MDAnalysis command line interface

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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 -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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