[Joelib-devel] GroupContributionMethod

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

Hi JOERG  =2C

Tuesday=2C I asked you a question about a Smiles file and you answered =

(thank you again) me =3A =


=D8	I would like to ask you if we can transform a Smiles file ( =

where the =

=3E smiles don=27t contain charges ) to a Smiles file where the molecules=
 =

are =

=3E charged (compounds and groups must be represented in their common =

state =

=3E in aqueous solution=2C at pH=3D7) =

I think we are talking about SMARTS=2C not SMILES=2E So we are talking on=
 =

regular expression patterns on graphs=2E SMILES is only a subset of =

SMARTS=2E

In fact =2C from your program joelib/src/joelib/desc/types/LogP and =

others programs=2C  I can develop a method that estimates Gibbs energy =

of  small biochemical compounds  with a contribution group method=2E

From a file Mol (with about 10000 compounds) I obtained a file Smiles=2E =

Therefore=2C with the classes that treat =22smiles parser =2C smarts pars=
er =

=85) I could predict   Gibbs energy of  small biochemical compounds =2E

But the trouble is that I was obliged to transform =22manually=22 each =

smiles of my smiles file because in the mol files are not charged and=2C =

compounds and groups must be represented in their common state =

=3E in aqueous solution=2C at pH=3D7=2EThat=27s why I would like to obtai=
n =

directly a smiles File where compounds and groups must be represented =

in their common state =

=3E in aqueous solution=2C at pH=3D7=2E

A question if I use the Smarts in order to transform=2C for example (In =

pH =3D7)=2C COOH to COO-  =

 and  you advice me   ( http=3A//www-ra=2Einformatik=2Euni-
tuebingen=2Ede/software/joelib/tutorial/functionalities/mol-
smarts=2Ehtml )  HOW COULD I MAKE TO HAVE A SMILES FILE WHERE MOLECULES =

ARE REPRESENTED IN PHYSIOLOGICAL PH) without change manually each =

smiles of my file=2E


Kind Regards

Naji
  =