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mda

:hammer: Analysis Tools for MD Simulations

https://github.com/ipudu/mda

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: rsc.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.4%) to scientific vocabulary

Keywords

molecular-dynamics-simulation trajectory-analysis
Last synced: 6 months ago · JSON representation

Repository

:hammer: Analysis Tools for MD Simulations

Basic Info
  • Host: GitHub
  • Owner: ipudu
  • License: mit
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 395 KB
Statistics
  • Stars: 4
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
molecular-dynamics-simulation trajectory-analysis
Created over 6 years ago · Last pushed about 5 years ago
Metadata Files
Readme License

README.md

mda: Analysis tools for MD simulations

MDA: Analysis Tools for MD Simulations

version python license

Installation

Clone and install the latest version of MDA:

bash git clone https://github.com/ipudu/mda cd mda python setup.py install

Or use the package manager pip to install stable MDA:

bash pip install mda

Usage

python import mda

Feature Support

MDA can be used to calculate following properties:

  • Diffusion coefficient (Mean square displacement)
  • Inertia tensor (Acylindricity, Asphericity, Shape)
  • Gyration tensor
  • Order parameters
    • Orientational tetrahedral order
    • Translational tetrahedral order
  • Radial distribution function
  • Radius of gyration
  • Solvent accessible surface area
  • and more

MDA can be used to download scientific papers:

```bash

using link:

mda https://pubs.rsc.org/en/content/articlehtml/2017/cp/c7cp01602f

using DOI number:

mda 10.1039/C7CP01602F ```

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.

License

MIT

Owner

  • Name: Pu Du
  • Login: ipudu
  • Kind: user
  • Location: Metaverse

Engineer, gamer, geek, Bitcoin maxi and NFT degen.

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 63
  • Total Committers: 3
  • Avg Commits per committer: 21.0
  • Development Distribution Score (DDS): 0.032
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Pu Du r****y@g****m 61
Pu Du p****g@g****m 1
Pu Du i****u 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total 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
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
View more stats
Top Authors
Issue Authors
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 67 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 3
  • Total maintainers: 1
pypi.org: mda

Analysis Tools for MD Simulations

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 67 Last month
Rankings
Dependent packages count: 10.0%
Dependent repos count: 21.7%
Average: 22.3%
Stargazers count: 23.1%
Downloads: 27.0%
Forks count: 29.8%
Maintainers (1)
pudu
Last synced: 6 months ago

Dependencies

requirements.txt pypi
  • beautifulsoup4 *
  • mdanalysis *
  • numba *
  • numpy *
  • pyyaml *
  • retrying *
  • tkinter *
  • tqdm *