Tools for Analyzing and Debugging (SA)FEP calculations. See also the SAFEP Tutorial: https://github.com/jhenin/SAFEP_tutorial/tree/main Documentation: https://safep-alchemy.readthedocs.io/en/latest/
Most functionality has been migrated to AFEP_parse.py and imported to the notebook.
Data can now be decorrelated (default for large files) by setting the decorrelate flag
Large data sets are automatically read piece-wise, decorrelated to reduce bloat, and saved. They are then read in and concatenated to create the u_nk. This needed because pandas stores all dataframes in RAM and u_nk is a (very) sparse matrix.
QC demonstration is probably unnecessary. Remove?
Addition of a CDF estimator for comparison with normal distributions without losing information to binning. "Optional" section at the end.
Key additions: