diff options
Diffstat (limited to 'test/descriptor.rb')
| -rw-r--r-- | test/descriptor.rb | 45 |
1 files changed, 27 insertions, 18 deletions
diff --git a/test/descriptor.rb b/test/descriptor.rb index d7d1385..563cdce 100644 --- a/test/descriptor.rb +++ b/test/descriptor.rb @@ -4,15 +4,17 @@ 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 @@ -26,43 +28,50 @@ class DescriptorTest < MiniTest::Test 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 |