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

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

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)