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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"
result = OpenTox::Algorithm::Descriptor.smarts_match c, "FF"
assert_equal [[1]], result
smarts = ["CC", "C", "C=C", "CO", "FF", "C1CCCC1", "NN"]
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, result[0].size
assert_equal 1.12518, result[0][0]
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]["Cdk.AtomCount.nAtom"]
c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
result = OpenTox::Algorithm::Descriptor.physchem c, ["Cdk.AtomCount"]
assert_equal 17, result[c]["Cdk.AtomCount.nAtom"]
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 c_types, result[c]
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[c]["Joelib.LogP"]
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[c].size
{
"Cdk.LongestAliphaticChain.nAtomLAC"=>5,
"Joelib.count.HeavyBonds"=>7,
"Openbabel.MR"=>30.905,
#"Cdk.LengthOverBreadthDescriptor.LOBMAX"=>1.5379006098352144,
#"Joelib.GeometricalShapeCoefficient"=>5.210533887682899,
}.each do |d,v|
assert_equal v, result[c][d]
end
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" ]
assert_equal 12, result[c].size
expect = {"Openbabel.logP"=>1.12518, "Cdk.AtomCount.nAtom"=>17, "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, "Joelib.LogP"=>2.65908}
assert_equal expect, result[c]
end
def test_dataset_descriptor_parameters
dataset = OpenTox::Dataset.new
dataset.upload File.join(DATA_DIR,"hamster_carcinogenicity.mini.csv")
d = OpenTox::Algorithm::Descriptor.physchem dataset, [ "Openbabel.logP", "Cdk.AtomCount", "Cdk.CarbonTypes", "Joelib.LogP" ]
assert_equal dataset.compounds.size, d.keys.size
assert_equal 12, d.first.last.size
end
end
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