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
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.