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.