Thanks Thomas and Tsjerk for pointing me back to the path...from my
quicksand and brambles where I knew I was off! Brilliant. Seems to be an
unfortunate habit I have in scripting where it's like "Why use a simple,
elegant one-liner when a mess of impenetrable hack-arounds would do?" I had
forgotten about those get_<goodstuff> commands.
Much appreciated!
-Seth
On Sun, Jan 23, 2011 at 5:58 AM, Thomas Holder <
spel...@users.sourceforge.net> wrote:
> 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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