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
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.