Standardizer exception

User da00f5c453

01-03-2013 19:16:30

I ran into a problem with standardizer when custom_aminoacids.dict file is present in $HOME/.chemaxon folder. The standardizer raises an error although it is produces correct output. To reporduce the error the  custom_aminoacids.dict file must be present with any custom aminoacid definition including the examples at http://www.chemaxon.com/marvin/help/formats/seq-doc.html. The command line is


standardize -c "keepone..aromatize..[O-][N+]=O>>O=N=O" "[O-][N+](=O)C1=CC=CC=C1"


exception:


 


java.lang.reflect.InvocationTargetException


at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)


at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)


at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)


at java.lang.reflect.Constructor.newInstance(Constructor.java:513)


at chemaxon.standardizer.StandardizerActionFactory.getStandardizerAction(StandardizerActionFactory.java:260)


at chemaxon.standardizer.StandardizerActionFactory.getAvailableStandardizerActions(StandardizerActionFactory.java:182)


at chemaxon.standardizer.configuration.reader.StandardizerActionStringReader.initializeMap(StandardizerActionStringReader.java:110)


at chemaxon.standardizer.configuration.reader.StandardizerActionStringReader.<init>(StandardizerActionStringReader.java:99)


at chemaxon.standardizer.configuration.reader.StandardizerActionStringReader.<init>(StandardizerActionStringReader.java:81)


at chemaxon.standardizer.StandardizerUtil.initializeReader(StandardizerUtil.java:146)


at chemaxon.standardizer.Standardizer.<init>(Standardizer.java:179)


at chemaxon.reaction.Standardizer.<init>(Standardizer.java:217)


at chemaxon.reaction.ConcurrentStandardizerProcessor.main(ConcurrentStandardizerProcessor.java:893)


Caused by: java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 5


at chemaxon.struc.MoleculeGraph.getAtom(Unknown Source)


at chemaxon.marvin.io.formats.peptide.AminoAcidSource.getExportMols(AminoAcidSource.java:341)


at chemaxon.standardizer.advancedactions.GroupList.getDefaultAminoAcids(GroupList.java:166)


at chemaxon.standardizer.advancedactions.GroupList.setAll(GroupList.java:269)


at chemaxon.standardizer.advancedactions.CreateGroupAction.createGroupList(CreateGroupAction.java:94)


at chemaxon.standardizer.advancedactions.CreateGroupAction.<init>(CreateGroupAction.java:47)


... 13 more


 


 


correct output is created "O=N(=O)c1ccccc1"


 


OS: OSX 10.7, Java 1.6.0_41, Standardizer 5.11.5


Removing  custom_aminoacids.dict from $HOME/.chemaxon doesn't raise the exception anymore.


 


Oleg.

ChemAxon e08c317633

04-03-2013 07:51:20

Thank you for reporting this issue. We will examine it and get back to you in few days.

Zsolt

ChemAxon e08c317633

18-03-2013 09:23:12

This bug affects only the "create group" action. "Create group" action will not handle amino acids defined in custom_aminoacids.dict file until it is fixed, but otherwise Standardizer will work correctly.


The fix can be expected in JChem 6.0.