Re: [PyMOL] command-line and python scripts

Dear Markus,

> 1) How can I supply arguments to a python script,
> when I invoke it from 
> the pymol command line?

Write the python script like

def bla(arg1,arg2):
    any.python.commands(arg1,arg2)
    return

from pymol import cmd
cmd.extend('blacommand',bla)

Now you can call your function 'bla' from the PyMOL 
command line:

PyMOL> blacommand pdb1cso,42

Which would be like in Python:

bla('pdb1cso','42')



> 2) Can I set user variables in the pymol command
> line and access them 
> in a python script?

same answer as for 1).

 
> 3) Can I rerun a python script and use generator
> functions that I 
> initialised in the run before?

Sorry, I did not understand this question completely
(might be same answer as above two).


> 4) Can I temporarily return control to pymol from
> within a running a 
> python script and continue running the script after
> I have finished 
> interacting with pymol?

You should probably check out the Script Box utility,
if You have not already (http://www.rubor.de/bioinf

 
> 5) Can I query the active state of a pymol object
> (and other properties 
> as well) from withing a python script?

Yes. Look at: 
http://www.rubor.de/bioinf/pymol_tips.html#getcoord


> 6) 
dunno
 
> 7) 
also.

Good luck,

Kristian Rother

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