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From: abhik <ab...@eb...> - 2018-04-25 19:52:30
|
Dear Till, Thank you very much. I will try this from command line and let you know. Regards, Abhik On 2018-04-25 13:55, Till Schäfer wrote: > Hi Abhik, > > this is not supported by the GUI, but can be done via the command line > interface. Please run > > java -jar scaffoldhunter-XXX.jar > edu.udo.scaffoldhunter.cli.ScaffoldGenerator --help > > for more information. This will generate and output a tree for a given > dataset. > > Regards, > Till > > On Dienstag, 24. April 2018 15:48:02 CEST abhik wrote: >> Hi, >> >> I am using Scaffold hunter to generate scaffold tree for a chemical >> dataset. Is there any way to export the smiles of the scaffolds that >> have been generated. >> >> Thanks, >> Abhik >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Scaffoldhunter-users mailing list >> Sca...@li... >> https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users >> |
|
From: Till S. <til...@tu...> - 2018-04-25 13:53:38
|
Hi Abhik, this is not supported by the GUI, but can be done via the command line interface. Please run java -jar scaffoldhunter-XXX.jar edu.udo.scaffoldhunter.cli.ScaffoldGenerator --help for more information. This will generate and output a tree for a given dataset. Regards, Till On Dienstag, 24. April 2018 15:48:02 CEST abhik wrote: > Hi, > > I am using Scaffold hunter to generate scaffold tree for a chemical > dataset. Is there any way to export the smiles of the scaffolds that > have been generated. > > Thanks, > Abhik > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Scaffoldhunter-users mailing list > Sca...@li... > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users > -- 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 |
|
From: abhik <ab...@eb...> - 2018-04-24 13:48:12
|
Hi, I am using Scaffold hunter to generate scaffold tree for a chemical dataset. Is there any way to export the smiles of the scaffolds that have been generated. Thanks, Abhik |
|
From: <nic...@in...> - 2016-08-02 14:05:52
|
Hi Nils, Do you think it is possible or not? :) Your last sentence let me think it is, but reading again the help of each existing rules I don't see how. Regards, Nicolas On 02-08-2016 09:09, nl...@us... wrote: > Hi Nicolas, > > unfortunately this is not possible. Whenever the custom rules are not > sufficient to determine a unique parent scaffold, a tie-break rule is > applied. > This is repeated until a scaffold with a single ring is obtained. In > general, > all scaffold with the same number of rings have the same depth in the > scaffold > tree. > > However, it should be possible to define a set of rules such that fused > rings > are preserved until no other rings can be removed. > > > Regards, > Nils > > > > > > On Thursday 28 July 2016 11:57:54 nic...@in... wrote: >> Hello, >> >> I use scaffold hunter for a few days and despite some difficulties for >> using it I think it is a great tool for scaffold generations and tree >> visualization. >> >> I read the manual and also took a look of the related articles but I >> have some issues to use the ruleset management. Basically, when I >> generate the tree, I would like not to split "fused rings". >> >> As an example, in J. Chem. Inf. Model., 2007, 47 (1), pp 47–58, in >> scheme 18, I would like the molecules with the "fused rings" to be the >> smallest scaffolds. Could tell me how to perform? >> >> Thank you for any help. >> >> >> Regards, >> >> Nicolas >> >> ---------------------------------------------------------------------------- >> -- _______________________________________________ >> Scaffoldhunter-users mailing list >> Sca...@li... >> https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users > > ------------------------------------------------------------------------------ > _______________________________________________ > Scaffoldhunter-users mailing list > Sca...@li... > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users |
|
From: <nl...@us...> - 2016-08-02 13:11:50
|
Hi Nicolas, unfortunately this is not possible. Whenever the custom rules are not sufficient to determine a unique parent scaffold, a tie-break rule is applied. This is repeated until a scaffold with a single ring is obtained. In general, all scaffold with the same number of rings have the same depth in the scaffold tree. However, it should be possible to define a set of rules such that fused rings are preserved until no other rings can be removed. Regards, Nils On Thursday 28 July 2016 11:57:54 nic...@in... wrote: > Hello, > > I use scaffold hunter for a few days and despite some difficulties for > using it I think it is a great tool for scaffold generations and tree > visualization. > > I read the manual and also took a look of the related articles but I > have some issues to use the ruleset management. Basically, when I > generate the tree, I would like not to split "fused rings". > > As an example, in J. Chem. Inf. Model., 2007, 47 (1), pp 47–58, in > scheme 18, I would like the molecules with the "fused rings" to be the > smallest scaffolds. Could tell me how to perform? > > Thank you for any help. > > > Regards, > > Nicolas > > ---------------------------------------------------------------------------- > -- _______________________________________________ > Scaffoldhunter-users mailing list > Sca...@li... > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users |
|
From: <nic...@in...> - 2016-07-28 10:15:38
|
Hello, I use scaffold hunter for a few days and despite some difficulties for using it I think it is a great tool for scaffold generations and tree visualization. I read the manual and also took a look of the related articles but I have some issues to use the ruleset management. Basically, when I generate the tree, I would like not to split "fused rings". As an example, in J. Chem. Inf. Model., 2007, 47 (1), pp 47–58, in scheme 18, I would like the molecules with the "fused rings" to be the smallest scaffolds. Could tell me how to perform? Thank you for any help. Regards, Nicolas |
|
From: Till S. <til...@tu...> - 2016-02-17 17:38:30
|
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 |
|
From: Jing Lu <aj...@gm...> - 2016-02-16 18:44:38
|
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
>
|
|
From: Till S. <til...@tu...> - 2016-02-15 17:27:24
|
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 |
|
From: Jing Lu <aj...@gm...> - 2016-02-15 16:27:52
|
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 > |
|
From: Till S. <til...@tu...> - 2016-02-15 13:25:40
|
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 |
|
From: Jing Lu <aj...@gm...> - 2016-02-12 17:18:22
|
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)
|
|
From: Till S. <til...@tu...> - 2015-09-29 08:24:52
|
Hi, you can configure the tooltip delay under "session -> preferences -> general configuration" searching is not implemented yet, but you can sort the table view by a property and find the desired molecule thereby. The views selection is synchonised. Therefore, it is possible to select the appropriate molecule(s) in the table view and your will find them highlighted in the scaffoldtreeview, too. Viele Grüße Till Am Montag, 28. September 2015, 11:19:03 schrieben Sie: > Thanks, Till and Shamshad, > > Ctrl-M is very helpful and also the tooltip dialog. But, I need to wait for > a while for tooltip to show up. I also find the table view useful as I need > to find a particular molecule. Does Scaffold Hunter have function for > searching? > > > Best, > Jing > > On Mon, Sep 28, 2015 at 5:56 AM, Till Schäfer <til...@tu... > > wrote: > > > Dear Jing, > > > > As Shamshad already said, the Scaffold Tree View only displays scaffolds > > of the imported molecules, but you can toggle the display of the molecules > > which are assigned to the scaffold nodes. If you like to learn more about > > the chemical purpose of the scaffold tree you can read the publication [1]. > > The molecules are shown directly in other views such as the heatmap, table, > > dendrogram and plot view. > > > > > > > > To keep track of your imported data, you have to do two steps: > > > > 1. Ensure that you import the ID as a property together with your > > molecules (see the manual.pdf file contained in the Scaffold Hunter zip > > bundle for further details) > > > > 2. Configure the Tool-Tip-Dialog to display them (Menu: Session -> > > Configure Tooltip) or use the table view > > > > > > > > The ID will be not displayed for scaffolds but for molecules, as the > > scaffolds are generated and not contained in the input data. > > > > > > > > If you are importing smiles data, Scaffold Hunter re-generates the smiles > > in order to calculate canonical smiles (to keep track of the molecules). > > This smiles might be different from your input data, as there may exist > > different correct smiles for a single molecule. If you want to keep your > > old smiles string, please import it as a property. You will then be able to > > see both, the canonical smiles generated from Scaffold Hunter and the > > original smiles from your imported data. > > > > > > > > @Shamshad: thx for explaining the scaffold tree > > > > > > > > Regards, > > > > Till > > > > > > > > [1] Interactive exploration of chemical space with Scaffold Hunter > > Stefan Wetzel, Karsten Klein, Steffen Renner, Daniel Rauh, Tudor I. Oprea, > > Petra Mutzel, Herbert Waldmann > > Nature Chemical Biology, 2009, 5, 581-583 > > > > > > > > Am Samstag, 26. September 2015, 23:31:53 schrieb Shamshad Alam: > > > > > Hi Jing, > > > > > > > > > > I contributed to scaffold hunter a year ago and worked on some feature > > > > > requests. > > > > > > > > > > As far as I know scaffolds are generated by pruning terminal chains and > > > > > thereafter cycles. So SMILE string is likely to differ from original > > > > > molecules. > > > > > > > > > > >> How to keep track of the exact molecule? > > > > > Tree view only shows scaffolds by default. If you want to see molecules > > > > > too, press Ctrl + M, or in Tree menu check 'Show Scaffold Molecules'. I > > > > > guess it might help you. > > > > > > > > > > >> Does Scaffold Hunter convert the original input molecules to a > > scaffold > > > > > first? > > > > > It does when you generate scaffold tree. > > > > > > > > > > >> Because, when I was checking the leaf nodes, the structure does not > > > > > really exist in my input file. How to interpret that? > > > > > In scaffold view at the leaf node what you see may exist as a > > substructure > > > > > of one or more molecules. > > > > > > > > > > I hope it will help you and clear your some doubts. If you have any > > further > > > > > queries let us know. > > > > > > > > > > > > > > > Cheers, > > > > > Shamshad > > > > > > > > > > On Sat, Sep 26, 2015 at 9:29 PM, Jing Lu <aj...@gm...> wrote: > > > > > > > > > > > Dear Scaffold Hunter developers, > > > > > > > > > > > > > > > > > > Sorrry to send this again. But, I am not sure where to ask questions. I > > > > > > try to put ligand id to tooltip to keep track of each molecule. It > > seems > > > > > > like impossible. Moreover, I find Scaffold Hunter changes the SMILE > > string > > > > > > I put in the input file. How to keep track of the exact molecule? > > > > > > > > > > > > Does Scaffold Hunter convert the original input molecules to a scaffold > > > > > > first? Because, when I was checking the leaf nodes, the structure does > > not > > > > > > really exist in my input file. How to inteperate that? > > > > > > > > > > > > > > > > > > > > > > > > Thanks, > > > > > > Jing > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------------ > > > > > > > > > > > > _______________________________________________ > > > > > > Scaffoldhunter-devel mailing list > > > > > > Sca...@li... > > > > > > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-devel > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > 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 |
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From: Jing Lu <aj...@gm...> - 2015-09-25 21:22:16
|
Dear Scaffold Hunter developers, I try to put ligand id to tooltip to keep track of each molecule. It seems like not possible. Moreover, I find Scaffold Hunter even change the SMILE string I put in the input file. How to keep track of the exact molecule? Does Scaffold Hunter convert the original input molecules to a scaffold first? Because, when I checking the leaf nodes, the structure does not really exist in my input file. How to inteperate that? Thanks, Jing |
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From: Till S. <til...@tu...> - 2014-02-26 10:55:37
|
Hi, thanks for the positive feedback. Currently, there is no TreeMap export feature. However, i created a feature request on the source forge tracker [1]. Feel free to create such requests on your own if you find bugs or feel that something is missing. We are trying to implement/fix as many of this requests as possible. [1] https://sourceforge.net/p/scaffoldhunter/feature-requests/39/ Greetings Till Am Dienstag, 25. Februar 2014, 16:02:24 schrieb Markus Heller: > Hello all, > > first of all, I'd like to say that the new version of ScaffoldHunter, > especially the TreeMap, rocks!! > > But here's my question: Are there any plans to offer the option to export > the TreeMap as an image, preferably including the color-scale legend? Or > am I missing something? If so, I'd be grateful for a hint ... > > Thanks and Cheers > Markus -- 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 |
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From: Markus H. <hel...@gm...> - 2014-02-26 00:02:32
|
Hello all, first of all, I'd like to say that the new version of ScaffoldHunter, especially the TreeMap, rocks!! But here's my question: Are there any plans to offer the option to export the TreeMap as an image, preferably including the color-scale legend? Or am I missing something? If so, I'd be grateful for a hint ... Thanks and Cheers Markus |
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From: Till S. <til...@tu...> - 2013-12-04 10:34:29
|
Hi, Am Dienstag, 3. Dezember 2013, 15:16:55 schrieb Markus Heller: > Hi Till, > > sorry about my slow response, things have been hectic over here ... > > D'uh, of course! The issue here must be the fact that my structures > contain different conformations and diastereomers. I will double-check and > report back if this is NOT the case, otherwise I'll remain quiet on this. > I always seem to forget about this ... > > Sorry for the noise and thanks for the explanation! No Problem :-) May i ask for what you are using Scaffold Hunter (educational, research, etc). We are always curious about what the concrete use cases are. Greetings Till > > Cheers > Markus > > > On Fri, Nov 29, 2013 at 3:28 AM, Till Schäfer <til...@tu... > > wrote: > > > Hi, > > > > Am Freitag, 29. November 2013, 12:26:16 schrieb Till Schäfer: > > > Hi Markus, > > > > > > Am Donnerstag, 28. November 2013, 11:37:35 schrieb Markus Heller: > > > > Hi all, > > > > > > > > when importing data (SDF file containing docking results) into a new or > > > > existing database, SH will only import structures that have not been > > > > imported yet. In the process, the number of docking results gets cut > > down > > > > considerably, in my case here from over 400 to just over 200, which > > has a > > > > big impact on my ability to analyze the scaffolds. The manual doesn't > > seem > > > > to address this; at least I haven't been able to find it if it does. > > > > > > > > How can I get SH to import *all* structures in a given SDF file, > > regardless > > > > of whether they've been imported before? > > > If you create a new Dataset all structures from the SDF should be > > imported. Therefore, the manual cannot mention it :-). That means this is a > > bug in the software or some misunderstanding about how the import works. > > > I tried to reproduce the behavior here with version 2.2.0 and was not > > able to do so with the mysql and hsqldb backend. > > > > > > That means we have to dig a bit deeper about what is going wrong: > > > > > > If you create a new database schema (you can just use a fresh temporary > > hasqldb) and import the dataset: Are all structures imported or at least > > most of them? The reason for this question is, that there are several > > circumstance in which some of the entries of a SDF are not imported or the > > the imported dataset and the sdf differ in size: > > > > > > 1. There are errors parsing the file. > > > This should be visible in the progress window. Can you provide a quick > > summarization about the top level entries, which are listed here? > > > > > > 2. There are several entries with the same structure. > > > We consider two structures identical iff they have the same SMILES > > string. That means also that we do NOT distinguish between different > > confirmations, etc. If there are some structures with the same SMILES > > during the import, the structure properties are merged regarding the merge > > strategy you select. > > I forget to mention, that this is indicated by a log entry during import, > > which tells you that a structure with the same smiles was already imported. > > > > > > > > > > 3. There is another software bug, because you use another Version of > > some software, such as the database. I think we should first inspect point > > 1 and 2, but maybe you can give me some information about the database you > > are using (name, version). > > > > > > If that all does not help and you are able to send me your SDF (no > > private data), i can also try it out here and see what is happening. If the > > error is located in the file (or in the way we interact with that file), we > > should be able to reproduce the behavior here. > > > > > > > Greetings > > Till > > -- > > Dipl.-Inf. Till Schäfer > > Technische Universität Dortmund > > Chair 11 - Algorithm Engineering > > Otto-Hahn-Str. 14 / Raum 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 Technische Universität Dortmund Chair 11 - Algorithm Engineering Otto-Hahn-Str. 14 / Raum 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 |
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From: Till S. <til...@tu...> - 2013-12-04 09:58:22
|
Hi, Am Dienstag, 3. Dezember 2013, 15:21:40 schrieb Markus Heller: > Hi Till, > > all I did was export docking results from OpenEye's VIDA application. I > can send you a sample .sdf to your private e-mail, if that's ok with you. Thats fine. Greetings Till > > Thanks > Markus > > > On Fri, Nov 29, 2013 at 5:40 AM, Till Schäfer <til...@tu... > > wrote: > > > Hi, > > to my knowledge this can lead to non-canonical SMILES. This means that the > > same structure can be imported more than one time. I am not aware of any > > other side affects this warning should have. > > > > @Nils: Do you think there are other places where failing in adding > > implicit hydrogens can have side effects? > > > > We rely on the Chemistry Development Kit (CDK) for this calculations. If > > it should be possible to add implicit hydrogens for that special structure, > > but CDK fails to do so, we should open a bug in their bug tracker. Can you > > provide a sample mol file? > > > > Best regards > > Till > > > > Am Donnerstag, 28. November 2013, 11:39:19 schrieb Markus Heller: > > > Hello all, > > > > > > when importing or exporting SDF files, I get the following warning: > > > > > > Nov 25, 2013 12:07:08 PM > > > edu.udo.scaffoldhunter.model.util.MoleculeConfigurator > > > prepare > > > WARNING: Error adding implicit hydrogens! > > > CDK error message: IAtom is not typed! N > > > > > > > > > At first I suspected incorrect input files, but on quick inspection, they > > > look ok to me ... > > > > > > Any suggestions? > > > > > > Thanks and Cheers > > > Markus > > -- -- Dipl.-Inf. Till Schäfer Technische Universität Dortmund Chair 11 - Algorithm Engineering Otto-Hahn-Str. 14 / Raum 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 |
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From: Markus H. <hel...@gm...> - 2013-12-03 23:21:47
|
Hi Till, all I did was export docking results from OpenEye's VIDA application. I can send you a sample .sdf to your private e-mail, if that's ok with you. Thanks Markus On Fri, Nov 29, 2013 at 5:40 AM, Till Schäfer <til...@tu... > wrote: > Hi, > to my knowledge this can lead to non-canonical SMILES. This means that the > same structure can be imported more than one time. I am not aware of any > other side affects this warning should have. > > @Nils: Do you think there are other places where failing in adding > implicit hydrogens can have side effects? > > We rely on the Chemistry Development Kit (CDK) for this calculations. If > it should be possible to add implicit hydrogens for that special structure, > but CDK fails to do so, we should open a bug in their bug tracker. Can you > provide a sample mol file? > > Best regards > Till > > Am Donnerstag, 28. November 2013, 11:39:19 schrieb Markus Heller: > > Hello all, > > > > when importing or exporting SDF files, I get the following warning: > > > > Nov 25, 2013 12:07:08 PM > > edu.udo.scaffoldhunter.model.util.MoleculeConfigurator > > prepare > > WARNING: Error adding implicit hydrogens! > > CDK error message: IAtom is not typed! N > > > > > > At first I suspected incorrect input files, but on quick inspection, they > > look ok to me ... > > > > Any suggestions? > > > > Thanks and Cheers > > Markus > -- > Dipl.-Inf. Till Schäfer > Technische Universität Dortmund > Chair 11 - Algorithm Engineering > Otto-Hahn-Str. 14 / Raum 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 |
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From: Markus H. <hel...@gm...> - 2013-12-03 23:17:02
|
Hi Till, sorry about my slow response, things have been hectic over here ... D'uh, of course! The issue here must be the fact that my structures contain different conformations and diastereomers. I will double-check and report back if this is NOT the case, otherwise I'll remain quiet on this. I always seem to forget about this ... Sorry for the noise and thanks for the explanation! Cheers Markus On Fri, Nov 29, 2013 at 3:28 AM, Till Schäfer <til...@tu... > wrote: > Hi, > > Am Freitag, 29. November 2013, 12:26:16 schrieb Till Schäfer: > > Hi Markus, > > > > Am Donnerstag, 28. November 2013, 11:37:35 schrieb Markus Heller: > > > Hi all, > > > > > > when importing data (SDF file containing docking results) into a new or > > > existing database, SH will only import structures that have not been > > > imported yet. In the process, the number of docking results gets cut > down > > > considerably, in my case here from over 400 to just over 200, which > has a > > > big impact on my ability to analyze the scaffolds. The manual doesn't > seem > > > to address this; at least I haven't been able to find it if it does. > > > > > > How can I get SH to import *all* structures in a given SDF file, > regardless > > > of whether they've been imported before? > > If you create a new Dataset all structures from the SDF should be > imported. Therefore, the manual cannot mention it :-). That means this is a > bug in the software or some misunderstanding about how the import works. > > I tried to reproduce the behavior here with version 2.2.0 and was not > able to do so with the mysql and hsqldb backend. > > > > That means we have to dig a bit deeper about what is going wrong: > > > > If you create a new database schema (you can just use a fresh temporary > hasqldb) and import the dataset: Are all structures imported or at least > most of them? The reason for this question is, that there are several > circumstance in which some of the entries of a SDF are not imported or the > the imported dataset and the sdf differ in size: > > > > 1. There are errors parsing the file. > > This should be visible in the progress window. Can you provide a quick > summarization about the top level entries, which are listed here? > > > > 2. There are several entries with the same structure. > > We consider two structures identical iff they have the same SMILES > string. That means also that we do NOT distinguish between different > confirmations, etc. If there are some structures with the same SMILES > during the import, the structure properties are merged regarding the merge > strategy you select. > I forget to mention, that this is indicated by a log entry during import, > which tells you that a structure with the same smiles was already imported. > > > > > > 3. There is another software bug, because you use another Version of > some software, such as the database. I think we should first inspect point > 1 and 2, but maybe you can give me some information about the database you > are using (name, version). > > > > If that all does not help and you are able to send me your SDF (no > private data), i can also try it out here and see what is happening. If the > error is located in the file (or in the way we interact with that file), we > should be able to reproduce the behavior here. > > > > Greetings > Till > -- > Dipl.-Inf. Till Schäfer > Technische Universität Dortmund > Chair 11 - Algorithm Engineering > Otto-Hahn-Str. 14 / Raum 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 > |
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From: Till S. <til...@tu...> - 2013-11-29 13:40:54
|
Hi, to my knowledge this can lead to non-canonical SMILES. This means that the same structure can be imported more than one time. I am not aware of any other side affects this warning should have. @Nils: Do you think there are other places where failing in adding implicit hydrogens can have side effects? We rely on the Chemistry Development Kit (CDK) for this calculations. If it should be possible to add implicit hydrogens for that special structure, but CDK fails to do so, we should open a bug in their bug tracker. Can you provide a sample mol file? Best regards Till Am Donnerstag, 28. November 2013, 11:39:19 schrieb Markus Heller: > Hello all, > > when importing or exporting SDF files, I get the following warning: > > Nov 25, 2013 12:07:08 PM > edu.udo.scaffoldhunter.model.util.MoleculeConfigurator > prepare > WARNING: Error adding implicit hydrogens! > CDK error message: IAtom is not typed! N > > > At first I suspected incorrect input files, but on quick inspection, they > look ok to me ... > > Any suggestions? > > Thanks and Cheers > Markus -- Dipl.-Inf. Till Schäfer Technische Universität Dortmund Chair 11 - Algorithm Engineering Otto-Hahn-Str. 14 / Raum 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 |
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From: Till S. <til...@tu...> - 2013-11-29 11:28:17
|
Hi, Am Freitag, 29. November 2013, 12:26:16 schrieb Till Schäfer: > Hi Markus, > > Am Donnerstag, 28. November 2013, 11:37:35 schrieb Markus Heller: > > Hi all, > > > > when importing data (SDF file containing docking results) into a new or > > existing database, SH will only import structures that have not been > > imported yet. In the process, the number of docking results gets cut down > > considerably, in my case here from over 400 to just over 200, which has a > > big impact on my ability to analyze the scaffolds. The manual doesn't seem > > to address this; at least I haven't been able to find it if it does. > > > > How can I get SH to import *all* structures in a given SDF file, regardless > > of whether they've been imported before? > If you create a new Dataset all structures from the SDF should be imported. Therefore, the manual cannot mention it :-). That means this is a bug in the software or some misunderstanding about how the import works. > I tried to reproduce the behavior here with version 2.2.0 and was not able to do so with the mysql and hsqldb backend. > > That means we have to dig a bit deeper about what is going wrong: > > If you create a new database schema (you can just use a fresh temporary hasqldb) and import the dataset: Are all structures imported or at least most of them? The reason for this question is, that there are several circumstance in which some of the entries of a SDF are not imported or the the imported dataset and the sdf differ in size: > > 1. There are errors parsing the file. > This should be visible in the progress window. Can you provide a quick summarization about the top level entries, which are listed here? > > 2. There are several entries with the same structure. > We consider two structures identical iff they have the same SMILES string. That means also that we do NOT distinguish between different confirmations, etc. If there are some structures with the same SMILES during the import, the structure properties are merged regarding the merge strategy you select. I forget to mention, that this is indicated by a log entry during import, which tells you that a structure with the same smiles was already imported. > > 3. There is another software bug, because you use another Version of some software, such as the database. I think we should first inspect point 1 and 2, but maybe you can give me some information about the database you are using (name, version). > > If that all does not help and you are able to send me your SDF (no private data), i can also try it out here and see what is happening. If the error is located in the file (or in the way we interact with that file), we should be able to reproduce the behavior here. > Greetings Till -- Dipl.-Inf. Till Schäfer Technische Universität Dortmund Chair 11 - Algorithm Engineering Otto-Hahn-Str. 14 / Raum 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 |
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From: Till S. <til...@tu...> - 2013-11-29 11:26:32
|
Hi Markus, Am Donnerstag, 28. November 2013, 11:37:35 schrieb Markus Heller: > Hi all, > > when importing data (SDF file containing docking results) into a new or > existing database, SH will only import structures that have not been > imported yet. In the process, the number of docking results gets cut down > considerably, in my case here from over 400 to just over 200, which has a > big impact on my ability to analyze the scaffolds. The manual doesn't seem > to address this; at least I haven't been able to find it if it does. > > How can I get SH to import *all* structures in a given SDF file, regardless > of whether they've been imported before? If you create a new Dataset all structures from the SDF should be imported. Therefore, the manual cannot mention it :-). That means this is a bug in the software or some misunderstanding about how the import works. I tried to reproduce the behavior here with version 2.2.0 and was not able to do so with the mysql and hsqldb backend. That means we have to dig a bit deeper about what is going wrong: If you create a new database schema (you can just use a fresh temporary hasqldb) and import the dataset: Are all structures imported or at least most of them? The reason for this question is, that there are several circumstance in which some of the entries of a SDF are not imported or the the imported dataset and the sdf differ in size: 1. There are errors parsing the file. This should be visible in the progress window. Can you provide a quick summarization about the top level entries, which are listed here? 2. There are several entries with the same structure. We consider two structures identical iff they have the same SMILES string. That means also that we do NOT distinguish between different confirmations, etc. If there are some structures with the same SMILES during the import, the structure properties are merged regarding the merge strategy you select. 3. There is another software bug, because you use another Version of some software, such as the database. I think we should first inspect point 1 and 2, but maybe you can give me some information about the database you are using (name, version). If that all does not help and you are able to send me your SDF (no private data), i can also try it out here and see what is happening. If the error is located in the file (or in the way we interact with that file), we should be able to reproduce the behavior here. Greetings Till -- Dipl.-Inf. Till Schäfer Technische Universität Dortmund Chair 11 - Algorithm Engineering Otto-Hahn-Str. 14 / Raum 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 |
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From: Markus H. <hel...@gm...> - 2013-11-28 19:39:26
|
Hello all,
when importing or exporting SDF files, I get the following warning:
Nov 25, 2013 12:07:08 PM
edu.udo.scaffoldhunter.model.util.MoleculeConfigurator
prepare
WARNING: Error adding implicit hydrogens!
CDK error message: IAtom is not typed! N
At first I suspected incorrect input files, but on quick inspection, they
look ok to me ...
Any suggestions?
Thanks and Cheers
Markus
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From: Markus H. <hel...@gm...> - 2013-11-28 19:37:41
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Hi all, when importing data (SDF file containing docking results) into a new or existing database, SH will only import structures that have not been imported yet. In the process, the number of docking results gets cut down considerably, in my case here from over 400 to just over 200, which has a big impact on my ability to analyze the scaffolds. The manual doesn't seem to address this; at least I haven't been able to find it if it does. How can I get SH to import *all* structures in a given SDF file, regardless of whether they've been imported before? Thanks and Cheers Markus |
