Re: [PyMOL] Is it possible to pass command line arguments to a .pml file?

[Tsjerk W. <ts...@gm...>]

Hey :)

You don't even need the python block, as the pymol interpreter is a python
interpreter with just some added extras. Single lines of python code are
never a problem. This works nicely for me

File test-argv.pml:
================

print sys.argv
for i in sys.argv[1:]: print i


Run pymol:
================

pymol test-argv.pml -- bla bla bla


Output:
================

PyMOL>print sys.argv
['/martini/tsjerk/Programs/pymol-1.5.0.4/pymol.exe', 'bla', 'bla', 'bla']
PyMOL>for i in sys.argv[1:]: print i
bla
bla
bla


Enjoy!

Tsjerk


On Wed, Jun 26, 2013 at 11:21 AM, <lie...@vu...> wrote:

> On Wednesday 26 June 2013 08:52:39 Jordan Willis wrote:
> > I'm looking to pass a .pml file, do some stuff, and then save it as a
> > session. Pymol -c My.pml looks like a good option.  I'm trying to write
> > hundreds of sessions each with different arguments. I was wondering if
> its
> > possible to pass command line arguments that can then be seen by the
> python
> > interpreter inside a .pml
> >
> > While I'm at it, is it easy to pass objects, i.e. variable names, between
> > the python enviroment and the pml enviroment inside a .pml script? Is
> > cmd.extend the best option? Is there a way to go backwards (from the .pml
> > to the python interpreter)?
>
> This .pml sequence works for me:
>
> stored.a = 5
> python
> import sys
> print sys.argv
> print stored.a
> stored.a = 10
> python end
> print stored.a
>
> Cheers,
>
> --
> Lieven Buts, Postdoctoral Fellow
> Structural Biology Brussels, Vrije Universiteit Brussel
> Department of Structural Biology, VIB
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.