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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.
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 more or less correspond with the github master branch, but they're not built automatically and thus may fall out of sync at times.
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(reference_traj=traj[0])
rmsd = featurizer.partial_transform(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.
- Python 3.4+
The preferred installation mechanism for msmexplorer is with conda:
$ conda install -c omnia msmexplorerIf 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
https://github.com/msmexplorer/msmexplorer
Please submit any bugs you encounter to the Github issue tracker.
Released under a MIT license
@misc{msmexplorer,
author = {Carlos X. Hernández and
Vijay S. Pande},
title = {MSMExplorer},
month = aug,
year = 2016,
doi = {10.5281/zenodo.154092},
url = {http://dx.doi.org/10.5281/zenodo.154092}
}