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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
# 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)
common_p_sum = 0.0
all_p_sum = 0.0
size = [ a.size, b.size ].min
$logger.warn "fingerprints don't have equal size" if a.size != b.size
(0...size).each { |idx|
common_p_sum += [ a[idx].to_f, b[idx].to_f ].min
all_p_sum += [ a[idx].to_f, b[idx].to_f ].max
}
(all_p_sum > 0.0) ? (common_p_sum/all_p_sum) : 0.0
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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