IndexOutOfBoundsException: Index 4195577

Hi,


I had an SD file with 4 or 5 million structures and upon scrolling through them


I got the following error. Scrolling on top was fine, however scrolling to the end was not correct.


This is Marvin 5.1.3.2 under JAVA 1.6 and WIN32.


The error msg says its an incorrect mol file header, but thats not true,


because if I scroll slow through them it works.


Tobias





Invalid energy specification in molfile header: "0 0 0 0"


Exception in thread "AWT-EventQueue-0" java.lang.IndexOutOfBoundsException: Index 4195577 is out of range [0, 4041251]


at chemaxon.marvin.view.StoredRecordArray.set(StoredRecordArray.java:53)


at chemaxon.marvin.view.MDocStorage.setMolCenter(MDocStorage.java:1409)


at chemaxon.marvin.view.swing.modules.SpreadsheetView.setMolCenter(SpreadsheetView.java:692)


at chemaxon.marvin.view.swing.modules.MoleculeCellEditor.stopCellEditing(MoleculeCellEditor.java:81)


at javax.swing.plaf.basic.BasicTableUI$Handler.mousePressed(Unknown Source)


at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)


at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)


at java.awt.AWTEventMulticaster.mousePressed(Unknown Source)


at java.awt.AWTEventMulticaster.mousePressed(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.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)


------





chemaxon.marvin.io.MRecordParseException: Invalid counts line


at chemaxon.marvin.io.formats.mdl.MolRecordReader.readCtab(MolRecordReader.java:573)


at chemaxon.marvin.io.formats.mdl.MolRecordReader.readMol0(MolRecordReader.java:198)


at chemaxon.marvin.io.formats.mdl.MolRecordReader.nextRecord(MolRecordReader.java:140)


at chemaxon.marvin.io.formats.mdl.MolRecordReader.skipRecord(MolRecordReader.java:88)


at chemaxon.marvin.io.MRecordImporter.skipRecord(MRecordImporter.java:447)


at chemaxon.formats.MolImporter.skipRecord(MolImporter.java:868)


at chemaxon.marvin.io.MDocSource.skipRecords(MDocSource.java:265)


at chemaxon.marvin.io.MDocSource.seekForward(MDocSource.java:203)


at chemaxon.formats.MolImporter.seekRecord(MolImporter.java:968)


at chemaxon.marvin.view.MDocStorage.tryToExtend(MDocStorage.java:819)


at chemaxon.marvin.view.MDocStorage.getMainDoc(MDocStorage.java:761)


at chemaxon.marvin.view.swing.modules.RecordFetcher$2.run(RecordFetcher.java:82)


at chemaxon.marvin.util.ThreadSerializer$CmpThread.run(ThreadSerializer.java:49)

Hi Tobias!





We are sorry for the late answer, but we are still investigating the issue. If the file you got the exception with is not confidential, could you give us a link to it or send the file itself?





Best regards,


Istvan

Hi Istvan,


thanks for checking in, the file is too large to send or to FTP.


But some of the problematic files are from PubChem.


So if you download PubChem FTP and copy the files together


as in Compound_11975001_12000000.sdf.gz you could recreate


that problem.





Some of the problems are random, don't ask me on what they depend,


sometimes it is not possible to scroll up in matrix 8x8 view or sometimes


it is not possible to see all the molecule numbers. Sometimes I can scroll


in real time through several million molecules, sometimes it gets stuck.


At this point I would probably ignore that error, not so many people will


work with very large files and as long large the majority of files


work it should be fine.


Tobias