We don't support smirks. See
http://baoilleach.blogspot.co.uk/2012/08/transforming-molecules-intowellother.html?m=1
On 24 Mar 2016 9:33 p.m., "Stefano Forli" <fo...@scripps.edu> wrote:
> Hi all,
> for a while, now, I'm banging my head on how to perform simple
> modifications on molecules
> (I wouldn't dare to call them reactions), but I'm having a hard time
> getting anything
> done. I'm using v2.3.2 with Python, and the core of my code is basically
> this:
>
> reactor = ob.OBChemTsfm()
> reactor.Init(start_pattern, end_pattern)
> reactor.Apply(mol)
>
> Since I couldn't get it to work with my molecules, I've tested one simple
> reaction example
> from here [1]:
> [CH2:1]=[CH:2][CH:3]=[CH:4][CH2:5][H:6]>>
> [H:6][CH2:1][CH:2]=[CH:3][CH:4]=[CH2:5]
>
> and I found that it doesn't seem to work on a simple test molecule such
> "C/C=C\C=C".
> I think the problem is that the first part of the reaction is not
> recognized using it as
> SMARTS pattern, even without indexes (i.e. "[CH2]=[CH][CH]=[CH][CH2][H]").
>
> The documentation suggests that OBChemTsfm is indeed the one to use to
> perform chemical
> transformations, while OBReaction holds only the information about it.
>
> I suspect I'm doing something wrong, but I can't figure out what it is.
> Any advice on the matter?
>
> Thanks!
>
> S
>
>
>
> [1]
> http://www.daylight.com/meetings/summerschool01/course/basics/smirks.html
>
>
> --
>
> Stefano Forli, PhD
>
> Assistant Professor of Integrative
> Structural and Computational Biology,
> Molecular Graphics Laboratory
>
> Dept. of Integrative Structural
> and Computational Biology, MB-112A
> The Scripps Research Institute
> 10550 North Torrey Pines Road
> La Jolla, CA 92037-1000, USA.
>
> tel: +1 (858)784-2055
> fax: +1 (858)784-2860
> email: fo...@scripps.edu
> http://www.scripps.edu/~forli/
>
>
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