Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection

Algorithm 4

Extension filtering algorithm.

(1)   function filter_extension(extension)

(2)   INPUT: extension, a set of pairs of atoms

(3)   OUTPUT: result, a subset of the extension containing

      only pairs of atoms that match well

(4)   

(5)   VertexSet result = empty_set()

(6)   Matrix transformation = get_optimal_transformation(seed)

(7)   For each vertex in extension

(8)      Point = get_coordinates_in_first_protein(vertex)

(9)      Point _prime = get_coordinates_in_second_protein(vertex)

(10)    Point _transformed = apply_transformation(, transformation)

(11)     Float distance = dist(_transformed, _prime)

(12)    If (distance < threshold)

(13)       result.insert(vertex)

(14)    End If

(15) End For