Module: OpenTox::Algorithm

Includes:
OpenTox
Included in:
Dataset, FeatureSelection, Fminer, Generic, Lazar, Substructure, Model::Lazar
Defined in:
lib/algorithm.rb,
lib/utils.rb

Overview

Wrapper for OpenTox Algorithms

Defined Under Namespace

Modules: Dataset, FeatureSelection, Neighbors, Similarity, Substructure Classes: BBRC, Fminer, Generic, LAST, Lazar, StructuralClustering

Instance Attribute Summary

Attributes included from OpenTox

#metadata, #uri

Class Method Summary collapse

Instance Method Summary collapse

Methods included from OpenTox

#add_metadata, all, #delete, #initialize, #load_metadata, sign_in, text_to_html

Class Method Details

.effect(occurrences, db_instances) ⇒ Object

Effect calculation for classification

Parameters:

  • Array (Array) —

    of occurrences per class in the form of Enumerables.

  • Array (Array) —

    of database instance counts per class.



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# File 'lib/utils.rb', line 214

def self.effect(occurrences, db_instances)
  max=0
  max_value=0
  nr_o = self.sum_size(occurrences)
  nr_db = db_instances.to_scale.sum

  occurrences.each_with_index { |o,i| # fminer outputs occurrences sorted reverse by activity.
    actual = o.size.to_f/nr_o
    expected = db_instances[i].to_f/nr_db
    if actual > expected
      if ((actual - expected) / actual) > max_value
       max_value = (actual - expected) / actual # 'Schleppzeiger'
        max = i
      end
    end
  }
  max
end

.gauss(x, sigma = 0.3) ⇒ Float

Gauss kernel

Returns:

  • (Float) 


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# File 'lib/utils.rb', line 158

def self.gauss(x, sigma = 0.3) 
  d = 1.0 - x.to_f
  Math.exp(-(d*d)/(2*sigma*sigma))
end

.get_pc_descriptors(params) ⇒ Object

Calculates PC descriptors via Ambit – DO NOT OVERLOAD Ambit. @param Required keys: :compounds, :pc_type @return Ambit result uri, piecewise (1st: base, 2nd: SMILES, 3rd+: features



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# File 'lib/utils.rb', line 33

def self.get_pc_descriptors(params)

  begin

    ambit_ds_service_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/"
    ambit_mopac_model_uri = "http://apps.ideaconsult.net:8080/ambit2/model/69632"
    descs = YAML::load_file( File.join(ENV['HOME'], ".opentox", "config", "ambit_descriptors.yaml") )
    descs_uris = []
    params[:pc_type] = "electronic,cpsa" if params[:pc_type].nil? # rescue missing pc_type
    types = params[:pc_type].split(",")
    descs.each { |uri, cat_name| 
      if types.include? cat_name[:category]
        descs_uris << uri
      end
    }
    if descs_uris.size == 0
      raise "Error! Empty set of descriptors. Did you supply one of [geometrical, topological, electronic, constitutional, hybrid, cpsa] ?"
    end
    #LOGGER.debug "Ambit descriptor URIs: #{descs_uris.join(", ")}"

    begin
      # Create SMI
      smiles_array = []; smiles_to_inchi = {}
      params[:compounds].each do |n|
        cmpd = OpenTox::Compound.new(n)
        smiles_string = cmpd.to_smiles
        smiles_to_inchi[smiles_string] = URI.encode_www_form_component(cmpd.to_inchi)
        smiles_array << smiles_string
      end
      smi_file = Tempfile.open(['pc_ambit', '.csv'])
      pc_descriptors = nil

      # Create Ambit dataset
      smi_file.puts( "SMILES\n" )
      smi_file.puts( smiles_array.join("\n") )
      smi_file.flush
      ambit_ds_uri = OpenTox::RestClientWrapper.post(ambit_ds_service_uri, {:file => File.new(smi_file.path)}, {:content_type => "multipart/form-data", :accept => "text/uri-list"} )
    rescue Exception => e
      LOGGER.debug "#{e.class}: #{e.message}"
      LOGGER.debug "Backtrace:\n\t#{e.backtrace.join("\n\t")}"
    ensure
      smi_file.close! if smi_file
    end
    ambit_smiles_uri = OpenTox::RestClientWrapper.get(ambit_ds_uri + "/features", {:accept=> "text/uri-list"} ).chomp

    # Calculate 3D for CPSA
    if types.include? "cpsa"
      ambit_ds_mopac_uri = OpenTox::RestClientWrapper.post(ambit_mopac_model_uri, {:dataset_uri => ambit_ds_uri}, {:accept => "text/uri-list"} ) 
      LOGGER.debug "MOPAC dataset: #{ambit_ds_mopac_uri }"
    end

    # Get Ambit results
    ambit_result_uri = [] # 1st pos: base uri, then features
    ambit_result_uri << ambit_ds_uri + "?"
    ambit_result_uri << ("feature_uris[]=" + URI.encode_www_form_component(ambit_smiles_uri) + "&")
    descs_uris.each_with_index do |uri, i|
      algorithm = Algorithm::Generic.new(uri)
      result_uri = algorithm.run({:dataset_uri => ambit_ds_uri})
      ambit_result_uri << result_uri.split("?")[1] + "&"
      LOGGER.debug "Ambit (#{descs_uris.size}): #{i+1}"
    end
    #LOGGER.debug "Ambit result: #{ambit_result_uri.join('')}"
    [ ambit_result_uri, smiles_to_inchi ]

  rescue Exception => e
    LOGGER.debug "#{e.class}: #{e.message}"
    LOGGER.debug "Backtrace:\n\t#{e.backtrace.join("\n\t")}"
  end
end

.isnull_or_singular?(array) ⇒ Boolean

For symbolic features

Parameters:

  • Array (Array) —

    to test, must indicate non-occurrence with 0.

Returns:

  • (Boolean) —

    Whether the feature is singular or non-occurring or present everywhere.



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# File 'lib/utils.rb', line 167

def self.isnull_or_singular?(array)
  nr_zeroes = array.count(0)
  return (nr_zeroes == array.size) ||    # remove non-occurring feature
         (nr_zeroes == array.size-1) ||  # remove singular feature
         (nr_zeroes == 0)                # also remove feature present everywhere
end

.load_ds_csv(ambit_result_uri, smiles_to_inchi, subjectid = nil) ⇒ Object

Load dataset via CSV @param Ambit result uri, piecewise (1st: base, 2nd: SMILES, 3rd+: features @return dataset uri



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# File 'lib/utils.rb', line 107

def self.load_ds_csv(ambit_result_uri, smiles_to_inchi, subjectid=nil)
  
  master=nil
  (1...ambit_result_uri.size).collect { |idx|
    curr_uri = ambit_result_uri[0] + ambit_result_uri[idx]
    LOGGER.debug "Requesting #{curr_uri}"
    csv_data = CSV.parse( OpenTox::RestClientWrapper.get(curr_uri, {:accept => "text/csv", :subjectid => subjectid}) )
    if csv_data[0] && csv_data[0].size>1
      if master.nil? # This is the smiles entry
        (1...csv_data.size).each{ |idx| csv_data[idx][1] = smiles_to_inchi[csv_data[idx][1]] }
        master = csv_data
        next
      else
        index_uri = csv_data[0].index("SMILES")
        csv_data.map {|i| i.delete_at(index_uri)} if index_uri #Removes additional SMILES information
        
        nr_cols = (csv_data[0].size)-1
        LOGGER.debug "Merging #{nr_cols} new columns"
        master.each {|row| nr_cols.times { row.push(nil) }  } # Adds empty columns to all rows
        csv_data.each do |row|
          temp = master.assoc(row[0]) # Finds the appropriate line in master
          ((-1*nr_cols)..-1).collect.each { |idx|
            temp[idx] = row[nr_cols+idx+1] if temp # Updates columns if line is found
          }
        end
      end
    end
  }

  index_uri = master[0].index("Compound")
  master.map {|i| i.delete_at(index_uri)}
  master[0].each {|cell| cell.chomp!(" ")}
  master[0][0] = "Compound" #"SMILES" 
  index_smi = master[0].index("SMILES")
  master.map {|i| i.delete_at(index_smi)} if index_smi
  #master[0][0] = "SMILES" 
   
  #LOGGER.debug "-------- AM: Writing to dumpfile"
  #File.open("/tmp/test.csv", 'w') {|f| f.write( master.collect {|r| r.join(",")}.join("\n") ) }
 
  parser = OpenTox::Parser::Spreadsheets.new
  ds = OpenTox::Dataset.new(nil,subjectid)
  ds.save(subjectid)
  parser.dataset = ds
  ds = parser.load_csv(master.collect{|r| r.join(",")}.join("\n"))
  ds.save(subjectid)
end

.min_frequency(training_dataset, per_mil) ⇒ Object

Minimum Frequency return [Integer] min-frequency

Parameters:

  • per-mil (Integer) —

    value



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# File 'lib/utils.rb', line 204

def self.min_frequency(training_dataset,per_mil)
  minfreq = per_mil * training_dataset.compounds.size.to_f / 1000.0 # AM sugg. 8-10 per mil for BBRC, 50 per mil for LAST
  minfreq = 2 unless minfreq > 2
  Integer (minfreq)
end

.numeric?(value) ⇒ Boolean

Numeric value test @param value

Returns:

  • (Boolean) —

    Whether value is a number



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# File 'lib/utils.rb', line 178

def self.numeric?(value)
  true if Float(value) rescue false
end

.pc_descriptors(params) ⇒ Object

Calculate physico-chemical descriptors. @param Required keys: :dataset_uri, :pc_type @return dataset uri



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# File 'lib/utils.rb', line 14

def self.pc_descriptors(params)

  begin
    ds = OpenTox::Dataset.find(params[:dataset_uri])
    compounds = ds.compounds.collect
    ambit_result_uri, smiles_to_inchi = get_pc_descriptors( { :compounds => compounds, :pc_type => params[:pc_type] } )
    #ambit_result_uri = ["http://apps.ideaconsult.net:8080/ambit2/dataset/987103?" ,"feature_uris[]=http%3A%2F%2Fapps.ideaconsult.net%3A8080%2Fambit2%2Ffeature%2F4276789&", "feature_uris[]=http%3A%2F%2Fapps.ideaconsult.net%3A8080%2Fambit2%2Fmodel%2F16%2Fpredicted"] # for testing
    LOGGER.debug "Ambit result uri for #{params.inspect}: '#{ambit_result_uri.to_yaml}'"
    load_ds_csv(ambit_result_uri, smiles_to_inchi)
  rescue Exception => e
    LOGGER.debug "#{e.class}: #{e.message}"
    LOGGER.debug "Backtrace:\n\t#{e.backtrace.join("\n\t")}"
  end

end

.sum_size(array) ⇒ Integer

Sum of an array for Arrays.

Parameters:

  • Array (Array) —

    with values

Returns:

  • (Integer) —

    Sum of size of values



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# File 'lib/utils.rb', line 194

def self.sum_size(array)
  sum=0
  array.each { |e| sum += e.size }
  return sum
end

.zero_variance?(array) ⇒ Boolean

For symbolic features

Parameters:

  • Array (Array) —

    to test, must indicate non-occurrence with 0.

Returns:

  • (Boolean) —

    Whether the feature has variance zero.



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# File 'lib/utils.rb', line 186

def self.zero_variance?(array)
  return array.uniq.size == 1
end

Instance Method Details

#run(params = nil, waiting_task = nil) ⇒ String

Execute algorithm with parameters, consult OpenTox API and webservice documentation for acceptable parameters

Parameters:

  • params (optional, Hash) (defaults to: nil) —

    Algorithm parameters

  • waiting_task (optional, OpenTox::Task) (defaults to: nil) —

    (can be a OpenTox::Subtask as well), progress is updated accordingly

Returns:

  • (String) —

    URI of new resource (dataset, model, …)



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# File 'lib/algorithm.rb', line 22

def run(params=nil, waiting_task=nil)
  LOGGER.info "Running algorithm '"+@uri.to_s+"' with params: "+params.inspect
  RestClientWrapper.post(@uri, params, {:accept => 'text/uri-list'}, waiting_task).to_s
end

#to_rdfxml ⇒ application/rdf+xml

Get OWL-DL representation in RDF/XML format

Returns:

  • (application/rdf+xml) —

    RDF/XML representation



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# File 'lib/algorithm.rb', line 29

def to_rdfxml
  s = Serializer::Owl.new
  s.add_algorithm(@uri,@metadata)
  s.to_rdfxml
end