1 files changed, 0 insertions, 96 deletions
diff --git a/pubchem-test.rb b/pubchem-test.rb
deleted file mode 100644
index a3e7799..0000000
--- a/pubchem-test.rb
+++ /dev/null
@@ -1,96 +0,0 @@
-require 'test/unit'
-require '../opentox-client/lib/opentox-client'
-require './pubchem.rb'
-require 'yaml'
-
-class AOPTest < Test::Unit::TestCase
-
-  def setup
-    @pug_uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/"
-    @compound = OpenTox::PubChemCompound.new #3036
-    @compound.cid = 1983
-    #@compound.from_name "2,4-D"
-  end
-
-  def test_initialize
-    print @compound.cid
-    print " "
-    puts @compound.to_smiles
-    puts "measured targets"
-    puts @compound.targets.collect{|t| t["Target Name"]}.to_yaml
-=begin
-    puts "predicted targets"
-    puts @compound.predicted_targets.select{|t| t[:prediction] == "active"}.size
-
-    puts "predicted non_targets"
-    puts @compound.predicted_targets.select{|t| t[:prediction] == "inactive"}.size
-    #puts @compound.predicted_non_targets.values.inspect
-    measured_target_gis = @compound.targets.collect{|t| t["Target GI"]}.compact.uniq
-    measured_nontarget_gis = @compound.non_targets.collect{|t| t["Target GI"]}.compact.uniq
-    predicted_target_gis = @compound.predicted_targets.collect{|t| t[:target_gi] if t[:prediction] == "active"}.compact.uniq
-    predicted_nontarget_gis = @compound.predicted_targets.collect{|t| t[:target_gi] if t[:prediction] == "inactive"}.compact.uniq
-    print "correct predicted targets: "
-    puts (measured_target_gis & predicted_target_gis).size
-    print "new predicted targets: "
-    puts (predicted_target_gis - measured_target_gis).size
-    print "correct predicted non-targets: "
-    puts (measured_nontarget_gis & predicted_nontarget_gis).size
-    print "new predicted non-targets: "
-    puts (predicted_nontarget_gis - measured_nontarget_gis).size
-    print "incorrect predicted targets: "
-    puts (measured_nontarget_gis & predicted_target_gis).size
-    puts (measured_nontarget_gis & predicted_target_gis).sort.to_yaml
-    puts @compound.predicted_targets.select{|t| t[:prediction] == "active"}.to_yaml
-    print "incorrect predicted non-targets: "
-    puts (measured_target_gis & predicted_nontarget_gis).size
-=end
-=begin
-    @compound.neighbors.each do |n|
-      #print n.cid
-      #print " "
-      print n.to_smiles
-      print " "
-      print n.similarity
-      print " "
-      puts n.p
-      puts n.targets.sort.inspect
-      #puts n.non_targets.inspect
-    end
-=end
-    #File.open("Acetaminophen.yaml","w+"){|f| f.puts @compound.to_yaml}
-    #puts @compound.neighbors.size
-    #assert_equal "7500", @p.cid
-    #assert_equal true, @p.aids[:active].include?(1188)
-    #assert_equal true, @p.aids[:inactive].include?(435)
-  end
-=begin
-  def test_similarity_search
-    #puts @p.to_smiles
-    @p.neighbors.each do |n|
-      #puts n.to_smiles
-      puts @p.target_similarity(n)
-    end
-    #puts @p.neighbors.inspect
-    #assert_equal 100, @p.neighbor_cids.size
-  end
-
-  def test_assay_description
-    puts @p.assay_description.to_yaml
-  end
-
-  def test_assay_genes
-    puts @p.assay_genes.to_yaml
-  end
-
-  def test_assay_similarity
-    @p2 = PubChem::Compound.new "OC(=O)C1=C(C=CC=C1)OC(=O)C"
-    puts @p.assay_similarity(@p2)
-  end
-
-  def test_target_similarity
-    @p2 = PubChem::Compound.new "OC(=O)C1=C(C=CC=C1)OC(=O)C"
-    puts @p.target_similarity(@p2)
-  end
-=end
-
-end