This section describes the tools that we have developed to analyze different intermolecular interactions that play important roles in the self-assembly of soft matter. We have developed novel methods for investigating the ring-ring interactions, which are commonly found within aggregates of conjugated polymers, proteins and other biopolymers, and for determining the solvation of different regions of molecules. Finally we have developed code that allows a more general assessment of all interactions between molecules within the simulated system.