Experiments with expanded ensemble simulation to explore chemical and mutational space.

This software is licensed under the MIT license, a permissive open source license.

Please be aware that this code is made available in the spirit of open science, but is currently pre-alpha--that is, it is not guaranteed to be completely tested or provide the correct results, and the API can change at any time without warning. If you do use this code, do so at your own risk. We appreciate your input, including raising issues about potential problems with the code, but may not be able to address your issue until other development activities have concluded.

See our installation instructions here.

In a fresh conda environment:

$ conda config --add channels conda-forge openeye
$ conda install perses openeye-toolkits

• perses/ - Package containing code for performing expanded ensemble simulations
• examples/ - Contains examples for various systems and methods of simulation
• attic/ - some old code that may be useful as part of the new setup
• devtools/ - Continuous integration and packaging utilities
• notes/ - LaTeX notes deriving acceptance criteria and stochastic approximation methods

A complete list of contributors can be found at GitHub Insights.

Major contributors include:

• Julie M. Behr
• Hannah E. Bruce Macdonald
• John D. Chodera
• Patrick B. Grinaway
• Mike M. Henry
• Iván J. Pulido
• Jaime Rodríguez-Guerra
• Dominic A. Rufa
• Ivy Zhang