getting-started

Introduction

SAFEP-related scripts and tools

These scripts and notebooks are broadly applicable to FEP analysis.

A complete tutorial is available at: SAFEP Tutorial.

Installation

  1. Clone this repository

  2. Enter the repository directory

  3. Run pip install .

OR

  1. Run pip install git+https://github.com/BranniganLab/safep.git

Notebooks

  • BAR_Estimator_Basic: General use FEP analysis. Includes cumulative dG estimates, error estimates, and measures of convergence.

  • BAR_Estimator_Expanded: Extended functionality including bootstrapped error estimates, kernel estimation of dL distributions, and more.

Examples

Sample data is available in Sample_Notebooks/Sample_Data or from the alchemtest package.