Isomorphism;
+import org.openscience.smsd.Substructure;
+import org.openscience.smsd.interfaces.Algorithm;
+
+/**
+ *
+ * @author Syed Asad Rahman <[email protected]>
+ *
+ */
+final public class MCSSThread implements Callable<List<IAtomContainer>> {
+
+ private final List<IAtomContainer> mcssList;
+ private final JobType jobType;
+ private int taskNumber = 0;
+ private TaskUpdater updater = null;
+
+ /**
+ *
+ * @param mcssList
+ * @param jobType MCS/Substructure
+ * @param taskNumber
+ */
+ public MCSSThread(List<IAtomContainer> mcssList, JobType jobType,
TaskUpdater updater, int taskNumber) {
+ this.mcssList = mcssList;
+ this.jobType = jobType;
+ this.taskNumber = taskNumber;
+ this.updater = updater;
+ }
+
+ @Override
+ public synchronized List<IAtomContainer> call() {
+
+// System.out.println("Calling MCSSTask " + taskNumber + " with " +
mcssList.size() + " items");
+ List<IAtomContainer> resultsList = new ArrayList<IAtomContainer>();
+ long startTime = Calendar.getInstance().getTimeInMillis();
+ IAtomContainer querySeed =
AtomContainerManipulator.removeHydrogens(mcssList.get(0));
+ long calcTime = startTime;
+
+
+ try {
+ for (int index = 1; index < mcssList.size(); index++) {
+ IAtomContainer target =
AtomContainerManipulator.removeHydrogens(mcssList.get(index));
+ Collection<Fragment> fragmentsFomMCS;
+ if (this.jobType == JobType.MCS) {
+ Isomorphism comparison = new Isomorphism(querySeed,
target, Algorithm.DEFAULT, true, true);
+ comparison.setChemFilters(true, true, true);
+ fragmentsFomMCS = getMCSS(comparison);
+ } else {
+ Substructure comparison = new Substructure(querySeed,
target, true, true, false);
+ comparison.setChemFilters(true, true, true);
+ fragmentsFomMCS = getMCSS(comparison);
+ }
+// System.out.println("MCSS for task " + taskNumber + " has " +
querySeed.getAtomCount() + " atoms, and " + querySeed.getBondCount() + "
bonds");
+// System.out.println("Target for task " + taskNumber + " has "
+ target.getAtomCount() + " atoms, and " + target.getBondCount() + " bonds");
+
+
+ long endCalcTime = Calendar.getInstance().getTimeInMillis();
+// System.out.println("Task " + taskNumber + " index " + index
+ " took " + (endCalcTime - calcTime) + "ms");
+ calcTime = endCalcTime;
+
+ if (querySeed == null || querySeed.getAtomCount() == 0) {
+ break;
+ }
+// System.out.println("comparison for task " + taskNumber + "
has " + fragmentsFomMCS.size()
+// + " unique matches of size " +
comparison.getFirstAtomMapping().getCount());
+ querySeed = fragmentsFomMCS.iterator().next().getContainer();
+ if (updater != null) updater.incrementCount();
+ }
+
+ } catch (Exception e) {
+ Logger.getLogger(MCSSThread.class.getName()).log(Level.SEVERE,
null, e);
+ if (updater != null)
updater.logException(MCSSThread.class.getName(),Level.SEVERE, null, e);
+ }
+ if (resultsList != null) {
+ resultsList.add(querySeed);
+ }
+
+ long endTime = Calendar.getInstance().getTimeInMillis();
+// System.out.print("Done: task " + taskNumber + " took " + (endTime -
startTime) + "ms");
+// System.out.println(" and mcss has " + querySeed.getAtomCount() + "
atoms, and " + querySeed.getBondCount() + " bonds");
+ return resultsList;
+ }
+
+ private synchronized Collection<Fragment> getMCSS(BaseMapping comparison) {
+ Set<Fragment> matchList = new HashSet<Fragment>();
+ // System.out.println("Found "+comparison.getAllAtomMapping().size()+"
mappings");
+ for (AtomAtomMapping mapping : comparison.getAllAtomMapping()) {
+ //IAtomContainer match = getMatchedSubgraph(mol1,
mapping.getMappings());
+ IAtomContainer match;
+ try {
+ match = mapping.getCommonFragmentInQuery();
+ try {
+ matchList.add(new Fragment(match));
+ } catch (CDKException ex) {
+
Logger.getLogger(MCSSThread.class.getName()).log(Level.SEVERE, null, ex);
+ if (updater != null)
updater.logException(MCSSThread.class.getName(),Level.SEVERE, null, ex);
+ }
+ } catch (CloneNotSupportedException ex) {
+ Logger.getLogger(MCSSThread.class.getName()).log(Level.SEVERE,
null, ex);
+ if (updater != null)
updater.logException(MCSSThread.class.getName(),Level.SEVERE, null, ex);
+ }
+ // System.out.println("match has "+match.getAtomCount()+" atoms,
and "+match.getBondCount()+" bonds");
+ }
+
+ return matchList;
+ }
+
+ /**
+ * Return SMILES
+ *
+ * @param ac
+ * @return
+ */
+ public synchronized String getMCSSSmiles(IAtomContainer ac) {
+ SmilesGenerator g = new SmilesGenerator();
+ g.setUseAromaticityFlag(true);
+ return g.createSMILES(ac);
+ }
+}
Added:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/TaskUpdater.java
===================================================================
---
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/TaskUpdater.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tools/mcss/TaskUpdater.java
2013-02-19 18:44:38 UTC (rev 31126)
@@ -0,0 +1,42 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package tools.mcss;
+
+import java.util.logging.Level;
+
+/**
+ *
+ * @author Scooter
+ */
+public interface TaskUpdater {
+
+ /**
+ * Set the number of iterations.
+ *
+ * @param nIterations
+ **/
+ public void setTotalCount(int nIterations);
+
+ /**
+ * Update the count
+ **/
+ public void incrementCount();
+
+ /**
+ * Update the status message
+ **/
+ public void updateStatus(String status);
+
+ /**
+ * This logs an exception and provides a mechanism
+ * for tools to integrate with the caller's logging mechanism
+ *
+ * @param className the class name of the reporter
+ * @param level the level of the error
+ * @param message the log message
+ * @param exception the exception itself
+ */
+ public void logException(String className, Level level, String message,
Exception exception);
+}
Modified: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ui/CompoundTable.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ui/CompoundTable.java
2013-02-15 22:35:56 UTC (rev 31125)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ui/CompoundTable.java
2013-02-19 18:44:38 UTC (rev 31126)
@@ -395,7 +395,7 @@
try {
SMARTSQueryTool queryTool = new
SMARTSQueryTool(smartsQuery);
for (Compound compound: compoundList) {
- boolean status =
queryTool.matches(compound.getIMolecule());
+ boolean status =
queryTool.matches(compound.getIAtomContainer());
if (status && queryTool.countMatches()
> 0)
matches.add(compound);
}
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