From 23ecfc6fa5ae4913e5cd17b7d58432d1f88d780c Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 10 Aug 2015 09:48:57 +0200
Subject: transfer to new git project started

---
 test/compound.rb | 93 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 93 insertions(+)
 create mode 100644 test/compound.rb

(limited to 'test/compound.rb')

diff --git a/test/compound.rb b/test/compound.rb
new file mode 100644
index 0000000..7bbba58
--- /dev/null
+++ b/test/compound.rb
@@ -0,0 +1,93 @@
+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
+    assert_equal "[B-](F)(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c.smiles, "A failure here might be caused by a compound webservice running on 64bit architectures using an outdated version of OpenBabel.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(CC(=O)C)C#N", 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 "c1ccc(cc1)[N+]#N.[B-](F)(F)(F)F", 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"
+    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
+
+  # OpenBabel segfaults randomly during inchikey calculation
+  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 "data/EPAFHM.csv"
+    d.compounds.each do |c|
+      refute_nil c.fp4
+    end
+    c = d.compounds[371]
+    assert_equal 19, c.neighbors.size
+  end
+
+end
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