mview problem with polymer structures

Hi,


I downloaded the Biometa DB (the curated KEGG DB) and


there are some molecules (I guess) with CH3-[CH2]n-CH3 notation.


(Same problem in Instant-JChem)





http://cheminf.cmbi.ru.nl/biometa/flat/





Mview 4.1.11





Tobias


Exception in thread "Thread-49" 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:3194)


at chemaxon.marvin.view.swing.modules.GridBagView.access$800(GridBagView.java:45)


at chemaxon.marvin.view.swing.modules.GridBagView$8.run(GridBagView.java:3162)


at chemaxon.marvin.util.ThreadSerializer$1.run(ThreadSerializer.java:97)

Hi,


I just looked into it, there are some weird Markush structures contained,


a general "ignore error" would be fine (also for I-JChem).





The substance is or was wrong, it looks like this


http://www.genome.jp/dbget-bin/www_bget?drug+D00361





The original file in Biometa is mc006057.mol (I cannot post it here, but you can downlad it from Biometa DB mol files.


Tobias

Hi Tobias,





The faulty structure contains a Multiple Sgroup where the subscript is a letter instead of a number. You can remove that faulty structure with molconvert -g option (continue with next molecule on error) and then use the converted sdf file.





Erika.

Hi Erika,


thank you, I already converted it with molconvert from the single molfiles. My concern was with Marvin and Instant-JChem, because Marvin crashes (instead of catching the error) and Instant-JChem stopped the import instead of ignoring the error.





Tobias