VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jul 27 2012 - 11:26:23 CDT

As Axel already mentioned, try compiling VMD with the "SHARED" option and
you should be able to load into Python as a module.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 26, 2012 at 04:40:40PM -0300, Caio Silva Souza wrote:
> Hi
>
> 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?
>
> Thanks
> Caio S.
> Computational and Theorical Biophysics Lab
> University of Brasilia
>
> 2012/7/25 Olaf Lenz <olenz_at_icp.uni-stuttgart.de>
>
> 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 fu:r Computerphysik, Pfaffenwaldring 27, D-70569 Stuttgart
> Phone: +49-711-685-63607 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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