ArrayIndexOutOfBoundsException when inserting rxn

We have a couple thousand structures in rxn format that I'm trying to insert into


a db-table using the UpdateHandler from jchem. On a few of this structures a


ArrayIndexOutOfBoundsException is thrown, always on the same row in MdlCompressor (384)


but on different indexes.





I have also tried to use chemaxon.formats.MdlCompressor directly on the failing


rxn-files and get a similar exception.


(chemaxon.formats.MdlCompressor.main( new String[] { "c", "0401011031_14.rxn" } );)





Importing the structure into ISIS/Draw the structure looks ok.





Opening the structure in a Marvin applet the structure looks


all garbled up, and the parts are drawn on top of each other.





I have attached one of the failing rxn-files.





Is the exception due to errors in the rxn or is the problem somewhere else?





program versions:


jchem 3.1.5


java 1.5.0_03


DB is MySql





rxn file i s attached.





Partial stacktrace:


java.lang.ArrayIndexOutOfBoundsException: 26


at chemaxon.formats.MdlCompressor.convertCtab(MdlCompressor.java:384)


at chemaxon.formats.MdlCompressor.convert(MdlCompressor.java:179)


at chemaxon.formats.MdlCompressor.convert(MdlCompressor.java:673)


at chemaxon.jchem.db.UpdateHandler.setFields(UpdateHandler.java:853)


at chemaxon.jchem.db.UpdateHandler.setFields(UpdateHandler.java:1064)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1441)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1384)


....





Johan, Biotage AB

Dear Johan,





A quick workaround is to switch off molfile compressor in JChem Manager. You can do that using Options/Advanced/Compress MOL, RXN, ...





We will check the exception and the coordinates issues.





Best regards,





Szabolcs

Johan,





We have fixed the exception, it will be OK in the next Marvin version (4.0.5) and the next JChem version that will include that version of Marvin. We are also working on the other problem, and that will be also fixed soon.





Best regards,


Szabolcs

Hi,





Just to let you know that we have finished the fix of the coordinate problem. The components were translated from overlap even in the latest alpha version (Marvin 4.1.0alpha13 http://www.chemaxon.com/shared/alpha/ and Jchem jchemTEST_2006_03_25 http://www.chemaxon.com/download.php?d=/data/download/jchem/test ), but now we solved the component center alignment and the nice layout of salts also. The next major release (Marvin 4.1, JChem 3.2 and in fact the next alphas also) will contain the full functionality.





Best regards,


Szabolcs