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All Projects → bowman-lab → enspara

bowman-lab / enspara

Licence: GPL-3.0 license
Modeling molecular ensembles with scalable data structures and parallel computing

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python
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Labels

clusteringprotein-structuremolecular-dynamicsmarkov-state-modelbiophysicskinetic-modelingmolecular-modeling

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DOI:10.1007/978-3-319-76207-4_15 Circle CI

enspara

MSMs at Scale

Reference

If you use enspara for published research, please cite us:

Porter, J.R., Zimmerman, M.I. and Bowman, G.R., 2019. Enspara: Modeling molecular ensembles with scalable data structures and parallel computing. The Journal of chemical physics, 150(4), p.044108.

Installation

Installation is documented here.

Building the docs

Enspara uses sphinx for documentation. They're a bit of a work in progress, but most of the most important stuff is documented already.

cd docs
make html

Running the tests

Enspara uses nosetests as a test discovery and running tool. To run the tests, you should first make sure you have the development dependencies installed then, from the enspara directory, run:

nosetests enspara

If you want to run the MPI tests, you can run

mpiexec -n 2 nosetests enspara -a mpi

where -a mpi asks nose to run only the tests that are MPI tests.

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