Some edges created during the first step form sharp angles that are not chemically or physically meaningful. Therefore, the second step is to remove the longer of the two edges that form such angles, as depicted in Figure (II). The threshold defining sharp angles differs from system to system and should be set manually. We found that taking this threshold as half of the smallest angle formed by translation vectors of a super-cell in the case of a periodic system is an excellent choice to obtain a structural-informative graph. After performing the first two steps, a graph representation is formed for each system configuration at our disposal. In practice, we can use only a limited number of representative structures, making the method easily applicable for large datasets.