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

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

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:

export MDANALYSIS_DATA=/my/chosen/path/MDAnalysis_data

Add it to your .bashrc for a permanent change.

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.