1 files changed, 92 insertions, 0 deletions
diff --git a/pubchem-test.rb b/pubchem-test.rb
new file mode 100644
index 0000000..273698e
--- /dev/null
+++ b/pubchem-test.rb
@@ -0,0 +1,92 @@
+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
+    @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
+    puts "predicted targets"
+    puts @compound.predicted_targets.select{|t| t[:prediction] == "active"}.to_yaml
+
+    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
+    print "incorrect predicted non-targets: "
+    puts (measured_target_gis & predicted_nontarget_gis).size
+=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