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|
include OpenTox
configure :production do
$logger = Logger.new(STDOUT)
enable :reloader
end
configure :development do
$logger = Logger.new(STDOUT)
enable :reloader
end
before do
@version = File.read("VERSION").chomp
end
not_found do
redirect to('/predict')
end
error do
@error = request.env['sinatra.error']
haml :error
end
helpers do
def embedded_svg image, options={}
doc = Nokogiri::HTML::DocumentFragment.parse image
svg = doc.at_css 'svg'
title = doc.at_css 'title'
if options[:class].present?
svg['class'] = options[:class]
end
if options[:title].present?
title.children.remove
text_node = Nokogiri::XML::Text.new(options[:title], doc)
title.add_child(text_node)
end
doc.to_html.html_safe
end
def to_csv(m,predictions,compounds)
model = (m != "Cramer" ? Model::Validation.find(m.to_s) : "Cramer")
csv = ""
if model == "Cramer"
compounds = compounds.collect{|c| c.smiles}
prediction = [Toxtree.predict(compounds, "Cramer rules"), Toxtree.predict(compounds, "Cramer rules with extensions")]
output = {}
output["model_name"] = "Oral toxicity (Cramer rules)"
output["model_type"] = false
output["model_unit"] = false
["measurements", "converted_measurements", "prediction_value", "converted_value", "interval", "converted_interval", "probability", "db_hit", "warnings", "info", "toxtree", "sa_prediction", "sa_matches", "confidence"].each do |key|
output["#{key}"] = false
end
output["toxtree"] = true
output["cramer_rules"] = prediction.collect{|array| array.collect{|hash| hash["Cramer rules"]}}.flatten.compact
output["cramer_rules_extensions"] = prediction.collect{|array| array.collect{|hash| hash["Cramer rules, with extensions"]}}.flatten.compact
# header
csv = "ID,Endpoint,Unique SMILES,Cramer rules,Cramer rules with extensions\n"
compounds.each_with_index do |smiles, idx|
csv << "#{idx+1},#{output["model_name"]},#{smiles},"\
"#{output["cramer_rules"][idx] != "nil" ? output["cramer_rules"][idx] : "none" },"\
"#{output["cramer_rules_extensions"][idx] != "nil" ? output["cramer_rules_extensions"][idx] : "none"}\n"
end
else
output = {}
predictions.each_with_index do |prediction,idx|
compound = compounds[idx]
line = ""
output["model_name"] = "#{model.endpoint.gsub('_', ' ')} (#{model.species})"
output["model_type"] = model.model.class.to_s.match("Classification") ? type = "Classification" : type = "Regression"
output["model_unit"] = (type == "Regression") ? "(#{model.unit})" : ""
output["converted_model_unit"] = (type == "Regression") ? "#{model.unit =~ /\b(mmol\/L)\b/ ? "(mg/L)" : "(mg/kg_bw/day)"}" : ""
["measurements", "converted_measurements", "prediction_value", "converted_value", "interval", "converted_interval", "probability", "db_hit", "warnings", "info", "toxtree", "sa_prediction", "sa_matches", "confidence"].each do |key|
output["#{key}"] = false
end
if prediction[:value]
inApp = (prediction[:warnings].join(" ") =~ /Cannot/ ? "no" : (prediction[:warnings].join(" ") =~ /may|Insufficient/ ? "maybe" : "yes"))
if prediction[:info] =~ /\b(identical)\b/i
prediction[:info] = "This compound was part of the training dataset. All information "\
"from this compound was removed from the training data before the "\
"prediction, to obtain unbiased results."
end
note = "\"#{prediction[:warnings].uniq.join(" ")}\""
output["prediction_value"] = (type == "Regression") ? "#{prediction[:value].delog10.signif(3)}" : "#{prediction[:value]}"
output["converted_value"] = "#{compound.mmol_to_mg(prediction[:value].delog10).signif(3)}" if type == "Regression"
output["db_hit"] = prediction[:info] if prediction[:info]
if prediction[:measurements].is_a?(Array)
output["measurements"] = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10.signif(3)} (#{model.unit})"} : prediction[:measurements].collect{|value| "#{value}"}
output["converted_measurements"] = (type == "Regression") ? prediction[:measurements].collect{|value| "#{compound.mmol_to_mg(value.delog10).signif(3)} #{model.unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"} : false
else
output["measurements"] = (type == "Regression") ? "#{prediction[:measurements].delog10.signif(3)} (#{model.unit})}" : "#{prediction[:measurements]}"
output["converted_measurements"] = (type == "Regression") ? "#{compound.mmol_to_mg(prediction[:measurements].delog10).signif(3)} #{(model.unit =~ /\b(mmol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : false
end #db_hit
if type == "Regression"
if !prediction[:prediction_interval].nil?
interval = prediction[:prediction_interval]
output['interval'] = "#{interval[1].delog10.signif(3)} - #{interval[0].delog10.signif(3)}"
output['converted_interval'] = "#{compound.mmol_to_mg(interval[1].delog10).signif(3)} - #{compound.mmol_to_mg(interval[0].delog10).signif(3)}"
end #prediction interval
line += "#{idx+1},#{output['model_name']},#{compound.smiles},"\
"\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{prediction[:measurements].join("; ") if prediction[:info]}\","\
"#{output['prediction_value'] != false ? output['prediction_value'] : ""},"\
"#{output['converted_value'] != false ? output['converted_value'] : ""},"\
"#{output['interval'].split(" - ").first.strip unless output['interval'] == false},"\
"#{output['interval'].split(" - ").last.strip unless output['interval'] == false},"\
"#{output['converted_interval'].split(" - ").first.strip unless output['converted_interval'] == false},"\
"#{output['converted_interval'].split(" - ").last.strip unless output['converted_interval'] == false},"\
"#{inApp},#{note.nil? ? "" : note.chomp}\n"
else # Classification
# consensus mutagenicity
sa_prediction = KaziusAlerts.predict(compound.smiles)
lazar_mutagenicity = prediction
confidence = 0
lazar_mutagenicity_val = (lazar_mutagenicity[:value] == "non-mutagenic" ? false : true)
if sa_prediction[:prediction] == false && lazar_mutagenicity_val == false
confidence = 0.85
elsif sa_prediction[:prediction] == true && lazar_mutagenicity_val == true
confidence = 0.85 * ( 1 - sa_prediction[:error_product] )
elsif sa_prediction[:prediction] == false && lazar_mutagenicity_val == true
confidence = 0.11
elsif sa_prediction[:prediction] == true && lazar_mutagenicity_val == false
confidence = ( 1 - sa_prediction[:error_product] ) - 0.57
end
output['sa_prediction'] = sa_prediction
output['sa_matches'] = sa_prediction[:matches].collect{|a| a.first}.join("; ") unless sa_prediction[:matches].blank?
output['confidence'] = confidence.signif(3)
output['model_name'] = "Lazar #{model.endpoint.gsub('_', ' ').downcase} (#{model.species}):"
output['probability'] = prediction[:probabilities] ? prediction[:probabilities].collect{|k,v| "#{k}: #{v.signif(3)}"} : false
line += "#{idx+1},Consensus mutagenicity,#{compound.smiles},"\
"\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{prediction[:measurements].join("; ") if prediction[:info]}\","\
"#{sa_prediction[:prediction] == false ? "non-mutagenic" : "mutagenic"},"\
"#{output['confidence']},#{output['sa_matches'] != false ? "\"#{output['sa_matches']}\"" : "none"},"\
"#{output['prediction_value']},"\
"#{output['probability'][0] != false ? output['probability'][0].split(":").last : ""},"\
"#{output['probability'][1] != false ? output['probability'][1].split(":").last : ""},"\
"#{inApp},#{note.nil? ? "" : note}\n"
end
output["warnings"] = prediction[:warnings] if prediction[:warnings]
else #no prediction value
inApp = "no"
if prediction[:info] =~ /\b(identical)\b/i
prediction[:info] = "This compound was part of the training dataset. All information "\
"from this compound was removed from the training data before the "\
"prediction, to obtain unbiased results."
end
note = "\"#{prediction[:warnings].join(" ")}\""
output["warnings"] = prediction[:warnings]
output["info"] = prediction[:info] if prediction[:info]
if type == "Regression"
line += "#{idx+1},#{output['model_name']},#{compound.smiles},#{prediction[:info] ? prediction[:info] : "no"},"\
"#{prediction[:measurements] if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n"
else
line += "#{idx+1},Consensus mutagenicity,#{compound.smiles},#{prediction[:info] ? prediction[:info] : "no"},"\
"#{prediction[:measurements] if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n"
end
end
csv += line
end
csv
end
end
end
get '/?' do
redirect to('/predict')
end
get '/predict/?' do
@models = Model::Validation.all
@models = @models.delete_if{|m| m.model.name =~ /\b(Net cell association)\b/}
@endpoints = @models.collect{|m| m.endpoint}.sort.uniq
@endpoints << "Oral toxicity (Cramer rules)"
@models.count <= 0 ? (haml :info) : (haml :predict)
end
get '/task/?' do
if params[:turi]
task = Task.find(params[:turi].to_s)
return JSON.pretty_generate(:percent => task.percent)
elsif params[:predictions]
pageSize = params[:pageSize].to_i - 1
pageNumber= params[:pageNumber].to_i - 1
compound = Compound.find @@compounds_ids[pageNumber]
image = compound.svg
smiles = compound.smiles
task = Task.find(params[:predictions].to_s)
unless task.predictions[params[:model]].nil?
if params[:model] == "Cramer"
prediction = task.predictions[params[:model]]
html = "<table class=\"table table-bordered single-batch\"><tr>"
html += "<td>#{image}</br>#{smiles}</br></td>"
string = "<td><table class=\"table\">"
string += "<tr class=\"hide-top\"><td>Cramer rules:</td><td>#{prediction["Cramer rules"][pageNumber.to_i]}</td>"
string += "<tr><td>Cramer rules, with extensions:</td><td>#{prediction["Cramer rules, with extensions"][pageNumber.to_i]}</td>"
string += "</table></td>"
html += "#{string}</tr></table>"
else
html = "<table class=\"table table-bordered single-batch\"><tr>"
html += "<td>#{image}</br>#{smiles}</br></td>"
string = "<td><table class=\"table\">"
prediction = task.predictions[params[:model]][pageNumber.to_i]
sorter = []
$logger.debug prediction
if prediction[:info]
sorter << {"Info" => prediction[:info]}
if prediction[:measurements_string].kind_of?(Array)
sorter << {"Measured activity" => "#{prediction[:measurements_string].join(";")}</br>#{prediction[:converted_measurements].join(";")}"}
else
sorter << {"Measured activity" => "#{prediction[:measurements_string]}</br>#{prediction[:converted_measurements]}"}
end
end
# regression
if prediction[:prediction_interval]
sorter << {"Prediction" => "#{prediction[:prediction_value]}</br>#{prediction[:converted_prediction_value]}"}
sorter << {"95% Prediction interval" => "#{prediction[:interval]}</br>#{prediction[:converted_interval]}"}
sorter << {"Warnings" => prediction[:warnings].join("</br>")}
# classification
elsif prediction[:probabilities]
sorter << {"Consensus prediction" => prediction["Consensus prediction"]}
sorter << {"Consensus confidence" => prediction["Consensus confidence"]}
sorter << {"Structural alerts for mutagenicity" => prediction["Structural alerts for mutagenicity"]}
sorter << {"Lazar mutagenicity (Salmonella typhimurium)" => ""}
sorter << {"Prediction" => prediction[:value]}
sorter << {"Probability" => prediction[:probabilities].collect{|k,v| "#{k}: #{v.signif(3)}"}.join("</br>")}
else
sorter << {"Warnings" => prediction[:warnings].join("</br>")}
end
sorter.each_with_index do |hash,idx|
k = hash.keys[0]
v = hash.values[0]
string += (idx == 0 ? "<tr class=\"hide-top\">" : "<tr>")+(k =~ /lazar/i ? "<td colspan=\"2\">" : "<td>")
# keyword
string += "#{k}:"
string += "</td><td>"
# values
string += "#{v}"
string += "</td></tr>"
end
string += "</table></td>"
html += "#{string}</tr></table>"
end
end
return JSON.pretty_generate(:predictions => [html])
end
end
get '/predict/modeldetails/:model' do
model = Model::Validation.find params[:model]
crossvalidations = Validation::RepeatedCrossValidation.find(model.repeated_crossvalidation_id).crossvalidations
return haml :model_details, :layout=> false, :locals => {:model => model, :crossvalidations => crossvalidations}
end
get '/jme_help/?' do
File.read(File.join('views','jme_help.html'))
end
get '/predict/dataset/:name' do
response['Content-Type'] = "text/csv"
dataset = Dataset.find_by(:name=>params[:name])
csv = dataset.to_csv
csv
end
get '/predict/csv/:task/:model/:filename/?' do
response['Content-Type'] = "text/csv"
task = Task.find params[:task].to_s
tempfile = Tempfile.new
tempfile.write(task.csv)
tempfile.rewind
send_file tempfile, :filename => "#{Time.now.strftime("%Y-%m-%d")}_lazar_batch_prediction_#{params[:model]}_#{params[:filename]}", :type => "text/csv", :disposition => "attachment"
end
post '/predict/?' do
# process batch prediction
if !params[:fileselect].blank?
if params[:fileselect][:filename] !~ /\.csv$/
bad_request_error "Please submit a csv file."
end
File.open('tmp/' + params[:fileselect][:filename], "w") do |f|
f.write(params[:fileselect][:tempfile].read)
end
@filename = params[:fileselect][:filename]
begin
input = Dataset.from_csv_file File.join("tmp", params[:fileselect][:filename]), true
$logger.debug "save dataset #{params[:fileselect][:filename]}"
if input.class == OpenTox::Dataset
@dataset = Dataset.find input
@compounds = @dataset.compounds
else
bad_request_error "Could not serialize file '#{@filename}'."
end
rescue
bad_request_error "Could not serialize file '#{@filename}'."
end
if @compounds.size == 0
message = dataset[:warnings]
@dataset.delete
bad_request_error message
end
@models = params[:selection].keys
# for single predictions in batch
@@compounds_ids = @compounds.collect{|c| c.id.to_s}
@tasks = []
@models.each{|m| t = Task.new; t.save; @tasks << t}
@predictions = {}
task = Task.run do
@models.each_with_index do |model,idx|
t = @tasks[idx]
unless model == "Cramer"
m = Model::Validation.find model
type = (m.regression? ? "Regression" : "Classification")
# add header for regression
if type == "Regression"
unit = (type == "Regression") ? "(#{m.unit})" : ""
converted_unit = (type == "Regression") ? "#{m.unit =~ /\b(mmol\/L)\b/ ? "(mg/L)" : "(mg/kg_bw/day)"}" : ""
header = "ID,Endpoint,Unique SMILES,inTrainingSet,Measurements,Prediction #{unit},Prediction #{converted_unit},"\
"Prediction Interval Low #{unit},Prediction Interval High #{unit},"\
"Prediction Interval Low #{converted_unit},Prediction Interval High #{converted_unit},"\
"inApplicabilityDomain,Note\n"
end
# add header for classification
if type == "Classification"
av = m.prediction_feature.accept_values
header = "ID,Endpoint,Unique SMILES,inTrainingSet,Measurements,Consensus Prediction,Consensus Confidence,"\
"Structural alerts for mutagenicity,Lazar Prediction,"\
"Lazar predProbability #{av[0]},Lazar predProbability #{av[1]},inApplicabilityDomain,Note\n"
end
# predict compounds
p = 100.0/@compounds.size
counter = 1
predictions = []
@compounds.each do |compound|
prediction = m.predict(compound)
if type == "Classification"# consensus mutagenicity
sa_prediction = KaziusAlerts.predict(compound.smiles)
lazar_mutagenicity = prediction
confidence = 0
lazar_mutagenicity_val = (lazar_mutagenicity[:value] == "non-mutagenic" ? false : true)
if sa_prediction[:prediction] == false && lazar_mutagenicity_val == false
confidence = 0.85
elsif sa_prediction[:prediction] == true && lazar_mutagenicity_val == true
confidence = 0.85 * ( 1 - sa_prediction[:error_product] )
elsif sa_prediction[:prediction] == false && lazar_mutagenicity_val == true
confidence = 0.11
elsif sa_prediction[:prediction] == true && lazar_mutagenicity_val == false
confidence = ( 1 - sa_prediction[:error_product] ) - 0.57
end
prediction["Consensus prediction"] = sa_prediction[:prediction] == false ? "non-mutagenic" : "mutagenic"
prediction["Consensus confidence"] = confidence.signif(3)
prediction["Structural alerts for mutagenicity"] = sa_prediction[:matches].blank? ? "none" : sa_prediction[:matches].collect{|a| a.first}.join("; ")
end
# regression
unless prediction[:value].blank?
if type == "Regression"
prediction[:prediction_value] = "#{prediction[:value].delog10.signif(3)} #{unit}"
prediction["converted_prediction_value"] = "#{compound.mmol_to_mg(prediction[:value].delog10).signif(3)} #{converted_unit}"
end
end
unless prediction[:prediction_interval].blank?
interval = prediction[:prediction_interval]
prediction[:interval] = "#{interval[1].delog10.signif(3)} - #{interval[0].delog10.signif(3)} #{unit}"
prediction[:converted_interval] = "#{compound.mmol_to_mg(interval[1].delog10).signif(3)} - #{compound.mmol_to_mg(interval[0].delog10).signif(3)} #{converted_unit}"
end
prediction["unit"] = unit
prediction["converted_unit"] = converted_unit
if prediction[:measurements].is_a?(Array)
prediction["measurements_string"] = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10.signif(3)} #{unit}"} : prediction[:measurements].join("</br>")
prediction["converted_measurements"] = prediction[:measurements].collect{|value| "#{compound.mmol_to_mg(value.delog10).signif(3)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"} if type == "Regression"
else
output["measurements_string"] = (type == "Regression") ? "#{prediction[:measurements].delog10.signif(3)} #{unit}}" : prediction[:measurements]
output["converted_measurements"] = "#{compound.mmol_to_mg(prediction[:measurements].delog10).signif(3)} #{(unit =~ /\b(mmol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if type == "Regression"
end
predictions << prediction.delete_if{|k,v| k =~ /neighbors|prediction_feature_id|r_squared|rmse/i}
t.update_percent((counter*p).ceil)
counter += 1
end
# write csv
t[:csv] = header + to_csv(model,predictions,@compounds)
# write predictions
@predictions["#{model}"] = predictions
else # Cramer model
#t[:csv] = to_csv(model,nil,@compounds)
compounds = @compounds.collect{|c| c.smiles}
prediction = [Toxtree.predict(compounds, "Cramer rules"), Toxtree.predict(compounds, "Cramer rules with extensions")]
output = {}
output["model_name"] = "Oral toxicity (Cramer rules)"
output["cramer_rules"] = prediction.collect{|array| array.collect{|hash| hash["Cramer rules"]}}.flatten.compact
output["cramer_rules_extensions"] = prediction.collect{|array| array.collect{|hash| hash["Cramer rules, with extensions"]}}.flatten.compact
# header
csv = "ID,Endpoint,Unique SMILES,Cramer rules,Cramer rules with extensions\n"
# content
compounds.each_with_index do |smiles, idx|
csv << "#{idx+1},#{output["model_name"]},#{smiles},"\
"#{output["cramer_rules"][idx] != "nil" ? output["cramer_rules"][idx] : "none" },"\
"#{output["cramer_rules_extensions"][idx] != "nil" ? output["cramer_rules_extensions"][idx] : "none"}\n"
end
#predictions = []
#predictions << {"Cramer rules" => output["cramer_rules"]}
#predictions << {"Cramer rules, with extensions" => output["cramer_rules_extensions"]}
predictions = {}
predictions["Cramer rules"] = output["cramer_rules"].collect{|rule| rule != "nil" ? rule : "none"}
predictions["Cramer rules, with extensions"] = output["cramer_rules_extensions"].collect{|rule| rule != "nil" ? rule : "none"}
# write csv
t[:csv] = csv
# write predictions
@predictions["#{model}"] = predictions
t.update_percent(100)
end
# save task
# append predictions as last action otherwise they won't save
# mongoid works with shallow copy via #dup
t[:predictions] = @predictions
t.save
end#models
end#main task
File.delete File.join("tmp", params[:fileselect][:filename])
return haml :task
end
# single compound prediction
# validate identifier input
if !params[:identifier].blank?
@identifier = params[:identifier].strip
$logger.debug "input:#{@identifier}"
# get compound from SMILES
@compound = Compound.from_smiles @identifier
bad_request_error "'#{@identifier}' is not a valid SMILES string." if @compound.blank?
@models = []
@predictions = []
@toxtree = false
params[:selection].keys.each do |model_id|
if model_id == "Cramer"
@toxtree = true
@predictions << [Toxtree.predict(@compound.smiles, "Cramer rules"), Toxtree.predict(@compound.smiles, "Cramer rules with extensions")]
else
model = Model::Validation.find model_id
@models << model
if model.model.name =~ /kazius/
sa_prediction = KaziusAlerts.predict(@compound.smiles)
lazar_mutagenicity = model.predict(@compound)
confidence = 0
lazar_mutagenicity_val = (lazar_mutagenicity[:value] == "non-mutagenic" ? false : true)
if sa_prediction[:prediction] == false && lazar_mutagenicity_val == false
confidence = 0.85
elsif sa_prediction[:prediction] == true && lazar_mutagenicity_val == true
confidence = 0.85 * ( 1 - sa_prediction[:error_product] )
elsif sa_prediction[:prediction] == false && lazar_mutagenicity_val == true
confidence = 0.11
elsif sa_prediction[:prediction] == true && lazar_mutagenicity_val == false
confidence = ( 1 - sa_prediction[:error_product] ) - 0.57
end
@predictions << [lazar_mutagenicity, {:prediction => sa_prediction, :confidence => confidence}]
else
@predictions << model.predict(@compound)
end
end
end
haml :prediction
end
end
get '/style.css' do
headers 'Content-Type' => 'text/css; charset=utf-8'
scss :style
end
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