The core of the code is based on the Cavity class, featuring several functions: file reading, center of mass calculation, 3D grid setup, identification of grid points within the cage calculation. Of MHP and ESP, and the subsequent saving of results in PDB and/or PyMol formats. Additionally, the GridPoint and CageGrid classes define attributes associated with each grid point in the 3D grid. The code also includes different functions for assigning hydrophobic values to the cage atoms, computing partial charges of the cage atoms, and calculating the maximum radius escape sphere, among other functions (See SI §S1 for a full description). Additionally, it offers a PyMol plugin with the corresponding C3 graphical user interface to set up all calculation parameters of C3 (see details in SI). Figure illustrates a simplified schematic diagram of C3 functionality.