Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection

Algorithm 2

Seed enumeration.

(1)   function enumerate_seeds(graph)

(2)   INPUT: graph, an alignment graph between atoms from two proteins

(3)   OUTPUT: seedList, a list of suitable 3-cliques (i.e. triplets of vertices that are connected

      to each other and correspond to non-degenerated triangles in both proteins)

(4)   

(5)   SeedList seedList = empty_seed_list()

(6)   For each vertex1 in graph

(7)      For each vertex2 in get_successors(vertex1)

(8)         For each vertex3 in get_successors(vertex2)

(9)            If is_edge(vertex1, vertex3)

(10)             If collinearity_check(vertex1, vertex2, vertex3)

(11)                 seedList. add(vertex1, vertex2, vertex3)

(12)             End If

(13)          End If

(14)       End For

(15)    End For

(16) End For