Re: [PyMOL] Faster way to find polymer chains?

[Tsjerk W. <ts...@gm...>]

Hi Seth,

So you just want to have all unique chain identifiers for the
'polymer' selection? Does the following give what you want?:

polychains = set([i.chain for i in cmd.get_model('polymer')])

Hope it helps,

Tsjerk

On Sun, Jan 23, 2011 at 10:04 AM, Seth Harris <se...@gm...> wrote:
> Hi All,
> I am script-plowing through PDB files and extracting unique chain
> identifiers only for "polymers" using PyMOL's polymer selection. Right now
> my code is a kind of brute force thing like this:
> <code>
>   cmd.create ("justpolys","polymer")
>   polymer_chains=[]
>   for a in cmd.index("justpolys"):
>     q_sel = "%s`%d"%a
>     #print q_sel+":",
>     cmd.iterate(q_sel, "stored.qry_info = (chain,resn,resi,name)")
>     #cmd.iterate_state(1,q_sel, "stored.qry_xyz = (x,y,z)")
>     #print
> stored.qry_info[0],stored.qry_info[1],stored.qry_info[2],stored.qry_info[3]
>     # Track any unique chains by adding to polymer_chains list if not
> already there
>     # first reformat to get rid of flanking ' marks
>     thischain=`stored.qry_info[0]`
>     thischain=thischain.replace("'","")
>     if thischain not in polymer_chains:
>       polymer_chains.append(thischain)
> </code>
> This works, but is quite slow as it iterates over every atom in every pdb
> just to get out the chain so it is quite redundant.
> Is there any way to iterate in a 'chain by chain' fashion? This q_sel stuff
> is recycled from something Warren suggested for a different purpose years
> ago, and I only have a loose idea of how that is interacting with the
> cmd.index part. Maybe there's a way to get just the chain from the get-go
> instead of all the individual atoms? Any reminders on that one or better
> method suggestions?
> Thanks,
> Seth
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands