Fig. 1

The coarse graining process of a macromolecule (macromolecule 1F1B). Subfigure (a) shows all atoms in macromolecule 1F1B. As shown in (b), all of the atoms in 1F1B are separated into 3 clusters using k-means clustering method. Three cluster centers are represented by red triangles, and the atoms in different clusters are marked by different colors. Our methods represent each macromolecule with several balls, and the 3D visualization result of our multiple-ball model on 1F1B is shown in subfigure (c). All the balls in a macromolecule are connected with each other. This fully connected topology guarantees its non-deformable nature. The topological structure of 1F1B is shown in (d) with a ball-stick model