MDAnalysis command line interface
=================================
|pypi| |mdanalysis| |codecov| |docs| |test|
``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 <https://github.com/MDAnalysis/mdacli/blob/main/docs/CONTRIBUTING.rst>`_!
To install `mdacli` refer to the `INSTALL file <https://github.com/MDAnalysis/mdacli/blob/main/docs/rst/installation.rst>`_.
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
.. list-table::
:widths: 25 50
:header-rows: 1
* - 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`_.
.. _argparse: https://docs.python.org/3/library/argparse.html
.. _MDAnalysis: https://www.mdanalysis.org
.. _`MDAnalysis installed`: https://userguide.mdanalysis.org/stable/installation.html
.. _`MDAnalysis documentation`: https://docs.mdanalysis.org/stable/documentation_pages/analysis_modules.html
.. |pypi| image:: https://img.shields.io/pypi/v/mdacli.svg
:alt: PyPI Package latest release
:target: https://pypi.org/project/mdacli
.. |mdanalysis| image:: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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
:alt: Powered by MDAnalysis
:target: https://www.mdanalysis.org
.. |docs| image:: https://readthedocs.org/projects/mdacli/badge/?version=latest
:target: https://mdacli.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. |test| image:: https://github.com/MDAnalysis/mdacli/actions/workflows/test.yml/badge.svg?branch=main
:alt: Github Actions Test Status
:target: https://github.com/MDAnalysis/mdacli/actions/workflows/test.yml
.. |codecov| image:: https://codecov.io/gh/MDAnalysis/mdacli/branch/main/graph/badge.svg?token=ets2mZ6xJD
:alt: Codecov mdacli
:target: https://codecov.io/gh/MDAnalysis/mdacli
Raw data
{
"_id": null,
"home_page": null,
"name": "mdacli",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.9",
"maintainer_email": null,
"keywords": "python, cli, science, command-line, molecular-dynamics, computational-chemistry, molecular-dynamics-simulation, command-line-tool, trajectory-analysis mdanalysis",
"author": null,
"author_email": "MDAnalysis Development Team and contributors <mdanalysis@numfocus.org>",
"download_url": "https://files.pythonhosted.org/packages/d0/85/a26fd91a80b6106d75dcb1e5bda6203102be4de489022b4268a84115001b/mdacli-0.1.32.tar.gz",
"platform": null,
"description": "MDAnalysis command line interface\n=================================\n\n|pypi| |mdanalysis| |codecov| |docs| |test|\n\n``mdacli`` is a simple command line interface (CLI) to the analysis classes of `MDAnalysis`_\nusing argparse_. This project is in an **early development stage** and\nwork in progress. `Contributions are welcome <https://github.com/MDAnalysis/mdacli/blob/main/docs/CONTRIBUTING.rst>`_!\n\nTo install `mdacli` refer to the `INSTALL file <https://github.com/MDAnalysis/mdacli/blob/main/docs/rst/installation.rst>`_.\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 <module> -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 \u03c7_1 and \u03c7_2 dihedral angles of selected group\n * - Ramachandran\n - Calculate \u03d5 and \u03c8 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\n .. |pypi| image:: https://img.shields.io/pypi/v/mdacli.svg\n :alt: PyPI Package latest release\n :target: https://pypi.org/project/mdacli\n\n .. |mdanalysis| image:: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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\n :alt: Powered by MDAnalysis\n :target: https://www.mdanalysis.org\n\n .. |docs| image:: https://readthedocs.org/projects/mdacli/badge/?version=latest\n :target: https://mdacli.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n .. |test| image:: https://github.com/MDAnalysis/mdacli/actions/workflows/test.yml/badge.svg?branch=main\n :alt: Github Actions Test Status\n :target: https://github.com/MDAnalysis/mdacli/actions/workflows/test.yml\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",
"bugtrack_url": null,
"license": "GPL-3.0-or-later",
"summary": "A command line client for MDAnalysis Analysis classes.",
"version": "0.1.32",
"project_urls": {
"blog": "https://www.mdanalysis.org/blog",
"changelog": "https://github.com/MDAnalysis/mdacli/blob/main/docs/CHANGELOG.rst",
"discord": "https://discord.com/channels/807348386012987462",
"documentation": "https://mdacli.mdanalysis.org",
"homepage": "https://mdacli.mdanalysis.org",
"issues": "https://github.com/MDAnalysis/mdacli/issues/",
"repository": "https://github.com/MDAnalysis/mdacli",
"twitter": "https://twitter.com/mdanalysis",
"user_group": "https://groups.google.com/g/mdnalysis-discussion"
},
"split_keywords": [
"python",
" cli",
" science",
" command-line",
" molecular-dynamics",
" computational-chemistry",
" molecular-dynamics-simulation",
" command-line-tool",
" trajectory-analysis mdanalysis"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "9229d305144134ad9729e199d7b448d7eeaedae275e6dde64b753d9d66980741",
"md5": "0103c5c10d47ff37733334a8f6d41bf0",
"sha256": "32e8d22ab970b99353e669381b45a61ecddf09c82199293312c81792ba2c8912"
},
"downloads": -1,
"filename": "mdacli-0.1.32-py3-none-any.whl",
"has_sig": false,
"md5_digest": "0103c5c10d47ff37733334a8f6d41bf0",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.9",
"size": 36785,
"upload_time": "2024-07-09T11:50:28",
"upload_time_iso_8601": "2024-07-09T11:50:28.514324Z",
"url": "https://files.pythonhosted.org/packages/92/29/d305144134ad9729e199d7b448d7eeaedae275e6dde64b753d9d66980741/mdacli-0.1.32-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "d085a26fd91a80b6106d75dcb1e5bda6203102be4de489022b4268a84115001b",
"md5": "6d9754005b0ea1243c3f497c639ee8ca",
"sha256": "f4c4fc8664d6a4abbb90751bfc500adaec6d0c29b0f83e174c379b457d426f37"
},
"downloads": -1,
"filename": "mdacli-0.1.32.tar.gz",
"has_sig": false,
"md5_digest": "6d9754005b0ea1243c3f497c639ee8ca",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.9",
"size": 237849,
"upload_time": "2024-07-09T11:50:30",
"upload_time_iso_8601": "2024-07-09T11:50:30.949381Z",
"url": "https://files.pythonhosted.org/packages/d0/85/a26fd91a80b6106d75dcb1e5bda6203102be4de489022b4268a84115001b/mdacli-0.1.32.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-07-09 11:50:30",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "MDAnalysis",
"github_project": "mdacli",
"travis_ci": false,
"coveralls": true,
"github_actions": true,
"tox": true,
"lcname": "mdacli"
}
JSON
