MDAnalysisTestData

Oliver Beckstein edited this page Sep 26, 2015 · 3 revisions

The instructions below are outdated and do not apply anymore (since 2011-12-21). They are kept for historical purposes. See UnitTests for explanations.

Notes on the test data are in the report for Issue 87 and Source.


MDAnalysis contains a large number of tests of the core functionality, described in UnitTests. For many tests we are using real simulation trajectories and structures to check that everything is working as expected. These tests make it very unlikely that new code or fixes introduce new bugs. The test trajectories are also used in examples throughout the documentation, allowing anyone to try out MDAnalysis right away.

The test trajectories are fairly big (about 20 GB) so we put them in a package separate from MDAnalysis. If you want to run the UnitTests or try out the examples then you must install MDAnalysisTestData (as described in INSTALL.

Installation

You can download a file such as MDAnalysisTestData-0.7.4.tar.gz from the Download page, unpack it and install as usual:

tar -zxvf MDAnalysisTestData-0.7.4.tar.gz
cd MDAnalysisTestData-0.7.4
python setup.py install

You might also be able to directly install from the web if you have easy_install available

easy_install http://mdanalysis.googlecode.com/files/MDAnalysisTestData-0.7.4.tar.gz

Running tests

See UnitTests.

Running examples

Once both MDAnalysis and MDAnalysisTestData are installed you can access the bundles files within the MDAnalysis.tests.datafiles module. For instance, on my machine

>>> from MDAnalysis.tests.datafiles import PSF,DCD
>>> print PSF
/Users/oliver/.local/lib/python2.6/site-packages/MDAnalysisTestData-0.7.4-py2.6.egg/MDAnalysisTestData/data/adk.psf
>>>  print DCD
/Users/oliver/.local/lib/python2.6/site-packages/MDAnalysisTestData-0.7.4-py2.6.egg/MDAnalysisTestData/data/adk_dims.dcd
>>> import MDAnalysis
>>> u = MDAnalysis.Universe(PSF,DCD)
>>> print u
<Universe with 3341 atoms>

Project Information

About
GNU GPL v2 code license
Labels: python, molecular dynamics, analysis, DCD, CHARMM, LAMMPS, NAMD, Gromacs, computer simulation, atoms, coordinates, trajectory, XTC, Library, object-oriented
Core Developers

Essentials

Applications
Downloads
Install
Release Notes
Guide for Developers
Google Summer of Code

Code of Conduct

Links

@mdanalysis on Twitter
Documentation
Tutorials
Downloads (PyPi)
Mailing Lists:
User discussion group
Developer mailing list

Clone this wiki locally
You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.
Press h to open a hovercard with more details.