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=begin
* Name: similarity.rb
* Description: Similarity algorithms
* Author: Andreas Maunz <andreas@maunz.de
* Date: 10/2012
=end
module OpenTox
module Algorithm
class Similarity
#TODO weighted tanimoto
# Tanimoto similarity
# @param [Array] a fingerprints of first compound
# @param [Array] b fingerprints of second compound
# @return [Float] Tanimoto similarity
def self.tanimoto(a,b)
bad_request_error "fingerprints #{a} and #{b} don't have equal size" unless a.size == b.size
#common = 0.0
#a.each_with_index do |n,i|
#common += 1 if n == b[i]
#end
#common/a.size
# TODO check if calculation speed can be improved
common_p_sum = 0.0
all_p_sum = 0.0
(0...a.size).each { |idx|
common_p_sum += [ a[idx], b[idx] ].min
all_p_sum += [ a[idx], b[idx] ].max
}
common_p_sum/all_p_sum
end
# Cosine similarity
# @param [Array] a fingerprints of first compound
# @param [Array] b fingerprints of second compound
# @return [Float] Cosine similarity, the cosine of angle enclosed between vectors a and b
def self.cosine(a, b)
val = 0.0
if a.size>0 and b.size>0
if a.size>12 && b.size>12
a = a[0..11]
b = b[0..11]
end
a_vec = a.to_gv
b_vec = b.to_gv
val = a_vec.dot(b_vec) / (a_vec.norm * b_vec.norm)
end
val
end
end
end
end
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