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-rw-r--r--test/descriptor.rb83
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+require_relative "setup.rb"
+
+class DescriptorTest < MiniTest::Test
+
+ def test_list
+ # check available descriptors
+ @descriptors = OpenTox::Algorithm::Descriptor::DESCRIPTORS.keys
+ assert_equal 111,@descriptors.size,"wrong num physchem descriptors"
+ @descriptor_values = OpenTox::Algorithm::Descriptor::DESCRIPTOR_VALUES
+ assert_equal 356,@descriptor_values.size,"wrong num physchem descriptors"
+ sum = 0
+ [ @descriptors, @descriptor_values ].each do |desc|
+ {"Openbabel"=>16,"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 (111+356),sum
+ end
+
+ def test_smarts
+ c = OpenTox::Compound.from_smiles "N=C=C1CCC(=F=FO)C1"
+ s = Smarts.find_or_create_by(:smarts => "FF")
+ result = OpenTox::Algorithm::Descriptor.smarts_match c, s
+ assert_equal [1], result
+ smarts = ["CC", "C", "C=C", "CO", "FF", "C1CCCC1", "NN"].collect{|s| Smarts.find_or_create_by(:smarts => s)}
+ result = OpenTox::Algorithm::Descriptor.smarts_match c, 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
+ 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
+ end
+
+ def test_compound_cdk_single
+ c = OpenTox::Compound.from_smiles "c1ccccc1"
+ result = OpenTox::Algorithm::Descriptor.physchem c, ["Cdk.AtomCount"]
+ assert_equal [12], result
+ 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"]
+ 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
+ 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
+ end
+
+ def test_compound_all
+ c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
+ result = OpenTox::Algorithm::Descriptor.physchem c
+ assert_equal 332, result.size
+ assert_equal 30.8723, result[2]
+ assert_equal 1.12518, result[328]
+ 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.last.size
+ assert_equal ["Openbabel.logP", "Cdk.AtomCount.nAtom", "Cdk.CarbonTypes.C1SP1", "Cdk.CarbonTypes.C2SP1", "Cdk.CarbonTypes.C1SP2", "Cdk.CarbonTypes.C2SP2", "Cdk.CarbonTypes.C3SP2", "Cdk.CarbonTypes.C1SP3", "Cdk.CarbonTypes.C2SP3", "Cdk.CarbonTypes.C3SP3", "Cdk.CarbonTypes.C4SP3", "Joelib.LogP"], result.first
+ assert_equal [1.12518, 17, 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
+ end
+
+end