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MSMExplorer

MSMExplorer: Data Visualizations for Biomolecular Dynamics - Published in JOSS (2017)

https://github.com/msmexplorer/msmexplorer

Science Score: 95.0%

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    Found 3 DOI reference(s) in README and JOSS metadata
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Data visualizations for biomolecular dynamics

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Fork of msmbuilder/msmexplorer
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Metadata Files
Readme Contributing License

README.md

MSMExplorer: data visualizations for biomolecular dynamics

Build Status Build status Coverage Status PyPI version License DOI Documentation

MSMExplorer is a Python visualization library for statistical models of biomolecular dynamics. It provides a high-level interface for drawing attractive statistical graphics with MSMBuilder.

Documentation

Online documentation is available here. It includes IPython notebooks, detailed API documentation, and other useful info.

There are docs for the development version here. These should correspond with the github master branch.

Examples

```python from msmbuilder.example_datasets import FsPeptide from msmbuilder.featurizer import RMSDFeaturizer

import msmexplorer as msme

Load Fs Peptide Data

traj = FsPeptide().get().trajectories[0]

Calculate RMSD

featurizer = RMSDFeaturizer(referencetraj=traj[0]) rmsd = featurizer.partialtransform(traj).flatten()

Plot Trace

msme.plot_trace(rmsd, label='traj0', xlabel='Timestep', ylabel='RMSD (nm)') ```

The documentation has an example gallery with short scripts showing how to use different parts of the package.

Dependencies

  • Python 3.4+

Mandatory

The latest versions of the following packages are required:

Installation

The preferred installation mechanism for msmexplorer is with conda:

bash $ conda install -c omnia msmexplorer

If you don't have conda, or are new to scientific python, we recommend that you download the Anaconda scientific python distribution.

To install from PyPI, just do:

pip install msmexplorer

You may instead want to use the development version from Github, by running

pip install git+git://github.com/msmexplorer/msmexplorer.git#egg=msmexplorer

Development

All development happens here, on Github.

If you're interested in contributing to MSMExplorer, please refer to our Contributing guide.

Support

Please submit any bugs or questions to the Github issue tracker.

License

Released under a MIT license

Citing

bibtex @article{msmexplorer, doi = {10.21105/joss.00188}, url = {https://doi.org/10.21105%2Fjoss.00188}, year = {2017}, month = {apr}, publisher = {The Open Journal}, volume = {2}, number = {12}, author = {Carlos X. Hern{\'{a}}ndez and Matthew P. Harrigan and Mohammad M. Sultan and Vijay S. Pande}, title = {{MSMExplorer}: Data Visualizations for Biomolecular Dynamics}, journal = {The Journal of Open Source Software} }

Owner

  • Name: MSMExplorer
  • Login: msmexplorer
  • Kind: organization
  • Location: Stanford University

Analytics for Markov state models

JOSS Publication

MSMExplorer: Data Visualizations for Biomolecular Dynamics
Published
April 08, 2017
DOI
Volume 2, Issue 12, Page 188
Authors
Carlos X. Hernández ORCID
Stanford University
Matthew P. Harrigan ORCID
Stanford University
Mohammad M. Sultan ORCID
Stanford University
Vijay S. Pande
Stanford University
Editor
Ariel Rokem ORCID
Tags
plotting molecular dynamics markov model
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Carlos Hernandez c****h@s****u 133
Carlos Hernández c****z 43
Juan Eiros j****z@g****m 27
Matthew Harrigan h****n@s****u 9
msultan m****n@s****u 4
Juan Eiros j****4@i****k 3
Shyam Saladi s****i 2
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Dependencies

docs/requirements.txt pypi
  • jinja2 *
  • jupyter *
  • msmb_data *
  • msmbuilder *
  • nbconvert *
  • numpydoc *
  • pyparsing *
  • python *
  • traitlets *
requirements.txt pypi
  • corner *
  • matplotlib *
  • mdtraj *
  • mpld3 *
  • msmbuilder *
  • nglview *
  • numpy *
  • pandas *
  • seaborn *
setup.py pypi