mdacli's Introduction

MDAnalysis command line interface

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.