.. Molli documentation master file, created by
   sphinx-quickstart on Sat Apr  8 20:25:17 2023.
   You can adapt this file completely to your liking, but it should at least
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Table of Contents
*****************

.. toctree::
   :caption: Table of Contents

.. toctree::
   :maxdepth: 2
   :caption: Introduction

   01-molli-preamble.md
   02-basics.md

.. toctree::
   :maxdepth: 3
   :caption: Detailed Package Documentation

   API/molli.chem/_index
   API/molli.data/_index
   API/molli.descriptor/_index
   API/molli.external/_index
   API/molli.ftypes/_index
   API/molli.math/_index
   API/molli.pipeline/pipeline-notes.md
   

.. toctree::
   :maxdepth: 2
   :caption: Command Line Reference 

   command_line/commands

.. toctree::
   :maxdepth: 2
   :caption: Molli Cookbook

   cookbook/001-helloworld.ipynb
   cookbook/002-atom.ipynb
   cookbook/003-bond.ipynb
   cookbook/004-geometry.ipynb
   cookbook/005-conformerensemble.ipynb
   cookbook/006-libraries.ipynb
   cookbook/007-visualization.ipynb
   cookbook/008-chemdraw.ipynb
   cookbook/009-openbabel.ipynb
   cookbook/010-rdkit.ipynb
   cookbook/011-gbca.ipynb
   cookbook/012-jobmap.ipynb
   cookbook/013-BOX_workflow.ipynb
   cookbook/014-map.ipynb
   cookbook/015-libmanip.ipynb
   
.. toctree::
   :maxdepth: 2
   :caption: Benchmarks and Workflows

   zenodo/001-molnet.ipynb
   zenodo/002-crude.ipynb
   zenodo/003-buildlibrary.ipynb
   zenodo/004-readwrite
   zenodo/05-gbca-benchmark/_index
   zenodo/06-gbca-calculation-vis/_index
   zenodo/07-kras-inhibitor-rotation-barrier/_index
   zenodo/08-workflow-nmr-prediction/_index

.. toctree::
   :maxdepth: 2
   :caption: Miscellaneous 
   
   miscellaneous/inheritance_diagram
   miscellaneous/extensions


Indices and tables
******************
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`