dataset tests cleanup

1 files changed, 4 insertions, 3 deletions

diff --git a/lib/compound.rb b/lib/compound.rb
index 143c4f2..6cb7f78 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -22,6 +22,7 @@ module OpenTox
 
     # Overwrites standard Mongoid method to create fingerprints before database insertion
     def self.find_or_create_by params
+      #PhysChem.descriptors # load descriptor features
       compound = self.find_or_initialize_by params
       compound.default_fingerprint_size = compound.fingerprint(DEFAULT_FINGERPRINT).size
       compound.save
@@ -77,7 +78,7 @@ module OpenTox
 
     def physchem descriptors=PhysChem.openbabel_descriptors
       # TODO: speedup java descriptors
-      calculated_ids = physchem.keys
+      calculated_ids = physchem_descriptors.keys
       # BSON::ObjectId instances are not allowed as keys in a BSON document.
       new_ids = descriptors.collect{|d| d.id.to_s} - calculated_ids
       descs = {}
@@ -90,11 +91,11 @@ module OpenTox
       # avoid recalculating Cdk features with multiple values
       descs.keys.uniq.each do |k|
         descs[k].send(k[0].downcase,k[1],self).each do |n,v|
-          physchem[algos[n].id.to_s] = v # BSON::ObjectId instances are not allowed as keys in a BSON document.
+          physchem_descriptors[algos[n].id.to_s] = v # BSON::ObjectId instances are not allowed as keys in a BSON document.
         end
       end
       save
-      physchem.select{|id,v| descriptors.collect{|d| d.id.to_s}.include? id}
+      physchem_descriptors.select{|id,v| descriptors.collect{|d| d.id.to_s}.include? id}
     end
 
     def smarts_match smarts, count=false