VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jul 27 2012 - 12:30:16 CDT

Caio,
  I think that supporting Python 3.x would be great. I would also
love to see the IED plugin get completely fixed so it works with the
newer revs of Python, works completely with NumPy etc. In truth, my
own preference has always been to maintain compatibility with the latest
revs of the scripting languages when feasible.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jul 27, 2012 at 02:19:07PM -0300, Caio Silva Souza wrote:
> Hi,
>
> And what about bringing Python 3 to VMD as I said? I think this won't be
> difficult and I'm willing to help on fixing the plugins that get crashed.
>
> Thanks
> Caio S.
> Computational and Theorical Biophysics Lab
> University of Brasilia
>
> 2012/7/27 John Stone <johns_at_ks.uiuc.edu>
>
> 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
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078