.. -*- coding: utf-8 -*-
.. _datasets:
============
Example data
============
MDAnalysis offers a collection of example data files and datasets to run tests and tutorials. These are split into two packages:
* MDAnalysisTests: primarily for unit tests of the code
* MDAnalysisData: datasets for workshops and tutorials
.. _mdanalysistests:
MDAnalysisTests
===============
While this is installed as a separate package, you should import files like so::
import MDAnalysis as mda
from MDAnalysis.tests.datafiles import PSF, DCD
u = mda.Universe(PSF, DCD)
A complete list of files and descriptions is in the ``mdanalysis/testsuite/MDAnalysisTests/datafiles.py`` file. The actual files are stored in the ``mdanalysis/testsuite/MDAnalysisTests/data/`` directory.
.. _mdanalysisdata:
MDAnalysisData
==============
The `MDAnalysisData `_ package is an interface to download, cache, and access certain datasets hosted on external repositories (e.g. figshare_, zenodo_, DataDryad_). Data is not downloaded upon installation, so the package itself is small; but the directory where the datasets are cached can grow significantly.
You can access datasets like so::
import MDAnalysis as mda
from MDAnalysisData import datasets
adk = datasets.fetch_adk_equilibrium()
u = mda.Universe(adk.topology, adk.trajectory)
# to see the description of the dataset
print(adk.DESCR)
The cached files are stored by default in the ``~/MDAnalysis_data`` directory. This can be changed by setting the environment variable ``MDANALYSIS_DATA``. You can change this for a Terminal session with the below command:
.. code-block:: bash
export MDANALYSIS_DATA=/my/chosen/path/MDAnalysis_data
Add it to your ``.bashrc`` for a permanent change.
.. code-block:: bash
echo 'export MDANALYSIS_DATA=/my/chosen/path/MDAnalysis_data' >> ~/.bashrc
In Python, you can check the location of your caching directory::
MDAnalysisData.base.get_data_home()
And clear the directory with::
MDAnalysisData.base.clear_data_home()
`A list of datasets `_ can be found at the MDAnalysisData documentation.
.. _figshare: https://figshare.com/
.. _zenodo: https://zenodo.org/
.. _DataDryad: https://www.datadryad.org/