Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection

Algorithm 3

Seed extension.

(1)   function extend_seed(vertexA, vertexB, vertexC)

(2)   INPUT: a seed represented by three vertices (or pairs of atoms) from the alignment graph

(3)   OUTPUT: res, a set of pairs of atoms that potentially match well when atoms from the

      seed are optimally superimposed;

(4)         size, the size of the returned set

(5)   

(6)   BinaryVertexSet setA = get_neighbors(vertexA)

(7)   BinaryVertexSet setB = get_neighbors(vertexB)

(8)   BinaryVertexSet setC = get_neighbors(vertexC)

(9)   BinaryVertexSet tmp = intersection(setA, setB)

(10) BinaryVertexSet res = intersection(tmp, vertexC)

(11)  int size = pop_count(res)