VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jul 27 2012 - 12:51:58 CDT

Caio,
  There must be, but IED is the one that is most complex, so if we
get IED fixed, we can tell other people to look at the changes needed
to bring it up to date, and their Python scripts/plugins can likely
make the same/similar changes and they will be working.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jul 27, 2012 at 02:46:27PM -0300, Caio Silva Souza wrote:
> Hi,
> Great! Besides IED, are there another plugins that you think would crash
> with this transition?
>
> Thanks
> Caio S.
> Computational and Theorical Biophysics Lab
> University of Brasilia
>
> 2012/7/27 John Stone <johns_at_ks.uiuc.edu>
>
> 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 

-- 
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