Re: [Cdk-devel] SymbolQueryAtom vs AliphaticAtom

[Jiao, D. <dj...@in...>]

Egon Willighagen wrote:
> On Saturday 14 April 2007, Jiao, Dazhi wrote:
>   
>>>> The only problem is when there is a recursive Smarts inside the
>>>> brackets. Then we not only have QueryAtom, but also QueryAtomContainer.
>>>> I don't see how to modify the SmartsAtom. So I think instead, when
>>>> parsing smarts, we need to build a QueryAtomContainer when there is
>>>> Recursive Smarts in the Brackets. When there is no Recursive Smarts,
>>>> return a SmartsAtom.
>>>>         
>>> This is probably right; however it seems that when you have a
>>> QueryAtomContainer as a node in the parse tree, we might hit problems
>>> with the UniversalIsomoprhismTester which considers atoms/bonds but not
>>> whole containers.
>>>       
>> This is bothering me as well. As I am getting myself more familiar with
>> the API, I am not sure if this is doable just using the
>> QueryAtomContainer for the RecursiveSmarts. Maybe we need a
>> SMARTSAtomContainer, which could contain the logical relationship. But I
>> am not sure due to my lack of understanding of how the query are
>> actually done. What do you think?
>>     
>
> OK, this would indeed be a problem. I do not feel that the UIT will be able to 
> support this.
>
> Might you show some SMARTS examples that use such set up? Does anyone know if 
> MQL also have such constructs?
>
> Egon
>
>   
Hi, Egon,

There are examples in the Daylight Smarts example page at 
http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html. 
Be careful, there are some smarts that could make people dizzy :) Here 
is one I copied from it.

N-Oxide
    [$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])] 
    Hits both forms. Won't hit azoxy, nitro, nitroso,or nitrate.


The daylight tutorial has some examples of recursive smarts.

http://www.daylight.com/dayhtml_tutorials/languages/smarts/index.html#RECURSIVE

David