Modified the prepare_files.py code to allow two-step processing. In the first step the system graph with the selected appropriate atomistic fragment is built and saved. Next, with an external tool (see examples/network_backmapping/abx/scan_bonds.py) the actual list of active sites for atomistic cross bonds can be prepared and included into the settings file (tag predefined_active_sites) for the next step.
The last step uses the predefined active sites to build the hybrid topology file.