Re: [PyMOL] How to pass a list of selections into pymol script

[Jordan W. <jwi...@gm...>]

Could you just initialize your helix class with the object at the time of creation? Also why are you passing the superclass object to Helix?

> class Helix():
>     def __init__(self,selection):
>         self.selection = selection
> 
> def my_module(*selections):
>     helices = [Helix(x) for x in selections]
>     for helix  in helices:
>         selection = helix.selection
>     """ Do some more things with these selections"""


On Oct 8, 2013, at 11:59 AM, David Johnson <da....@gm...> wrote:

> I would like to create a module for pymol which accepts several 
> selections for processing. The number of selections passed to the 
> modules is not fixed and thus I want to pass a list of selections into 
> the applications. I have tried something like the following.
> 
> from pymol import cmd, stored, CmdException
> 
> class Helix(object):
>     def __init__(self):
>         self.selection = None
> 
> def my_module(*selections):
>     helices = [Helix() for x in selections]
>     for helix, sele in zip(helices, selections):
>         helix.selection = sele
>     """ Do some more things with these selections"""
> 
> 
> Within pymol I load it up and import the module without any trouble. I 
> make several selections and try to pass them in as follows.
> 
> sele S1, resi 1-10
> sele S2, resi 11-15
> sele S3, resi 16-30
> import my_module
> my_module S1, S2, S3
> 
> I receive the following error
> Traceback (most recent call last):
>   File 
> "/Volumes/Data/scm/vikki/bld/MacPyMOL.app/pymol/modules/pymol/parser.py", line 
> 254, in parse
> TypeError: my_module() got an unexpected keyword argument '_self'
> 
> I have tried modifying the code as follows.
> 
> def my_module(selections):
>     ...
> 
> I get an error that my_module expects only one argument.
> 
> It has been suggested that I pass a list of strings and then access the 
> selections based on the string name of the selections, however, I have 
> not been able to find the syntax to put this into the code.
> 
> Thanks.
> 
> David
> 
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