MDEntropy
MDEntropy: Information-Theoretic Analyses for Molecular Dynamics - Published in JOSS (2017)
Science Score: 95.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 7 DOI reference(s) in README and JOSS metadata -
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Links to: joss.theoj.org -
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2 of 4 committers (50.0%) from academic institutions -
○Institutional organization owner
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✓JOSS paper metadata
Published in Journal of Open Source Software
Scientific Fields
Repository
Analyze correlated motions in MD trajectories with only a few lines of Python.
Basic Info
Statistics
- Stars: 32
- Watchers: 4
- Forks: 13
- Open Issues: 12
- Releases: 4
Metadata Files
README.md
MDEntropy
MDEntropy is a python library that allows users to perform information-theoretic analyses on molecular dynamics (MD) trajectories. It includes methods to calculate:
- Bias-Corrected Entropy
- Conditional Entropy
- Mutual Information
- Normalized Mutual Information
- Conditional Mutual Information
- Normalized Conditional Mutual Information
Documentation
Full documentation can be found at http://msmbuilder.org/mdentropy/. For information about installation, please refer to our Installation page.
We also have example notebooks with common use cases for MDEntropy. Please feel free to add your own as a pull-request!
Requirements
python>=3.4numpy>=1.10.4scipy>=0.17.0scikit-learn>=0.17.0msmbuilder>=3.5.0nose(optional, for testing)
Citing
Please cite:
bibtex
@article{mdentropy,
author = {Carlos X. Hern{\'{a}}ndez and Vijay S. Pande},
title = {{MDEntropy: Information-Theoretic Analyses for Molecular Dynamics}},
month = nov,
year = 2017,
doi = {10.21105/joss.00427},
url = {https://doi.org/10.21105/joss.00427}
}
Owner
- Name: MSMBuilder
- Login: msmbuilder
- Kind: organization
- Email: msmbuilder-user@lists.stanford.edu
- Website: http://msmbuilder.org
- Repositories: 12
- Profile: https://github.com/msmbuilder
Statistical models for biomolecular dynamics
JOSS Publication
MDEntropy: Information-Theoretic Analyses for Molecular Dynamics
Authors
Stanford University
Stanford University
Editor
Ariel Rokem
Tags
information theory molecular dynamics time-seriesGitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Carlos Hernandez | c****h@s****u | 150 |
| Carlos Hernández | c****z | 31 |
| Muneeb | m****n@i****r | 3 |
| server user for FAH | s****r@v****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 44
- Total pull requests: 32
- Average time to close issues: 4 months
- Average time to close pull requests: 7 days
- Total issue authors: 13
- Total pull request authors: 3
- Average comments per issue: 1.52
- Average comments per pull request: 0.75
- Merged pull requests: 29
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- cxhernandez (26)
- rupeshagarwal (3)
- MamtaMohan (2)
- MidhunkMadhu (2)
- evanfeinberg (2)
- Martin1937 (2)
- cing (1)
- autodataming (1)
- jgpattis (1)
- brookehus (1)
- jiajiexiao (1)
- anotherjoshsmith (1)
- tharpole-chwy (1)
Pull Request Authors
- cxhernandez (30)
- evanfeinberg (1)
- msultan (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- jinja2 *
- jupyter *
- matplotlib *
- msmb_data *
- msmbuilder *
- msmexplorer *
- nbconvert *
- numpydoc *
- pyparsing *
- python *
- traitlets *
- mdtraj *
- msmbuilder *
- numpy *
- pandas *
- scipy *