test/descriptor.rb in lazar-0.9.3 vs test/descriptor.rb in lazar-1.0.0

@@ -2,19 +2,21 @@
 
 class DescriptorTest < MiniTest::Test
 
   def test_list
     # check available descriptors
-    assert_equal 355,PhysChem.descriptors.size,"incorrect number of physchem descriptors"
     assert_equal 15,PhysChem.openbabel_descriptors.size,"incorrect number of Openbabel descriptors"
-    assert_equal 295,PhysChem.cdk_descriptors.size,"incorrect number of Cdk descriptors"
     assert_equal 45,PhysChem.joelib_descriptors.size,"incorrect number of Joelib descriptors"
+    assert_equal 286,PhysChem.cdk_descriptors.size,"incorrect number of Cdk descriptors"
+    assert_equal 346,PhysChem.descriptors.size,"incorrect number of physchem descriptors"
   end
 
   def test_smarts
     c = OpenTox::Compound.from_smiles "N=C=C1CCC(=F=FO)C1"
-    File.open("tmp.png","w+"){|f| f.puts c.png}
+    File.open("/tmp/tmp.png","w+"){|f| f.puts c.png}
+    assert_match /^PNG/,`file -b /tmp/tmp.png`
+    File.delete "/tmp/tmp.png"
     s = Smarts.find_or_create_by(:smarts => "F=F")
     result = c.smarts_match [s]
     assert_equal [1], result
     smarts = ["CC", "C", "C=C", "CO", "F=F", "C1CCCC1", "NN"].collect{|s| Smarts.find_or_create_by(:smarts => s)}
     result = c.smarts_match smarts
@@ -24,45 +26,52 @@
     assert_equal smarts_count, result
   end
 
   def test_compound_openbabel_single
     c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
-    result = c.physchem [PhysChem.find_or_create_by(:name => "Openbabel.logP")]
-    assert_equal 1.12518, result.first.last.round(5)
+    feature = PhysChem.find_or_create_by(:name => "Openbabel.logP")
+    result = c.calculate_properties([feature])
+    assert_equal 1.12518, result.first.round(5)
+    assert_equal 1.12518, c.properties[feature.id.to_s].round(5)
   end
 
   def test_compound_cdk_single
     c = OpenTox::Compound.from_smiles "c1ccccc1"
-    result = c.physchem [PhysChem.find_or_create_by(:name => "Cdk.AtomCount.nAtom")]
-    assert_equal 12, result.first.last
+    feature = PhysChem.find_or_create_by(:name => "Cdk.AtomCount.nAtom")
+    result = c.calculate_properties([feature])
+    assert_equal 12, result.first
     c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
-    result = c.physchem [PhysChem.find_or_create_by(:name => "Cdk.AtomCount.nAtom")]
-    assert_equal 17, result.first.last
+    feature = PhysChem.find_or_create_by(:name => "Cdk.AtomCount.nAtom")
+    result = c.calculate_properties([feature])
+    assert_equal 17, result.first
     c_types = {"Cdk.CarbonTypes.C1SP1"=>1, "Cdk.CarbonTypes.C2SP1"=>0, "Cdk.CarbonTypes.C1SP2"=>0, "Cdk.CarbonTypes.C2SP2"=>1, "Cdk.CarbonTypes.C3SP2"=>0, "Cdk.CarbonTypes.C1SP3"=>2, "Cdk.CarbonTypes.C2SP3"=>1, "Cdk.CarbonTypes.C3SP3"=>1, "Cdk.CarbonTypes.C4SP3"=>0}
     physchem_features = c_types.collect{|t,nr| PhysChem.find_or_create_by(:name => t)}
-    result = c.physchem physchem_features
-    assert_equal [1, 0, 0, 1, 0, 2, 1, 1, 0], result.values
+    result = c.calculate_properties physchem_features
+    assert_equal [1, 0, 0, 1, 0, 2, 1, 1, 0], result
   end
 
   def test_compound_joelib_single
     c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
-    result = c.physchem [PhysChem.find_or_create_by(:name => "Joelib.LogP")]
-    assert_equal 2.65908, result.first.last
+    result = c.calculate_properties [PhysChem.find_or_create_by(:name => "Joelib.LogP")]
+    assert_equal 2.65908, result.first
   end
 
   def test_compound_all
     c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
-    result = c.physchem PhysChem.descriptors
     amr = PhysChem.find_or_create_by(:name => "Cdk.ALOGP.AMR", :library => "Cdk")
     sbonds = PhysChem.find_by(:name => "Openbabel.sbonds")
-    assert_equal 30.8723, result[amr.id.to_s]
-    assert_equal 5, result[sbonds.id.to_s]
+    result = c.calculate_properties([amr,sbonds])
+    assert_equal 30.8723, result[0]
+    assert_equal 5, result[1]
   end
 
   def test_compound_descriptor_parameters
+    PhysChem.descriptors
     c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
-    result = c.physchem [ "Openbabel.logP", "Cdk.AtomCount.nAtom", "Joelib.LogP" ].collect{|d| PhysChem.find_or_create_by(:name => d)}
+    result = c.calculate_properties [ "Openbabel.logP", "Cdk.AtomCount.nAtom", "Joelib.LogP" ].collect{|d| PhysChem.find_or_create_by(:name => d)}
     assert_equal 3, result.size
-    assert_equal [1.12518, 17.0, 2.65908], result.values.collect{|v| v.round 5}
+    assert_equal 1.12518, result[0].round(5)
+    assert_equal 17.0, result[1].round(5)
+    assert_equal 2.65908, result[2].round(5)
   end
 
 end