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
--
Never mistake motion for action.
E. Hemingway
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