aromatize problem (exception in molconvert setupDB)

Tried molconvert smiles:aun on the molfile at


http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=720921





I know that I might be pushing my luck with this one, but if so, there's a larger problem here. Assuming that you're always going to run into unfortunate problems like this one every once in a while, can't molconvert be changed to catch exceptions, write out info about the problem to the error stream, and then continue (perhaps add a force option at the command line)?











Ran in to the following bizarre exception:





java.lang.ArrayIndexOutOfBoundsException: -1


at chemaxon.marvin.modules.SmilesExport.setupDB(SmilesExport.java:2592)


at chemaxon.marvin.modules.SmilesExport.walkIslands(SmilesExport.java:23


90)


at chemaxon.marvin.modules.SmilesExport.initStereo2(SmilesExport.java:19


19)


at chemaxon.marvin.modules.SmilesExport.singleMolToSMILES(SmilesExport.j


ava:627)


at chemaxon.marvin.modules.SmilesExport.toSMILES(SmilesExport.java:558)


at chemaxon.marvin.modules.CxsmilesExport.convert(CxsmilesExport.java:18


7)


at chemaxon.formats.MolExporter.write(MolExporter.java:217)


at chemaxon.formats.MolConverter.convert0(MolConverter.java:597)


at chemaxon.formats.MolConverter.convert(MolConverter.java:431)


at chemaxon.formats.MolConverter.main(MolConverter.java:1067)


java.lang.ArrayIndexOutOfBoundsException: -1


at chemaxon.marvin.modules.SmilesExport.setupDB(SmilesExport.java:2592)


at chemaxon.marvin.modules.SmilesExport.walkIslands(SmilesExport.java:23


90)


at chemaxon.marvin.modules.SmilesExport.initStereo2(SmilesExport.java:19


19)


at chemaxon.marvin.modules.SmilesExport.singleMolToSMILES(SmilesExport.j


ava:627)


at chemaxon.marvin.modules.SmilesExport.toSMILES(SmilesExport.java:558)


at chemaxon.marvin.modules.CxsmilesExport.convert(CxsmilesExport.java:18


7)


at chemaxon.formats.MolExporter.write(MolExporter.java:217)


at chemaxon.formats.MolConverter.convert0(MolConverter.java:597)


at chemaxon.formats.MolConverter.convert(MolConverter.java:431)


at chemaxon.formats.MolConverter.main(MolConverter.java:1067)

I have sketched the molecule you mention, but I could not reproduce the problem with Marvin 4.1.0.


I have tried the following:

Code:

scripts/molconvert smiles:aun 1.mol N#CC1=C/C=N(/C=C\1)=C2\C(=C3c4cccc5cccc(C/3=C2c6ccccc6)c45)c7ccccc7

Can you attach the problematic molfile.

The force option is already done.


molconvert can continue the conversion with the -g option:


-g continue with next molecule on error