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module OpenTox
module Algorithm
class Generic
attr_accessor :uri, :title, :date
def self.find(uri)
owl = OpenTox::Owl.from_uri(uri, "Algorithm")
return self.new(owl)
end
protected
def initialize(owl)
@title = owl.get("title")
@date = owl.get("date")
@uri = owl.uri
end
end
class Fminer
def self.create_feature_dataset(params)
LOGGER.debug File.basename(__FILE__) + ": creating feature dataset"
resource = RestClient::Resource.new(params[:feature_generation_uri], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
resource.post :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri]
end
def self.uri
File.join(@@config[:services]["opentox-algorithm"], "fminer")
end
end
class Lazar
def self.create_model(params)
LOGGER.debug params
LOGGER.debug File.basename(__FILE__) + ": creating model"
LOGGER.debug File.join(@@config[:services]["opentox-algorithm"], "lazar")
resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "lazar"), :user => @@users[:users].keys[0], :password => @@users[:users].values[0], :content_type => "application/x-yaml")
@uri = resource.post(:dataset_uri => params[:dataset_uri], :prediction_feature => params[:prediction_feature], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")).body.chomp
end
def self.uri
File.join(@@config[:services]["opentox-algorithm"], "lazar")
end
end
class Similarity
def self.weighted_tanimoto(fp_a,fp_b,p)
common_features = fp_a & fp_b
all_features = (fp_a + fp_b).uniq
common_p_sum = 0.0
if common_features.size > 0
common_features.each{|f| common_p_sum += OpenTox::Utils.gauss(p[f])}
all_p_sum = 0.0
all_features.each{|f| all_p_sum += OpenTox::Utils.gauss(p[f])}
common_p_sum/all_p_sum
else
0.0
end
end
def self.euclidean(prop_a,prop_b)
common_properties = prop_a.keys & prop_b.keys
if common_properties.size > 1
dist_sum = 0
common_properties.each do |p|
dist_sum += (prop_a[p] - prop_b[p])**2
end
1/(1+Math.sqrt(dist_sum))
else
nil
end
end
end
end
end
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