#########################
 CHEMSMART Documentation
#########################

.. image:: _static/chemsmart_logo.png
   :width: 400
   :align: center

CHEMSMART is a Python-based toolkit for automating quantum chemistry workflows. It provides tools for creating input
files, submitting jobs to HPC clusters, and analyzing simulation results from Gaussian, ORCA, and other computational
chemistry software.

.. toctree::
   :maxdepth: 2
   :caption: Getting Started

   introduction
   installation-linux-macos
   installation-windows-wsl
   installation-windows-gitbash
   installation-windows-powershell
   installation-hpc-cluster

.. toctree::
   :maxdepth: 2
   :caption: Configuration

   configuration-overview
   configuration-test
   configuration-user-settings
   configuration-server-settings
   configuration-project-settings

.. toctree::
   :maxdepth: 2
   :caption: CLI Reference

   cli-overview
   molecule-input-formats
   chemdraw-organometallic

.. toctree::
   :maxdepth: 2
   :caption: Gaussian Jobs

   gaussian-cli-options
   gaussian-structure-optimization
   gaussian-transition-state
   gaussian-conformational-sampling
   gaussian-qrc
   gaussian-electronic-structure
   gaussian-qmmm-jobs
   gaussian-other-jobs

.. toctree::
   :maxdepth: 2
   :caption: ORCA Jobs

   orca-cli-options
   orca-structure-optimization
   orca-transition-state
   orca-direct-input
   orca-multiscale-calculations

..
   .. toctree::

..
   :maxdepth: 2

..
   :caption: ITERATE

..

..
   iterate-cli-options

..
   iterate-structure-generation

.. toctree::
   :maxdepth: 2
   :caption: Thermochemistry

   thermochemistry-analysis

.. toctree::
   :maxdepth: 2
   :caption: PyMOL Visualization

   pymol-cli-options
   pymol-visualization
   pymol-reaction-analysis
   pymol-electronic-structure
   pymol-interaction-analysis

..
   .. toctree::

..
   :maxdepth: 2

..
   :caption: Grouper Tool

..

..
   grouper-cli-options

..
   grouper-strategies

..
   grouper-crest-or-traj-workflow

.. toctree::
   :maxdepth: 2
   :caption: NCIPLOT

   nciplot-tutorial

.. toctree::
   :maxdepth: 2
   :caption: Auxiliary Scripts

   scripts-overview
   scripts-data-management
   scripts-electronic-analysis

.. toctree::
   :maxdepth: 2
   :caption: API Reference

   modules

********************
 Indices and Tables
********************

-  :ref:`genindex`
-  :ref:`modindex`
-  :ref:`search`