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+require_relative "setup.rb"
+
+class CompoundTest < MiniTest::Test
+
+ def test_0_compound_from_smiles
+ c = OpenTox::Compound.from_smiles "F[B-](F)(F)F.[Na+]"
+ assert_equal "InChI=1S/BF4.Na/c2-1(3,4)5;/q-1;+1", c.inchi.chomp
+ assert_equal "F[B-](F)(F)F.[Na+]", c.smiles, "A failure here might be caused by a compound webservice running on 64bit architectures using an outdated version of OpenBabel. Please install OpenBabel version 2.3.2 or higher." # seems to be fixed in 2.3.2
+ end
+
+ def test_1_compound_from_smiles
+ c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
+ assert_equal "InChI=1S/C6H9NO/c1-5(4-7)3-6(2)8/h5H,3H2,1-2H3", c.inchi
+ assert_equal "CC(C#N)CC(=O)C", c.smiles
+ end
+
+ def test_2_compound_from_smiles
+ c = OpenTox::Compound.from_smiles "N#[N+]C1=CC=CC=C1.F[B-](F)(F)F"
+ assert_equal "InChI=1S/C6H5N2.BF4/c7-8-6-4-2-1-3-5-6;2-1(3,4)5/h1-5H;/q+1;-1", c.inchi
+ assert_equal "F[B-](F)(F)F.N#[N+]c1ccccc1", c.smiles
+ end
+
+ def test_compound_from_name
+ c = OpenTox::Compound.from_name "Benzene"
+ assert_equal "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H", c.inchi
+ assert_equal "c1ccccc1", c.smiles
+ end
+
+ def test_compound_from_inchi
+ c = OpenTox::Compound.from_inchi "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
+ assert_equal "c1ccccc1", c.smiles
+ end
+
+ def test_sdf_import
+ c = OpenTox::Compound.from_sdf File.read(File.join DATA_DIR, "acetaldehyde.sdf")
+ assert_equal "InChI=1S/C2H4O/c1-2-3/h2H,1H3", c.inchi
+ assert_equal "CC=O", c.smiles
+ assert c.names.include? "Acetylaldehyde"
+ end
+
+ def test_sdf_export
+ c = OpenTox::Compound.from_smiles "CC=O"
+print c.sdf
+ assert_match /7 6 0 0 0 0 0 0 0 0999 V2000/, c.sdf
+ end
+
+ def test_compound_image
+ c = OpenTox::Compound.from_inchi "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
+ testbild = "/tmp/testbild.png"
+ File.open(testbild, "w"){|f| f.puts c.png}
+ assert_match "image/png", `file -b --mime-type /tmp/testbild.png`
+ File.unlink(testbild)
+ end
+
+ def test_inchikey
+ c = OpenTox::Compound.from_inchi "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
+ assert_equal "UHOVQNZJYSORNB-UHFFFAOYSA-N", c.inchikey
+ end
+
+ def test_cid
+ c = OpenTox::Compound.from_inchi "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
+ assert_equal "241", c.cid
+ end
+
+ def test_chemblid
+ c = OpenTox::Compound.from_inchi "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
+ #assert_equal "CHEMBL277500", c.chemblid
+ assert_equal "CHEMBL581676", c.chemblid
+ end
+
+ def test_sdf_storage
+ c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
+ c.sdf
+ assert !c.sdf_id.nil?
+ end
+
+ def test_fingerprint
+ c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
+
+ assert_equal 9, c.fingerprint("FP4").size
+ end
+
+ def test_neighbors
+ d = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.csv")
+ d.compounds.each do |c|
+ refute_nil c.fingerprint("MP2D")
+ end
+ c = d.compounds[371]
+ n = c.fingerprint_neighbors({:type => "FP4", :min_sim => 0.7, :training_dataset_id => d.id })
+ assert n.size >= 18, "Neighbors size (#{n.size}) should be larger than 17"
+ end
+
+ def test_openbabel_segfault
+ inchi = "InChI=1S/C19H27NO7/c1-11-9-19(12(2)27-19)17(23)26-14-6-8-20(4)7-5-13(15(14)21)10-25-16(22)18(11,3)24/h5,11-12,14,24H,6-10H2,1-4H3/b13-5-/t11-,12-,14-,18-,19?/m1/s1"
+
+ c = Compound.from_inchi(inchi)
+ assert_equal inchi, c.inchi
+ end
+
+ def test_openbabel_fingerprint
+ [
+ "CC(=O)CC(C)C#N",
+ "CC(=O)CC(C)C",
+ "C(=O)CC(C)C#N",
+ ].each do |smi|
+ c = OpenTox::Compound.from_smiles smi
+ refute_nil c.fingerprint("FP4")
+ end
+ end
+
+ def test_fingerprint_neighbors
+ types = ["FP2", "FP3", "FP4", "MACCS"]
+ min_sim = 0.7
+ training_dataset = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.csv")
+ [
+ "CC(=O)CC(C)C#N",
+ "CC(=O)CC(C)C",
+ "C(=O)CC(C)C#N",
+ ].each do |smi|
+ c = OpenTox::Compound.from_smiles smi
+ types.each do |type|
+ neighbors = c.fingerprint_neighbors({:type => type, :training_dataset_id => training_dataset.id, :min_sim => min_sim})
+ unless type == "FP2" and smi == "CC(=O)CC(C)C#N" or smi == "C(=O)CC(C)C#N" and (type == "FP2" or type == "MACCS")
+ refute_empty neighbors
+ end
+ end
+ end
+ end
+
+ def test_mna
+ c = OpenTox::Compound.from_smiles "N#[N+]C1=CC=CC=C1.F[B-](F)(F)F"
+ assert_equal 18, c.fingerprint("MNA").size
+ assert_equal 9, c.fingerprint("MNA").uniq.size
+ end
+
+ def test_mpd
+ c = OpenTox::Compound.from_smiles "N#[N+]C1=CC=CC=C1.F[B-](F)(F)F"
+ assert 13, c.fingerprint("MP2D").size
+ assert 7, c.fingerprint("MP2D").uniq.size
+ end
+
+ def test_fingerprint_count_neighbors
+ types = ["MP2D", "MNA"]
+ min_sim = 0.0
+ training_dataset = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.csv")
+ [
+ "CC(=O)CC(C)C#N",
+ "CC(=O)CC(C)C",
+ "C(=O)CC(C)C#N",
+ ].each do |smi|
+ c = OpenTox::Compound.from_smiles smi
+ types.each do |type|
+ neighbors = c.fingerprint_count_neighbors({:type => type, :training_dataset_id => training_dataset.id, :min_sim => min_sim})
+ if type == "FP4"
+ fp4_neighbors = c.neighbors
+ neighbors.each do |n|
+ assert_includes fp4_neighbors, n
+ end
+ end
+ end
+ end
+ end
+
+ def test_fingerprint_db_neighbors
+ skip
+ training_dataset = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.csv")
+ [
+ "CC(=O)CC(C)C#N",
+ "CC(=O)CC(C)C",
+ "C(=O)CC(C)C#N",
+ ].each do |smi|
+ c = OpenTox::Compound.from_smiles smi
+ neighbors = c.db_neighbors(:training_dataset_id => training_dataset.id, :min_sim => 0.2)
+ p neighbors
+ end
+ end
+end
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