From a361230e88d7abe6b61139467e1514578399da87 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Thu, 12 Oct 2017 11:04:30 +0000
Subject: changes to catch unpredictable compounds

---
 lib/toxtree.rb  | 24 +++++++++++++++++-------
 test/toxtree.rb | 14 ++++++++++++++
 2 files changed, 31 insertions(+), 7 deletions(-)

diff --git a/lib/toxtree.rb b/lib/toxtree.rb
index f395968..3677071 100644
--- a/lib/toxtree.rb
+++ b/lib/toxtree.rb
@@ -72,14 +72,24 @@ class Toxtree
       rules.each do |name|
         `cd #{File.join(File.dirname(__FILE__),"..","Toxtree-v2.6.13","Toxtree")}; java -jar Toxtree-2.6.13.jar -i #{input.path} -m #{RULES[name][:java_class]} -n -o #{output}`
         prediction = CSV.read(output)
-        header = prediction.shift
-        header.pop # remove last empty element
-        prediction.each do |line|
-          p = {"rule" => name}
-          header.each_with_index do |h,i|
-            p[h] = line[i]
+        unless prediction.empty?
+          header = prediction.shift
+          header.pop # remove last empty element
+          smiles.each do |smi|
+            line = prediction.flatten.include?(smi) ? prediction.find{|array| array[0 ]== smi} : ["nil","nil","nil","nil"]
+            p = {"rule" => name}
+            header.each_with_index do |h,i|
+              p[h] = line[i]
+            end
+            predictions << p
+          end
+        else
+          smiles.each do |smi|
+            p = {"rule" => name}
+            p["SMILES"] = smi
+            p[name] = nil
+            predictions << p
           end
-          predictions << p
         end
       end
     ensure
diff --git a/test/toxtree.rb b/test/toxtree.rb
index b1d6274..772eee8 100644
--- a/test/toxtree.rb
+++ b/test/toxtree.rb
@@ -22,5 +22,19 @@ class ToxtreeTest < MiniTest::Test
     skip
   end
 
+  def test_no_prediction
+    assert_equal Toxtree.predict("O=S(=O)(Oc1ccccc1)CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCS(=O)(=O)Oc1ccccc1"), {"rule"=>"Cramer rules", "SMILES"=>"O=S(=O)(Oc1ccccc1)CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCS(=O)(=O)Oc1ccccc1", "Cramer rules"=>nil}
+  end
+
+  def test_no_prediction_array
+    assert_equal Toxtree.predict(["O=S(=O)(Oc1ccccc1)CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCS(=O)(=O)Oc1ccccc1","O=S(=O)(Oc1ccccc1)CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCS(=O)(=O)Oc1ccccc1"]), [{"rule"=>"Cramer rules", "SMILES"=>"O=S(=O)(Oc1ccccc1)CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCS(=O)(=O)Oc1ccccc1", "Cramer rules"=>nil}, {"rule"=>"Cramer rules", "SMILES"=>"O=S(=O)(Oc1ccccc1)CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCS(=O)(=O)Oc1ccccc1", "Cramer rules"=>nil}]
+  end
+
+  def test_with_and_without_prediction_array
+    predictions = Toxtree.predict(["c1ccccc1NN","O=S(=O)(Oc1ccccc1)CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCS(=O)(=O)Oc1ccccc1"])
+    assert_equal predictions.size, 2
+    assert_equal predictions, [{"rule"=>"Cramer rules", "SMILES"=>"c1ccccc1NN", "CRAMERFLAGS"=>nil, "Cramer rules"=>"High (Class III)", "toxTree.tree.cramer.CramerTreeResult"=>"1N,2N,3N,5N,6N,7N,16N,17N,19N,23Y,27Y,28N,30Y,31N,32N,22N,33N"}, {"rule"=>"Cramer rules", "SMILES"=>"nil", "CRAMERFLAGS"=>"nil", "Cramer rules"=>"nil", "toxTree.tree.cramer.CramerTreeResult"=>"nil"}]
+  end
+
 end
 
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