molecular_weight fixed

1 files changed, 5 insertions, 88 deletions

diff --git a/test/compound.rb b/test/compound.rb
index c78acb1..76471ac 100644
--- a/test/compound.rb
+++ b/test/compound.rb
@@ -2,19 +2,16 @@ require_relative "setup.rb"
 
 class CompoundTest < MiniTest::Test
 
-  def test_0_compound_from_smiles
+  def test_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c.smiles, "A failure here might be caused by a compound webservice running on 64bit architectures using an outdated version of OpenBabel.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
+  def test_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
@@ -79,22 +76,6 @@ print c.sdf
     assert_equal 9, c.fingerprint("FP4").size
   end
 
-  def test_neighbors
-    d = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM_log10.csv")
-    d.compounds.each do |c|
-      refute_nil c.fingerprint("MP2D")
-    end
-    c = d.compounds[371]
-    n = c.neighbors(
-      descriptors: {:method => "fingerprint", :type => "FP4"},
-      similarity: {:method => "Algorithm::Similarity.tanimoto", :min => 0.7},
-      dataset_id: d.id,
-      prediction_feature_id: d.features.first.id 
-    )
-
-    assert n.size >= 8, "Neighbors size (#{n.size}) should be larger than 7"
-  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"
 
@@ -113,30 +94,6 @@ print c.sdf
     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_log10.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(
-          descriptors: {:method => "fingerprint",:type => type},
-          dataset_id: training_dataset.id,
-          similarity: {:method => "Algorithm::Similarity.tanimoto", :min => min_sim},
-          prediction_feature_id: training_dataset.features.first.id
-        )
-        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
@@ -149,47 +106,6 @@ print c.sdf
     assert 7, c.fingerprint("MP2D").uniq.size
   end
 
-  def test_fingerprint_count_neighbors
-    skip
-    types = ["MP2D", "MNA"]
-    min_sim = 0.0
-    training_dataset = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM_log10.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, :dataset_id => training_dataset.id, :min_sim => min_sim, :prediction_feature_id => training_dataset.features.first.id})
-        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_log10.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(:dataset_id => training_dataset.id, :min_sim => 0.2)
-      neighbors2 = c.fingerprint_neighbors({:type => "MP2D", :dataset_id => training_dataset.id, :min_sim => 0.2, :prediction_feature_id => training_dataset.features.first.id})
-      #p neighbors
-      #p neighbors2
-      #p neighbors2 - neighbors
-      assert_equal neighbors, neighbors2
-    end
-  end
-
   def test_molecular_weight
     c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C"
     assert_equal 100.15888, c.molecular_weight
@@ -208,8 +124,9 @@ print c.sdf
 
   def test_physchem
     c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C"
-    assert_equal PhysChem::OBDESCRIPTORS.size, c.calculated_physchem.size
-    assert_equal PhysChem::OBDESCRIPTORS.size, c.calculated_physchem(PhysChem.openbabel_descriptors).size
+    p c.calculated_properties
+    assert_equal PhysChem::OPENBABEL.size, c.calculated_properties.size
+    assert_equal PhysChem::OPENBABEL.size, c.calculated_properties(PhysChem.openbabel_descriptors).size
     assert_equal PhysChem::unique_descriptors.size, c.calculated_physchem(PhysChem.unique_descriptors).size
   end
 end