Caution

This is module is undergoing heavy development. None of the API calls are final. This software is provided without any guarantees of correctness, you will likely encounter bugs.

If you are interested in this code, please wait for the official release to use it. In the mean time, to stay informed of development progress you are encouraged to:

• Follow this feed for updates on releases.

• Check out the github repository .

perses

A Python framework for automated small molecule free energy driven design.

perses is a Python framework that uses OpenMM for GPU-accelerated molecular design driven by alchemical free energy calculations.

Contents:

• Installation
  • Installing via conda
• Changelog

Modules

• Alchemical transformations
  • Nonequilibrium switching
  • Relative alchemical transformations
  • Principle of HybridTopologyFactory
  • Basic Usage of HybridTopologyFactory
• Bias engine
  • perses.bias.BiasEngine
  • perses.bias.MinimizedPotentialBias
• Molecular geometry generation via RJMC
  • Topology proposal engines
  • OpenMM System generation utilities
  • Geometry proposal engines
  • Geometry utility classes
• Sampler stack
• Storage handling
  • perses.storage.NetCDFStorage
• Analysis
  • Cache objects

Indices and tables

• Index

• Module Index

• Search Page