joelib-devel

[Joelib-devel] pHmodels.txt

[NAJI H. <naj...@ul...>]

Hi all,


I would like to ask you if we can transform a Smiles file ( where the 
smiles don't contain charges ) to a Smiles file where the molecules are 
charged (compounds and groups must be represented in their common state 
in aqueous solution, at pH=7) 

For example  
CC(N)C(O)=O>> CC([NH3+])C([O-])=O

In the JOELib  I  observe source\src\joelib\data\plain/phmodel.txt

#charged amine
TRANSFORM [N^3;!$(N~[!#6;!#1]):1] >> [N+:1]

#carboxylic acid
TRANSFORM O=C[OQ1-0:1] >> O=C[O-:1]


Therefore, can I change automatically with a programme in Joelib and 
with a phmodel.txt file a  Smiles file   file ( where the smiles don't 
contain charges ) to a Smiles file where the molecules are charged 
(compounds and groups must be represented in their common state in 
aqueous solution, at pH=7) 

If I can Could you tell me What classes I could use.

Kind Regards

Naji

Re: [Joelib-devel] pHmodels.txt

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

Hi NAJI,

> I would like to ask you if we can transform a Smiles file ( where the 
> smiles don't contain charges ) to a Smiles file where the molecules are 
> charged (compounds and groups must be represented in their common state 
> in aqueous solution, at pH=7) 
I think we are talking about SMARTS, not SMILES. So we are talking on 
regular expression patterns on graphs. SMILES is only a subset of SMARTS.

Sure you can that's what i expect. If you have time you can also invent 
tautomer transfomation rules with the same mechansim.
I would be happy if you will do.

Two possibilities:

1. Modify phmodel.txt and store in myPhModel.txt or what you like
    Then change in src/joelib.properties the line
    joelib.data.JOEPhModel.resourceFile=joelib/data/plain/phmodel.txt
    to
    joelib.data.JOEPhModel.resourceFile=joelib/data/plain/myPhModel.txt

2. If you want to use SMARTS transformations in general you can use the
    joelib.data.JOEChemTransformation class
    see tutorial
http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/functionalities/mol-smarts.html
    So for each tranformation you want to apply you need such an instance.
    The pH model uses simply a vector of such rules and applys them all.

For N tautomers or biotransformations you can simply call them NxN 
times. Then you can try to remove duplicates by using a clever hash code 
or whatever. Or you can try to avoid calculating them NxN by assuming a 
clever heuristic, ... but's that's another thread, isn't it ? :-)

Kind regards, Joerg


> For example  
> CC(N)C(O)=O>> CC([NH3+])C([O-])=O
> In the JOELib  I  observe source\src\joelib\data\plain/phmodel.txt 
> #charged amine
> TRANSFORM [N^3;!$(N~[!#6;!#1]):1] >> [N+:1]
> #carboxylic acid
> TRANSFORM O=C[OQ1-0:1] >> O=C[O-:1]
> Therefore, can I change automatically with a programme in Joelib and 
> with a phmodel.txt file a  Smiles file   file ( where the smiles don't 
> contain charges ) to a Smiles file where the molecules are charged 
> (compounds and groups must be represented in their common state in 
> aqueous solution, at pH=7)

-- 
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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