MDAnalysis example data
Project description
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
or install with conda
conda install --channel conda-forge 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.
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