to study nanopartiles with a distinct core-shell structure is the intrinsic core-shell interface method (ICSI). This approach divides the constituent molecules within a molecular aggregate into the core and shell region with an intermediate region in between these. The masses of the core and shell are determined, and the volumes of the core, shell, and interface are calculated. The total density of the aggregate is then computed by dividing the total mass by the sum of the volumes of the core, shell, and interface, which accounts for the varying properties of the core and shell. PySoftK's intrinsic_density class harnesses the ICSI method to perform intrinsic density calculations. PySoftK's implementation enables seamless processing of the entire reconstructed coordinate set provided by make_micelle_whole . Also, it can handle varying numbers of molecules constituting the structure of interest at each time step. The usage of this function closely resembles that of the spherical density function. Additionally, there is a intrinsic_density_water class for the computation of the intrinsic density of water.