initial k-nn weighted average implementation, validation test added

3 files changed, 30 insertions, 1 deletions

diff --git a/test/compound.rb b/test/compound.rb
index 86930b6..2bf0204 100644
--- a/test/compound.rb
+++ b/test/compound.rb
@@ -74,4 +74,20 @@ class CompoundTest < MiniTest::Test
     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]
+    #p c
+    p c.neighbors
+  end
+
 end
diff --git a/test/setup.rb b/test/setup.rb
index cfa670d..d8f05d5 100644
--- a/test/setup.rb
+++ b/test/setup.rb
@@ -2,7 +2,7 @@ require 'minitest/autorun'
 require 'bundler'
 Bundler.require
 require 'opentox-client'
-require File.join(ENV["HOME"],".opentox","config","test.rb")
+#require File.join(ENV["HOME"],".opentox","config","test.rb")
 
 include OpenTox
 TEST_DIR ||= File.expand_path(File.dirname(__FILE__))
diff --git a/test/validation.rb b/test/validation.rb
new file mode 100644
index 0000000..80055f2
--- /dev/null
+++ b/test/validation.rb
@@ -0,0 +1,13 @@
+require_relative "setup.rb"
+
+class ValidationTest < MiniTest::Test
+
+  def test_classification_crossvalidation
+    dataset = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv"
+    features = Algorithm::Fminer.bbrc dataset
+    model = Model::Lazar.create dataset, features
+    cv = CrossValidation.create model
+    p cv
+  end
+
+end