Welcome to PyMEMENTO’s documentation!

PyMEMENTO is a simple implementation of the MEMENTO method (Morphing Endstates by Modelling Ensembles with iNdependent TOpologies) — a manuscript describing the method is in preparation. This documentation includes some background on MEMENTO, installation information for PyMEMENTO as well as several worked examples as used in our validation paper. This is alongside the full API documentation of all the python code.

Contents:

• Background on MEMENTO
• Installation
  • PyPI installation
  • Installation from source
  • Additional packages
• Examples and tutorial
  • Simple use case — deca-alanine
  • Setting up umbrella sampling
  • Handling ligands
  • Handling lipids
• Python API Documentation
  • Auxiliary functions

• Index