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 <tsje...@gmail.com> 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
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