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

2013-10-08 Thread Jordan Willis
For some reason David, you have to pass the **kwargs keyword list too. I'm not sure why but this worked for me, python from pymol import cmd, stored, CmdException class Helix(): def __init__(self,selection): self.selection = selection def my_module(*args,**kwargs): helices = [He

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

2013-10-08 Thread Jordan Willis
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 i

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

2013-10-08 Thread David Johnson
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, Cm

Re: [PyMOL] Trouble with saving mol2 format

2013-10-08 Thread David Hall
One feature request, it would be nice if I open a mol2 and then save that molecule as mol2, it would remember the atom types and charges. No need for assignment, just remember what the user read in. -David On Thu, Sep 19, 2013 at 1:03 PM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: >