Figure 4

Illustration of 2D representation of a channel in a synthetic 2D example.Top: The molecule is shown as a set of disks (grey). The channel is shown as a path (red) and as a set of triangles (blue). In 2D, each node in the path corresponds to a triangle, while a path edge corresponds to an edge in the triangulation. Each disk is given an alphabetic label, while the nodes of the path are given numeric labels. Bottom: The proposed 2D visual metaphor of the channel is shown. Each vertical box denotes a node in the path (and thus denotes a triangle within the channel). The three small boxes within the node box denote the disks incident on the triangle corresponding to the particular node box. Also, consecutive nodes boxes are connected by two edges. These edges denote the edge shared by the consecutive triangles in the channel. For example, node boxes 3 and 4 denote triangles cbf and cgf, respectively. Their shared edge is cf, so the atom boxes corresponding to discs c and f are connected by edges. This representation naturally extends to the 3D case, with the only modification that each node box will denote a tetrahedron and will thus contain four atom boxes. Two consecutive node boxes will be connected by three edges denoting the common triangle shared by the adjacent tetrahedra.