VMD-L Mailing List

From: Caio Silva Souza (caiobiounb_at_gmail.com)
Date: Fri Jul 27 2012 - 12:19:07 CDT

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
>