This document should help you to install the GromacsWrapper package. The installation uses setuptools (also known as easy_install or “egg install”); if this is not available on your system you can either let the installer download it automatically from the internet (so just go to Quick installation instructions) or install it using your package manager, eg:
aptitude install python-setuptools
or similar.
Please do not hesitate to contact Oliver Beckstein if problems occur or if you have suggestions on how to improve the package or these instructions.
If you have easy_install on your system you can directly install from the interweb:
easy_install -f http://sbcb.bioch.ox.ac.uk/users/oliver/download/Python GromacsWrapper
This will automatically download and install the latest version.
If your prefer to download manually, get the latest version from
and use any of the following methods (in increasing order of complexity):
From an egg install file, eg GromacsWrapper-0.1-py2.5.egg:
easy_install GromacsWrapper-0.1-py2.5.egg
From a tar ball, eg GromacsWrapper-0.1.tar.gz:
easy_install GromacsWrapper-0.1.tar.gz
From the unpacked source:
tar -zxvf GromacsWrapper-0.1.tar.gz
cd GromacsWrapper-0.1
python setup.py install
See the easy_install instructions for explanation of the options that allow you to install into non-standard places.
The tar archive from http://sbcb.bioch.ox.ac.uk/users/oliver/download/Python contains a full source code distribution.
In order to follow code development you can also browse the code git repository at http://github.com/orbeckst/GromacsWrapper or clone the git repository from
git://github.com/orbeckst/GromacsWrapper.git
Python and Gromacs must be installed. ipython is very much recommended. These packages might already be available through your local package manager such as aptitude/apt, yum, yast, fink or macports.
Tested with python 2.5, 2.6 on Linux and Mac OS X. Earlier python versions will likely fail.
The basic package makes use of numpy and can use matplotlib (in the form of the pylab package). Only numpy is immediately required (and automatically installed with easy_install).
For the gromacs.analysis library additional packages are required:
package version source matplotlib >=0.91.3 http://matplotlib.sourceforge.net/ scipy http://www.scipy.org/ RecSQL >=0.3 http://sbcb.bioch.ox.ac.uk/users/oliver/software/RecSQL/
See Installing all packages and requirements for hints on how to install these package.
If you want to make sure that easy_install also installs requirements for optional modules then you will have to add the additional requirement [analysis] to the command line. For a web install this would look like
easy_install -f http://sbcb.bioch.ox.ac.uk/users/oliver/download/Python GromacsWrapper[analysis]
For installation from a downloaded source distribution
easy_install GromacsWrapper-0.1.tar.gz[analysis]
or from within the unpacked source
cd GromacsWrapper-0.1
easy_install . GromacsWrapper[analysis]
In each case this will try to download additional packages for the extra analysis module.
A common problem appears to be the error Could not find matplotlib as discussed below.
For problems with easy_install please read the User setuptools instructions.
Inform yourself about how to use easy_install to install packages in Custom Installation Locations.
For code hacking and development a developer installation is often useful. In the unpacked source:
python setup.py develop --install-dir python-lib-dir
where python-lib-dir must be on the PYTHONPATH.
Online installation can run into issues where the installation dies with the error:
ImportError: No module named ez_setup
If EasyInstall Troubleshooting does not help then try downloading the source distribution package manually, unpack, and install from inside with something like:
python setup.py install
If this is still not working contact the author and complain.
Automatic downloading of matplotlib often fails:
Searching for matplotlib>=0.91.3
Reading http://pypi.python.org/simple/matplotlib/
Reading http://matplotlib.sourceforge.net
Reading https://sourceforge.net/project/showfiles.php?group_id=80706&package_id=278194
Reading https://sourceforge.net/project/showfiles.php?group_id=80706&package_id=82474
Reading http://sourceforge.net/project/showfiles.php?group_id=80706
No local packages or download links found for matplotlib>=0.91.3
error: Could not find suitable distribution for Requirement.parse('matplotlib>=0.91.3')
If automatic downloading of matplotlib fails then the best approach is to install it through your package management system. Search for “matplotlib” or “pylab” in the list of available packages.
If this is not an option then download matplotlib manually and install matplotlib manually first. For example,
wget http://kent.dl.sourceforge.net/sourceforge/matplotlib/matplotlib-0.98.5.3-py2.5-macosx-10.3-fat.egg \
-O matplotlib-0.98.5.3-py2.5.egg
easy_install matplotlib-0.98.5.3-py2.5.egg
Note that you should look at the download matplotlib page to get the latest distribution. As highlighted in the matplotlib installation FAQ it is important to rename the egg file (as done in the example above).
Possibly the following installation from the source distribution works, too:
easy_install matplotlib-0.98.5.3.tar.gz
Once this has been accomplished, try the above installation instructions again; easy_install should now pick up the newly installed matplotlib.