.. image:: _static/logo.png
   :alt: PolyzyMD Logo
   :align: center
   :width: 320px

PolyzyMD Documentation
======================

PolyzyMD is a molecular dynamics toolkit for building, running, and analyzing
enzyme-polymer simulations.

Use this site by *need*:

- Start here if you need to install PolyzyMD or run a first simulation.
- Use Tutorials for guided, end-to-end learning.
- Use How-To Guides for specific tasks such as SLURM submission, restraints,
  polymers, GROMACS export, or condition comparisons.
- Use Reference for command lookup, configuration details, benchmarks, and API
  docs.
- Use Explanation for concepts, rationale, interpretation, and best practices.
- Use Contributor Guide for development architecture and extension workflows.

.. note::

   PolyzyMD is under active development. If you encounter issues, please
   `open an issue <https://github.com/joelaforet/polyzymd/issues>`_ on GitHub.

.. note::

   Stable analysis workflows for the `v1.2.0` release are RMSF, contacts,
   distances, catalytic triad, and secondary structure. Binding preference,
   exposure dynamics, binding free energy, and polymer affinity remain
   available, but are documented as experimental.

Choose Your Path
----------------

- :doc:`Get Started <get_started/index>`
  Install PolyzyMD with pixi and run your first simulation.
- :doc:`Tutorials <tutorials/index>`
  Follow guided, end-to-end workflows with clear success states.
- :doc:`How-To Guides <how_to/index>`
  Solve a specific task quickly without wading through background material.
- :doc:`Reference <reference/index>`
  Look up commands, config schema, API modules, and benchmark data.
- :doc:`Explanation <explanation/index>`
  Understand why workflows are structured the way they are and how to
  interpret results.
- :doc:`Contributor Guide <contributor_guide/index>`
  Extend PolyzyMD, understand the architecture, and contribute safely.

Common Workflows
----------------

- Install locally and validate the CLI:
  :doc:`Install PolyzyMD with pixi <tutorials/installation>`
- Build and submit a first simulation:
  :doc:`Run Your First PolyzyMD Simulation <tutorials/quickstart>`
- Run a comparison study across multiple conditions:
  :doc:`Compare Simulation Conditions <tutorials/analysis_compare_conditions>`
- Generate comparison figures as a smoke test:
  :doc:`Analyze a Multi-Condition Study <tutorials/analysis_complete_workflow>`

.. IMAGE OPPORTUNITY: Add a single workflow schematic showing Build -> Submit ->
   Analyze -> Compare -> Plot, with stable and experimental analysis branches.
..

.. toctree::
   :hidden:
   :maxdepth: 2

   Get Started <get_started/index>
   Tutorials <tutorials/index>
   How-To Guides <how_to/index>
   Reference <reference/index>
   Explanation <explanation/index>
   Contributor Guide <contributor_guide/index>

Indices and Tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`