Re: [Joelib-devel] smarts

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

And again,

see also:
joelib.desc.types.SSKey3DS in method getFingerprintPatterns()

see also:
joelib/data/plain/*.contributions for MR, PSA, LogP SMARTS contribution 
patterns.
They contain no $(...) environments, which is the most powerfull tool in 
SMARTS expression searching, so i recommend to use it heavily, although 
it is also time consuming.

Here are three more examples:
patty.addRule("[$([NH2]-c),ND1H3,ND2H2,ND3H1,ND2H1,$(Cl-[C,c]),$(Br-[C,c]),$(I-[C,c])]",
             "donor");
         patty.addRule("[$(N#C-[C,c]),OD1X1,OD2X2,ND3X3,ND2X2]", 
"acceptor");
         patty.addRule("[$([NH2]-C),$([OH]-C),$([OH]-c)]", "donoracceptor");

So, now you've nearly all public examples in JOELib collected in these 
mails.
I've also a SMARTS testing environment with side effect testing when 
changing the atom typer. Very usefull, for changing the expert system. 
I've used it also to resolve the aromaticity typer problems without 
loosing generalization ability.

So i will publish these classes and all molecular structures with the 
next release, so please be patient. Once a time if already submitted 
these classes to the JOELib/OpenBabel mailing list, but i will it make 
more official and write some documentation for this pretty piece of code.

Kind, regards, Joerg

> 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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