molecular_weight fixed

3 files changed, 5 insertions, 5 deletions

diff --git a/lib/compound.rb b/lib/compound.rb
index 0f178ce..ca9d5e3 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -75,9 +75,10 @@ module OpenTox
       fingerprints[type]
     end
 
-    def calculated_properties types=["OPENBABEL"]
+    def calculated_properties types=["PhysChem::OPENBABEL"]
       descriptors = []
       types.each do |t|
+        p t
         descriptors += PhysChem.descriptors OpenTox.const_get(t)
       end
       # TODO: speedup java descriptors
@@ -304,7 +305,7 @@ module OpenTox
     # @return [Float] molecular weight
     def molecular_weight
       mw_feature = PhysChem.find_or_create_by(:name => "Openbabel.MW")
-      calculated_physchem([mw_feature])[mw_feature.id.to_s]
+      calculated_properties[mw_feature.id.to_s]
     end
 
     private
diff --git a/lib/model.rb b/lib/model.rb
index f3f0603..859df8b 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -126,7 +126,8 @@ module OpenTox
           end
           model.descriptor_ids = model.fingerprints.flatten.uniq
           model.descriptor_ids.each do |d|
-            model.independent_variables << model.substance_ids.collect_with_index{|s,i| model.fingerprints[i].include? d}
+            # resulting model may break BSON size limit (e.g. f Kazius dataset
+            model.independent_variables << model.substance_ids.collect_with_index{|s,i| model.fingerprints[i].include? d} if model.algorithms[:prediction][:method].match /Caret/
           end
         else
           # parse independent_variables
@@ -225,7 +226,6 @@ module OpenTox
         else
           # call prediction algorithm
           result = Algorithm.run algorithms[:prediction][:method], dependent_variables:neighbor_dependent_variables,independent_variables:neighbor_independent_variables ,weights:neighbor_similarities, query_variables:query_descriptors
-          p result
           prediction.merge! result
           prediction[:neighbors] = neighbor_ids.collect_with_index{|id,i| {:id => id, :measurement => neighbor_dependent_variables[i], :similarity => neighbor_similarities[i]}}
         end
diff --git a/lib/regression.rb b/lib/regression.rb
index bed6df8..d1724fd 100644
--- a/lib/regression.rb
+++ b/lib/regression.rb
@@ -4,7 +4,6 @@ module OpenTox
     class Regression
 
       def self.weighted_average dependent_variables:, independent_variables:nil, weights:, query_variables:
-      #def self.weighted_average descriptors:nil, neighbors:, parameters:nil, method:nil, relevant_features:nil
         # TODO: prediction_interval
         weighted_sum = 0.0
         sim_sum = 0.0