Directed string assembly index calculator using the smallest grammar algorithm re-pair. This will find a short, valid path. But there is no guarantee that it will find the shortest possible valid path.
CFG/cfg_ai.py has two useful functions: ai_upper and ai_upper_with_pathways. Both return the same path length, but ai_upper_with_pathways prints the joining operations of the path.
Prerequisites: networkx >= 3.4.2 rdkit >=2024.03.5
conda install conda-forge::networkx
Use pip to install this package.
pip install git+https://github.com/ELIFE-ASU/assemblycfg.git
See the examples folder for examples of how to use the package.