A Parallel Framework for Multipoint Spiral Search in ab Initio Protein Structure Prediction

Algorithm 3

evaluate(AA).

(1) for (𝑖=1   to   seqLength − 1) do

(2)  for (𝑘=𝑖+2   to   seqLength − 1) do

(3)    if   AAType[𝑖] = AAType[𝑘] = H then

(4)       nodeI  ⟵  AA[𝑖]

(5)       nodeJ  ⟵  AA[𝑘]

(6)       sqrD  ⟵  getSqrDist(nodeI, nodeJ)

(7)       if   sqrD = 2 then

(8)         fitness  ⟵  fitness – 1

(9) return fitness