.. image:: https://gitlab.com/maicos-devel/maicos/-/raw/main/docs/static/logo_MAICOS_small.png
:align: left
:alt: MAICoS
.. inclusion-readme-intro-start
**MAICoS** is the acronym for Molecular Analysis for Interfacial and Confined Systems.
It is an object-oriented python toolkit for analysing the structure and dynamics of
interfacial and confined fluids from molecular simulations. Combined with MDAnalysis_,
MAICoS can be used to extract density profiles, dielectric constants, structure factors,
or transport properties from trajectories files, including LAMMPS, GROMACS, CHARMM or
NAMD data. MAICoS is open source and is released under the GNU general public license
v3.0.
MAICoS is a tool for beginners of molecular simulations with no prior Python experience.
For these users MAICoS provides a descriptive command line interface. Also experienced
users can use the Python API for their day to day analysis or use the provided
infrastructure to build their own analysis for interfacial and confined systems.
Keep up to date with MAICoS news by following us on Twitter_. If you find an issue, you
can report it on Gitlab_. You can also join the developer team on Discord_ to discuss
possible improvements and usages of MAICoS.
.. _`MDAnalysis`: https://www.mdanalysis.org
.. _`Twitter`: https://twitter.com/maicos_analysis
.. _`Gitlab`: https://gitlab.com/maicos-devel/maicos
.. _`Discord`: https://discord.gg/mnrEQWVAed
.. inclusion-readme-intro-end
Basic example
=============
This is a simple example showing how to use MAICoS to extract the density profile from a
molecular dynamics simulation. The files ``conf.gro`` and ``traj.trr`` correspond to
simulation files from a GROMACS_ simulation package. In a Python environment, type:
.. code-block:: python
import MDAnalysis as mda
import maicos
u = mda.Universe("conf.gro", "traj.trr")
dplan = maicos.DensityPlanar(u.atoms).run()
The density profile can be accessed from ``dplan.results.profile`` and the position of
the bins from ``dplan.results.bin_pos``.
.. _`GROMACS` : https://www.gromacs.org/
Documentation
=============
For details, tutorials, and examples, please have a look at our documentation_. If you
are using an older version of MAICoS, you can access the corresponding documentation on
ReadTheDocs_.
.. _`documentation`: https://maicos-devel.gitlab.io/maicos/index.html
.. _`ReadTheDocs` : https://readthedocs.org/projects/maicos/
.. inclusion-readme-installation-start
Installation
============
Install MAICoS using `pip`_ with::
pip install maicos
or using conda_ with::
conda install -c conda-forge maicos
.. _`pip`: https://pip.pypa.io
.. _`conda`: https://www.anaconda.com
.. inclusion-readme-installation-end
List of analysis modules
========================
.. inclusion-marker-modules-start
Currently, MAICoS supports the following analysis modules:
.. list-table::
:widths: 25 50
:header-rows: 1
* - Module Name
- Description
* - DensityPlanar
- Compute cartesian partial density profiles
* - DensityCylinder
- Compute cylindrical partial densitiy profiles
* - DensitySphere
- Compute spherical partial density profiles
* - TemperaturePlanar
- Compute temperature profiles in a cartesian geometry
* - DielectricPlanar
- Compute planar dielectric profiles
* - DielectricCylinder
- Compute cylindrical dielectric profiles
* - DielectricSphere
- Compute spherical dielectric profiles
* - DielectricSpectrum
- Compute the linear dielectric spectrum
* - Saxs
- Compute small angle X-Ray scattering intensities (SAXS)
* - DiporderPlanar
- Compute planar dipolar order parameters
* - DiporderCylinder
- Compute cylindrical dipolar order parameters
* - DiporderSphere
- Compute spherical dipolar order parameters
* - PDFPlanar
- Compute slab-wise planar 2D pair distribution functions
* - PDFCylinder
- Compute cylindrical shell-wise 1D pair distribution functions
* - DipoleAngle
- Compute angle timeseries of dipole moments
* - KineticEnergy
- Compute the timeseries of energies
* - VelocityPlanar
- Compute the velocity profile in a cartesian geometry
* - VelocityCylinder
- Compute the cartesian velocity profile across a cylinder
.. inclusion-marker-modules-end
Raw data
{
"_id": null,
"home_page": "",
"name": "maicos",
"maintainer": "Philip Loche, Henrik Stoo\u00df, Alexander Schlaich",
"docs_url": null,
"requires_python": ">=3.9",
"maintainer_email": "",
"keywords": "Science,Molecular Dynamics,Confined Systems,MDAnalysis",
"author": "MAICoS Developer Team",
"author_email": "",
"download_url": "https://files.pythonhosted.org/packages/da/d3/17f9c35132274f70ced3e80087cd8d684d8c9fdf9bd89ffc191842087aec/maicos-0.8.tar.gz",
"platform": null,
"description": ".. image:: https://gitlab.com/maicos-devel/maicos/-/raw/main/docs/static/logo_MAICOS_small.png\n :align: left\n :alt: MAICoS\n\n.. inclusion-readme-intro-start\n\n**MAICoS** is the acronym for Molecular Analysis for Interfacial and Confined Systems.\nIt is an object-oriented python toolkit for analysing the structure and dynamics of\ninterfacial and confined fluids from molecular simulations. Combined with MDAnalysis_,\nMAICoS can be used to extract density profiles, dielectric constants, structure factors,\nor transport properties from trajectories files, including LAMMPS, GROMACS, CHARMM or\nNAMD data. MAICoS is open source and is released under the GNU general public license\nv3.0.\n\nMAICoS is a tool for beginners of molecular simulations with no prior Python experience.\nFor these users MAICoS provides a descriptive command line interface. Also experienced\nusers can use the Python API for their day to day analysis or use the provided\ninfrastructure to build their own analysis for interfacial and confined systems.\n\nKeep up to date with MAICoS news by following us on Twitter_. If you find an issue, you\ncan report it on Gitlab_. You can also join the developer team on Discord_ to discuss\npossible improvements and usages of MAICoS.\n\n.. _`MDAnalysis`: https://www.mdanalysis.org\n.. _`Twitter`: https://twitter.com/maicos_analysis\n.. _`Gitlab`: https://gitlab.com/maicos-devel/maicos\n.. _`Discord`: https://discord.gg/mnrEQWVAed\n\n.. inclusion-readme-intro-end\n\nBasic example\n=============\n\nThis is a simple example showing how to use MAICoS to extract the density profile from a\nmolecular dynamics simulation. The files ``conf.gro`` and ``traj.trr`` correspond to\nsimulation files from a GROMACS_ simulation package. In a Python environment, type:\n\n.. code-block:: python\n\n import MDAnalysis as mda\n import maicos\n\n u = mda.Universe(\"conf.gro\", \"traj.trr\")\n dplan = maicos.DensityPlanar(u.atoms).run()\n\nThe density profile can be accessed from ``dplan.results.profile`` and the position of\nthe bins from ``dplan.results.bin_pos``.\n\n.. _`GROMACS` : https://www.gromacs.org/\n\nDocumentation\n=============\n\nFor details, tutorials, and examples, please have a look at our documentation_. If you\nare using an older version of MAICoS, you can access the corresponding documentation on\nReadTheDocs_.\n\n.. _`documentation`: https://maicos-devel.gitlab.io/maicos/index.html\n.. _`ReadTheDocs` : https://readthedocs.org/projects/maicos/\n\n.. inclusion-readme-installation-start\n\nInstallation\n============\n\nInstall MAICoS using `pip`_ with::\n\n pip install maicos\n\nor using conda_ with::\n\n conda install -c conda-forge maicos\n\n.. _`pip`: https://pip.pypa.io\n.. _`conda`: https://www.anaconda.com\n\n.. inclusion-readme-installation-end\n\nList of analysis modules\n========================\n\n.. inclusion-marker-modules-start\n\nCurrently, MAICoS supports the following analysis modules:\n\n.. list-table::\n :widths: 25 50\n :header-rows: 1\n\n * - Module Name\n - Description\n\n * - DensityPlanar\n - Compute cartesian partial density profiles\n * - DensityCylinder\n - Compute cylindrical partial densitiy profiles\n * - DensitySphere\n - Compute spherical partial density profiles\n * - TemperaturePlanar\n - Compute temperature profiles in a cartesian geometry\n * - DielectricPlanar\n - Compute planar dielectric profiles\n * - DielectricCylinder\n - Compute cylindrical dielectric profiles\n * - DielectricSphere\n - Compute spherical dielectric profiles\n * - DielectricSpectrum\n - Compute the linear dielectric spectrum\n * - Saxs\n - Compute small angle X-Ray scattering intensities (SAXS)\n * - DiporderPlanar\n - Compute planar dipolar order parameters\n * - DiporderCylinder\n - Compute cylindrical dipolar order parameters\n * - DiporderSphere\n - Compute spherical dipolar order parameters\n * - PDFPlanar\n - Compute slab-wise planar 2D pair distribution functions\n * - PDFCylinder\n - Compute cylindrical shell-wise 1D pair distribution functions\n * - DipoleAngle\n - Compute angle timeseries of dipole moments\n * - KineticEnergy\n - Compute the timeseries of energies\n * - VelocityPlanar\n - Compute the velocity profile in a cartesian geometry\n * - VelocityCylinder\n - Compute the cartesian velocity profile across a cylinder\n\n.. inclusion-marker-modules-end\n",
"bugtrack_url": null,
"license": "GPL-3.0-or-later",
"summary": "Analyse molecular dynamics simulations of interfacial and confined systems.",
"version": "0.8",
"project_urls": {
"changelog": "https://maicos-devel.gitlab.io/maicos/get-started/changelog.html",
"discord": "https://discord.gg/mnrEQWVAed",
"documentation": "https://maicos-devel.gitlab.io/maicos",
"homepage": "https://www.maicos-analysis.org",
"issues": "https://gitlab.com/maicos-devel/maicos/-/issues",
"repository": "https://gitlab.com/maicos-devel/maicos",
"twitter": "https://twitter.com/maicos_analysis"
},
"split_keywords": [
"science",
"molecular dynamics",
"confined systems",
"mdanalysis"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "1f5f6474bf5f734850939898b5aeb7a4357cc1b3335a955f899e8f6aa4701511",
"md5": "363e9611755748b584c38bab3f378d59",
"sha256": "10d958dc8805d49e7cd4dd365a03d0f51ea75943a26655f5a6410c6762246833"
},
"downloads": -1,
"filename": "maicos-0.8-cp310-cp310-macosx_13_0_arm64.whl",
"has_sig": false,
"md5_digest": "363e9611755748b584c38bab3f378d59",
"packagetype": "bdist_wheel",
"python_version": "cp310",
"requires_python": ">=3.9",
"size": 323723,
"upload_time": "2024-02-05T20:38:21",
"upload_time_iso_8601": "2024-02-05T20:38:21.016400Z",
"url": "https://files.pythonhosted.org/packages/1f/5f/6474bf5f734850939898b5aeb7a4357cc1b3335a955f899e8f6aa4701511/maicos-0.8-cp310-cp310-macosx_13_0_arm64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "635e03bb8b31c83288078994dcaa7275a01d935b92e7e0115be710affbc7cc8d",
"md5": "88455483d46b2b64c0ef1c91b7671337",
"sha256": "7272ddd1f78cef13f11452fcec5213bdbbd4354aa96d0bcf56f130d451900b79"
},
"downloads": -1,
"filename": "maicos-0.8-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
"has_sig": false,
"md5_digest": "88455483d46b2b64c0ef1c91b7671337",
"packagetype": "bdist_wheel",
"python_version": "cp310",
"requires_python": ">=3.9",
"size": 724676,
"upload_time": "2024-02-05T20:38:24",
"upload_time_iso_8601": "2024-02-05T20:38:24.895476Z",
"url": "https://files.pythonhosted.org/packages/63/5e/03bb8b31c83288078994dcaa7275a01d935b92e7e0115be710affbc7cc8d/maicos-0.8-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "014991f02ed4a77412694900b911f16184a7d9a6c5442ee927431b356f484c80",
"md5": "dd8d61ab8ea9115e0e1564e6ae49567f",
"sha256": "ddcc2acf6bc59bc9c3a1c7fccc1db3485515be0e1c1619fd668c86e75efc1a2b"
},
"downloads": -1,
"filename": "maicos-0.8-cp310-cp310-win_amd64.whl",
"has_sig": false,
"md5_digest": "dd8d61ab8ea9115e0e1564e6ae49567f",
"packagetype": "bdist_wheel",
"python_version": "cp310",
"requires_python": ">=3.9",
"size": 320444,
"upload_time": "2024-02-05T20:38:26",
"upload_time_iso_8601": "2024-02-05T20:38:26.887317Z",
"url": "https://files.pythonhosted.org/packages/01/49/91f02ed4a77412694900b911f16184a7d9a6c5442ee927431b356f484c80/maicos-0.8-cp310-cp310-win_amd64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "bdc85887a15741fd688f595eb68c1b2fbe3c09a957efc7567ba7257d406740c0",
"md5": "2a1e553e825cd27f5f02a730f380e0d3",
"sha256": "dd949aa9041cef95c30d891006975c6041553b95226d07b67288ed9490342bd3"
},
"downloads": -1,
"filename": "maicos-0.8-cp311-cp311-macosx_13_0_arm64.whl",
"has_sig": false,
"md5_digest": "2a1e553e825cd27f5f02a730f380e0d3",
"packagetype": "bdist_wheel",
"python_version": "cp311",
"requires_python": ">=3.9",
"size": 323806,
"upload_time": "2024-02-05T20:38:28",
"upload_time_iso_8601": "2024-02-05T20:38:28.907465Z",
"url": "https://files.pythonhosted.org/packages/bd/c8/5887a15741fd688f595eb68c1b2fbe3c09a957efc7567ba7257d406740c0/maicos-0.8-cp311-cp311-macosx_13_0_arm64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "c74f9fe17a12daa5976bab936e8c46f19c318b7bbbab4097ed2576eb4c774a6d",
"md5": "b4e964184e75460a30e9981380407b29",
"sha256": "afc840931880b40974a0f410f7b6153c1f2554049af6148d301756de69265615"
},
"downloads": -1,
"filename": "maicos-0.8-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
"has_sig": false,
"md5_digest": "b4e964184e75460a30e9981380407b29",
"packagetype": "bdist_wheel",
"python_version": "cp311",
"requires_python": ">=3.9",
"size": 761341,
"upload_time": "2024-02-05T20:38:31",
"upload_time_iso_8601": "2024-02-05T20:38:31.242330Z",
"url": "https://files.pythonhosted.org/packages/c7/4f/9fe17a12daa5976bab936e8c46f19c318b7bbbab4097ed2576eb4c774a6d/maicos-0.8-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "233d27532f138a1cb4df75f4f9ebaa81b4d2f075a0923751bc94ab74d7407ec3",
"md5": "1feae2f79c9c7fad56bd632da0af9f33",
"sha256": "c6f91169c61626563c022a1d0653443e526382648bbc323004c1f5a0c546f688"
},
"downloads": -1,
"filename": "maicos-0.8-cp311-cp311-win_amd64.whl",
"has_sig": false,
"md5_digest": "1feae2f79c9c7fad56bd632da0af9f33",
"packagetype": "bdist_wheel",
"python_version": "cp311",
"requires_python": ">=3.9",
"size": 320556,
"upload_time": "2024-02-05T20:38:33",
"upload_time_iso_8601": "2024-02-05T20:38:33.397061Z",
"url": "https://files.pythonhosted.org/packages/23/3d/27532f138a1cb4df75f4f9ebaa81b4d2f075a0923751bc94ab74d7407ec3/maicos-0.8-cp311-cp311-win_amd64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "cf49ca698f0705e797d88533be78ecec97cf85e04c346a9ee771d2f2815fe0b3",
"md5": "bbf0bbd77303725b2948e34600b71caa",
"sha256": "d01e47ad9bf8625d76e2845e62abe72e254c62d2c609d0b45c749438bcee8965"
},
"downloads": -1,
"filename": "maicos-0.8-cp312-cp312-macosx_13_0_arm64.whl",
"has_sig": false,
"md5_digest": "bbf0bbd77303725b2948e34600b71caa",
"packagetype": "bdist_wheel",
"python_version": "cp312",
"requires_python": ">=3.9",
"size": 324919,
"upload_time": "2024-02-05T20:38:35",
"upload_time_iso_8601": "2024-02-05T20:38:35.734945Z",
"url": "https://files.pythonhosted.org/packages/cf/49/ca698f0705e797d88533be78ecec97cf85e04c346a9ee771d2f2815fe0b3/maicos-0.8-cp312-cp312-macosx_13_0_arm64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "1d22c2105a1c05d76108ef63a30b401451bdffa121d90fb1ecab6076866560fd",
"md5": "906d398962476181ee992da7f5bd8175",
"sha256": "789154186a7ac2244580abbfa52b48b65cfafe0cd8151e257ac54cc8f023bbce"
},
"downloads": -1,
"filename": "maicos-0.8-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
"has_sig": false,
"md5_digest": "906d398962476181ee992da7f5bd8175",
"packagetype": "bdist_wheel",
"python_version": "cp312",
"requires_python": ">=3.9",
"size": 753116,
"upload_time": "2024-02-05T20:38:37",
"upload_time_iso_8601": "2024-02-05T20:38:37.035048Z",
"url": "https://files.pythonhosted.org/packages/1d/22/c2105a1c05d76108ef63a30b401451bdffa121d90fb1ecab6076866560fd/maicos-0.8-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "2a402c74175247118f3febb87bc10bdfa66204dc0f742b1f1b723ae395b170c4",
"md5": "8b374f227e67127ae334907e17c57c19",
"sha256": "44937e3c508776d38d00a973b6f46b20914214bc53abbef60f1d6d09fb70fc8b"
},
"downloads": -1,
"filename": "maicos-0.8-cp312-cp312-win_amd64.whl",
"has_sig": false,
"md5_digest": "8b374f227e67127ae334907e17c57c19",
"packagetype": "bdist_wheel",
"python_version": "cp312",
"requires_python": ">=3.9",
"size": 320905,
"upload_time": "2024-02-05T20:38:39",
"upload_time_iso_8601": "2024-02-05T20:38:39.410662Z",
"url": "https://files.pythonhosted.org/packages/2a/40/2c74175247118f3febb87bc10bdfa66204dc0f742b1f1b723ae395b170c4/maicos-0.8-cp312-cp312-win_amd64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "57bc1364d54910cfc1f52a01a50d64abf10c25b1f07734eff806e1088a91d853",
"md5": "6a2761f5b502236096ee354994b3a4b7",
"sha256": "3e11670fa190b43b4c4f3bb0dc8b2266ddcae8842752f0ec5fb626e87a52bf80"
},
"downloads": -1,
"filename": "maicos-0.8-cp39-cp39-macosx_13_0_arm64.whl",
"has_sig": false,
"md5_digest": "6a2761f5b502236096ee354994b3a4b7",
"packagetype": "bdist_wheel",
"python_version": "cp39",
"requires_python": ">=3.9",
"size": 324289,
"upload_time": "2024-02-05T20:38:40",
"upload_time_iso_8601": "2024-02-05T20:38:40.947031Z",
"url": "https://files.pythonhosted.org/packages/57/bc/1364d54910cfc1f52a01a50d64abf10c25b1f07734eff806e1088a91d853/maicos-0.8-cp39-cp39-macosx_13_0_arm64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "5ab5516909aa9816b3030e4f976833fe7caf00c5c7566f0cd1a4174b4687816c",
"md5": "a655bd397fa179099ee2065c1a6498e5",
"sha256": "6267b49e30aa0ea510518393fdaa27f3ede3ed2484bf5cf3f7657fe889697abe"
},
"downloads": -1,
"filename": "maicos-0.8-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
"has_sig": false,
"md5_digest": "a655bd397fa179099ee2065c1a6498e5",
"packagetype": "bdist_wheel",
"python_version": "cp39",
"requires_python": ">=3.9",
"size": 727328,
"upload_time": "2024-02-05T20:38:42",
"upload_time_iso_8601": "2024-02-05T20:38:42.904083Z",
"url": "https://files.pythonhosted.org/packages/5a/b5/516909aa9816b3030e4f976833fe7caf00c5c7566f0cd1a4174b4687816c/maicos-0.8-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "71122a5a375094cd39b52b05408f9aa176ff176532f3f45b10a0d5f05e70635a",
"md5": "90440d0b194520aea4bf2b0da6a0d005",
"sha256": "99ef9b642a7b1d90105c61adcd32d44ec28eaaf2e976161f2e38a0773204fef5"
},
"downloads": -1,
"filename": "maicos-0.8-cp39-cp39-win_amd64.whl",
"has_sig": false,
"md5_digest": "90440d0b194520aea4bf2b0da6a0d005",
"packagetype": "bdist_wheel",
"python_version": "cp39",
"requires_python": ">=3.9",
"size": 321001,
"upload_time": "2024-02-05T20:38:44",
"upload_time_iso_8601": "2024-02-05T20:38:44.354108Z",
"url": "https://files.pythonhosted.org/packages/71/12/2a5a375094cd39b52b05408f9aa176ff176532f3f45b10a0d5f05e70635a/maicos-0.8-cp39-cp39-win_amd64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "dad317f9c35132274f70ced3e80087cd8d684d8c9fdf9bd89ffc191842087aec",
"md5": "46ab285e5277dd0d93558c6015a2a8f3",
"sha256": "15d242d638f15ab1fa8f8888df45b4f4e1a746529b33128b1555f45b839bc04f"
},
"downloads": -1,
"filename": "maicos-0.8.tar.gz",
"has_sig": false,
"md5_digest": "46ab285e5277dd0d93558c6015a2a8f3",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.9",
"size": 45219306,
"upload_time": "2024-02-05T20:38:46",
"upload_time_iso_8601": "2024-02-05T20:38:46.914318Z",
"url": "https://files.pythonhosted.org/packages/da/d3/17f9c35132274f70ced3e80087cd8d684d8c9fdf9bd89ffc191842087aec/maicos-0.8.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-02-05 20:38:46",
"github": false,
"gitlab": true,
"bitbucket": false,
"codeberg": false,
"gitlab_user": "maicos-devel",
"gitlab_project": "maicos",
"lcname": "maicos"
}
JSON