Installation¶
Although it’s not possible to cover all possible ways to install PBxplore on any operating system, we try in this document to provide few guidelines regarding PBxplore setup.
Supported Platforms¶
Currently, PBxplore run with Python 2.7, 3.3 and 3.4 on Linux and Mac OS X.
Dependencies¶
To use PBxplore, the following libraries have to be installed.
- NumPy >= 1.6.0
- NumPy is the base package for numerical computing in python.
- matplotlib [1] >= 1.4.0
- All ploting functions use matplotlib package.
- MDAnalysis [2] >= 0.11
- We use MDAnalysis to read Gromacs molecular dynamics trajectories. Many other trajectory files are also supported, see list here.
Optionally, PBxplore can use the following packages:
Installing PBxplore¶
The most straightforward way is to use pip:
$ pip install pbxplore
PBxplore can also be installed for the current user only:
$ pip install --user pbxplore
See the documentation of pip for more information. You may also want to look at virtualenv.
Testing PBxplore¶
PBxplore comes with unit tests and regression tests. It requires the package nose. You have several options to run the tests:
$ nosetests -v pbxplore/tests
$ python setup.py nosetests
Or from the PBxplore module:
import pbxplore
pbxplore.test()
Uninstalling PBxplore¶
Run the simple command:
$ pip uninstall pbxplore
[1] | J. D. Hunter. Matplotlib: A 2D graphics environment. Computing In Science and Engineering 9 (2007), 90-95. doi:10.1109/MCSE.2007.55 |
[2] | N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319–2327. doi:10.1002/jcc.21787 |
[3] | G. E. Crooks, G. Hon, J.-M. Chandonia, and S. E. Brenner. WebLogo: A Sequence Logo Generator. Genome Research 14: 1188–90 (2004) doi:10.1101/gr.849004 |