Class: Toxtree

Inherits:
Object
  • Object
show all
Defined in:
lib/toxtree.rb

Constant Summary collapse

RULES = 
{
  "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",
  },

}

Class Method Summary collapse

Class Method Details

.predict(smiles, rules = "Cramer rules") ⇒ Object 



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# File 'lib/toxtree.rb', line 62

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
      header.pop # remove last empty element
      prediction.each do |line|
        p = {"rule" => name}
        header.each_with_index do |h,i|
          p[h] = line[i]
        end
        predictions << p
      end
    end
  ensure
    input.unlink
  end
  predictions.size == 1 ? predictions[0] : predictions
end