[gmx-developers] Python interface for Gromacs

[Roland Schulz]

Hi,

I was aware of pymacs but I wanted something which is pythonic from the
interface.
Also I wanted something which doesn't generate any dependencies and doesn't
add any complexity to the makefile. This is why I chose to use ctypes.

How many functions did you wrap with swig? Would it really be much more work
to do it with ctypes? Can you upload you lib somewhere so we can take a look
at the interface? The problem with the libs, I have seen so far which have
been wrapped with swig, is that they keep the C interface. I think you only
have half the advantage of using python if the interface is still C-like. I
think reading a trajectory has to work the same way as you read any other
file in python. Thus I made sure this works:

from xdrfile import *
x=xdrfile("test.xtc")
for f in x: #f frame
    print f.x

the same way e.g. reading pdb should work as
p=pdb("some.pdb")
for a in p: #a atom
   print a.x,a.y,a.z,a.type,a.beta

The wrapper now also autodetects trr and numpy (if numpy is installed the
coordinates are a Numpy array). Still it is very small.
latest version: https://cmb.ornl.gov/Members/z8g/xdr.tgz/at_download/file

I think it would be great to have also wrapper for the analysis library and
for reading other files. But I wouldn't like to have a SWIG interface with
is not pythonic.

We certainly don't want to have depencies of Gromacs on Python. You can't
run python everywhere. But I think it would be good to have a CVS repository
for a python wrapper of the other Gromacs libs (and python tools) so that it
is possible to collabrate. I asked whether the xdr python wrapper can be
added to the xdrlib because it only reads trajectories and thus fits best in
that repository. Also by keeping it seperate to the rest of Gromacs it is
possible to use it without installing all of Gromacs.

Roland

On Sat, Mar 28, 2009 at 12:35 AM, nizamov.shawkat at gmail.com <
nizamov.shawkat at gmail.com> wrote:

> Hi all!
>
> It looks like there is a plenty of developers trying to create a Python
> interface for this or that particular function of Gromacs. There is
> fairly functional (and stable?) pymacs package. I didn't look much in
> it, but it goes directly extending Python with manually crafted C
> wrapper. Others are creating some useful wrappers using ctypes (previous
> message in the list). Lately I also did some work in this area, but
> wasn't interested in discussing it before some actual results obtained.
> But as surprisingly much effort of different researchers got devoted to
> Pythonic interface, maybe it's time to discuss before reinventing the
> wheel?
>
> Last week I created a single SWIG wrapper around all 3 libraries -
> libgmx, libmd and libgmxana. As a proof of concept I also successfully
> (but implemented only partially) ported gmxdump.c to Python using this
> wrapper. Rewriting gmxdump.c in pure Python was straightforward. I hope,
> that there will be no large obstacles for using other library routines
> also. The task of creating wrapper for scripting language is on
> developers section of Gromacs wiki right after the task of moving
> analyzing functions to core library (libgmxana). But it is not clear -
> if scripting interface with Python wrapper is going to be mainline tool
> for analyzing  data, converting to and from different formats (XML and
> gnuplot are also mentioned on developers section), setup the simulation,
> interfacing with user,  etc? That means that in the long term Gromacs
> will be strictly dependent on Python and its bindings and only a
> simulation core will remain in pure C and available mostly as a library.
> Did I get the idea correctly?
>
> Practical question is - how can different developers collaborate on such
> Python wrapper for Gromacs ? I would spend some of my spare time for
> improving SWIG wrapper (that is already usable) for my own research, but
> working in a team makes much more sense in the open-source world.
>
> WBR
> Shawkat
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20090328/0f8428df/attachment.html>