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taurenmd

taurenmd: A command-line interface for analysis of Molecular Dynamics simulations. - Published in JOSS (2020)

https://github.com/joaomcteixeira/taurenmd

Science Score: 93.0%

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

  • ○
    CITATION.cff file
  • ✓
    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
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software
Last synced: 6 months ago · JSON representation

Repository

A command-line interface for analysis of Molecular Dynamics simulations.

Basic Info
Statistics
  • Stars: 9
  • Watchers: 1
  • Forks: 2
  • Open Issues: 6
  • Releases: 31
Created over 6 years ago · Last pushed over 3 years ago
Metadata Files
Readme Changelog Contributing License Authors

README.rst 

taurenmd
========

.. image:: https://raw.githubusercontent.com/joaomcteixeira/taurenmd/master/docs/img/taurenmd_logo_black_readme.png

.. start-description

.. image:: https://img.shields.io/pypi/v/taurenmd.svg
    :alt: PyPI Package latest release
    :target: https://pypi.org/project/taurenmd

.. image:: https://joss.theoj.org/papers/10.21105/joss.02175/status.svg
    :target: https://doi.org/10.21105/joss.02175
    :alt: joss

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3551990.svg
    :target: https://doi.org/10.5281/zenodo.3551990
    :alt: Zenodo

.. image:: https://github.com/joaomcteixeira/taurenmd/workflows/tests/badge.svg?branch=master
    :target: https://github.com/joaomcteixeira/taurenmd/actions?workflow=tests
    :alt: Test Status

.. image:: https://img.shields.io/readthedocs/taurenmd/latest?label=Read%20the%20Docs
    :target: https://taurenmd.readthedocs.io/en/latest/index.html
    :alt: Read the Docs (latest)

.. image:: https://codecov.io/gh/joaomcteixeira/taurenmd/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/joaomcteixeira/taurenmd
    :alt: Codecov master branch

.. image:: https://api.codeclimate.com/v1/badges/d69e2e9866338d88955c/maintainability
   :target: https://codeclimate.com/github/joaomcteixeira/taurenmd
   :alt: Code Climate

.. image:: https://img.shields.io/codeclimate/tech-debt/joaomcteixeira/taurenmd?label=Code%20Climate%20tech%20debt
    :target: https://codeclimate.com/github/joaomcteixeira/taurenmd
    :alt: Code Climate technical debt

.. image:: https://img.shields.io/pypi/wheel/taurenmd.svg
    :alt: PyPI Wheel
    :target: https://pypi.org/project/taurenmd

.. image:: https://img.shields.io/pypi/pyversions/taurenmd.svg
    :alt: Supported versions
    :target: https://pypi.org/project/taurenmd

.. image:: https://img.shields.io/pypi/dm/taurenmd?label=PyPI%20Downloads
    :alt: PyPI - Downloads
    :target: https://pypistats.org/packages/taurenmd

**A command-line interface for analysis routines of Molecular Dynamics data.**

**Taurenmd** provides an easy, flexible and extensible, **command-line** interface for the most common *(and not so common)* routines of analysis and representation of Molecular Dynamics (MD) data.

It bridges the gap between the highly complex (and powerful) Python libraries available for analysis of MD data and the *non-developer* users that lack the programming skills to perform a thorough and proficient use those libraries. *But not only*, **taurenmd** also facilitates high throughput operations, even to those proficient *devs*, because complex executions are reduced to single argument-rich command-lines that can be concatenated or aliased.

**Taurenmd** wraps around feature-rich and powerful MD analysis libraries such as `MDAnalysis `_ and `MDTraj `_ *(but not only)*, combining them to extract the best of *those worlds*. We use these libraries to access and extract MD data and calculate observables, and we have also added our own routines of analysis when needed. When using this software, you **should** cite **taurenmd** together with the dependencies used, please read our `Citing `_ page for a detailed explanation.

Though designed to perform as a command-line user-directed interface, all **taurenmd**'s core functions are openly distributed and documented. Currently, there are already `several command-line interfaces available `_, some that perform only single tasks, while others allow complex setups, all are *one-liners*.

With this said, **taurenmd** aims to be a flexible and extensible peace of software, built as simple and modular as we can think of, to *agile* the incorporation of new functionalities as needed.

.. end-description

Documentation
=============

**taurenmd**'s full documentation is available at: https://taurenmd.readthedocs.io, read there:

#. how to install
#. usage examples
#. citing
#. *etc...*

Owner

  • Name: João M.C. Teixeira
  • Login: joaomcteixeira
  • Kind: user
  • Location: Padova
  • Company: University of Padova

Creator of IDPConformerGenerator (@julie-forman-kay-lab) and previous lead developer of HADDOCK3 (@haddocking). Passionate about software architecture.

JOSS Publication

taurenmd: A command-line interface for analysis of Molecular Dynamics simulations.
Published
June 03, 2020
DOI
Volume 5, Issue 50, Page 2175
Authors
João M.C. Teixeira ORCID
Previous, Biomolecular NMR Laboratory, Organic Chemistry Section, Inorganic and Organic Chemistry Department, University of Barcelona, Baldiri Reixac 10-12, Barcelona 08028, Spain, Current, Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
Editor
Richard Gowers ORCID
Tags
Molecular Dynamics Structural Biology Proteins DNA RNA Biochemistry
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GitHub Events

Total
Last Year

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 536
  • Total Committers: 1
  • Avg Commits per committer: 536.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
joaomcteixeira j****a@g****m 536

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 13
  • Total pull requests: 53
  • Average time to close issues: 22 days
  • Average time to close pull requests: 6 days
  • Total issue authors: 6
  • Total pull request authors: 1
  • Average comments per issue: 2.23
  • Average comments per pull request: 1.72
  • Merged pull requests: 47
  • 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
  • joaomcteixeira (5)
  • Luthaf (4)
  • amritagos (1)
  • menoliu (1)
  • vsheg (1)
  • richardjgowers (1)
Pull Request Authors
  • joaomcteixeira (53)
Top Labels
Issue Labels
enhancement (5) documentation (4) bug (2) question (2) continous integration (2) wontfix (1)
Pull Request Labels
enhancement (21) documentation (15) continous integration (9) bug (7) good first issue (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 41 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 40
  • Total maintainers: 1
pypi.org: taurenmd

A command-line interface for analysis routines in Molecular Dynamics data.

  • Versions: 40
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 41 Last month
Rankings
Dependent packages count: 10.1%
Downloads: 14.6%
Average: 16.9%
Forks count: 19.1%
Stargazers count: 19.3%
Dependent repos count: 21.6%
Maintainers (1)
joaomcteixeira
Last synced: 6 months ago

Dependencies

docs/requirements.txt pypi
  • CommonMark *
  • mock *
  • sphinx >=2
  • sphinx-argparse *
  • sphinx-rtd-theme *