crossvalidation.rb, neighbor.rb addedmongodb

1 files changed, 25 insertions, 0 deletions

diff --git a/lib/neighbor.rb b/lib/neighbor.rb
new file mode 100644
index 0000000..a2c28d4
--- /dev/null
+++ b/lib/neighbor.rb
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+module OpenTox
+  module Algorithm
+    class Neighbor
+
+      def self.fingerprint_similarity compound, params={}
+        compound.neighbors params[:min_sim]
+      end
+
+      def self.fminer_similarity compound, params
+        feature_dataset = Dataset.find params[:feature_dataset_id]
+        query_fingerprint = Algorithm::Descriptor.smarts_match(compound, feature_dataset.features.collect{|f| f.smarts} )
+        neighbors = []
+
+        # find neighbors
+        feature_dataset.data_entries.each_with_index do |fingerprint, i|
+          sim = Algorithm::Similarity.tanimoto fingerprint, query_fingerprint
+          if sim > params[:min_sim]
+            neighbors << [feature_dataset.compound_ids[i],sim] # use compound_ids, instantiation of Compounds is too time consuming
+          end
+        end
+        neighbors
+      end
+    end
+  end
+end