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https://github.com/mdanalysis/mdacli

Command line interface for MDAnalysis
https://github.com/mdanalysis/mdacli

cli command-line command-line-tool computational-chemistry mdanalysis molecular-dynamics molecular-dynamics-simulation python science trajectory-analysis

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Command line interface for MDAnalysis

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README 

        
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 `_!



To install `mdacli` refer to the `INSTALL file `_.



Run `mdacli`::



   mda -h



For a help and an overview of the supported modules. A help

message for each module is available using::



   mda  -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



 .. |pypi| image:: https://img.shields.io/pypi/v/mdacli.svg

   :alt: PyPI Package latest release

   :target: https://pypi.org/project/mdacli



 .. |mdanalysis| image:: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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

   :alt: Powered by MDAnalysis

   :target: https://www.mdanalysis.org



 .. |docs| image:: https://readthedocs.org/projects/mdacli/badge/?version=latest

   :target: https://mdacli.readthedocs.io/en/latest/?badge=latest

   :alt: Documentation Status



 .. |test| image:: https://github.com/MDAnalysis/mdacli/actions/workflows/test.yml/badge.svg?branch=main

   :alt: Github Actions Test Status

   :target: https://github.com/MDAnalysis/mdacli/actions/workflows/test.yml



 .. |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