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.

Contents:

• FastEnsemble
  • Citation
  • Table of Contents
  • Features
  • Installation
  • Dependencies
  • Documentation
  • OS Requirements
  • Usage
  • Troubleshooting
  • Download Sample Files
  • Contributing
  • License
  • Acknowledgements
• Usage
• Installing on Linux
• Installing on Windows (WSL)
• Running FastConformation on Windows
• Running the GUI
• Using the Command-Line Interface (CLI)
• Additional Notes
• Command-Line Interface (CLI) Guide
  • MSA Generation Tool Documentation
  • JackHMMeR Multiple Sequence Alignment
  • mmseqs2 Multiple Sequence Alignment
  • Configuration Files
  • Output
  • Ensemble Prediction
  • Command-Line Interface (CLI) Usage
  • Configuration
  • Overview
  • Available CLI Tools
• API reference
  • fast_conformation package

Installation Guide

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

• 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:

• Usage

Command-Line Interface (CLI)

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

• Command-Line Interface (CLI) Guide

API Reference

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

• API reference

Additional Resources

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