Metadata-Version: 2.1
Name: cg-r-pathway
Version: 0.1.6
Summary: A comprehensive protein reaction coordinate optimization framework
Home-page: https://github.com/simura-works/cg_r_pathway
Author: Bernard Kwadwo Essuman
Author-email: simura.pathway@gmail.com
Classifier: Programming Language :: Python :: 3
Classifier: License :: Other/Proprietary License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: matplotlib
Requires-Dist: torch
Requires-Dist: numba

# cg_r_pathway

`cg_r_pathway` is a comprehensive protein reaction coordinate optimization framework that integrates:

- **Physics-based Modeling:** Residue-specific parameters (mass, charge, ε, σ, hydrophobicity), bonds, angles, nonbonded interactions.
- **Advanced Optimization:** Global path optimization using Adaptive PSO+SA and local refinement using Double-Nested Simulated Annealing (DSA-ASA).
- **Self-Learning ML Model:** A placeholder neural network force field for continuous improvement.
- **Coarse-Graining and Backmapping:** Converting full-atom PDB structures to a coarse-grained model and reconstructing all-atom models via rigid-body transformation.
- **Advanced Visualization:** Reaction coordinate (RMSD vs Energy) plots and 3D path visualization.

## Installation

Clone the repository and install with pip:

```bash
pip install .

