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

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

Hi, 
glad to hear, that it works with the new version. 

THX for sharing the info,
Till

Am Montag, 15. Februar 2016, 11:27:25 schrieb Jing Lu:
> 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
> > pgp:
> > https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84DED79
> >
-- 
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
pgp: https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84DED79