From: Giacomo Fiorin (
Date: Mon May 25 2020 - 12:32:27 CDT

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.



On Mon, May 25, 2020 at 1:09 PM MD Simulation <>

> 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