Mview 5.0.1 MolFormatException

Hi,


I created a smiles file using the markush generator in marvin


and later created unique smiles with molconvert. If I view the created files I get the following error (see below). The problem is, the mentioned problematic SMILES code is not existing in both files. This is Marvin 5.0.1





In the file: [H]c1c(I)c(Br)c(F)c2c(Cl)c(Br)c(Cl)c(Br)c12


Problem: (I)c(Br)c(F)c2c(Cl)c(Br)c(Cl)c(Br)c12 ( no such SMILES in the file)





That happens during scrolling through the file with a 2x2 or 10x10 matrix display. See attached one smiles file as 7ZIP


Tobias








Error in mview 5.0.1


chemaxon.formats.MolFormatException: Unmatched ring closure number 1 in SMILES string (I)c(Br)c(F)c2c(Cl)c(Br)c(Cl)c(Br)c12


at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol0(SmilesImport.java:937)


at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol(SmilesImport.java:531)


at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol(SmilesImport.java:489)


at chemaxon.marvin.io.MRecordImporter.readDoc(MRecordImporter.java:170)


at chemaxon.formats.MolImporter.readDoc(MolImporter.java:698)


at chemaxon.formats.MolImporter.nextDoc(MolImporter.java:638)


at chemaxon.marvin.view.MDocStorage.readDoc(MDocStorage.java:2477)


at chemaxon.marvin.view.MDocStorage.getMainDoc(MDocStorage.java:758)


at chemaxon.marvin.view.swing.modules.GridBagView.getDocument(GridBagView.java:628)


at chemaxon.marvin.view.swing.modules.GridBagView.setVisibleCanvas(GridBagView.java:1097)


at chemaxon.marvin.view.swing.ViewPanel.setVisibleCanvas(ViewPanel.java:2475)


at chemaxon.marvin.view.swing.modules.GridBagView.setVisibleCell(GridBagView.java:1542)


at chemaxon.marvin.view.swing.modules.GridBagView.visibleCells(GridBagView.java:1743)


at chemaxon.marvin.view.swing.modules.GridBagView.update(GridBagView.java:3388)


at chemaxon.marvin.view.swing.modules.GridBagView.access$1200(GridBagView.java:46)


at chemaxon.marvin.view.swing.modules.GridBagView$9.run(GridBagView.java:3341)


at java.awt.event.InvocationEvent.dispatch(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)

We are checking it.

Hi,


its also in version 5.1.0 for different locations. Thats weird.

Code:

chemaxon.formats.MolFormatException: Unmatched ring closure number 1 in SMILES string (Cl)c(I)c2c([H])c(F)c(F)c(F)c2c1Cl    at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol0(SmilesImport.java:937)    at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol(SmilesImport.java:531)    at chemaxon.marvin.io.formats.smiles.SmilesImport.readMol(SmilesImport.java:489)    at chemaxon.marvin.io.MRecordImporter.readDoc(MRecordImporter.java:170)    at chemaxon.formats.MolImporter.readDoc(MolImporter.java:698)    at chemaxon.formats.MolImporter.nextDoc(MolImporter.java:638)    at chemaxon.marvin.view.MDocStorage.readDoc(MDocStorage.java:2477)    at chemaxon.marvin.view.MDocStorage.getMainDoc(MDocStorage.java:758)    at chemaxon.marvin.view.swing.modules.GridBagView.getDocument(GridBagView.java:628)    at chemaxon.marvin.view.swing.modules.GridBagView.setVisibleCanvas(GridBagView.java:1097)    at chemaxon.marvin.view.swing.ViewPanel.setVisibleCanvas(ViewPanel.java:2475)    at chemaxon.marvin.view.swing.modules.GridBagView.setVisibleCell(GridBagView.java:1542)    at chemaxon.marvin.view.swing.modules.GridBagView.visibleCells(GridBagView.java:1743)    at chemaxon.marvin.view.swing.modules.GridBagView.update(GridBagView.java:3388)    at chemaxon.marvin.view.swing.modules.GridBagView.access$1200(GridBagView.java:46)    at chemaxon.marvin.view.swing.modules.GridBagView$9.run(GridBagView.java:3341)    at java.awt.event.InvocationEvent.dispatch(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)

Tobias

Hi,


Not reproducible here. (although I only tried it with the latest version)


What is your JVM version, CPU and OS?


How do you "scroll" exactly? Using the page down key only (do you hold it down, or press it multiple times?) or by dragging the scrollbar with the mouse (how quickly?)? Or by clicking a point on the scrollbar? Do you scroll in one direction only (down) or by changing the direction frequently?


Peter

(Andras: It is not a SMILES bug, that invalid SMILES string is simply the end of the valid SMILES "[H]c1c(I)c(Br)c(F)c2c(Cl)c(Br)c(Cl)c(Br)c12". If the bug exists at all, then it may be an mview multithreading bug, two threads may read the file at the same time. Currently, I cannot imagine anything else...)

Dear Tobias,


I realized the problem, so I removed my previous comment.





Andras

The problem seems to be the same as in


http://www.chemaxon.com/forum/viewtopic.php?p=19325 ,


GridBagView.getDocument is called on the event dispatch thread and it performs I/O operations simultaneously with another thread. The fix is the same, the bug hopefully disappeared.