MDAnalysisData

Access to data for workshops and extended tests of MDAnalysis.

Data sets are stored at external stable URLs (e.g., on figshare, zenodo, or DataDryad) and this package provides a simple interface to download, cache, and access data sets.

Installation

To use, install the package

pip install --upgrade MDAnalysisData

Accessing data sets

Import the datasets and access your data set of choice:

from MDAnalysisData import datasets

adk = datasets.fetch_adk_equilibrium()

The returned object contains attributes with the paths to topology and trajectory files so that you can use it directly with, for instance, MDAnalysis:

import MDAnalysis as mda
u = mda.Universe(adk.topology, adk.trajectory)

The metadata object also contains a DESCR attribute with a description of the data set, including relevant citations:

print(adk.DESCR)

Managing data

Data are locally stored in the data directory ~/MDAnalysis_data (i.e., in the user's home directory). This location can be changed by setting the environment variable MDANALYSIS_DATA, for instance

export MDANALYSIS_DATA=/tmp/MDAnalysis_data

The location of the data directory can be obtained with

MDAnalysisData.base.get_data_home()

If the data directory is removed then data are downloaded again. Data file integrity is checked with a SHA256 checksum when the file is downloaded.

The data directory can we wiped with the function

MDAnalysisData.base.clear_data_home()

Credits

This package is modelled after sklearn.datasets. It uses code from sklearn.datasets (under the BSD 3-clause license).

No data are included; please see the DESCR attribute for each data set for authorship, citation, and license information for the data.