Class: OpenTox::Nanoparticle

Inherits:
Substance show all
Includes:
OpenTox
Defined in:
lib/nanoparticle.rb

Overview

Nanoparticles

Instance Method Summary collapse

Instance Method Details

#add_feature(feature, value, dataset) ⇒ Object

Add (measured) feature values



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# File 'lib/nanoparticle.rb', line 46

def add_feature feature, value, dataset
  unless feature.name == "ATOMIC COMPOSITION" or feature.name == "FUNCTIONAL GROUP" # redundand
    case feature.category
    when "P-CHEM"
      properties[feature.id.to_s] ||= []
      properties[feature.id.to_s] << value
      properties[feature.id.to_s].uniq!
    when "Proteomics"
      properties[feature.id.to_s] ||= []
      properties[feature.id.to_s] << value
      properties[feature.id.to_s].uniq!
    when "TOX"
      if feature.name.match("Cell Viability Assay") and !feature.name.match("SLOPE") # -log10 transformation
        value = -Math.log10(value)
        feature.unit = "-log10(#{feature.unit})" unless feature.unit.match "log10"
        feature.warnings += ["-log10 transformed values"]  unless feature.warnings.include? "-log10 transformed values"
        feature.save
      end
      dataset.add self, feature, value
    else
      warn "Unknown feature type '#{feature.category}'. Value '#{value}' not inserted."
    end
    dataset_ids << dataset.id
    dataset_ids.uniq!
  end
end

#calculate_properties(descriptors = PhysChem::OPENBABEL) ⇒ Array<Float>

Calculate physchem properties



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# File 'lib/nanoparticle.rb', line 34

def calculate_properties descriptors=PhysChem::OPENBABEL
  if core.smiles and !coating.collect{|c| c.smiles}.compact.empty?
    core_prop = core.calculate_properties descriptors
    coating_prop = coating.collect{|c| c.calculate_properties descriptors if c.smiles}
    descriptors.collect_with_index{|d,i| [core_prop[i],coating_prop.collect{|c| c[i] if c}]}
  end
end

#coating ⇒ Array<OpenTox::Compound>

Get coatings



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# File 'lib/nanoparticle.rb', line 18

def coating
  coating_ids.collect{|i| Compound.find i }
end

#core ⇒ OpenTox::Compound

Get core compound



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# File 'lib/nanoparticle.rb', line 12

def core
  Compound.find core_id
end

#fingerprint(type = DEFAULT_FINGERPRINT) ⇒ Array<String>

Get nanoparticle fingerprint (union of core and coating fingerprints)



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# File 'lib/nanoparticle.rb', line 25

def fingerprint type=DEFAULT_FINGERPRINT
  core_fp = core.fingerprint type
  coating_fp = coating.collect{|c| c.fingerprint type}.flatten.uniq.compact
  (core_fp.empty? or coating_fp.empty?) ? [] : (core_fp+coating_fp).uniq.compact
end

#parse_ambit_value(feature, v, dataset) ⇒ Object

Parse values from Ambit database



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# File 'lib/nanoparticle.rb', line 77

def parse_ambit_value feature, v, dataset
  # TODO add study id to warnings
  v.delete "unit"
  # TODO: ppm instead of weights
  if v.keys == ["textValue"]
    add_feature feature, v["textValue"], dataset
  elsif v.keys == ["loValue"]
    add_feature feature, v["loValue"], dataset
  elsif v.keys.size == 2 and v["errorValue"]
    add_feature feature, v["loValue"], dataset
    #warn "Ignoring errorValue '#{v["errorValue"]}' for '#{feature.name}'."
  elsif v.keys.size == 2 and v["loQualifier"] == "mean"
    add_feature feature, v["loValue"], dataset
    #warn "'#{feature.name}' is a mean value. Original data is not available."
  elsif v.keys.size == 2 and v["loQualifier"] #== ">="
    #warn "Only min value available for '#{feature.name}', entry ignored"
  elsif v.keys.size == 2 and v["upQualifier"] #== ">="
    #warn "Only max value available for '#{feature.name}', entry ignored"
  elsif v.keys.size == 3 and v["loValue"] and v["loQualifier"].nil? and v["upQualifier"].nil?
    add_feature feature, v["loValue"], dataset
    #warn "loQualifier and upQualifier are empty."
  elsif v.keys.size == 3 and v["loValue"] and v["loQualifier"] == "" and v["upQualifier"] == ""
    add_feature feature, v["loValue"], dataset
    #warn "loQualifier and upQualifier are empty."
  elsif v.keys.size == 4 and v["loValue"] and v["loQualifier"].nil? and v["upQualifier"].nil?
    add_feature feature, v["loValue"], dataset
    #warn "loQualifier and upQualifier are empty."
  elsif v.size == 4 and v["loQualifier"] and v["upQualifier"] and v["loValue"] and v["upValue"]
    #add_feature feature, [v["loValue"],v["upValue"]].mean, dataset
    #warn "Using mean value of range #{v["loValue"]} - #{v["upValue"]} for '#{feature.name}'. Original data is not available."
  elsif v.size == 4 and v["loQualifier"] == "mean" and v["errorValue"]
    #warn "'#{feature.name}' is a mean value. Original data is not available. Ignoring errorValue '#{v["errorValue"]}' for '#{feature.name}'."
    add_feature feature, v["loValue"], dataset
  elsif v == {} # do nothing
  else
    warn "Cannot parse Ambit eNanoMapper value '#{v}' for feature '#{feature.name}'."
  end
end