diff options
Diffstat (limited to 'lib/compound.rb')
-rw-r--r-- | lib/compound.rb | 16 |
1 files changed, 9 insertions, 7 deletions
diff --git a/lib/compound.rb b/lib/compound.rb index 4541816..17cc240 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -257,12 +257,13 @@ module OpenTox def fingerprint_neighbors(type:, min_sim: 0.1, dataset_id:, prediction_feature_id:) neighbors = [] dataset = Dataset.find(dataset_id) - if type == DEFAULT_FINGERPRINT - neighbors = db_neighbors(min_sim: min_sim, dataset_id: dataset_id) - neighbors.each do |n| - n["measurements"] = dataset.values(n["_id"],prediction_feature_id) - end - else + # TODO: fix db_neighbors +# if type == DEFAULT_FINGERPRINT +# neighbors = db_neighbors(min_sim: min_sim, dataset_id: dataset_id) +# neighbors.each do |n| +# n["measurements"] = dataset.values(n["_id"],prediction_feature_id) +# end +# else query_fingerprint = self.fingerprint type dataset.compounds.each do |compound| values = dataset.values(compound,prediction_feature_id) @@ -271,7 +272,7 @@ module OpenTox sim = Algorithm::Similarity.tanimoto(query_fingerprint , candidate_fingerprint) neighbors << {"_id" => compound.id, "measurements" => values, "similarity" => sim} if sim >= min_sim end - end +# end end neighbors.sort{|a,b| b["similarity"] <=> a["similarity"]} end @@ -294,6 +295,7 @@ module OpenTox # end def db_neighbors min_sim: 0.1, dataset_id: + p fingerprints[DEFAULT_FINGERPRINT] # from http://blog.matt-swain.com/post/87093745652/chemical-similarity-search-in-mongodb #qn = default_fingerprint_size |