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author | Christoph Helma <helma@in-silico.ch> | 2015-08-10 13:26:06 +0200 |
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committer | Christoph Helma <helma@in-silico.ch> | 2015-08-10 13:26:06 +0200 |
commit | b7cd3ebbb858a8891c35c45896f1bdd525f3534e (patch) | |
tree | a9df6b1f4fc15f2f953e9a23c6dd00b74a967754 /lib/similarity.rb | |
parent | 23ecfc6fa5ae4913e5cd17b7d58432d1f88d780c (diff) |
algorithm libraries added, fminer tests pass
Diffstat (limited to 'lib/similarity.rb')
-rw-r--r-- | lib/similarity.rb | 58 |
1 files changed, 58 insertions, 0 deletions
diff --git a/lib/similarity.rb b/lib/similarity.rb new file mode 100644 index 0000000..91e18db --- /dev/null +++ b/lib/similarity.rb @@ -0,0 +1,58 @@ +=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 |