mdacli is a simple command line interface (CLI) to the analysis classes of MDAnalysis using argparse. 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.
2 maintainers
Metadata
2 maintainers
Release files for mdacli 0.2.1
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