tautomerization module and certain charged moeties

I was eager to try out the latest tautomerization plugin for the standardizer (new in 3.2) - and it mostly behaves as expected, except for throwing a wierd exception with a number of charged molecules.





Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1


at chemaxon.calculations.Tautomerization.getChargedAtomCount(Tautomerization.java:3639)


at chemaxon.calculations.Tautomerization.postFiltering(Tautomerization.java:7060)


at chemaxon.calculations.Tautomerization.calculateDACouples(Tautomerization.java:3521)


at chemaxon.calculations.Tautomerization.createDACouples(Tautomerization.java:3432)


at chemaxon.marvin.calculations.MultiformPlugin.run(MultiformPlugin.java:266)


at chemaxon.reaction.Standardizer.performTautomerize(Standardizer.java:1506)


at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1669)


at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1741)


at chemaxon.reaction.Standardizer.run(Standardizer.java:1869)


at chemaxon.reaction.Standardizer.main(Standardizer.java:1953)








<StandardizerConfiguration Version ="0.1">


<Actions>


<Tautomerize ID="tautomer"/> <!-- This implicitly includes keepOne and dearomatize?! -->


</Actions>


</StandardizerConfiguration>





Some problematic molecules include:


CCCOP([O-])([O-])=O phosphate


[Br-]ON1C(C)(C)CC([N+](C)(CCCCCCCCCCCC)C)CC1(C)C 4-(dodecyldimethylammonium)-1-oxyl-2,2,6,6-tetramethylpiperidine


C[N+]1(C)C(CO)CCCC1.OC(C2=CC=CC=C2)(C3=CC=CC=C3)C([O-])=O 2-(hydroxymethyl)-N,N-dimethylpiperidinium benzilate





Thanks





Noel

Hi,





Thanks for sending this error message.


This error have been fixed even now.





Jozsi