From: Caio Silva Souza (
Date: Thu Jul 26 2012 - 14:40:40 CDT


I understand the problems of supporting Python, but I think nowadays this
language has reached a mature level in which these problems no longer
occurs. For example, since version 1.5 Numpy is working with Python 2.x and
3.x releases. And as Python is backported, if the version of the
interpreter changes, these modules will still work. Related to old plugins
(like IED), I think I can repair them. Also, are there another plugins that
would crash with new Python versions? Finally, you could choose just one
version of the interpreter to work with, and the users will be still be
able to use newer releases (e.g. I compiled VMD 1.9.1 with Python 2.7.3 and
everything worked out of the box).

With all these ideas in mind, I think it's time to VMD to support version
3.x of Python (since 2.x no more has support). I took a look at the source
code, and I guess this transition won't be difficulty, as most of the
changes doesn't modify the original function's return values.

As you can see, I'm very interested on this transition and I hope to be of
help in the process.

Olaf's point of view is interesting. How feasable it would be to make VMD
(only for analysis, without a GUI) a Python module in the future?

Caio S.
Computational and Theorical Biophysics Lab
University of Brasília

2012/7/25 Olaf Lenz <>

> Hi!
> On 07/24/2012 06:48 PM, John Stone wrote:
>> Going forward, I am hoping that we can choose to support just one
>> major version of Python and that we can start removing the remnants
>> of the oldest Python interface code in VMD to streamline future
>> efforts. If Python itself ends up being more stable in the next few
>> years, that would go a long way toward making it feasible to provide
>> a greater degree of integration in VMD than is currently provided.
> What I do not completely understand is why you chose to integrate the
> Python interpreter into VMD instead of making VMD a Python module. We
> have done this with our software ESPResSo, and we see various advantages:
> * It removes the versioning problem, as the API for Python extensions is
> pretty stable over various versions - in contrast to the interpreter API.
> * It would allow users to run VMD with the version of Python provided by
> their system.
> * It would allow users to use VMD in conjunction with any of the various
> other Python modules.
> BTW, the same goes for Tcl: one could also make VMD a package for Tcl,
> instead of integrating the interpreter into VMD. But I see that the
> effort is probably not well spent, as Tcl is mostly a dying language
> anyway.
> Olaf
> --
> Dr. rer. nat. Olaf Lenz
> Institut für Computerphysik, Pfaffenwaldring 27, D-70569 Stuttgart
> Phone: +49-711-685-63607