VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 24 2012 - 11:48:52 CDT

Hi,
  The state of Python in VMD could probably best be described as
being in a "holding pattern" at present. This is in large part due
to the fact that there have been several incompatible major revisions
to Python in the past few years that have made it very difficult to
support Python at the level of sophistication that we had originally
hoped to. If things like Numeric / NumPy weren't getting broken so
easily with major Python releases, it would be far easier for me to
justify putting more effort into advancing the state of Python support
in VMD. In regards to these troubles, you may find that the existing
IED plugin is a case study of the difficulties I mention above.

Python has been a bit of an "always moving target" in terms of
providing a stable set of VMD functionality via the most widely
used Python APIs. Now that Python 3.x has been out for a while and
the dust is beginning to settle, we might hope to make more progress
in this area as fewer and fewer people are expecting their old Python 2.x
scripts and plugins to continue to work without updates.

We have a mechanism to allow Python scripts to make calls into the
Tcl-only APIs and Tcl plugins, that allows full coverage of VMD features,
albeit with a less convenient mechanism than if there was 100% coverage
via Python-native APIs. Given this, I would say that there's probably
not a need to "reinvent" existing plugins in Python-native versions
except in a limited set of cases where it would be very helpful
for providing starting examples and tutorial materials for other people
interested in developing Python scripts and plugins. If you are interested
in doing some of this, I would be happy to work with you as time allows.

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.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Jul 21, 2012 at 08:47:13PM -0300, Caio Silva Souza wrote:
> Hi,
>
> I am a VMD user and have some experience with Python. Recently I
> discovered the VMD's Python support and its development difficulties,
> mainly the lack of plugins written in this language.
> I am interested in helping the development of the Python layer mainly by
> translating some plugins written in TCL to this language and maybe
> creating new modules. Will this be helpful?
> Furthermore, what are the future plans about Python support on VMD?
>
> Thanks
> Caio S.
> Computational and Theorical Biophysics Lab
> University of Brasilia 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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