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!
Provided you have MDAnalysis installed, get the mdacli source from
https://github.com/MDAnalysis/mdacli and install mdacli with the following:
python setup.py develop
and run:
mda -h
for a help and an overview of the supported modules. A help message for each module is available using:
mda module -h
Currentlty 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, |
| Contacts | Calculate contacts based observables. |
| DensityAnalysis | Volumetric density analysis. |
| DistanceMatrix | Calculate the pairwise distance between each frame in a trajectory |
| Janin | Calculate \chi_1 and \chi_2 dihedral angles of selected group |
| Ramachandran | Calculate \phi and \psi dihedral angles of selected group |
| GNMAnalysis | Basic tool for GNM analysis. |
| closeContactGNMAnalysis | GNMAnalysis only using close contacts. |
| HELANAL | Perform HELANAL helix analysis on your trajectory. |
| HoleAnalysis | Run program hole 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.