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:

Weblogo3 [3]
Weblogo3 is required to create logo from PB sequences.

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