Figure 1
From: Rule-based spatial modeling with diffusing, geometrically constrained molecules
Exemplary rule-based system: Two elementary molecule types (blue, green) with their subdomains (or components) are displayed (a). Each component can be bound to another component or can be modified, e.g. denoting a phosphorylation or a conformational change. Site names need not be unique and hence a wide spectrum of possibilities for the system's specification is offered. Multiple elementary molecules can be connected at their components to form complex molecule graphs (b). Reaction rules, for example the binding reaction (c), are specified by using patterns graphs (or reactant patterns). A reactant pattern fits to a molecule graph, if it is contained as a subgraph in the molecule graph. Note that some components are missing in the reactant pattern's definition, which are then ignored in the matching process. Two different instances of the reaction rule are symbolized (d). In the upper realization, two independent molecule graphs are connected. For the lower example on the other hand, both of the rules' reactant patterns are found in a single connected molecule graph.