hi warren.
if i were to do something like:
cd some_module_source_tarball
pymol -qc setup.py install
would that compile and install the module somewhere/way the pymol
interpreter can import it in scripts? (given that the some_module
corresponds to a python version matching the version of the pymol
interpreter)
thanks,
wlad
On Jun 8, 2009, at 10:01 PM, Warren DeLano wrote:
> As for the your general question: can you "import pymol; from pymol
> import cmd; pymol.finish_launching(); etc"?
>
> Answer 1: Yes, if you manually compile PyMOL open-source code into an
> existing Python interpreter.
>
> Or
>
> Answer 2: Yes, if you run your Python script using PyMOL's built-in
> Python interpreter (launch PyMOL as follows):
>
> ./pymol your-script.py # with full 3D GUI
>
> ./pymol -qc your-script.py # command-line only (in a terminal)
>
> Or
>
> Answer 3: Yes, if you call your Python script from a PyMOL script via
> the "run" or "spawn" commands inside PyMOL.
>
> However,
>
> Answer 4: No, if you want precompiled PyMOL build to work with an
> external precompiled Python build. This approach has proved
> impractical
> due unavoidable application binary interface (ABI) version mismatches
> between PyMOL, Python, and the host environment.
>
> As for your specific question, this is something you could do with a
> plain old script without even introducing the complexity of Python:
>
>
> load $TUT/1hpv.pdb, query
>
> remove not polymer
>
> create tmp, query
>
> set dot_solvent
>
> get_area tmp, load_b=1
>
> # threshold on what one considers an "exposed" atom (in A**2):
>
> remove tmp and b<2.5
>
> tmp_dict = {}
>
> iterate tmp, tmp_dict[(chain,resv)]=1
>
> select exposed
>
> exposed = tmp_dict.keys()
>
> exposed.sort()
>
> print "Solvent exposed residues (chain,residue):"
>
> for res in exposed: print res
>
> select exposed, query in tmp
>
> dele tmp
>
>
> # visual confirmation
>
> color white
>
> color red, byres exposed
>
> set sphere_solvent
>
> as spheres
>
> orient
>
>
> Cheers,
> Warren
>
>> -----Original Message-----
>> From: Yasser Almeida Hernandez [mailto:[email protected]]
>> Sent: Friday, June 05, 2009 9:18 AM
>> To: [email protected]
>> Subject: [PyMOL] Hi all...
>>
>> I want to make a python script to list the surface residues of a
>> protein. The idea is import the pymol module inside the script,
>> receive the pdb file to be analyzed and run the pymol's commands to
>> do
>> this task. It is possible..? the script is to tun in a classical
>> terminal...
>>
>> Thanks...
>>
>> ----------------------------------------------------------------
>> Correo FENHI
>>
>>
>>
>>
>>
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