[Joelib-devel] Debugging+Logging+Testing

[Joerg K. W. <we...@in...>]

Hi all,

this is just a reminder, that nearly all classes contains a specific 
Logger with a debugging functionality.
If we take the aromatic typer for example you can switch on this 
functionality by changing
log4j.category.joelib.data.JOEAromaticTyper=INFO
in the file joelib/src/log4j.properties

to
log4j.category.joelib.data.JOEAromaticTyper=DEBUG

and recompile the project, which copies the resource files to the 
joelib/build directory.

This will show you the assigned SMARTS pattern with the number of 
electrons and the typer process, when calling any method which requires 
this functionality.

This can be *VERY* helpfull when trying to resolve, why e.g. some atoms 
are not recognized as aromatic (see my last bug fix mail !;-)
It's recommended to use one one or two molecule for such tasks, or you 
will have a lot of console filling messages, e.g. for testing a 
SMILES/SMARTS match i used and you can use:

SMILESTest       to generate a molecule file
SMARTTest        for substructure search in the generated file and
MoleculeLoadTest for showing the atom properties, e.g. aromaticity flags

Regards, Joerg

-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
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