[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