Hi Seth,
I think this one-liner will do the job for you:
print cmd.get_chains('polymer')
Cheers,
Thomas
Seth Harris wrote, On 01/23/11 10:04:
> 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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