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From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon May 25 2020 - 12:32:27 CDT
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Whatever the search algorithm you want to use, you may take advantage of
selections based on the "withinbonds" keyword to get all the atoms of the
same ring starting from a given selection. To handle napthalene, you may
want to use a starting selection of containing two adjacent carbons at the
far end of each ring, and "withinbonds 2" from them.
Giacomo
Giacomo
On Mon, May 25, 2020 at 1:09 PM MD Simulation <mdsimulationgroup_at_gmail.com>
wrote:
> Hello,
>
> I would like to get a list of atoms in each ring. I know there is
> "atomselect ringsize" but this returns a single list of all atoms. If, for
> example, the molecule is naphthalene, "atomselect ringsize 6 in all" would
> return a single list of all carbon atoms. Is there a function or away to
> program a proc to return a list of lists for each ring system of a specific
> size?
>
> My first thought is some kind of non-binary tree traversal.
>
> Thanks for the help,
> Stacey
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Research collaborator, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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