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require 'csv'
require 'tempfile'
class Toxtree
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",
},
}
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
end
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