Re: [Open Babel] Combine two SMARTS patterns

[Andrew D. <da...@da...>]

On Mar 7, 2009, at 9:21 AM, Rajarshi Guha wrote:
> 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.

Yes, the "*" gets turned into a PseudoAtom in CDK. There is a  
mismatch between those two, which caused the problems reported in  
issue 2596061.

> 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.

It's probably in the conversion from IQueryAtomContainer to  
IAtomContainer.

You probably want Roger Sayle's "1st-class SMARTS patterns" at
   http://www.daylight.com/meetings/emug97/Sayle/index.html

He writes that while canonical bond expressions in SMARTS are  
possible, canonical atom expressions are an NP-complete problem. Then  
again, so is graph canonicalization.


				Andrew
				da...@da...