A system of algorithms for compiling a mathematical model of physical systems, the structure of which is given using graphs of great complexity, is proposed. The proposed algorithms can be used not only to develop new systems, but also to diagnose operating equipment and troubleshooting. The resulting mathematical model of the system, presented in the form of a system of equations, allows us to obtain a unique solution. The operation of the algorithms is illustrated using the example of a mechanical system, but the results of the work can be extended to systems of a different nature using electromechanical or electroeconomic analogies.