{"id":18524271,"url":"https://github.com/mdanalysis/mdacli","last_synced_at":"2026-01-23T10:41:15.599Z","repository":{"id":41952774,"uuid":"287262645","full_name":"MDAnalysis/mdacli","owner":"MDAnalysis","description":"Command line interface for MDAnalysis","archived":false,"fork":false,"pushed_at":"2024-07-09T15:51:42.000Z","size":7499,"stargazers_count":19,"open_issues_count":9,"forks_count":7,"subscribers_count":5,"default_branch":"main","last_synced_at":"2024-12-14T09:25:15.977Z","etag":null,"topics":["cli","command-line","command-line-tool","computational-chemistry","mdanalysis","molecular-dynamics","molecular-dynamics-simulation","python","science","trajectory-analysis"],"latest_commit_sha":null,"homepage":"https://mdacli.readthedocs.io/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MDAnalysis.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":"docs/CONTRIBUTING.rst","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-08-13T11:35:13.000Z","updated_at":"2024-07-09T15:50:50.000Z","dependencies_parsed_at":"2024-04-12T12:20:29.531Z","dependency_job_id":"929b4117-f1d7-45b1-9a4c-6f243bf1c78a","html_url":"https://github.com/MDAnalysis/mdacli","commit_stats":{"total_commits":246,"total_committers":6,"mean_commits":41.0,"dds":0.5487804878048781,"last_synced_commit":"92e788ebab15c4dcad8c92319aa678558baf9e94"},"previous_names":[],"tags_count":33,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2Fmdacli","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2Fmdacli/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2Fmdacli/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2Fmdacli/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MDAnalysis","download_url":"https://codeload.github.com/MDAnalysis/mdacli/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":230340130,"owners_count":18211162,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["cli","command-line","command-line-tool","computational-chemistry","mdanalysis","molecular-dynamics","molecular-dynamics-simulation","python","science","trajectory-analysis"],"created_at":"2024-11-06T17:40:21.069Z","updated_at":"2026-01-23T10:41:15.594Z","avatar_url":"https://github.com/MDAnalysis.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"MDAnalysis command line interface\n=================================\n\n|tests| |codecov| |docs-stable| |docs-latest| |mdanalysis|\n\n``mdacli`` is a simple command line interface (CLI) to the analysis classes of `MDAnalysis`_\nusing argparse_. `Contributions are welcome \u003chttps://github.com/MDAnalysis/mdacli/blob/main/docs/CONTRIBUTING.rst\u003e`_!\n\nTo install ``mdacli`` refer to the `INSTALL file \u003chttps://github.com/MDAnalysis/mdacli/blob/main/docs/src/installation.rst\u003e`_.\n\nRun ``mdacli``::\n\n   mda -h\n\nFor a help and an overview of the supported modules. A help\nmessage for each module is available using::\n\n   mda \u003cmodule\u003e -h\n\n\nAvailable modules\n-----------------\n\nCurrently the following analysis modules are available\n\n.. list-table::\n   :widths: 25 50\n   :header-rows: 1\n\n   * - Module Name\n     - Description\n\n   * - AlignTraj\n     - RMS-align trajectory to a reference structure using a selection.\n   * - AverageStructure\n     - RMS-align trajectory to a reference structure using a selection,\n       and calculate the average coordinates of the trajectory.\n   * - Contacts\n     - Calculate contacts based observables.\n   * - DensityAnalysis\n     - Volumetric density analysis.\n   * - DistanceMatrix\n     - Calculate the pairwise distance between each frame in a trajectory\n   * - Dihedral\n     - Calculate dihedral angles for specified atomgroups.\n   * - Janin\n     - Calculate χ_1 and χ_2 dihedral angles of selected group\n   * - Ramachandran\n     - Calculate ϕ and ψ dihedral angles of selected group\n   * - DielectricConstant\n     - Computes the average dipole moment.\n   * - GNMAnalysis\n     - Basic tool for GNM analysis.\n   * - closeContactGNMAnalysis\n     - GNMAnalysis only using close contacts.\n   * - HELANAL\n     - Perform HELANAL helix analysis on your trajectory.\n   * - HoleAnalysis\n     - Run ``hole`` program on a trajectory.\n   * - LinearDensity\n     - Linear density profile\n   * - EinsteinMSD\n     - Class to calculate Mean Squared Displacement by the Einstein relation.\n   * - PCA\n     - Principal component analysis on an MD trajectory.\n   * - InterRDF\n     - Intermolecular pair distribution function\n   * - RMSD\n     - Class to perform RMSD analysis on a trajectory.\n   * - RMSF\n     - Calculate RMSF of given atoms across a trajectory.\n\nMore information about each module is available through the help\npage or at the `MDAnalysis documentation`_.\n\n.. _argparse: https://docs.python.org/3/library/argparse.html\n.. _MDAnalysis: https://www.mdanalysis.org\n.. _`MDAnalysis installed`: https://userguide.mdanalysis.org/stable/installation.html\n.. _`MDAnalysis documentation`: https://docs.mdanalysis.org/stable/documentation_pages/analysis_modules.html\n.. _`documentation`: https://mdacli.mdanalysis.org\n.. _`latest documentation`: https://mdacli.mdanalysis.org/latest\n\n.. |tests| image:: https://github.com/MDAnalysis/mdacli/workflows/Tests/badge.svg\n   :alt: GitHub Actions Tests Job Status\n   :target: https://github.com/MDAnalysis/mdacli/actions?query=branch%3Amain\n\n.. |codecov| image:: https://codecov.io/gh/MDAnalysis/mdacli/branch/main/graph/badge.svg?token=ets2mZ6xJD\n    :alt: Codecov mdacli\n    :target: https://codecov.io/gh/MDAnalysis/mdacli\n\n.. |docs-stable| image:: https://img.shields.io/badge/📚_Documentation-stable-success\n   :alt: Documentation of stable released version\n   :target: `documentation`_\n\n.. |docs-latest| image:: https://img.shields.io/badge/📒_Documentation-latest-yellow.svg\n   :alt: Documentation of latest unreleased version\n   :target: `latest documentation`_\n\n.. |mdanalysis| image:: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16\u0026logo=data:image/x-icon;base64,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\n   :alt: Powered by MDAnalysis\n   :target: https://www.mdanalysis.org`\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmdanalysis%2Fmdacli","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmdanalysis%2Fmdacli","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmdanalysis%2Fmdacli/lists"}