VMD-L Mailing List

From: Caio Silva Souza (caiobiounb_at_gmail.com)
Date: Fri Jul 27 2012 - 12:46:27 CDT

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
>