Re: [Joelib-devel] GroupContributionMethod

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

Hi NAJI,

> A question if I use the Smarts in order to transform, for example (In 
> pH =7), COOH to COO-  
> HOW COULD I MAKE TO HAVE A SMILES FILE WHERE MOLECULES 
> ARE REPRESENTED IN PHYSIOLOGICAL PH) without change manually each 
> smiles of my file.
So if i understand this correctly you are interested in:
SMILES --> tranform to protonation state at pH=7 --> SMILES.

Why do you not simply convert your structures from:
sh convert.sh yourOriginalFile.smi phCorrectedFile.smi

JOELib applys in the conversion process the pH state defined in
joelib/src/joelib/data/plain/phmodel.txt

So the only thing you must do is to provide JOElib with the correct 
protonation transofmation rules given there.
So create and check e.g.
joelib/src/joelib/data/plain/phmodel_pH7.txt
and
use in joelib/src/joelib.properties

joelib.data.JOEPhModel.resourceFile=joelib/data/plain/phmodel_pH7.txt
instead of the default entry.

Kind 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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