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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
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