Re: [Joelib-help] SMARTS search

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

Hi Gerd,

> I'm trying to use subtructure search with SMARTS, but somehow 
> it doesn't work. I do the following:
> 1. Load a Molecule from the SMILES string 'C1CCCCC1 .'
> 2. Create a SMARTS pattern with 'c1ccccc1'
> 
> But the match method returns false. I have to admit that I'm
> not chemist but a computer scientist, so maybe I've overseen
> something. But shouldn't the pattern match the given structure
> since they are the same ?
No, the patterns are really different.

The SMILES string creates a 6ring with single bonds.
The SMARTS string looks for an aromatic ring with conjugated 
single-bond-double-bond system (aromatic).

In SMILES/SMARTS all kind of aromatic atoms, are described by lowerCase 
letters.

So C, c and #6 describes
aliphatic C, aromatic C and aliphatic/aromatic C

Please have a look at the SMILES/SMARTS references in the tutorial.
http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/bibliography.html

The SMARTS Patterns can get really complex, so you can always refer to 
the examples in joelib/src/joelib/data/plain/*, especially when handling 
  atom environments [$(#6);$(*=O);$(*~c)] which means any carbon 
connected with a double bond to an oxygen and with an any bond to an 
aromatic C.

Best regards, Joerg

> 
> Best Regards,
> gerd
> 
> ________________________________________________________________
> Gerd Mueller                                    ge...@sm...     
> SMB GmbH                                  http://www.smb-tec.com
> 
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-- 
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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