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

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Hi, ScaffoldHunter developers

For molecule cloud function, I got the following error:

150828 [SwingWorker-pool-441706900-thread-4] INFO
 net.sf.jnati.deploy.artefact.
ConfigManager  - Loading global configuration
150828 [SwingWorker-pool-441706900-thread-4] DEBUG
net.sf.jnati.deploy.artefact.
ConfigManager  - Loading defaults:
jar:file:/C:/Users/ajing/Documents/CompareMet
hods/scaffold-hunter-2.6.0/lib/cdk/cdk-1.5.13-SNAPSHOT-custom.jar!/META-INF/jnat
i/jnati.default-properties
150828 [SwingWorker-pool-441706900-thread-4] INFO
 net.sf.jnati.deploy.artefact.
ConfigManager  - Loading artefact configuration: jniinchi-1.03_1
150828 [SwingWorker-pool-441706900-thread-4] DEBUG
net.sf.jnati.deploy.artefact.
ConfigManager  - Loading instance defaults: jar:file:/C:/Users//Documents/C
ompareMethods/scaffold-hunter-2.6.0/lib/cdk/cdk-1.5.13-SNAPSHOT-custom.jar!/META
-INF/jnati/jnati.instance.default-properties
150828 [SwingWorker-pool-441706900-thread-4] INFO
 net.sf.jnati.deploy.repositor
y.ClasspathRepository  - Searching classpath for:
jniinchi-1.03_1-WINDOWS-AMD64
150828 [SwingWorker-pool-441706900-thread-4] INFO
 net.sf.jnati.deploy.repositor
y.LocalRepository  - Searching local repository for:
jniinchi-1.03_1-WINDOWS-AMD
64
150828 [SwingWorker-pool-441706900-thread-4] DEBUG
net.sf.jnati.deploy.repositor
y.LocalRepository  - Artefact path: C:\Users\\.jnati\repo\jniinchi\1.03_1\W
INDOWS-AMD64
150828 [SwingWorker-pool-441706900-thread-4] INFO
 net.sf.jnati.deploy.repositor
y.LocalRepository  - Creating artefact: C:\Users\\.jnati\repo\jniinchi\1.03
_1\WINDOWS-AMD64
150843 [SwingWorker-pool-441706900-thread-4] DEBUG
net.sf.jnati.deploy.source.Ja
rSource  - Opening jar: C:\Users\\Documents\CompareMethods\scaffold-hunter-
2.6.0\lib\cdk\cdk-1.5.13-SNAPSHOT-custom.jar
150843 [SwingWorker-pool-441706900-thread-4] INFO
 net.sf.jnati.deploy.artefact.
ManifestReader  - Reading manifest
150890 [SwingWorker-pool-441706900-thread-4] INFO
 net.sf.jnati.deploy.resolver.
ArtefactResolver  - Copying files to repository: C:\Users\\.jnati\repo\jnii
nchi\1.03_1\WINDOWS-AMD64
151109 [SwingWorker-pool-441706900-thread-4] INFO
 net.sf.jnati.deploy.NativeArt
efactLocator  - Artefact (jniinchi-1.03_1-WINDOWS-AMD64) location:
C:\Users\ajin
g\.jnati\repo\jniinchi\1.03_1\WINDOWS-AMD64
151109 [SwingWorker-pool-441706900-thread-4] DEBUG
net.sf.jnati.deploy.NativeLib
raryLoader  - Loading library: C:\Users\\.jnati\repo\jniinchi\1.03_1\WINDOW
S-AMD64\JniInchi-1.03_1-WINDOWS-AMD64.dll
Feb 15, 2016 11:09:52 AM
edu.udo.scaffoldhunter.model.util.CanonicalSmilesGenera
tor createSMILES
SEVERE: Smiles generation failed
org.openscience.cdk.exception.CDKException: An InChI could not be generated
and
used to canonise SMILES: null
        at
org.openscience.cdk.smiles.SmilesGenerator.inchiNumbers(SmilesGenerat
or.java:503)
        at
org.openscience.cdk.smiles.SmilesGenerator.labels(SmilesGenerator.jav
a:471)
        at
org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.jav
a:375)
        at
org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.jav
a:325)
        at
edu.udo.scaffoldhunter.model.util.CanonicalSmilesGenerator.createSMIL
ES(CanonicalSmilesGenerator.java:73)
        at
edu.udo.scaffoldhunter.model.dataimport.MergeIterator.getNextMolecule
(MergeIterator.java:517)
        at
edu.udo.scaffoldhunter.model.dataimport.MergeIterator.next(MergeItera
tor.java:306)

On Mon, Feb 15, 2016 at 12:27 PM, Till Schäfer <
til...@tu...> wrote:

> 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
>