Hi @mroguljic ,
one way to do it is by calling GenerateDictionary
as I do here: Generate dictionary for dinamically created custom STL collections - #2 by eguiraud .
Otherwise I think adding the right #pragma link C++ class
(inside a #ifdef __CLING__
guard) in FatJetStruct.h
should do the job.
Cheers,
Enrico