mdacli 0.1.12

A command line client for MDAnalysis Analysis classes.

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,
Contacts	Calculate contacts based observables.
DensityAnalysis	Volumetric density analysis.
DistanceMatrix	Calculate the pairwise distance between each frame in a trajectory
Janin	Calculate χ_1 and χ_2 dihedral angles of selected group
Ramachandran	Calculate ϕ and ψ 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.

Changelog

v0.1.12 (2022-01-19)

• Support list of AtomGroups as parameters (#82)

• Simplify add_argument logic in create_CLI (#82)

• Allow list of reference classes in module detection (#82)

• Support for generic classes as reference in module detection (#82)

• Rename save_results` to save (#82)

• More tests for docstring parsing and CLI creation (#82)

v0.1.11 (2022-01-19)

• Improved help for run parameters (#83)

v0.1.10 (2022-01-18)

• Removed conda dependency from CI and tox (#86)

v0.1.9 (2022-01-16)

• Fix test banner in README.rst (#85)

v0.1.8 (2022-01-16)

• Use Github actions matrix for tests (#68)

• Fix Conda permissions on MacOS (#68)

• Fix Tests failing on Windows (#68)

v0.1.7 (2021-12-18)

• Improves regex to convert from time to frame (#81)

v0.1.6 (2021-12-01)

• Fixed URL in docs (#80)

v0.1.5 (2021-12-01)

• Add doc deployment to CI (#78)

v0.1.4 (2021-11-24)

• Link docs to mdacli.mdanalysis.org (#75)

v0.1.3 (2021-11-24)

• MDA-style documentation pages (#70)

v0.1.2 (2021-11-18)

• Added option to manually set box dimensions (#65)

v0.1.1 (2021-11-18)

• corrects .bumpversion.cfg for CHANGELOG

• updates docs/CONTRIBUTING.rst accordingly

v0.1.0 (2021-11-18)

• Initial release