[gmx-developers] Python interface for Gromacs

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Thu Sep 9 00:26:57 CEST 2010

Also, I can't help but mention -- the Jules Verne University of Picardy!
That's awesome.  We definitely need more imagination in science and
engineering :)

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

> From: Sébastien Buchoux <sebastien.buchoux at u-picardie.fr>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Wed, 8 Sep 2010 15:51:47 -0400
> To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
> Subject: [gmx-developers] Python interface for Gromacs
> Dear Gromacs developers,
> Interfacing Gromacs with Python have been discussed on this
> list last year (mainly here:
> http://lists.gromacs.org/pipermail/gmx-developers/2009-March/003177.html) but,
> according to the Gromacs roadmap
> (http://www.gromacs.org/Developer_Zone/Roadmap), things are still to be done.
> Sorry if decisions were made in the meantime making this email out of scope.
> I have been using Gromacs for a few years now and lately I have been
> playing with Gromacs source code. More precisely, I wanted to interface
> some of the Gromacs core stuff (pbc, neighbour searching...) with Python.
> To do so, I used pure C extensions (no C types nor SWIG) to handle calls
> to the C libs and to define new Python types to store gromacs-friendly C
> objects while allowing a more "pythonic" way to access them. (This
> approach is actually close to what the Numpy/Scipy guys did.)
> This is still at pretty early stage but it could be extended to
> interface all the Gromacs libraries with Python.
> Where is my point? While I don't think inserting Python-related stuff
> directly into Gromacs source code would be a good idea, a kind of
> "official Python interface for Gromacs" developed at the same time as
> Gromacs would great because:
> - This would be a way to reflect Gromacs API changes into the interface
> more or less seamlessly.
> - "Modularizing the analysis tools" and "making the analysis library a
> true callable library" (cf. roadmap) could also be done.
> - One project would be more visible than a few ones.
> - Python is cool!
> What do you think?
> Sébastien
> --
> Sébastien Buchoux, MC
> UMR 6022 - Génie Enzymatique et Cellulaire / Enzyme and Cell
> Engineering Université Picardie Jules Verne (UPJV)
> 33, rue Saint Leu, 80000 Amiens, France
> tel: +33(0)3 22 82 74 73 - email: sebastien.buchoux[at]u-picardie.fr
> -- 
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