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# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the Lesser GNU Public Licence, v2.1 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# 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
#
"""
=========================
Test cases for MDAnalysis
=========================
Test cases are stored in a separate packacge (:mod:`MDAnalysisTests`)
that has to be installed separately from
https://www.mdanalysis.org. For more details on the tests see
https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests .
We are using the NumPy_ testing frame work; thus, numpy *must* be
installed for the tests to run at all.
Run all the tests with
.. code-block:: bash
pytest --pyargs MDAnalysisTests
Data
====
The simulation data used in some tests are from [Beckstein2009]_ (``adk.psf``,
``adk_dims.dcd``) or unpublished simulations (O. Beckstein).
adk_dims
Trajectory of a macromolecular transition of the enzyme adenylate kinase
between a closed and an open conformation. The simulation was run in
Charmm_ c35a1.
adk_oplsaa
Ten frames from the first 1 ns of a equilibrium trajectory of AdK in
water with Na+ counter ions. The OPLS/AA forcefield is used with the
TIP4P water model. The simulation was run with Gromacs_ 4.0.2.
.. [Beckstein2009] O. Beckstein, E.J. Denning, J.R. Perilla and
T.B. Woolf, Zipping and Unzipping of Adenylate Kinase: Atomistic
Insights into the Ensemble of Open ↔ Closed Transitions. J Mol Biol
394 (2009), 160–176, doi:10.1016/j.jmb.2009.09.009
Writing test cases
==================
The unittests use the :mod:`pytest_` module. See the
examples provided alongside the ``MDAnalysisTests`` module.
The `SciPy testing guidelines`_ are also a good howto for writing test cases.
.. _pytest:
https://docs.pytest.org/en/latest/
.. _SciPy testing guidelines:
http://projects.scipy.org/numpy/wiki/TestingGuidelines#id11
.. _Charmm: http://www.charmm.org
.. _Gromacs: http://www.gromacs.org
"""
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