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authorChristoph Helma <helma@in-silico.ch>2016-06-08 18:26:07 +0200
committerChristoph Helma <helma@in-silico.ch>2016-06-08 18:26:07 +0200
commit0f31c884d1bcfa448a1bf43a41d8fd6cf88bfc52 (patch)
treeb50005c5211487a0bfac93ac918f06d1bcd476ba /lib/compound.rb
parentf7e87b45f15083e5fcdea64821f06ed93ece4c4e (diff)
compound tests fixed
Diffstat (limited to 'lib/compound.rb')
-rw-r--r--lib/compound.rb16
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