molconvert ignore error argument (-g) broken

Hi,


I have some broken molecules as Markush structures,


they come out of ISIS BASE (they are infact from BioMetaDB)


and I want that molconvert ignores those broken structures


during conversion. (ISIS itself can not show those structures, still


I just want to ignore them).





I use:


molconvert -g cxsmarts:a-H molfiles.sdf





An get (just as example, not from the ZIP file)


[#6]CN(C[#6])CC(=O)Nc1c(-[#6])cccc1-[#6]


[#6]C[C@H]([#6])C(=O)O[C@H]1C[C@@H]([#6])C=C2C=C[C@H]([#6])[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@@H]12 |c:13,t:11|


Cl[C@H]1[C@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H]1Cl |r|


molfiles.sdf:732102: error in molecule 12312: Bad multiple group subscript, not an integer


java.lang.IllegalArgumentException: Bad multiple group subscript, not an integer


at chemaxon.struc.sgroup.MultipleSgroup.setSubscript(MultipleSgroup.java:372)


at chemaxon.marvin.modules.MolImport.setSgroupSubscript(MolImport.java:2088)


at chemaxon.marvin.modules.MolImport.readPropertiesBlockV2(MolImport.java:1500)


at chemaxon.marvin.modules.MolImport.readCtab(MolImport.java:992)


at chemaxon.marvin.modules.MolImport.readMol0(MolImport.java:681)


at chemaxon.marvin.modules.MolImport.readMol(MolImport.java:265)


at chemaxon.formats.MolImporter.readDoc(MolImporter.java:697)


at chemaxon.formats.MolConverter.readDoc(MolConverter.java:694)


at chemaxon.formats.MolConverter.convert0(MolConverter.java:642)


at chemaxon.formats.MolConverter.convert(MolConverter.java:515)


at chemaxon.formats.MolConverter.main(MolConverter.java:1245)





--------------


## mview or Instant JCHem error from problematic molecules





Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException: Bad multiple group subscript, not an integer


at chemaxon.struc.sgroup.MultipleSgroup.setSubscript(MultipleSgroup.java:372)


at chemaxon.marvin.modules.MolImport.setSgroupSubscript(MolImport.java:2088)


at chemaxon.marvin.modules.MolImport.readPropertiesBlockV2(MolImport.java:1500)


at chemaxon.marvin.modules.MolImport.readCtab(MolImport.java:992)


at chemaxon.marvin.modules.MolImport.readMol0(MolImport.java:681)


at chemaxon.marvin.modules.MolImport.readMol(MolImport.java:265)


at chemaxon.formats.MolImporter.readDoc(MolImporter.java:697)


at chemaxon.formats.MolImporter.nextDoc(MolImporter.java:622)


at chemaxon.marvin.view.MDocStorage.readDoc(MDocStorage.java:2289)


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


at chemaxon.marvin.view.swing.modules.GridBagView.getDocument(GridBagView.java:601)


at chemaxon.marvin.view.swing.modules.GridBagView.setVisibleCanvas(GridBagView.java:1028)


at chemaxon.marvin.view.swing.ViewPanel.setVisibleCanvas(ViewPanel.java:1817)


at chemaxon.marvin.view.swing.modules.GridBagView.setVisibleCell(GridBagView.java:1467)


at chemaxon.marvin.view.swing.modules.GridBagView.visibleCells(GridBagView.java:1668)


at chemaxon.marvin.view.swing.modules.GridBagView.update(GridBagView.java:3212)


at chemaxon.marvin.view.swing.modules.GridBagView.access$1200(GridBagView.java:45)


at chemaxon.marvin.view.swing.modules.GridBagView$9.run(GridBagView.java:3169)


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


at java.awt.EventQueue.dispatchEvent(Unknown Source)


at java.awt.EventDispatchThread.pumpOneEventForHierarchy(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)


Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: unable to create new native thread


at java.lang.Thread.start0(Native Method)


at java.lang.Thread.start(Unknown Source)


at java.awt.EventQueue.initDispatchThread(Unknown Source)


at java.awt.EventDispatchThread.run(Unknown Source)


--------------


The same problem for still exists for Instant-JChem.


The only way to get around would be to use my own API molconverter,


to ignore the problem and just go on. Thanks! See ZIP file with 3 broken structures.


Tobias

Thanks for reporting this issue. We will check it.

I fixed the exception handling bug, the bugfix will appear in the next Marvin 5.0 beta. The stack trace is not printed, only the error message. Option -g works, you will be able to ignore the bug.