Re: [Joelib-devel] smarts

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

Hi,

sorry, replace all
,=or statement
;=and statement

> Hi naji,
> 
> so here are my guesses, no gurantee that the SMART patterns work. So 
> please resend the tested/working patterns.
> 
>>> C= (participating in two fused benzene rings)
> 
> c~[#6]~c two benzene rings connected via aliphatic/aromatic via any bonds
> or general aromatic rings ?
> [r;a]~[#6]~[r;a]
> 
>>> C= (participating in two fused non-benzene rings)
> 
> [r;!a]~[#6]~[r;!a] two non-aromatic rings connected via 
> aliphatic/aromatic via any bonds
> 
>>> C= (participating in two fused  rings: one benzene ring and one 
>>> non-benzene ring)
> 
> [r;!a]~[#6]~[r;a]
> 
>> -CH=( participating in a benzene ring)
>>
>>> C= (the formal double bond and a formal single bond participating in 
>>> a benzene ring)
> 
> [#6,a,Q2,$(*-*),$(*=*)] so two heavy weight neighbors and neighbour 
> environments with $(...), here general aromatic ring.
> You can also work with hybridisation states using ^2, see 
> joelib/data/plain/*.txt for examples
> 
>>> C= (two single bonds participating in a non- benzene ring)
> 
> with or without implicite hydrogens, so X or D or Q
> http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/functionalities/mol-smarts.html 
> 
> and reference and link to daylight tutorial.
> [#6,!a,r,Q2,$(*-*),$(*-*)] so two heavy weight neighbours, here general 
> non-aromatic ring
> 
>> -CH=( participating in a non- benzene ring)
> 
> [#6,!a,r,Q2,$(*-*),$(*=*)]
> 
>>> C= (the formal double bond and a formal single bond participating in 
>>> a non-benzene ring)
> 
> difference to -CH= ?
> 
>> =N- (participating in a ring )
> 
> [#7,r,Q2,$(*-*),$(*-*)] so assuming any ring, or only aliphatic ones ?
> 
>>> NH(participating in a ring )
> 
> [#7,r,H1,$(*-*),$(*-*)]
> 
>> -N< (participating in a ring )
>> -N< (participating in two fused rings )
> 
> analogue to C, more or less.
> 
>> Any suggestions?
> 
> Yes :-)
> 
>> Thanks
> 
> Was me a pleasure.
> 
> 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
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