MOFUN: a Python package for molecular find and replace

Abstract

MOFUN is an open-source Python package that can find and replace molecular substructures in a larger, potentially periodic, system. In the context of molecular simulations, find and replace is a useful operation for adding/swapping functional groups, adding/removing solvent molecules or defect sites, and many other helpful system perturbations. MOFUN can also be used to alter force field terms on certain atoms while leaving the geometry/composition otherwise unchanged. The package is easily automated, which is particularly helpful for preparing input files for large-scale screenings. The package is freely available on GitHub at https://github.com/WilmerLab/mofun.