User 380f434589
26-03-2012 15:01:54
Hello everyone.
I tried to export a database with about 100.000 structures to a SDF-File, but the process always aborted after 62.800 lines with an exceptional error.
This are the details:
java.lang.ArrayIndexOutOfBoundsException: 112
at chemaxon.calculations.clean.Clean2D.postProcess(Clean2D.java:9717)
at chemaxon.calculations.clean.Clean2D.generateCoordinates(Clean2D.java:8922)
at chemaxon.calculations.clean.Clean2D.calcInitialGeometry(Clean2D.java:1820)
at chemaxon.calculations.clean.Clean2D.cleanFragment(Clean2D.java:1375)
at chemaxon.calculations.clean.Clean2D.cleanMoleculeStructure(Clean2D.java:1149)
at chemaxon.calculations.clean.Clean2D.clean(Clean2D.java:633)
at chemaxon.calculations.clean.Clean2D.clean(Clean2D.java:613)
at chemaxon.calculations.clean.Cleaner.cleanMolGraph(Cleaner.java:205)
at chemaxon.calculations.clean.Cleaner.cleanMol(Cleaner.java:288)
at chemaxon.calculations.clean.Cleaner.clean(Cleaner.java:54)
at chemaxon.calculations.clean.CleanerUtil.clean(CleanerUtil.java:28)
at chemaxon.struc.MoleculeGraph.clean(MoleculeGraph.java:5436)
at chemaxon.struc.MoleculeGraph.clean(MoleculeGraph.java:5301)
at com.im.ijc.io.impl.exporter.MarvinExporter.doExport(MarvinExporter.java:181)
at com.im.ijc.io.impl.exporter.MarvinExporter$MarvinExportConfiguration.performExport(MarvinExporter.java:473)
at com.im.ijc.io.export.ExportRunner.startExport(ExportRunner.java:78)
at com.im.ijc.io.export.ExportToFileWizardPanel3$1.run(ExportToFileWizardPanel3.java:97)
at org.openide.util.Task.run(Task.java:248)
at org.openide.util.RequestProcessor$Task.run(RequestProcessor.java:1418)
at org.openide.util.RequestProcessor$Processor.run(RequestProcessor.java:1957)
Caused: org.openide.util.RequestProcessor$SlowItem: task failed due to
at org.openide.util.RequestProcessor.post(RequestProcessor.java:422)
at com.im.ijc.io.export.ExportToFileWizardPanel3.readSettings(ExportToFileWizardPanel3.java:106)
at org.openide.WizardDescriptor.updateStateOpen(WizardDescriptor.java:903)
at org.openide.WizardDescriptor.updateState(WizardDescriptor.java:854)
at org.openide.WizardDescriptor.goToNextStep(WizardDescriptor.java:1065)
at org.openide.WizardDescriptor.access$1200(WizardDescriptor.java:130)
at org.openide.WizardDescriptor$Listener$1.run(WizardDescriptor.java:2022)
at org.openide.WizardDescriptor$8.run(WizardDescriptor.java:1430)
at org.openide.WizardDescriptor.lazyValidate(WizardDescriptor.java:1470)
at org.openide.WizardDescriptor.access$1300(WizardDescriptor.java:130)
at org.openide.WizardDescriptor$Listener.actionPerformed(WizardDescriptor.java:2041)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.openide.util.WeakListenerImpl$ProxyListener.invoke(WeakListenerImpl.java:459)
at $Proxy42.actionPerformed(Unknown Source)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$000(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue$2.run(Unknown Source)
[catch] at java.awt.EventQueue$2.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:137)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.Dialog$1.run(Unknown Source)
at java.awt.Dialog$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Dialog.show(Unknown Source)
at org.netbeans.core.windows.services.NbPresenter.superShow(NbPresenter.java:1006)
at org.netbeans.core.windows.services.NbPresenter.doShow(NbPresenter.java:1040)
at org.netbeans.core.windows.services.NbPresenter.run(NbPresenter.java:1028)
at org.netbeans.core.windows.services.NbPresenter.run(NbPresenter.java:121)
at org.openide.util.Mutex$1AWTWorker.run(Mutex.java:1377)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$000(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:137)
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)
Do you have any idea why this happens and how I can avoid it? I need the transformation to sdf.
Best,
Daniel
ChemAxon 2bdd02d1e5
27-03-2012 08:42:16
User 380f434589
27-03-2012 09:24:26
Hi.
This is the copy to clipboard information, hope it helps. Can't find the logfile and meanwhile I found the reason for the cancellation. There was a corrupt structure in the database in row 62.850, after deleting it the process worked out just fine.
Thanks for your help anyway.
Daniel
Instant JChem Version: 5.9.0 (build: 201203081907-180776)
JChem Version: 5.9.0
JChem Table Version: 5080100
Marvin Version: 5.9.0 (build date: 2012-03-02)
Java: 1.6.0_26; Java HotSpot(TM) 64-Bit Server VM 20.1-b02
System: Windows 7 version 6.1 running on amd64; Cp1252; de_DE (instantjchem)
NetBeans build: 110214-aec102d89c78
Userdir: C:\Users\Daniel\AppData\Roaming\.instantjchem\ijc_5_8
Java Web Start: No
Plugins:
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ChemAxon 2bdd02d1e5
27-03-2012 09:42:11
I thought it could be caused by a wrong structure. Logfile would show it. You don't need to search for that file if IJC is running. Simply View-> Instant JChem Log File and then in the log window r-click and Save As...
Cheers!
Filip
ChemAxon 2bdd02d1e5
27-03-2012 10:10:46
One more thing, the structure which was wrong. Could you please send us the structure(send an email if you prefer that) ? You can open it in MarvinSketch and save it (try different format if it doesn't work). It helps to fix this problem.
Thanks!
User 380f434589
27-03-2012 10:47:54
Hi Filip,
I'm sorry, but I can only send you the SMILES String of the structure. The import into IJC seemed to have worked, but even if I just scrolled over the structure in the table view an error occured.
1st column SMILES
C2=C(N\N=C1/C(=O)C=C(N)C=C1)C=CC8=C2C(=O)C(=N/NC7=CC(=C(NC6=CC=C(N\N=C3/C(=CC5=C(C3=O)C=C(N\N=C4\C(=O)C=C(N)C=C4)C=C5)([O-])(=O)=O)C=C6)C=C7)([O-])(=O)=O)/C(=C8)([O-])(=O)=O.[Na+].[Na+].[Na+]
2nd column Name
trisodium 6-[(4-amino-2-hydroxyphenyl)azo]-3-[[4-[[4-[[7-[(4-amino-2-hydroxyphenyl)azo]-1-hydroxy-3-sulphonato-2-naphthyl]azo]phenyl]amino]-3-sulphonatophenyl]azo]-4-hydroxynaphthalene-2-sulphonate
I've had a look at the log file, it does not contain data from this day any more. The error occured like 7 days ago. Just wanted to let you know.
Cheers,
Daniel
ChemAxon 2bdd02d1e5
31-03-2014 04:18:13
This problem should have been fixed a while ago, in 5.11.2.
