require_relative "setup.rb" 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" 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 = 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 assert_equal [1, 1, 1, 0, 1, 1, 0], result smarts_count = [10, 6, 2, 0, 2, 10, 0] 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 = 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 = 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 = 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} 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 = 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 = 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 = 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