Hsim is an agent-based simulator used to model the interactions of macromolecules in a 3D virtual cell surrounded by a membrane. This simulator is not dedicated to a specific model of macromolecular interactions but allows the modelling of any kind of interactions, described using a modelling language, written by the user of the simulator and representing reactions between the various molecules, including the formation of complexes. Our aim was to verify the validity of the user's model and to exhibit properties of the model without needing to run a simulation. To this end, we construct a Petri Net to determine all the possible macromolecular assemblies and use the Petri Net algebra to verify chosen properties.