Re: [PyMOL] list of polar contacts

[Jason V. <jas...@sc...>]

Thomas,

When you hash by coordinates you could get odd results from alternate
locations and multi-state objects. I like how Takanori solved the
problem, but it's not a strictly perfect solution. What I need to do
is provide access to the C-object for real. We plan to provide
something for this soon.

Cheers,

-- Jason

On Wed, Feb 1, 2012 at 10:41 AM, Thomas Holder
<sp...@us...> wrote:
> Jason, what pitfalls? Are they still present in this script?
>
> http://pymolwiki.org/index.php/Get_raw_distances
>
> Cheers,
>  Thomas
>
>
> On 02/01/2012 04:01 PM, Jason Vertrees wrote:
>>
>> 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.n...@ma...>  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)
>
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120