From 0c5d2e678908a2d4aea43efbedbedc2c0439be30 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 14 Mar 2016 15:25:50 +0100
Subject: descriptor tests

---
 lib/similarity.rb | 58 -------------------------------------------------------
 1 file changed, 58 deletions(-)
 delete mode 100644 lib/similarity.rb

(limited to 'lib/similarity.rb')

diff --git a/lib/similarity.rb b/lib/similarity.rb
deleted file mode 100644
index 91e18db..0000000
--- a/lib/similarity.rb
+++ /dev/null
@@ -1,58 +0,0 @@
-=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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