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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c.smiles, "A failure here might be caused by a compound webservice running on 64bit architectures using an outdated version of OpenBabel.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 c.fp4.collect{|fid| Feature.find(fid).name}.include? ("1,3-Tautomerizable")
assert_equal c.fp4.size, c.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.fp4
end
c = d.compounds[371]
n = c.neighbors
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
assert_equal c.openbabel_fingerprint("FP4").size, c.fp4.size
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
p c.smiles
types.each do |type|
p type
neighbors = c.fingerprint_neighbors({:type => type, :training_dataset_id => training_dataset.id, :min_sim => min_sim})
p neighbors.collect{|n| [Compound.find(n.first).smiles,n.last]}
if type == "FP4"
fp4_neighbors = c.neighbors
neighbors.each do |n|
p [Compound.find(n.first).smiles,n.last] unless fp4_neighbors.include?(n)
assert_includes fp4_neighbors, n
end
end
end
end
end
end
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