On Jul 11, 2010, at 9:17 AM, Nina Jeliazkova wrote:

>>> The reason of c1cccccc1 (7membered ring in your first example) being
>>> displayed as C1CCCCCC1 is the aromaticity is somehow lost when  
>>> parsing the
>>> aromatic SMILES.
>>>
>>
>> A 7 membered ring should not be aromatic according to Hueckels rule
>
>
>
> Then this smiles should be perceived as invalid, and parsing should  
> fail -
> isn't it?


Hmm, not sure I'd say that it is a syntactically correct SMILES (in  
that the ring closure is correct and valid symbols are employed) but  
semantically it is incorrect - and CDK will indicate the latter by not  
detecting aromaticity

----------------------------------------------------
Rajarshi Guha        | NIH Chemical Genomics Center
http://www.rguha.net | http://ncgc.nih.gov
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