From 6ac119c32cef094d4f1c2fb5c2daa4e274401f70 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 17 Sep 2015 14:56:25 +0200
Subject: neighbor calculation moved to Compound class

---
 test/compound.rb   | 26 ++++++++++++++++++++++++++
 test/experiment.rb | 31 +++++++++++++++++++++++++++++--
 2 files changed, 55 insertions(+), 2 deletions(-)

(limited to 'test')

diff --git a/test/compound.rb b/test/compound.rb
index 6deba4e..6a3c696 100644
--- a/test/compound.rb
+++ b/test/compound.rb
@@ -108,4 +108,30 @@ print c.sdf
       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
diff --git a/test/experiment.rb b/test/experiment.rb
index cad4fa7..4b54768 100644
--- a/test/experiment.rb
+++ b/test/experiment.rb
@@ -18,7 +18,7 @@ class ExperimentTest < MiniTest::Test
         }
       ]
     )
-    experiment.run
+    #experiment.run
     puts experiment.report.to_yaml
     assert_equal datasets.size, experiment.results.size
     experiment.results.each do |dataset_id, result|
@@ -48,7 +48,7 @@ class ExperimentTest < MiniTest::Test
         #}
       ]
     )
-    experiment.run
+    #experiment.run
 =begin
     experiment = Experiment.find "55f944a22b72ed7de2000000"
 =end
@@ -61,4 +61,31 @@ class ExperimentTest < MiniTest::Test
       end
     end
   end
+
+  def test_regression_fingerprints
+    datasets = [
+      "LOAEL_mmol_corrected_smiles.csv"
+    ]
+    min_sims = [0.3,0.7]
+    types = ["FP2","FP3","FP4","MACCS"]
+    experiment = Experiment.create(
+      :name => "Fminer vs fingerprint classification for datasets #{datasets}.",
+      :dataset_ids => datasets.collect{|d| Dataset.from_csv_file(File.join(DATA_DIR, d)).id},
+    )
+    types.each do |type|
+      min_sims.each do |min_sim|
+        experiment.model_settings << {
+          :algorithm => "OpenTox::Model::LazarRegression",
+          :neighbor_algorithm => "fingerprint_neighbors",
+          :neighbor_algorithm_parameter => {
+            :type => type,
+            :min_sim => min_sim,
+          }
+        }
+      end
+    end
+    experiment.run
+    p experiment.report
+
+  end
 end
-- 
cgit v1.2.3