MDAnalysis command line interface
=================================
|tests| |codecov| |docs-stable| |docs-latest| |mdanalysis|
``mdacli`` is a simple command line interface (CLI) to the analysis classes of `MDAnalysis`_
using argparse_. `Contributions are welcome <https://github.com/MDAnalysis/mdacli/blob/main/docs/CONTRIBUTING.rst>`_!
To install ``mdacli`` refer to the `INSTALL file <https://github.com/MDAnalysis/mdacli/blob/main/docs/rst/installation.rst>`_.
Run ``mdacli``::
mda -h
For a help and an overview of the supported modules. A help
message for each module is available using::
mda <module> -h
Available modules
-----------------
Currently the following analysis modules are available
.. list-table::
:widths: 25 50
:header-rows: 1
* - Module Name
- Description
* - AlignTraj
- RMS-align trajectory to a reference structure using a selection.
* - AverageStructure
- RMS-align trajectory to a reference structure using a selection,
and calculate the average coordinates of the trajectory.
* - Contacts
- Calculate contacts based observables.
* - DensityAnalysis
- Volumetric density analysis.
* - DistanceMatrix
- Calculate the pairwise distance between each frame in a trajectory
* - Dihedral
- Calculate dihedral angles for specified atomgroups.
* - Janin
- Calculate χ_1 and χ_2 dihedral angles of selected group
* - Ramachandran
- Calculate ϕ and ψ dihedral angles of selected group
* - DielectricConstant
- Computes the average dipole moment.
* - GNMAnalysis
- Basic tool for GNM analysis.
* - closeContactGNMAnalysis
- GNMAnalysis only using close contacts.
* - HELANAL
- Perform HELANAL helix analysis on your trajectory.
* - HoleAnalysis
- Run ``hole`` program on a trajectory.
* - LinearDensity
- Linear density profile
* - EinsteinMSD
- Class to calculate Mean Squared Displacement by the Einstein relation.
* - PCA
- Principal component analysis on an MD trajectory.
* - InterRDF
- Intermolecular pair distribution function
* - RMSD
- Class to perform RMSD analysis on a trajectory.
* - RMSF
- Calculate RMSF of given atoms across a trajectory.
More information about each module is available through the help
page or at the `MDAnalysis documentation`_.
.. _argparse: https://docs.python.org/3/library/argparse.html
.. _MDAnalysis: https://www.mdanalysis.org
.. _`MDAnalysis installed`: https://userguide.mdanalysis.org/stable/installation.html
.. _`MDAnalysis documentation`: https://docs.mdanalysis.org/stable/documentation_pages/analysis_modules.html
.. _`documentation`: https://mdacli.mdanalysis.org
.. _`latest documentation`: https://mdacli.mdanalysis.org/latest
.. |tests| image:: https://github.com/MDAnalysis/mdacli/workflows/Tests/badge.svg
:alt: GitHub Actions Tests Job Status
:target: https://github.com/MDAnalysis/mdacli/actions?query=branch%3Amain
.. |codecov| image:: https://codecov.io/gh/MDAnalysis/mdacli/branch/main/graph/badge.svg?token=ets2mZ6xJD
:alt: Codecov mdacli
:target: https://codecov.io/gh/MDAnalysis/mdacli
.. |docs-stable| image:: https://img.shields.io/badge/📚_Documentation-stable-success
:alt: Documentation of stable released version
:target: `documentation`_
.. |docs-latest| image:: https://img.shields.io/badge/📒_Documentation-latest-yellow.svg
:alt: Documentation of latest unreleased version
:target: `latest documentation`_
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:alt: Powered by MDAnalysis
:target: https://www.mdanalysis.org`
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