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

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Hi, 
the stack trace below only shows an error in the import process (maybe just for a single molecule), but no error for the molecule cloud. Can you please describe in more detail, what the problem is, that you are facing in the molecule cloud? How large is the subset you try to render?

Regards,
Till

Am Dienstag, 16. Februar 2016, 13:44:10 schrieben Sie:
> 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
> >
-- 
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