Takanori,
This is a very clever script -- well done! There are some pitfalls,
but in general this should work well.
Cheers,
-- Jason
On Tue, Jan 31, 2012 at 6:01 PM, Takanori Nakane
<t.nak...@mail.mfour.med.kyoto-u.ac.jp> wrote:
> Hi Abhinav and Jason,
>
>> The underlying C-object for a measurement does not support
>> iterate/alter. This is rather silly; PyMOL should be able to tell you
>> what's in the object.
>
> As an ad-hoc hack, I wrote a Python script to access internal C-object
> of distance representation and convert it to atom name.
>
> Save the script to somewhere and
>
> run script_name.py
> list_dist
>
> will do the job.
>
> Takanori Nakane
>
> === Script start ===
>
> from pymol import cmd
>
> def parseDistObj(obj):
> if (obj[5][0][3][10] != 1): # 'show dashed' flag
> return ""
> points = obj[5][2][0][1]
> ret = []
> for i in range(len(points) / 6):
> ret.append([(points[i * 6], points[i * 6 + 1], points[i * 6 + 2]),
> (points[i * 6 + 3], points[i * 6 + 4], points[i * 6
> + 5])])
> return ret
>
> def list_dist():
> names = cmd.get_session()['names']
>
> dist_pairs = []
> for obj in names:
> if (obj == None):
> continue
> if (obj[1] == 0 and obj[4] == 4):
> dist_pairs += parseDistObj(obj)
>
> namespace = {'dict': {}, 'a': 1}
> dict = {}
> cmd.iterate_state(1, 'all', 'dict[x,y,z] =
> chain+"/"+resn+resi+"/"+name' , space=namespace)
>
> dict = namespace['dict']
> for pair in dist_pairs:
> print dict.get(pair[0], '?') + " - " + dict.get(pair[1], '?')
>
> cmd.extend('list_dist', list_dist)
>
> ------------------------------------------------------------------------------
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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