joelib-devel

[Joelib-devel] smart modification and hydrogen

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

HI JOERG=3B


Thank very much for your advice =3A sh convert=2Esh yourOriginalFile=2Esm=
i =

phCorrectedFile=2Esmi=2E Now=2C I can transform my original file to =

pHcorrectedfile but in the transformations I don=27t manage to convert C
(=3DNH)(-NH2)(-NH-) to  C(=3DNH2+)(-NH2)(-NH-) ( a guanidium group found =

for example in the arginine   )

I have another question =3A Have you got some ideas how I could make in =

order to count the total number of hydrogen of a molecule from a smiles =

string=2E
For example =5BNH3+=5DCC(=5BO-=5D)=3DO  (glycine) we have got for this co=
mpound 6 =

hydrogen=27s  because I would like to convert Gibbs energy (pH=3D0) to =

Gibbs energy (pH=3D7) with the formula deltaG=270(pH=3D7)=3D deltaG=270(p=
H=3D0) =96 =

NHRTln10-pH=2C where NH is the hydrogen number  of the molecule=2E

Kind Regards

Naji

Re: [Joelib-devel] smart modification and hydrogen

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

Hi NAJI,

> Thank very much for your advice : sh convert.sh yourOriginalFile.smi 
> phCorrectedFile.smi. Now, I can transform my original file to 
> pHcorrectedfile but in the transformations I don't manage to convert C
> (=NH)(-NH2)(-NH-) to  C(=NH2+)(-NH2)(-NH-) ( a guanidium group found 
> for example in the arginine   )
As you can see at the bottom of this page
http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/functionalities/mol-smarts.html
1. you should only apply one change at time.
2. I can't see any vector binding in your pattern, it should be
    something like this, but please remember that not all imaginable
    rules are implementetd in the basic transformer class, so try and
    check, e.g.:
    [N:1](-NH2)(-NH) >> [N+:1](-NH2)(-NH)

> I have another question : Have you got some ideas how I could make in 
> order to count the total number of hydrogen of a molecule from a smiles 
> string.
Explicit or implicite hydrogens ?
Try:
numHAtoms=atom.getImplicitValence() + atom.getValence()

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
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-devel] a trouble to match a new element : R

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

Dear NAJI,

1. radicals R are not supported directly.

2. You can not simply add a new element entry in the element table
joelib/data/plain/element.txt, because this type must be anywhere 
assigned and this is not the case at all.
Typically this is done by the SMARTS atom types (PATTY algorithm) in
joelib/data/plain/atomtype.txt
So, radicals are much more difficult, because electron counts are at the 
moment not supported by SMARTS matching and therefore also not for the 
PATTY algorithm. See also:
joelib/smarts/JOESmartsPattern.java
joelib/smarts/ParseSmart.java
joelib/smarts/Patty.java

3. Smiles does not recognize 'R'. So there exists still a request for 
this feature, but there they requested the R-groups analogue to the 
entries in SDF files. So, what is the standard here ?
http://sourceforge.net/tracker/index.php?func=detail&aid=970983&group_id=39708&atid=425970

I've increased the priority to 6.

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
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)