getting-started
===============

.. toctree::
   :maxdepth: 4

Introduction
------------
SAFEP-related scripts and tools

These scripts and notebooks are broadly applicable to FEP analysis.

A complete tutorial is available at:
`SAFEP Tutorial <https://doi.org/10.33011/livecoms.5.1.2067>`_.

Installation
------------

.. Installation:
0. Clone this repository
1. Enter the repository directory
2. Run ``pip install .``

OR

0. 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.