The Fragmenstein codebase is a modular Python package that is dependent on RDKit for compound manipulation, PyRosetta for energy minimisation and some additional open-source purpose-written packages described in the GitHub repository. Its usage does not require external system calls, including the ligand parameterisation for Rosetta, which was rewritten to be both open source and usable within Python 3.6+. Thanks to the limited number of external dependencies, it can be easily deployed in both Linux and MacOS architectures.