Re: [Open Babel] Combine two SMARTS patterns

[Rajarshi G. <rg...@in...>]

On Mar 7, 2009, at 10:59 AM, Andrew Dalke wrote:

> On Mar 7, 2009, at 8:14 AM, Rajarshi Guha wrote:
>> Hmm, a simple case seems to work: http://blog.rguha.net/?p=168
>
> Sweet! I didn't know the CDK could handle that.
>
> Your test was the MCS of
>
>   c1ccccc1C(=O)C* and *C([N,S])C=O
>
> to get *CC=O. One observation though is that test doesn't check any
> properties which aren't simple atom properties, like the "and" in
> [N,S]. What does it report with
>
>   c1ccccc1[N,S](=O)C* and [N,S](=O)C* ?

Hmm, I get a 2 atom match: the aliphatic C and a PseudoAtom, which I  
think corresponds to the * - I think the issue here is with the way  
the logical operator gets represented.

I don't know of the top of my head how the logical operators get  
converted into the 'molecule graph' form. A crude way around for the  
"or" case is to expand the query into the two possibilities.

> Something else I was wondering about. In addition to normalization,
> should the two SMARTS terms
>
>    [C,c]  and [!c]
>
> be considered as a match, with the intersection being [C]?


Hmm, that would make sense.

I think these types of things would be done via transforming the AST  
somehow and then doing the graph ops.

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Rajarshi Guha  <rg...@in...>
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