From b7cd3ebbb858a8891c35c45896f1bdd525f3534e Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 10 Aug 2015 13:26:06 +0200
Subject: algorithm libraries added, fminer tests pass

---
 test/descriptor.rb | 83 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 83 insertions(+)
 create mode 100644 test/descriptor.rb

(limited to 'test/descriptor.rb')

diff --git a/test/descriptor.rb b/test/descriptor.rb
new file mode 100644
index 0000000..1143b87
--- /dev/null
+++ b/test/descriptor.rb
@@ -0,0 +1,83 @@
+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"
+    s = Smarts.find_or_create_by(:smarts => "FF")
+    result = OpenTox::Algorithm::Descriptor.smarts_match c, s
+    assert_equal [1], result
+    smarts = ["CC", "C", "C=C", "CO", "FF", "C1CCCC1", "NN"].collect{|s| Smarts.find_or_create_by(:smarts => s)}
+    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 [1.12518], result
+  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 = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
+    result = OpenTox::Algorithm::Descriptor.physchem c, ["Cdk.AtomCount"]
+    assert_equal [17], result
+    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 [1, 0, 0, 1, 0, 2, 1, 1, 0], result
+  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
+  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.size
+    assert_equal 30.8723, result[2]
+    assert_equal 1.12518, result[328]
+  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" ], true
+    assert_equal 12, result.last.size
+    assert_equal ["Openbabel.logP", "Cdk.AtomCount.nAtom", "Cdk.CarbonTypes.C1SP1", "Cdk.CarbonTypes.C2SP1", "Cdk.CarbonTypes.C1SP2", "Cdk.CarbonTypes.C2SP2", "Cdk.CarbonTypes.C3SP2", "Cdk.CarbonTypes.C1SP3", "Cdk.CarbonTypes.C2SP3", "Cdk.CarbonTypes.C3SP3", "Cdk.CarbonTypes.C4SP3", "Joelib.LogP"], result.first
+    assert_equal [1.12518, 17, 1, 0, 0, 1, 0, 2, 1, 1, 0, 2.65908], result.last
+  end
+
+  def test_dataset_descriptor_parameters
+    dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"hamster_carcinogenicity.mini.csv")
+    d = OpenTox::Algorithm::Descriptor.physchem dataset, [ "Openbabel.logP", "Cdk.AtomCount", "Cdk.CarbonTypes", "Joelib.LogP" ]
+    assert_kind_of Dataset, d
+    assert_equal dataset.compounds, d.compounds
+    assert_equal dataset.compounds.size, d.data_entries.size
+    assert_equal 12, d.data_entries.first.size
+  end
+
+end
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