Re: [PyMOL] Expose PyMOL API

[Thomas H. <sp...@us...>]

Hi Martin,

I don't have a Mac so I can't test this, sorry.

I suspect that the _cmd module is built into the MacPyMOL executable. 
This would imply that you cannot use MacPyMOL like in the 
"Launching_From_a_Script" examples. Maybe someone of the MacPyMOL users 
knows more?

Cheers,
   Thomas

Martin Hediger wrote, On 11/22/11 13:14:
> Thanks Thomas for the reply. I tried it under Mac OS X 10.5.8.
> 
> me @ ~/PROG_TEST $ python
> Python 2.6.5 (r265:79359, Mar 24 2010, 01:32:55)
> [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> imported numpy
> from PyQt4.QtGui imported *
> from PyQt4.QtCore imported *
>>>>  import os, sys
>>>>  import readline
>>>>  import rlcompleter
>>>>  readline.parse_and_bind('tab: complete')
>>>>  moddir='/Applications/PyMOLX11Hybrid.app/pymol/modules'
>>>>  sys.path.insert(0, moddir)
>>>>  os.environ['PYMOL_PATH'] = os.path.join(moddir, 'pymol/pymol_path')
>>>>  import pymol
> Traceback (most recent call last):
>   File "<stdin>", line 1, in<module>
>   File 
> "/Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/__init__.py", line 
> 472, in<module>
>     import _cmd
> ImportError: No module named _cmd
>>>>  import pymol
> 
> 
> What could be the problem? Could it be that the 'pymol/pymol_path' call 
> is not exactly right? In the modules/pymol directory, there is a module 
> 'pymol/launch_pymol', but I have a similar error ("No module named 
> _cmd") when I try to import it.
> Martin
> 
> 
> 
> 
> 
> 
> Am 22.11.11 09:47, schrieb Thomas Holder:
>> Hi Martin,
>>
>> the recommended way is to use PyMOL as your python interpreter, so 
>> instead of:
>>
>>   python file.py
>>
>> do this:
>>
>>   pymol -cqr file.py
>>
>>
>> However, launching a PyMOL process from a python terminal as you 
>> suggested is also possible. Have a look at Example 2 of 
>> http://pymolwiki.org/index.php/Launching_From_a_Script , the important 
>> lines are those:
>>
>> import pymol
>> pymol.pymol_argv = ['pymol','-qc']
>> pymol.finish_launching()
>>
>> Cheers,
>>   Thomas
>>
>>
>> Martin Hediger wrote, On 11/22/11 09:26:
>>> Dear PyMOL List
>>> It comes up once in a while, is it possible to use PyMOL features 
>>> from outside of PyMOL? An example, the below is a script (inspired by 
>>> Thomas Holder) which saves down to disk all amino acids of a protein 
>>> structure into separate PDB files.
>>>
>>> # *****************************************************************
>>> from pymol import cmd
>>> from pymol import stored
>>> from pymol.exporting import _resn_to_aa as one_letter
>>> # *****************************************************************
>>> def seq(state, selection="name ca or resn hoh or resn lig"):
>>>      print "Generating seqs."
>>>      cmd.select("prot", selection)
>>>      while cmd.pop("_tmp", "prot"):
>>>          cmd.iterate("_tmp", "stored.x=(resn,resv)")
>>>          #print stored.x[0], stored.x[1]
>>>
>>>          # Special case 1: Waters.
>>>          if stored.x[0] == 'HOH':
>>>              filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
>>>          # Special case 2: Substrate.
>>>          elif stored.x[0] == 'LIG':
>>>              filename = 'seq-x%s-%s.pdb' % (stored.x[1], state)
>>>          # Other: protein back-bone.
>>>          else:
>>>              filename = 'seq-%s%d-%s.pdb' % 
>>> (one_letter[stored.x[0]].lower(), stored.x[1], state)
>>>          cmd.save(filename, "byres _tmp")
>>>      cmd.delete('_tmp prot')
>>>
>>> cmd.extend('seq', seq)
>>> # -----------------------------------------------------------------
>>>
>>> Is it possible to somehow include this in a Python script, and 
>>> running it from the command line? If not, why?
>>>
>>>
>>> Thanks for any feedback.

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen