From d63b4729dc3af22c40e40b06d768ec24f8cdda4b Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Tue, 22 Aug 2017 19:41:21 +0200
Subject: initial commit

---
 lib/toxtree.rb  | 97 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 test/toxtree.rb | 20 ++++++++++++
 2 files changed, 117 insertions(+)
 create mode 100644 lib/toxtree.rb
 create mode 100644 test/toxtree.rb

diff --git a/lib/toxtree.rb b/lib/toxtree.rb
new file mode 100644
index 0000000..3234f6a
--- /dev/null
+++ b/lib/toxtree.rb
@@ -0,0 +1,97 @@
+require 'csv'
+require 'tempfile'
+
+class Toxtree
+  RULES = {
+#toxtree.plugins.lewis.LewisTree
+#toxtree.plugins.moa.MOARules
+#toxtree.plugins.search.CompoundLookup
+#toxtree.plugins.smartcyp.rules.SMARTCYPRuleHigherRank
+#toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank1
+#toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank2
+#toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank3
+    "Cramer rules" => {
+      :java_class => "toxTree.tree.cramer.CramerRules",
+      :url => "http://toxtree.sourceforge.net/cramer.html"
+    },
+    "Cramer rules with extensions" => {
+      :java_class => "cramer2.CramerRulesWithExtensions",
+      :url => ""
+    },
+    "Verhaar scheme" => {
+      :java_class => "verhaar.VerhaarScheme",
+    },
+    "Modified Verhaar scheme" => {
+      :java_class => "toxtree.plugins.verhaar2.VerhaarScheme2",
+    },
+    "Skin irritation" => {
+      :java_class => "sicret.SicretRules",
+    },
+    "Eye irritation" => {
+      :java_class => "eye.EyeIrritationRules",
+    },
+    "START biodegradation and persistence" => {
+      :java_class => "com.molecularnetworks.start.BiodgeradationRules",
+    },
+    "Benigni / Bossa rulebase for mutagenicity and carcinogenicity" => {
+      :java_class => "mutant.BB_CarcMutRules",
+    },
+    "In vitro mutagenicity (Ames test) alerts by ISS" => {
+      :java_class => "toxtree.plugins.ames.AmesMutagenicityRules",
+    },
+    "Structure Alerts for the in vivo micronucleus assay in rodents (ISSMIC)" => {
+      :java_class => "mic.MICRules",
+    },
+    "Structural Alerts for Functional Group Identification (ISSFUNC)" => {
+      :java_class => "toxtree.plugins.func.FuncRules",
+    },
+    "Structure Alerts for identification of Michael Acceptors" => {
+      :java_class => "michaelacceptors.MichaelAcceptorRules",
+    },
+    "Structure Alerts for skin sensitisation reactivity domains" => {
+      :java_class => "toxtree.plugins.skinsensitisation.SkinSensitisationPlugin",
+    },
+    "DNA binding alerts" => {
+      :java_class => "toxtree.plugins.dnabinding.DNABindingPlugin",
+    },
+    "Protein binding alerts" => {
+      :java_class => "toxtree.plugins.proteinbinding.ProteinBindingPlugin",
+    },
+    "Kroes TTC Decision tree" => {
+      :java_class => "toxtree.plugins.kroes.Kroes1Tree",
+    },
+    "SMARTCyp - Cytochrome P450-Mediated Drug Metabolism and metabolites prediction" => {
+      :java_class => "toxtree.plugins.smartcyp.SMARTCYPPlugin",
+    },
+
+  }
+
+  def self.predict smiles, rules="Cramer rules"
+    smiles = [smiles] unless smiles.is_a? Array
+    rules = [rules] unless rules.is_a? Array
+    predictions = []
+    input = Tempfile.new(["input",".csv"])
+    output = input.path.sub("input","result")
+    begin
+      input.write "SMILES\n"
+      input.write smiles.join("\n")
+      input.close
+      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
+        prediction.each do |line|
+          p = {"rule" => name}
+          header.each_with_index do |h,i|
+            p[h] = line[i] unless h == ""
+          end
+          predictions << p#{:smiles => line[0], :prediction => line[2], :rule => name}
+        end
+      end
+    ensure
+      input.unlink
+    end
+    predictions.size == 1 ? predictions[0] : predictions
+  end
+
+end
diff --git a/test/toxtree.rb b/test/toxtree.rb
new file mode 100644
index 0000000..9f67967
--- /dev/null
+++ b/test/toxtree.rb
@@ -0,0 +1,20 @@
+require 'json'
+require 'minitest/autorun'
+require_relative '../lib/toxtree.rb'
+
+class ToxtreeTest < MiniTest::Test
+  def test_cramer
+    skip
+    assert_equal Toxtree.predict("c1ccccc1NN"), {:smiles=>"c1ccccc1NN", :prediction=>"High (Class III)", :rule=>"Cramer rules"}
+  end
+  def test_all_rules
+    smiles = ["c1ccccc1NN","c1ccccc1N","CCC(CC)CC#N"]
+    Toxtree::RULES.each do |name,rule|
+      puts JSON.pretty_generate(Toxtree.predict(smiles,name))
+    end
+  end
+  def test_urls
+    skip
+  end
+end
+
-- 
cgit v1.2.3