name generation failing error

Hi,

I have a table with an column (IUPAC) that has automatic generation of preferred naming enabled. I am using JChem Web Services 5.3.1. I have been getting name generation error (pasted below) and as a result the structure table does not accept new compound addtions whenever it encounters this error. I cannot find a way to bypass this error and add new compounds. I have increased the 'iupac_name' column field length to 4000 characters in the structure table but that apparently is not the issue.

chemaxon.marvin.io.MolExportException: Name generation failed: java.lang.ArrayIndexOutOfBoundsException: 15
    at chemaxon.marvin.io.formats.name.NameExport.convert(Unknown Source)
    at chemaxon.marvin.calculations.IUPACNamingPlugin.a(Unknown Source)
    at chemaxon.marvin.calculations.IUPACNamingPlugin.getTraditionalName(Unknown Source)
    at chemaxon.marvin.calculations.IUPACNamingPlugin.run(Unknown Source)
    at chemaxon.marvin.plugin.CalculatorPluginManager.a(Unknown Source)
    at chemaxon.marvin.plugin.CalculatorPluginManager.a(Unknown Source)
    at chemaxon.marvin.plugin.CalculatorPluginManager.a(Unknown Source)
    at chemaxon.marvin.plugin.CalculatorPluginManager.callback(Unknown Source)
    at chemaxon.marvin.plugin.PluginManager.callback(Unknown Source)
    at chemaxon.marvin.common.swing.MolPanel$5.run(Unknown Source)
Caused by: chemaxon.marvin.io.formats.name.nameexport.IUPACNamer$Error: Name generation failed: java.lang.ArrayIndexOutOfBoundsException: 15
    at chemaxon.marvin.io.formats.name.nameexport.NamingCentral.a(Unknown Source)
    at chemaxon.marvin.io.formats.name.nameexport.IUPACNamerThread.run(Unknown Source)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 15
    at chemaxon.marvin.io.formats.name.nameexport.GeneralFusedRingSystem.a_(Unknown Source)
    at chemaxon.marvin.io.formats.name.nameexport.GeneralSpiroNamer.a(Unknown Source)
    at chemaxon.marvin.io.formats.name.nameexport.GeneralSpiroNamer.nameRingSystem(Unknown Source)
    at chemaxon.marvin.io.formats.name.nameexport.UnbranchedSpiroNamer.a(Unknown Source)
    at chemaxon.marvin.io.formats.name.nameexport.UnbranchedSpiroNamer.computePartNames(Unknown Source)
    at chemaxon.marvin.io.formats.name.nameexport.GeneralSpiroNamer.c_(Unknown Source)
    at chemaxon.marvin.io.formats.name.nameexport.GeneralSpiroNamer.d(Unknown Source)
    at chemaxon.marvin.io.formats.name.nameexport.Part.a(Unknown Source)
    at chemaxon.marvin.io.formats.name.nameexport.Part.f(Unknown Source)
    at chemaxon.marvin.io.formats.name.nameexport.Part.B(Unknown Source)
    at chemaxon.marvin.io.formats.name.nameexport.ParentFinder.a(Unknown Source)
    at chemaxon.marvin.io.formats.name.nameexport.ParentFinder.a(Unknown Source)
    at chemaxon.marvin.io.formats.name.nameexport.ParentFinder.a(Unknown Source)
    at chemaxon.marvin.io.formats.name.nameexport.TopologyAnalyser.b(Unknown Source)
    at chemaxon.marvin.io.formats.name.nameexport.TopologyAnalyser.a(Unknown Source)
    at chemaxon.marvin.io.formats.name.nameexport.NamingCentral.c(Unknown Source)
    ... 2 more

HI Renju,

How are you calling the JChem import functionality?  Are you using Web Services (perhaps through a web services client like our AJAX example) or are you using a java application using the JChem Base API directly?

 

Jon 

I am using the Web Services (5.3.1) client similar to the ajax example that you have. I used JChemBase 5.3.1 UI to set the IUPAC column to generate the preferred name automatically. So, when inserting a new structure, I don't explicitly calculate the name, since it is automatically done by the JChem API.

Renju,

Perhaps there is a bug that the later compounds are not added when there is a compound that we cannot automatically generate the name.  As a workaround, try to identify the problem compound and input the rest of the molecules. 

 

We'll have to investigate this issue further. 

 

Jon

Renju,

Can you attach a section of the file that you were having problem importing?

 

This would help us recreate the issue. 

Thanks,

Jon