Module: ViennaRna::Global::RnaExtensions::TwoStructureBasedMethods

Defined in:
lib/vienna_rna/global/rna_extensions.rb

Instance Method Summary collapse

Instance Method Details

#bp_distance(structure_1, structure_2) ⇒ Object 



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# File 'lib/vienna_rna/global/rna_extensions.rb', line 84

def bp_distance(structure_1, structure_2)
  # Takes two structures and calculates the distance between them by |symmetric difference(bp_in_a, bp_in_b)|
  raise "The two structures are not the same length" unless structure_1.length == structure_2.length

  bp_set_1, bp_set_2 = base_pairs(structure_1), base_pairs(structure_2)

  ((bp_set_1 - bp_set_2) + (bp_set_2 - bp_set_1)).count
end

#symmetric_bp_distance(structure_1, structure_2) ⇒ Object 



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# File 'lib/vienna_rna/global/rna_extensions.rb', line 93

def symmetric_bp_distance(structure_1, structure_2)
  # Takes two structures and calculates the distance between them by: sum { ((x_j - x_i) - (y_j - y_i)).abs }
  raise "The two structures are not the same length" unless structure_1.length == structure_2.length
  
  bp_dist = ->(array, i) { array[i] == -1 ? 0 : array[i] - i }
  
  structure_1_pairings = get_pairings(structure_1)
  structure_2_pairings = get_pairings(structure_2)
  
  structure_1.length.times.inject(0) do |distance, i|
    distance + (bp_dist[structure_1_pairings, i] - bp_dist[structure_2_pairings, i]).abs
  end
end