safep 0.1.3

Tools for Analyzing and Debugging (SA)FEP calculations

SAFEP

SAFEP-related scripts and tools

These scripts and notebooks are broadly applicable to FEP analysis.

Sample Notebooks:

• AlternativeParser_nBAR uses less RAM to read large fepout files. Rarely useful unless each fepout file is extremely large.
• BAR_Estimator_Basic: General use FEP analysis. Includes cumulative dG estimates, error estimates, and measures of convergence.
• BAR_Estimator_Expanded: Extendend functionality including bootstrapped error estimates, kernel estimation of dL distributions, and more.
• Batch_Basic: Like BAR_Estimator_Basic but designed for multiple replicas of the same calculation.

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