Re: [Scaffoldhunter-users] Is ScaffoldHunter not able to deal with more than 20, 000 molecules?

[Till S. <til...@tu...>]

Hi, 
the observed issue is not caused by the dataset size, but is a bug in the cdk library. Which version of SH are you using? The new SH version 2.6.0 has a new version of the cdk library. So if you are still using 2.5.1 or below, please try the new version.

Regards, 
Till Schäfer

Am Freitag, 12. Februar 2016, 12:17:55 CET schrieb Jing Lu:
> Hi Scaffold Hunters,
> 
> I have a dataset with >20,000 molecules. The software froze after loading
> about 6,000 molecules and gave me the following error (part of the error).
> 
> Is there any way to get around this?
> 
> Thanks,
> Jing
> 
> ble.actionPerformed(SwingWorker.java:958)
>         at javax.swing.Timer.fireActionPerformed(Unknown Source)
>         at javax.swing.Timer$DoPostEvent.run(Unknown Source)
>         at java.awt.event.InvocationEvent.dispatch(Unknown Source)
>         at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
>         at java.awt.EventQueue.access$500(Unknown Source)
>         at java.awt.EventQueue$3.run(Unknown Source)
>         at java.awt.EventQueue$3.run(Unknown Source)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionP
> rivilege(Unknown Source)
>         at java.awt.EventQueue.dispatchEvent(Unknown Source)
>         at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown
> Source)
>         at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
>         at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
> Source)
>         at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>         at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>         at java.awt.EventDispatchThread.run(Unknown Source)
> Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
>         at java.lang.AbstractStringBuilder.<init>(Unknown Source)
>         at java.lang.StringBuffer.<init>(Unknown Source)
>         at org.openscience.cdk.silent.AtomType.toString(AtomType.java:366)
>         at org.openscience.cdk.silent.Atom.toString(Atom.java:386)
>         at java.lang.String.valueOf(Unknown Source)
>         at java.lang.StringBuilder.append(Unknown Source)
>         at
> org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis$AuxiliaryG
> raph.auxVertex1(SimpleCycleBasis.java:854)
>         at
> org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis$AuxiliaryG
> raph.edgesOf(SimpleCycleBasis.java:831)
>         at
> org._3pq.jgrapht.traverse.CrossComponentIterator$UndirectedSpecifics.
> edgesOf(Unknown Source)
>         at
> org._3pq.jgrapht.traverse.CrossComponentIterator.addUnseenChildrenOf(
> Unknown Source)
>         at org._3pq.jgrapht.traverse.CrossComponentIterator.next(Unknown
> Source)
> 
>         at
> org.openscience.cdk.graph.MinimalPathIterator.createShortestPathGraph
> (MinimalPathIterator.java:143)
>         at
> org.openscience.cdk.graph.MinimalPathIterator.<init>(MinimalPathItera
> tor.java:78)
>         at
> org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis.relevantCy
> cles(SimpleCycleBasis.java:557)
>         at
> org.openscience.cdk.ringsearch.cyclebasis.CycleBasis.relevantCycles(C
> ycleBasis.java:239)
>         at
> org.openscience.cdk.ringsearch.SSSRFinder.findRelevantRings(SSSRFinde
> r.java:122)
>         at
> edu.udo.scaffoldhunter.model.util.SVGGen.calcSVGString(SVGGen.java:16
> 0)
>         at edu.udo.scaffoldhunter.model.util.SVGGen.getSVG(SVGGen.java:107)
>         at
> edu.udo.scaffoldhunter.model.dataimport.MergeIterator.newMolecule(Mer
> geIterator.java:360)
>         at
> edu.udo.scaffoldhunter.model.db.DbManagerHibernate.mergeMoleculesInto
> DBbySMILES(DbManagerHibernate.java:2545)
>         at
> edu.udo.scaffoldhunter.model.dataimport.Importer$MergeWorker.doInBack
> ground(Importer.java:426)
>         at
> edu.udo.scaffoldhunter.model.dataimport.Importer$MergeWorker.doInBack
> ground(Importer.java:373)
>         at
> edu.udo.scaffoldhunter.gui.util.SwingWorker$1.call(SwingWorker.java:3
> 18)
>         at java.util.concurrent.FutureTask.run(Unknown Source)
>         at
> edu.udo.scaffoldhunter.gui.util.SwingWorker$2.run(SwingWorker.java:32
> 5)
>         at
> edu.udo.scaffoldhunter.gui.util.SwingWorker.run(SwingWorker.java:362)
> 
>         at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
>         at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown
> Source)
>         at java.lang.Thread.run(Unknown Source)
> 
-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
44227 Dortmund, Germany

e-mail: til...@cs...
phone: +49(231)755-7706
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