You would need to specify the size of the ring and indicate that many
atoms. Then add "true" to the parameters of that find() call:
print {*}.find("SMARTS","[r]2[r][r][r][r]2", true)
for example, gives an array for 1crn:
({26 27 30:32})
({135 136 139:141})
({153 154 157:159})
({253 254 257:259})
({282 283 286:288})
These are the prolines, I think.
On Fri, Oct 26, 2012 at 11:03 AM, Rolf Huehne <[email protected]>wrote:
> Dear all,
>
> I would like to use SMARTS/SMILES to find specific groups of atoms but I
> am not sure about how to analyze and use the results.
>
> Let's s say I want to find all cycles within a structure and then use
> the center of mass of each cycle to do a further analysis with each cycle.
> I could run the following command:
>
> x = {*}.find("SMARTS","[r]")
>
> But then there is just a list of atoms in 'x' and I don't know which
> atom belongs to which cycle.
>
> Q: Is there a way to preserve the grouping defined by the SMARTS string
> within a search result?
>
> Q: Or do I have to loop through all atoms in the result list and search
> again somehow for each atom to find the other atoms belonging to it's
> group?
>
> Regards,
> Rolf
> --
>
> Rolf Huehne
> Postdoc
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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