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module OpenTox
class Nanoparticle < Substance
include OpenTox
field :core, type: String
field :coating, type: Array, default: []
field :bundles, type: Array, default: []
def nanoparticle_neighbors params
Dataset.find(params[:training_dataset_id]).nanoparticles
end
def add_feature feature, value
if feature.source.match /property\/P-CHEM/
physchem_descriptors[feature.id.to_s] ||= []
physchem_descriptors[feature.id.to_s] << value
elsif feature.source.match /property\/TOX/
toxicities[feature.id.to_s] ||= []
toxicities[feature.id.to_s] << value
else
warn "Unknown feature type '#{feature.source}'. Value '#{value}' not inserted."
end
end
def parse_ambit_value feature, v
# TODO: units, mmol/log10 conversion
if v.keys == ["loValue"]
#if v["loValue"].numeric?
add_feature feature, v["loValue"]
#else
#warn "'#{v["loValue"]}' is not a numeric value, entry ignored."
#end
elsif v.keys.size == 2 and v["loQualifier"] == "mean"
#add_feature feature, {:mean => v["loValue"]}
add_feature feature, v["loValue"]
warn "'#{feature.name}' is a mean value. Original data is not available."
elsif v.keys.size == 2 and v["loQualifier"] #== ">="
#add_feature feature, {:min => v["loValue"],:max => Float::INFINITY}
warn "Only min value available for '#{feature.name}', entry ignored"
elsif v.keys.size == 2 and v["upQualifier"] #== ">="
#add_feature feature, {:max => v["upValue"],:min => -Float::INFINITY}
warn "Only max value available for '#{feature.name}', entry ignored"
elsif v.size == 4 and v["loQualifier"] and v["upQualifier"]
#add_feature feature, {:min => v["loValue"],:max => v["upValue"]}
add_feature feature, [v["loValue"],v["upValue"]].mean
warn "Using mean value of range #{v["loValue"]} - #{v["upValue"]} for '#{feature.name}'. Original data is not available."
elsif v == {} # do nothing
else
$logger.warn "Cannot parse Ambit eNanoMapper value '#{v}' for feature '#{feature.name}'."
warnings << "Cannot parse Ambit eNanoMapper value '#{v}' for feature '#{feature.name}'."
end
end
end
end
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