compound tests fixed

1 files changed, 17 insertions, 10 deletions

diff --git a/lib/compound.rb b/lib/compound.rb
index 2554d54..89e9db2 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -254,13 +254,15 @@ module OpenTox
       self["chemblid"]
     end
 
-#    def fingerprint_count_neighbors params
-#      # TODO fix
-#      neighbors = []
-#      query_fingerprint = self.fingerprint params[:type]
-#      training_dataset = Dataset.find(params[:training_dataset_id]).compounds.each do |compound|
-#        unless self == compound
-#          candidate_fingerprint = compound.fingerprint params[:type]
+=begin
+    def fingerprint_neighbors(type:, min_sim: 0.1, dataset_id:, prediction_feature_id:)
+      neighbors = []
+      dataset = Dataset.find(dataset_id)
+      query_fingerprint = self.fingerprint type
+      dataset.compounds.each do |compound|
+        values = dataset.values(compound,prediction_feature_id)
+        if values
+          candidate_fingerprint = compound.fingerprint type
 #          features = (query_fingerprint + candidate_fingerprint).uniq
 #          min_sum = 0
 #          max_sum = 0
@@ -274,7 +276,13 @@ module OpenTox
 #        end
 #      end
 #      neighbors.sort{|a,b| b.last <=> a.last}
-#    end
+          sim = Algorithm::Similarity.tanimoto(query_fingerprint , candidate_fingerprint)
+          neighbors << {"_id" => compound.id, "toxicities" => values, "similarity" => sim} if sim >= min_sim
+        end
+      end
+      neighbors.sort{|a,b| b["similarity"] <=> a["similarity"]}
+    end
+=end
 
     def fingerprint_neighbors(type:, min_sim: 0.1, dataset_id:, prediction_feature_id:)
       neighbors = []
@@ -294,9 +302,8 @@ module OpenTox
             neighbors << {"_id" => compound.id, "toxicities" => values, "similarity" => sim} if sim >= min_sim
           end
         end
-        neighbors.sort!{|a,b| b["similarity"] <=> a["similarity"]}
       end
-      neighbors
+      neighbors.sort{|a,b| b["similarity"] <=> a["similarity"]}
     end
 
 #    def physchem_neighbors params