diff options
Diffstat (limited to 'test/descriptor.rb')
| -rw-r--r-- | test/descriptor.rb | 67 |
1 files changed, 26 insertions, 41 deletions
diff --git a/test/descriptor.rb b/test/descriptor.rb index 58149a7..d7d1385 100644 --- a/test/descriptor.rb +++ b/test/descriptor.rb @@ -4,80 +4,65 @@ class DescriptorTest < MiniTest::Test def test_list # check available descriptors - @descriptors = OpenTox::Algorithm::Descriptor::DESCRIPTORS.keys - assert_equal 110,@descriptors.size,"wrong num physchem descriptors" - @descriptor_values = OpenTox::Algorithm::Descriptor::DESCRIPTOR_VALUES - assert_equal 355,@descriptor_values.size,"wrong num physchem descriptors" - sum = 0 - [ @descriptors, @descriptor_values ].each do |desc| - {"Openbabel"=>15,"Cdk"=>(desc==@descriptors ? 50 : 295),"Joelib"=>45}.each do |k,v| - assert_equal v,desc.select{|x| x=~/^#{k}\./}.size,"wrong num #{k} descriptors" - sum += v - end - end - assert_equal (465),sum + 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" 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} s = Smarts.find_or_create_by(:smarts => "F=F") - result = OpenTox::Algorithm::Descriptor.smarts_match c, s + 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 = OpenTox::Algorithm::Descriptor.smarts_match c, smarts + result = c.smarts_match smarts assert_equal [1, 1, 1, 0, 1, 1, 0], result smarts_count = [10, 6, 2, 0, 2, 10, 0] - result = OpenTox::Algorithm::Descriptor.smarts_count c, smarts + result = c.smarts_match smarts, true assert_equal smarts_count, result end def test_compound_openbabel_single c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N" - result = OpenTox::Algorithm::Descriptor.physchem c, ["Openbabel.logP"] - assert_equal 1.12518, result.first + result = c.physchem [PhysChem.find_or_create_by(:name => "Openbabel.logP")] + assert_equal 1.12518, result.first.last.round(5) end def test_compound_cdk_single c = OpenTox::Compound.from_smiles "c1ccccc1" - result = OpenTox::Algorithm::Descriptor.physchem c, ["Cdk.AtomCount"] - assert_equal [12], result + result = c.physchem [PhysChem.find_or_create_by(:name => "Cdk.AtomCount.nAtom")] + assert_equal 12, result.first.last c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N" - result = OpenTox::Algorithm::Descriptor.physchem c, ["Cdk.AtomCount"] - assert_equal [17], result - result = OpenTox::Algorithm::Descriptor.physchem c, ["Cdk.CarbonTypes"] + result = c.physchem [PhysChem.find_or_create_by(:name => "Cdk.AtomCount.nAtom")] + assert_equal 17, result.first.last 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} - assert_equal [1, 0, 0, 1, 0, 2, 1, 1, 0], result + 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 end def test_compound_joelib_single c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N" - result = OpenTox::Algorithm::Descriptor.physchem c, ["Joelib.LogP"] - assert_equal [2.65908], result + result = c.physchem [PhysChem.find_or_create_by(:name => "Joelib.LogP")] + assert_equal 2.65908, result.first.last end def test_compound_all c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N" - result = OpenTox::Algorithm::Descriptor.physchem c - assert_equal 330, result.size - assert_equal 30.8723, result[2] - assert_equal 5, result[328] + 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] end def test_compound_descriptor_parameters c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N" - result = OpenTox::Algorithm::Descriptor.physchem c, [ "Openbabel.logP", "Cdk.AtomCount", "Cdk.CarbonTypes", "Joelib.LogP" ]#, true - assert_equal 12, result.size - assert_equal [1.12518, 17.0, 1, 0, 0, 1, 0, 2, 1, 1, 0, 2.65908], result#.last - end - - def test_dataset_descriptor_parameters - dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"hamster_carcinogenicity.mini.csv") - d = OpenTox::Algorithm::Descriptor.physchem dataset, [ "Openbabel.logP", "Cdk.AtomCount", "Cdk.CarbonTypes", "Joelib.LogP" ] - assert_kind_of Dataset, d - assert_equal dataset.compounds, d.compounds - assert_equal dataset.compounds.size, d.data_entries.size - assert_equal 12, d.data_entries.first.size + result = c.physchem [ "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} end end |