Re: [AMBER-Developers] Python request

From: Jason Swails <>
Date: Thu, 21 Oct 2010 16:12:10 -0400


I think I finally have a working branch that will build an Amber-specific
Python version alongside AmberTools as a part of the normal build process.
(This can be removed via a -nopython flag in configure).

It was fairly trivial to get it to work for Linux, since it requires nothing
but a ./configure make make install, but the only way I could get it to work
on Mac OS X (specifically 10.6 SL), was to steal the relevant Macports diff
files, specifically use the Xcode gcc-4.2, and build it as an Apple
Framework, though the end result is that I have a working copy tested and
running on both Ubuntu and Mac OS X 10.6, with the intel and gnu compilers.

This is all part of the branch MMPBSApy-dev, so for those that have
different machine configurations and/or would like to try out the new Python
integration, it's available.

Some notable advantages: all python module files can be dumped into the
python2.6 lib folder with all of the system modules, and python should
simply find the module without having to set PYTHONPATH or anything else.
I've also taken to writing wrapper shell scripts for my Python programs that
invoke the proper program with the Amber python.


$AMBERHOME/bin/python python_prog $*

more or less.

Improvements and suggestions welcome.


On Wed, Oct 20, 2010 at 8:54 AM, David A. Case <>wrote:

> On Sat, Oct 16, 2010, Jason Swails wrote:
> >
> > I have removed the python 2.6 requirement in the git tree;
> OK..thanks for the update. Looks like people in my group were not pulling
> recent git commits. Sorry for the noise.
> > The install is done in such a way that failures are non-fatal,
> OK...sounds good.
> > Ben and I are also working on creating a
> > library of useful python utilities for amber which could be included,
> > and installing our own python can help us keep track of dependencies and
> > make the install process more painless.
> Again, sounds good. I think it will probably turn out to be a good idea to
> bundle up a working (subset of?) python as part of our distribution.
> ....thx....dac
> _______________________________________________
> AMBER-Developers mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER-Developers mailing list
Received on Thu Oct 21 2010 - 13:30:04 PDT
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