Systems and methods for visualization of a molecule, comprising a set of particles, are provided. A set of three-dimensional coordinates is obtained, each coordinate describing a position for a corresponding particle. A cost function containing an error in a set of two-dimensional coordinates, where each two-dimensional coordinate corresponds to a three-dimensional coordinate in the set of three-dimensional coordinates, is minimized until an exit condition is achieved. The minimization alters the two-dimensional coordinate values. A set of physical properties SM is obtained, each such property representing a property shared by a pair of particles in the molecule. The coordinates are plotted as nodes of a two-dimensional graph after minimization, connected by a plurality of edges. An edge connects a coordinate pair in the graph that corresponds to a pair of particles in the molecule. A characteristic of the edge is determined by a physical property for the pair of particles.