Re: [PyMOL] Calling pymol from python - access to global variables

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

Hi Tsjerk,

use either the global pymol.stored variable or the alter_state 'space' argument.

--------------
#!/usr/bin/env python

if __name__ == "__main__":
 import __main__
 __main__.pymol_argv = [ 'pymol', '-cq' ]
 import pymol
 pymol.finish_launching()
else:
 import pymol

def identity(x,y,z):
  print "YEAH!"
  return x,y,z

pymol.editor.build_peptide("GGGGG")
pymol.cmd.alter_state(1,"all","(x,y,z)=identity(x,y,z)",
       space={'identity':identity})

# or:
# pymol.stored.identity = identity
# pymol.cmd.alter_state(1,"all","(x,y,z)=stored.identity(x,y,z)")
--------------

Cheers,
 Thomas

On Tue, Mar 29, 2011 at 6:18 PM, Tsjerk Wassenaar <ts...@gm...> wrote:
> Hi,
>
> I'm having some trouble accessing a function defined at top level with
> alter_state in a python script launching pymol. Maybe I shouldn't be
> wanting to do this, but what I'm trying, and failing to do is
> exemplified by this script:
>
> ###
>
> #!/usr/bin/env python
>
> import pymol
>
> if __name__ == "__main__":
>    pymol.finish_launching()
>
> def identity(x,y,z):
>    print "YEAH!"
>    return x,y,z
>
> # Fix:
> # setattr(pymol,"identity",identity)
>
> pymol.editor.build_peptide("GGGGG")
> pymol.cmd.alter_state(1,"all","(x,y,z)=identity(x,y,z)")
>
> ###
>
> The problem is that the function 'identity' (which may be given a more
> sensical form by actually doing something with the coordinates), is
> sought in the pymol namespace. I can't really figure out where I
> should be looking to directly call the function. Of course, I can
> register the function in the pymol module (uncomment the setattr
> line), but I don't think it's proper meddling with established modules
> like that. Does anyone know a better/cleaner solution?
>
> In addition, does anyone know how to suppress the GUI stuff when
> launching pymol like this?
>
> Groetjes,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands

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