From f46ba3b7262f5b551c81fc9396c5b7f0cac7f030 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Fri, 27 May 2016 19:16:16 +0200 Subject: first correlation of nanoparticle predictions --- lib/compound.rb | 30 ------------------------------ 1 file changed, 30 deletions(-) (limited to 'lib/compound.rb') diff --git a/lib/compound.rb b/lib/compound.rb index 89e9db2..a87678e 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -254,36 +254,6 @@ module OpenTox self["chemblid"] end -=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 -# features.each do |f| -# min,max = [query_fingerprint.count(f),candidate_fingerprint.count(f)].minmax -# min_sum += min -# max_sum += max -# end -# max_sum == 0 ? sim = 0 : sim = min_sum/max_sum.to_f -# neighbors << [compound.id, sim] if sim and sim >= params[:min_sim] -# end -# end -# neighbors.sort{|a,b| b.last <=> a.last} - 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 = [] dataset = Dataset.find(dataset_id) -- cgit v1.2.3