.. FastConformation documentation master file, created by
   sphinx-quickstart on Tue Aug 24 2024.

Welcome to FastConformation's Documentation!
=========================================

This documentation provides an overview of how to use FastConformation, a tool for MSA generation, AF2 prediction, and protein conformation analysis. Below, you will find documentation on installation, usage, and the API reference.

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   README.md
   usage
   cli_scripts/index
   api/modules


Installation Guide
==================

For installation instructions, please refer to the `requirements.txt` and `README.md` files:

- `README.md <README.md>`_: Provides a general overview and installation instructions.

Usage Guide
===========

To learn how to use FastConformation, including running the GUI and CLI tools, visit the `usage` guide:

- :doc:`usage`

Command-Line Interface (CLI)
============================

FastConformation includes several CLI scripts for various tasks. Each script is documented in detail on this page:

- :doc:`cli_scripts/index`

API Reference
=============

For developers and advanced users, the API reference provides detailed documentation on the internal workings of FastConformation:

- :doc:`api/modules`

Additional Resources
=====================

For more information on specific tasks, usage examples, and troubleshooting, explore the sections above.