1. A non-transitory computer-readable storage medium storing a program that causes a computer to perform a procedure comprising: calculating coordinates of a point with reference to structure data that includes coordinates of vertices of a plurality of polygons representing a three-dimensional structure, the point being to be used together with the vertices of the polygons to produce a graph from the structure data according to spatial arrangement of the polygons and further to calculate characteristic quantities based on the produced graph; and storing the calculated coordinates of the point in a memory device as a piece of information relating to the structure data.