This paper proposes a new mathematical framework that can be applied to biological problems such as analysis of the structures of proteins and protein complexes. In particular, it gives a new method for encoding the three-dimensional structure of a protein into a binary sequence, where proteins are approximated by a folded tetrahedron sequence. It also gives a new algebraic framework for describing molecular complexes and their interactions. For simplicity, we shall explain the framework in the case of two-dimensional objects. Then, the binary code of a plane curve is obtained as the ``second derivative'' of the curve and ``fusion and fission'' of closed trajectories is described algebraically.