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

[Jing Lu <aj...@gm...>]

Yes, you are right. The new version has no problem.



Thanks,
Jing

On Mon, Feb 15, 2016 at 8:25 AM, Till Schäfer <til...@tu...
> wrote:

> 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
> fax: +49(231)755-7740
> web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer
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