Welcome to MadraX’s documentation!

Madrax is a force field implemented as a differentiable PyTorch module and capable of estimate the energies that stabilize protein folding. This module can be used in the same way of a pytorch layer, which take as input a protein structure and return a tensor containing the Gibbs energies. The library is deep learining-ready

• Installation guide
  • How do I set it up?
  • Installing MadraX with pip:
  • Installing MadraX with Anaconda (Linux Only)
• Introduction
  • What is a force field?
  • Machine learning in structural biology
  • The Problem
  • Our Solution
  • What is MadraX?
  • Why is Differentiability Important?
  • Serendipity of Differentiability
  • What does MadraX mean?
• Quickstart
  • Importing libraries
  • Collecting the data
  • Parsing the structures
  • Running MadraX
• Tutorials
  • Optimizing a protein
  • Building a Non End-to-End network with Madrax
  • Implementing mutations in a protein
• Contacts
• madrax
  • ForceField module
  • dataStructures module
  • utils module
  • StructureOptimizer module
  • mutatingEngine module

Indices and tables

• Index

• Module Index

• Search Page