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docs/src/conf.py

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"MDAnalysis": ("https://docs.mdanalysis.org/stable/", None),
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"numpy": ("https://numpy.org/doc/stable/", None),
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"python": ("https://docs.python.org/3/", None),
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"maicos": ("https://maicos-analysis.org/stable/", None),
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}

docs/src/get-started/index.rst

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Getting started
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===============
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This sections describes MAICoS, how to install it, and its most basic commands.
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This sections describes Scatterkit, how to install it, and its most basic commands.
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.. toctree::
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:maxdepth: 0
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maicos
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scatterkit
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installation
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units
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changelog
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What is MAICoS
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==============
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What is Scatterkit
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==================
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.. include:: ../../../README.rst
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:start-after: inclusion-readme-intro-start

docs/src/index.rst

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Scatterkit Documentation
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========================
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This documentation covers everything you need to know about Scatterkit, the Molecular
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Analysis for Interfacial and Confined Systems toolkit. There are five sections:
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This documentation covers everything you need to know about Scatterkit.
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There are five sections:
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- :ref:`userdoc-get-started`
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- :ref:`userdoc-how-to`

examples/saxs.py

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Small-angle X-ray scattering
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============================
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Small-angle X-ray scattering (SAXS) can be extracted using MAICoS. To follow this how-to
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Small-angle X-ray scattering (SAXS) can be extracted using Scatterkit. To follow this how-to
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guide, you should download the :download:`topology <water.tpr>` and the
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:download:`trajectory <water.trr>` files of the water system.
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For more details on the theory see :ref:`saxs-explanations`.
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First, we import Matplotlib, MDAnalysis, NumPy and MAICoS:
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First, we import Matplotlib, MDAnalysis, NumPy and Scatterkit:
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""" # noqa: D415
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# %%
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# Extract small angle x-ray scattering (SAXS) intensities
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# -------------------------------------------------------
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#
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# Let us use the :class:`scatterkit.Saxs` class of MAICoS and apply it to all atoms in the
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# Let us use the :class:`scatterkit.Saxs` class of Scatterkit and apply it to all atoms in the
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# system:
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saxs = scatterkit.Saxs(u.atoms).run(stop=30)

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