Hsim is an agent-based simulator that allow the modelling of any kind of macro-molecules interactions in a 3D virtual cell using a description language. Theses models, which describe reactions between the various molecules are written by the user of the simulator. Our aim is to verify the validity of the user's model and to exhibit properties of these models without needing to run a simulation. To this end, we construct and analyse a Petri Net to determine all the possible macromolecular assemblies.