MDAnalysis command line interface
=================================
|pypi| |mdanalysis| |codecov| |docs| |test|
``mdacli`` is a simple command line interface (CLI) to the analysis classes of `MDAnalysis`_
using argparse_. This project is in an **early development stage** and
work in progress. `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
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:alt: PyPI Package latest release
:target: https://pypi.org/project/mdacli
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:alt: Powered by MDAnalysis
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.. |docs| image:: https://readthedocs.org/projects/mdacli/badge/?version=latest
:target: https://mdacli.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
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:target: https://codecov.io/gh/MDAnalysis/mdacli
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