This package is now renamed pele. All developement on pygmin will now be done on pele. You can find the new repository at

https://github.com/pele-python/pele

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PyGMIN: tools for global optimization and energy landscape exploration.

PyGMIN is a python partial-rewriting of GMIN, OPTIM, and PATHSAMPLE: fortran programs written by David Wales and collaborators.

The code is hosted at

https://github.com/js850/PyGMIN

for documentation, see

http://js850.github.com/PyGMIN/

The code project upon which this python package is based can be found at

http://www-wales.ch.cam.ac.uk/software.html

INSTALLATION

Required packages

for compilation:

1. fortran compiler
2. c compiler

python packages:

1. numpy:

   We use numpy everywhere for doing numerical work. It also installs f2py which is used to compile fortran code into modules callable by python.

2. scipy:

   For some of the optimizers and various scientific tools

3. networkx:

   For graph functionality. https://networkx.lanl.gov

4. matplotlib:

   For making plots (e.g. disconnectivity graphs)

5. SQLAlchemy 0.7:

   For managing database of stationary points. http://www.sqlalchemy.org/

6. hungarian:

   For permutational alignment

7. scikits.sparse: optional

   for use of sparse Cholesky decomposition methods when calculating rates

8. pymol: optional

   for viewing molecular structures

All the above packages can be installed via the python package manager pip (or easy_install). However, some of the packages (numpy, scipy) have additional dependencies and it can be more convenient to use the linux package manager (apt, yum, ...).

If you want to use the gui you will additionally need:

1. qt4 and qt4 python bindings
2. opengl python bindings

The Ubuntu packages (apt-get) for these are: python-qt4, python-opengl, and python-qt4-gl

In fedora Fedora (yum) you will want the packages: PyQt4, and PyOpenGl

Installing prerequisites on Ubuntu

if you're running ubuntu, you can get all the prerequisites with the following commands:

$ sudo apt-get install python-numpy python-scipy python-matplotlib python-qt4 python-opengl python-qt4-gl python-pip cython pymol
$ pip install --user networkx sqlalchemy hungarian

(in the above, the flag --user will install localy.)

Compilation

Compilation is required for use of the fast potentials, those written in C and/or fortran). Theoretically you should be able to use any fortran compiler, but we mostly use gfortran, so it's the least likely to have problems. This package uses the standard python setup utility (distutils). There are lots of options for how and where to install. For more information:

$ python setup.py --help
$ python setup.py --help-commands

Developers probably want to install "in-place", i.e. build the extension modules in their current directories:

$ python setup.py build_ext -i --fcompiler=gfortran

Users can install pygmin in the standard python package location:

$ python setup.py build --fcompiler=gfortran
$ python setup.py install [--user]

where --user installs it in $HOME/.local/

PYTHONPATH

If you do an in-place install, make sure to add the install directory to your PYTHONPATH environment variable. This is not necessary if you install to a standard location.

Installing on Mac

When I used macports, everything installed very easily. However, at least on my machine the OpenGL / Qt implementation (necessary for the gui) was broken and I could never get it to work. So I aborted using macports and installed everything by hand. I eventually got (almost) everything working. Here are a few hints

use the Enthought python distribution instead of the prepackaged one. This seems to be standard, plus it includes numpy and scipy http://www.enthought.com/products/epd.php

if you want to use the gui you have to install pyqt and its dependencies. This is not as simple as it should be. I roughly followed the instructions here http://www.noktec.be/python/how-to-install-pyqt4-on-osx . Even though my mac is 64 bit I had to compile things with --arch=i386. I think I even had to install Qt from source to get it with the 32 bit architecture. Also, when compiling pyqt, you have to point to the qmake in the Qt install folder, not /usr/bin/qmake as the website says. Sorry for the vague instructions, I'm writing this from memory. If you have more complete installation help please email or submit a pull request.

Installing pymol was easy with macports, but since I've abandoned macports I haven't gotten it installed and running (I haven't tried the pay version)

Running

You can find examples of how to run pygmin in the examples folder. More information can be found in the documentation at

http://js850.github.com/PyGMIN/