Re: [PyMOL] Performance of extended commands vs python function

[Thomas H. <tho...@sc...>]

OK thanks. I haven't seen such performance differences before and couldn't reproduce it so far. Could you share your script (and data files if possible) with me?

Thanks,
  Thomas


> On Dec 16, 2019, at 5:42 PM, Lorenzo Gaifas <br...@gm...> wrote:
> 
> Yes, it does. Both cases are with the GUI and ewual graphical representation.
> 
> On Mon, Dec 16, 2019, 17:37 Thomas Holder <tho...@sc...> wrote:
> Hi Lorenzo,
> 
> When you say "run from a python script", is that with the graphical GUI? That "instant update", does that include instant update of visual representations?
> 
> Thanks,
>   Thomas
> 
> 
> > On Dec 13, 2019, at 12:55 PM, Lorenzo Gaifas <br...@gm...> wrote:
> > 
> > Dear Pymol users,
> > 
> > I just discovered something I did not expect: the same python function can have extremely different performance when called as a python function or using the pymol api.
> > 
> > To be more specific: I have a function func that (among other things) uses cmd.alter several times over a big system to change the properties and representation.
> > 
> > If I run it calling func() from a python script, its effects are almost instant. If I call it with cmd.do('func') (or directly from within pymol with func), it’s extremely slow (up to 10 seconds) and Pymol freezes completely during this time.
> > 
> > I expected this to be due to an overhead of the api itself, but when I do the same thing with a simpler function, I see no noticeable difference.
> > 
> > Why exactly is this happening? And more importantly, how can I get the performance of func even when I call it from within pymol?
> > 
> > Thank you,
> > Lorenzo
> > 
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> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.