Standardizer exception

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.

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

Zsolt

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.