Introduction
============

This repository contains all code for the full Q4Bio pipeline.

Submodules
===========

The repository contains the following submodules:
- `NEQ_switching_ani2x` - Contains slurm scripts for running NEQ switching simulations with element embracing ML potentials and the ANI2x potential (see https://zenodo.org/records/14971120).
- `fep` - Contains `yank` scripts and input files to run the classical MM FEP simulations.
- `ml` - Contains the Python package that runs the active learning.
- `plot_energy_distribution` - Contains the Python scripts that plot the energy distribution of the QM region.
- `qm-mm` - Contains the Python package that facilitates interfacing with the database. It provides the scripts necessary to add calculations to the database and extract results.
   Furthermore, it contains `yml` configuration files providing easy access to the calculation settings and the database. These files are required by most scripts in the submodules.
- `work_distributions` - Contains a Python package for plotting the work distributions of the NEQ switching simulations and the final free energy difference.

Installation and Usage
======================

Please see the documentation of the submodules for installation instructions. Note that some dependencies are directly provided in the `packages` directory.