descriptor tests fixed

3 files changed, 8 insertions, 12 deletions

diff --git a/lib/compound.rb b/lib/compound.rb
index 72882d0..b47364c 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -75,11 +75,7 @@ module OpenTox
       fingerprints[type]
     end
 
-    def calculated_properties types=["PhysChem::OPENBABEL"]
-      descriptors = []
-      types.each do |t|
-        descriptors += PhysChem.descriptors OpenTox.const_get(t)
-      end
+    def calculate_properties descriptors=PhysChem::OPENBABEL
       # TODO: speedup java descriptors
       calculated_ids = properties.keys
       # BSON::ObjectId instances are not allowed as keys in a BSON document.
@@ -98,7 +94,8 @@ module OpenTox
         end
       end
       save
-      properties.select{|id,v| descriptors.collect{|d| d.id.to_s}.include? id}
+      descriptors.collect{|d| properties[d.id.to_s]}
+      #properties.select{|id,v| descriptors.collect{|d| d.id.to_s}.include? id}
     end
 
     def smarts_match smarts, count=false
@@ -303,8 +300,9 @@ module OpenTox
     # Calculate molecular weight of Compound with OB and store it in object
     # @return [Float] molecular weight
     def molecular_weight
-      mw_feature = PhysChem.find_or_create_by(:name => "Openbabel.MW")
-      calculated_properties[mw_feature.id.to_s]
+      mw_feature = PhysChem.find_or_create_by(:name => "Openbabel.MW").id.to_s
+      calculate_properties unless properties[mw_feature]
+      properties[mw_feature]
     end
 
     private
diff --git a/lib/model.rb b/lib/model.rb
index 859df8b..7029c31 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -131,7 +131,7 @@ module OpenTox
           end
         else
           # parse independent_variables
-          if (model.algorithms[:descriptors] & ["PhysChem::OPENBABEL","PhysChem::CDK","PhysChem::JOELIB"]).empty?
+          if (model.algorithms[:descriptors] & [PhysChem::OPENBABEL,PhysChem::CDK,PhysChem::JOELIB]).empty?
             properties = model.substances.collect { |s| s.properties }
             all_property_ids = properties.collect{|p| p.keys}.flatten.uniq
             model.descriptor_ids = all_property_ids.select{|id| model.algorithms[:descriptors].include? Feature.find(id).category }
@@ -139,7 +139,7 @@ module OpenTox
 
           # calculate physchem properties
           else
-            properties = model.substances.collect { |s| s.calculated_properties(model.algorithms[:descriptors]) }
+            properties = model.substances.collect { |s| s.calculate_properties(model.algorithms[:descriptors]) }
             model.descriptor_ids = properties.collect{|p| p.keys}.flatten.uniq
             model.independent_variables = model.descriptor_ids.collect{|i| properties.collect{|p| p[i]}}
           end
diff --git a/lib/nanoparticle.rb b/lib/nanoparticle.rb
index f74f263..23e155c 100644
--- a/lib/nanoparticle.rb
+++ b/lib/nanoparticle.rb
@@ -6,8 +6,6 @@ module OpenTox
     field :core, type: Hash, default: {}
     field :coating, type: Array, default: []
 
-    attr_accessor :scaled_values
- 
     def add_feature feature, value, dataset
       unless feature.name == "ATOMIC COMPOSITION" or feature.name == "FUNCTIONAL GROUP" # redundand
         case feature.category