A command line client for MDAnalysis Analysis classes.
Project description
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, 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.
Changelog
v0.1.19 (2022-04-12)
Update README.rst for MDAnalysis 2.1.0 modules
v0.1.18 (2022-04-12)
Fixed typo in libcli.py
v0.1.17 (2022-04-07)
Added dihedral module
v0.1.16 (2022-02-25)
Do not convert None types
v0.1.15 (2022-02-25)
Set positional arguments as required in cli
v0.1.14 (2022-02-17)
corrects bump2version changelog update
v0.1.13 (2022-02-16)
Added conda package install instructions (#88)
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
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