From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 01 2012 - 10:46:26 CDT

Hi,
  I don't have any test data for IED, but I bet that if you contact
John Mongan (the original author) he might have such test data.

Last time I checked, John had moved on to UCSF:
  http://www.linkedin.com/pub/john-mongan/49/24a/b75

If John doesn't have test data or can't be contacted, you might be able
to ask around within the AMBER communityk, since IED was developed to work
in concert with with the AMBER tools such as ptraj.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 31, 2012 at 04:21:44PM -0300, Caio Silva Souza wrote:
> John,
>
> So I will work on this plugin. Do you have any file that would help to
> test the plugin, such as projections file and eigenvector file?
>
> Thanks
> Caio S.
> Computational and Theorical Biophysics Lab
> University of Brasilia
>
> 2012/7/27 John Stone <johns_at_ks.uiuc.edu>
>
> 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

-- 
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