Brett,
What exactly do you mean one side vs the other? What separates a
"side"? Regardless, you can achieve what you want in two ways: you
can use PyMOL selections; or you can get a chempy model of your
object. Here is an example for each:
#1 -- get atoms bound to a given "sele" atom:
select vicinos, neighbor sele
#1a -- get atoms bound to a given atom and the atom itself:
select mySel, sele extend 1
#2 -- use a chempy model for a given object
x = cmd.get_model("yourObj")
print x.bond[0].index
Cheers,
-- Jason
On Fri, Mar 26, 2010 at 8:33 PM, Brett T. Hannigan
<[email protected]> wrote:
> When visualizing a protein, Pymol automatically connects the various atoms.
> Is there a method to access the connection graph in a pymol plug-in? What
> I want to do, is to write a plug-in so that I click on an atom and have it
> create 2 selections, one selection will have all atoms that are connected to
> each other on one side of the atom I clicked, and the other selection all of
> the atoms on the other side of the atom (I'm assuming for now that there are
> no connections joining the atoms on one side and the other side). This
> should be fairly straight forward I think, provided the info about the
> various atoms connectedness is accessible. Any help is much appreciated.
> -Brett
>
> --
> ******************************************
> Brett T. Hannigan
> ******************************************
>
> ------------------------------------------------------------------------------
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) [email protected]
(o) +1 (603) 374-7120
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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