Loading...
Loading...
working with data in the computational molecular sciences
Avg 28.4 stars per repo.
Coding for 11 years.
334 followers.
|numfocus|
|build| |cron| |cirruscron| |linters| |cov|
|docs| |devdocs| |discussions|
|pypi| |anaconda| |asv|
MDAnalysis_ is a Python library for the analysis of computer simulations of many-body systems at the molecular scale, spanning use cases from interactions of drugs with proteins to novel materials. It is widely used in the scientific community and is written by scientists for scientists.
It works with a wide range of popular simulation packages including GROMACS, Amber, NAMD, CHARMM, DL_POLY, HOOMD, LAMMPS and many others — see the lists of supported trajectory formats_ and topology formats.
MDAnalysis also includes widely used analysis algorithms in the MDAnalysis.analysis module.
.. _numfocus-fiscal-sponsor-attribution:
The MDAnalysis project uses an open governance model_ and is fiscally sponsored by NumFOCUS. Consider making
a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
.. image:: https://www.mdanalysis.org/public/images/numfocus-sponsored-small.png :alt: NumFOCUS (Fiscally Sponsored Project) :target: https://numfocus.org/project/mdanalysis :align: center
This project is bound by a Code of Conduct_.
|powered_by_MDA|
If you use MDAnalysis_ in your project consider letting your users and the world know about it by displaying the MDAnalysis_ badge! Embedding code_ is available for different markups.
.. code:: python
import MDAnalysis as mda
u = mda.Universe('topol.tpr','traj.trr')
ag = u.select_atoms('name OH')
ag.positions ag.velocities ag.forces
for ts in u.trajectory: print(ag.center_of_mass())
New users should read the Quickstart Guide_ and might want to
look at our videos_, in which core developers explain various aspects
of MDAnalysis.
All users should read the User Guide_.
Developers may also want to refer to the MDAnalysis API docs_.
A growing number of tutorials_ are available that explain how to
conduct RMSD calculations, structural alignment, distance and contact
analysis, and many more.
The latest release can be installed via pip or conda as
described in the Installation Quick Start_.
Source code is hosted in a git repository at https://github.com/MDAnalysis/mdanalysis and is packaged under the GNU Lesser General Public License, version 3 or any later version (LGPLv3+). Individual source code components are provided under the GNU Lesser General Public License, version 2.1 or any later version (LGPLv2.1+). Please see the file LICENSE_ for more information.
Please report bugs or enhancement requests through the Issue Tracker. Questions can also be asked on GitHub Discussions.
If you are a new developer who would like to start contributing to
MDAnalysis get in touch on GitHub Discussions. To set up a
development environment and run the test suite read the developer guide.
When using MDAnalysis in published work, please cite the following two papers:
10.25080/Majora-629e541a-00e_10.1002/jcc.21787_For citations of included algorithms and sub-modules please see the references_.
.. _NumFOCUS: https://numfocus.org/
.. _open governance model: https://www.mdanalysis.org/pages/governance/
.. _tax-deductible donation: https://numfocus.org/donate-to-mdanalysis
.. _Code of Conduct: https://www.mdanalysis.org/conduct/
.. _trajectory formats: https://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1
.. _topology formats: https://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats
.. _MDAnalysis: https://www.mdanalysis.org
.. _LICENSE:
https://github.com/MDAnalysis/mdanalysis/blob/develop/LICENSE
.. _Installation Quick Start:
https://www.mdanalysis.org/pages/installation_quick_start/
.. _MDAnalysis.analysis: https://docs.mdanalysis.org/documentation_pages/analysis_modules.html
.. _tutorials: https://userguide.mdanalysis.org/examples/README.html
.. _videos: https://www.mdanalysis.org/pages/learning_MDAnalysis/#videos
.. _Quickstart Guide:
https://userguide.mdanalysis.org/examples/quickstart.html
.. _User Guide: https://userguide.mdanalysis.org
.. _MDAnalysis API docs:
https://docs.mdanalysis.org
.. _Issue Tracker: https://github.com/mdanalysis/mdanalysis/issues
.. _GitHub Discussions:
https://github.com/MDAnalysis/mdanalysis/discussions
.. _developer guide:
https://userguide.mdanalysis.org/contributing.html
.. _10.1002/jcc.21787: https://dx.doi.org/10.1002/jcc.21787
.. _10.25080/Majora-629e541a-00e: https://doi.org/10.25080/Majora-629e541a-00e
.. _references: https://docs.mdanalysis.org/documentation_pages/references.html
.. _Embedding code: https://www.mdanalysis.org/pages/citations/#powered-by-mdanalysis
.. |docs| image:: https://img.shields.io/badge/docs-latest-brightgreen.svg :alt: Documentation (latest release) :target: https://docs.mdanalysis.org
.. |devdocs| image:: https://img.shields.io/badge/docs-development-yellow.svg :alt: Documentation (development version) :target: https://docs.mdanalysis.org/dev
.. |numfocus| image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A :alt: Powered by NumFOCUS :target: https://www.numfocus.org/
.. |build| image:: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci.yaml/badge.svg :alt: Github Actions Build Status :target: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci.yaml
.. |cron| image:: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci-cron.yaml/badge.svg :alt: Github Actions Cron Job Status :target: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci-cron.yaml
.. |cirruscron| image:: https://img.shields.io/cirrus/github/MDAnalysis/mdanalysis/develop :alt: Cirrus CI - Cron job status :target: https://cirrus-ci.com/github/MDAnalysis/mdanalysis/develop
.. |linters| image:: https://github.com/MDAnalysis/mdanalysis/actions/workflows/linters.yaml/badge.svg :alt: Github Actions Linters Status :target: https://github.com/MDAnalysis/mdanalysis/actions/workflows/linters.yaml
.. |cov| image:: https://codecov.io/gh/MDAnalysis/mdanalysis/branch/develop/graph/badge.svg :alt: Coverage Status :target: https://codecov.io/gh/MDAnalysis/mdanalysis
.. |pypi| image:: https://img.shields.io/pypi/v/MDAnalysis :alt: PyPI Version :target: https://pypi.org/project/MDAnalysis/
.. |anaconda| image:: https://anaconda.org/conda-forge/mdanalysis/badges/version.svg :alt: Anaconda :target: https://anaconda.org/conda-forge/mdanalysis
.. |asv| image:: https://img.shields.io/badge/benchmarked%20by-asv-blue.svg :alt: ASV Benchmarks :target: https://www.mdanalysis.org/benchmarks/
.. |powered_by_MDA| image:: https://img.shields.io/badge/Powered%20by-MDAnalysis-orange.svg?logoWidth=15&logo=data:image/x-icon;base64,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 :alt: Powered by MDAnalysis :target: https://www.mdanalysis.org
.. |discussions| image:: https://img.shields.io/github/discussions/MDAnalysis/MDAnalysis :alt: GitHub Discussions :target: https://github.com/MDAnalysis/mdanalysis/discussions