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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!

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 <module> -h

Available modules

Currently the following analysis modules are available

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.