Re: [Joelib-devel] smarts

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

Hi naji,

i will forward this also to the mailing list. Hope you don't mind. I=20
think this is a general question and also interesting for other=20
users/developers.

> 1) >NH(participating in a ring )
> [#7;r;H1;$(*-*);$(*-*)] it matches NH in C1CNC=3DCC=3DC1 but
>  it doesn't match a NH of a heteroaromatic ring for example : cytosine =
( how could I do?)
So as said aromatic, means aromatic bonds (:) and not aliphatic bonds (-)=
.
So use $(:) or try another representation, e.g. nitrogen in ring with=20
two heavy weight neighbours, implicite+explicite number of hydrogens is=20
still one.
[#7;r;H1;Q2]

> 2) [c+0X3&H0](:n)(:a) with this pattern I wanted to match  2*(ring> C=3D=
) (participating in two fused non-benzene rings)
> in the adenosine (heteroaromatic ring)
The number of participating rings to an atom is [R]
The ring size is [r]
So what's with
[c;R2](:n)
I think (:a) will match always if you use [c], so i will skip this.
Aromatic [c,n] or nonaromatic [C,N] ? I think i've still not completely=20
understood your pattern request.

> [c+0X3&H0](:n)(A)  with this pattern I wanted to match  1*(ring> C=3D) =
(two single bonds participating in a non- benzene ring) in the cytosine
> there is a problem when I run the program (the same program that joelib=
/src/joelib/desc/types/logP).Although   *(ring> C=3D)(adenosine) and *(ri=
ng> C=3D) (cytosine) are different ( in regard to contribution group) I d=
on't manage to differ them how could I make?). In fact , I would like to =
estimate standard Gibbs energy changes of biochemical compounds and I try=
 to convert from a table the different groups (nitrogen,oxygen,etc..)of t=
he contribution group to smarts pattern.For small molecules there is not =
very difficult but for the rings (benzene ,heteroaromatic rings=85) I enc=
ounter some problems to differ the different molecular fragments of those=
 rings.  =20
I recommend to use the added SMARTS matching code in the CVS, so you can=20
proceed much faster to generate and test different SMARTS patterns.
Just add the single molecule file MDL-SD with .mol extension to=20
joelib/src/resource/smartsEvaluation/*.mol
and add your test patterns to
joelib/src/resource/smartsEvaluation/evaluation.txt
So you can try different things and you can also see the internal=20
representation of these patterns in the result file. So you can work in=20
a kind of 'debugging mode'.

> 3)> C=3D (participating in two fused non-benzene rings)
>  [r;!a]~[#6]~[r;!a] two non-aromatic rings connected via=20
>  aliphatic/aromatic via any bonds but how could I find the smarts patte=
rn if I have adenosine as molecule.
Is the adenine part really non-aromatic ?
If you want only exclude aromatic six rings i would use.
[r6;!a]~[#6]~[r6;!a]
But i'm not sure if this will match, because the 5-ring looks really=20
imidazol like :-)

> 4) > C=3D (the formal double bond and a formal single bond participatin=
g in a non-benzene ring)
>  difference to -CH=3D ? for example,in the cytosine, there are 1 fragme=
nt of > C=3D (the formal double bond and a formal single bond participati=
ng in=20
>  a non-benzene ring) and an other fragment t -CH=3D (participating in a=
 non benzene ring)
Definitely aromatic in cytosine, because Keto-Enol-Tautomerism !
So, i would say
n:c:n

> 5) how could I differ(with smarts pattern) cH aromatic of the benzene =96=
CH=3D (participating in a benzene ring) and cH aromatic of the tyrosine (=
cH of the phenol fragment).The contribution of those fragments is difeere=
nt.
 From the SMARTS standpoint of view there does not exists -CH=3D in=20
benzene. Because the 'atom typer' expert systems (chemical kernel) in=20
JOELib assigns 'c:c' to all carbon atoms connected with aromatic bonds.

So the only difference to the phenol part of tyrosine is 'c-OH' the=20
aliphatic bond to the hydroxyl group.

Again, please use the matching module submitted to CVS, so you can try=20
the different options. Furthermore you can have a look at
http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/atomty=
per.html
and you can see that the aromaticity is the first step of the atom=20
typing process, followed by the hybridization and the implicite valence.
The SMARTS matching and also the real 'atom typer' works on the=20
previously assigned 'expert systems' of the chemical kernel.

Kind regards, Joerg

--=20
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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