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first draft for the documentation
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‎.gitignore‎

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sg_execution_times.rst
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# Allow scatterkit share text files
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!scatterkit/share/*.dat
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!src/scatterkit/share/*.dat
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# editors and IDEs
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*.sw[a-z]

‎README.md‎

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‎README.rst‎

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Scatterkit
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==========
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|tests| |codecov| |docs-stable| |docs-latest| |mdanalysis|
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.. inclusion-readme-intro-start
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Scatterkit does SAXS analysis of molecular dynamics simulations.
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.. inclusion-readme-intro-end
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Documentation
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=============
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For details, tutorials, and examples, visit our official `documentation`_. We also
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provide the `latest documentation`_ for the current development version of MAICoS.
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.. _`documentation`: https://maicos-analysis.org
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.. _`latest documentation`: https://maicos-analysis.org/latest
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.. inclusion-readme-installation-start
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Installation
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============
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Install Scatterkit using `pip`_::
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pip install scatterkit
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Or with `conda`_ from conda-forge::
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conda install -c conda-forge scatterkit
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.. _`pip`: https://pip.pypa.io
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.. _`conda`: https://www.anaconda.com
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.. inclusion-readme-installation-end
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List of Analysis Modules
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========================
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.. inclusion-marker-modules-start
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Currently, Scatterkit supports the following analysis modules (alphabetically):
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.. list-table::
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:widths: 25 50
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:header-rows: 1
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* - Module
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- Description
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* - SAXS
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- Small angle X-ray scattering
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.. inclusion-marker-modules-end
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Contributors
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============
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Thanks to all contributors who make **Scatterkit** possible:
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.. image:: https://contrib.rocks/image?repo=maicos-devel/maicos
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:target: https://github.com/maicos-devel/maicos/graphs/contributors
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.. |tests| image:: https://github.com/maicos-devel/maicos/workflows/Tests/badge.svg
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:alt: GitHub Actions Tests Job Status
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:target: https://github.com/maicos-devel/maicos/actions?query=branch%3Amain
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.. |codecov| image:: https://codecov.io/gh/maicos-devel/maicos/graph/badge.svg?token=9AXPLF6CR3
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:alt: Code coverage
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:target: https://codecov.io/gh/maicos-devel/maicos
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.. |docs-stable| image:: https://img.shields.io/badge/📚_Documentation-stable-success
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:alt: Documentation of stable released version
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:target: `documentation`_
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.. |docs-latest| image:: https://img.shields.io/badge/📒_Documentation-latest-yellow.svg
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:alt: Documentation of latest unreleased version
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:target: `latest documentation`_
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.. |mdanalysis| image:: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,AAABAAEAEBAAAAEAIAAoBAAAFgAAACgAAAAQAAAAIAAAAAEAIAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAJD+XwCY/fEAkf3uAJf97wGT/a+HfHaoiIWE7n9/f+6Hh4fvgICAjwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACT/yYAlP//AJ///wCg//8JjvOchXly1oaGhv+Ghob/j4+P/39/f3IAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAJH8aQCY/8wAkv2kfY+elJ6al/yVlZX7iIiI8H9/f7h/f38UAAAAAAAAAAAAAAAAAAAAAAAAAAB/f38egYF/noqAebF8gYaagnx3oFpUUtZpaWr/WFhY8zo6OmT///8BAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAgICAn46Ojv+Hh4b/jouJ/4iGhfcAAADnAAAA/wAAAP8AAADIAAAAAwCj/zIAnf2VAJD/PAAAAAAAAAAAAAAAAICAgNGHh4f/gICA/4SEhP+Xl5f/AwMD/wAAAP8AAAD/AAAA/wAAAB8Aov9/ALr//wCS/Z0AAAAAAAAAAAAAAACBgYGOjo6O/4mJif+Pj4//iYmJ/wAAAOAAAAD+AAAA/wAAAP8AAABhAP7+FgCi/38Axf4fAAAAAAAAAAAAAAAAiIiID4GBgYKCgoKogoB+fYSEgZhgYGDZXl5e/m9vb/9ISEjpEBAQxw8AAFQAAAAAAAAANQAAADcAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAjo6Mb5iYmP+cnJz/jY2N95CQkO4pKSn/AAAA7gAAAP0AAAD7AAAAhgAAAAEAAAAAAAAAAACL/gsAkv2uAJX/QQAAAAB9fX3egoKC/4CAgP+NjY3/c3Nz+wAAAP8AAAD/AAAA/wAAAPUAAAAcAAAAAAAAAAAAnP4NAJL9rgCR/0YAAAAAfX19w4ODg/98fHz/i4uL/4qKivwAAAD/AAAA/wAAAP8AAAD1AAAAGwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAALGxsVyqqqr/mpqa/6mpqf9KSUn/AAAA5QAAAPkAAAD5AAAAhQAAAAEAAAAAAAAAAAAAAAAAAAAAAAAAAAAAADkUFBSuZ2dn/3V1df8uLi7bAAAATgBGfyQAAAA2AAAAMwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAB0AAADoAAAA/wAAAP8AAAD/AAAAWgC3/2AAnv3eAJ/+dgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA9AAAA/wAAAP8AAAD/AAAA/wAKDzEAnP3WAKn//wCS/OgAf/8MAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAIQAAANwAAADtAAAA7QAAAMAAABUMAJn9gwCe/e0Aj/2LAP//AQAAAAAAAAAA
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:alt: Powered by MDAnalysis
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:target: https://www.mdanalysis.org

‎docs/requirements.txt‎

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furo
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setuptools # required for sphinxcontrib-bibtex together with Python 3.12
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sphinx>=7.2.2
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sphinx-gallery
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sphinxcontrib-bibtex
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sphinx-toggleprompt
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tomli

‎docs/src/.gitignore‎

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examples

‎docs/src/analysis-modules/index.rst‎

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.. _userdoc-analysis-modules:
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Analysis modules
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################
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This is a list of all analysis modules provided by MAICoS. Note that we do not have an
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example section for each module. Instead, we refer to :ref:`userdoc-how-to`.
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Once you understand the basic structure taught there, you can
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work with all modules. If not, feel free to raise an issue in GitHub_ or ask us on
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Discord_.
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.. _`GitHub`: https://github.com/maicos-devel/scatterkit/issues
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.. _`Discord`: https://discord.gg/mnrEQWVAed
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.. toctree::
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:maxdepth: 1
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:glob:
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./*

‎docs/src/analysis-modules/saxs.rst‎

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.. _Saxs:
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Saxs
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####
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.. autoclass:: maicos.Saxs
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:members: +run, save
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:undoc-members:
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:show-inheritance:
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.. footbibliography::

‎docs/src/api-documentation/index.rst‎

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.. _userdoc_api-documentation:
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API documentation
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#################
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The API documentation gives details on how the additional *functions* and classes can be
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used.
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.. toctree::
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:maxdepth: 2
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lib

‎docs/src/api-documentation/lib.rst‎

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.. _library_functions:
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Library functions
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#################
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.. automodule:: maicos.lib
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.. toctree::
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:titlesonly:
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:maxdepth: 4
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:caption: Library functions
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math
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util
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tables

‎docs/src/api-documentation/math.rst‎

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.. _mathematical_helper_functions:
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Mathematical helper functions
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#############################
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.. automodule:: maicos.lib.math
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:members:
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:undoc-members:
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:show-inheritance:
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.. automodule:: maicos.lib._cmath
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:members:
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:undoc-members:
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:show-inheritance:

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