Oops... That should've been:
polychains = set([i.chain for i in cmd.get_model('polymer').atom])
Sorry for that. :p
Tsjerk
On Sun, Jan 23, 2011 at 10:32 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
> 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 <set...@gmail.com> 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
>
--
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
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