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module OpenTox
# Wrapper for OpenTox Algorithms
class Algorithm
# Execute algorithm with parameters, please consult the OpenTox API and the webservice documentation for acceptable parameters
# @param [optional,Hash] params Algorithm parameters
# @param [optional,Boolean] wait set to false if method should return a task uri instead of the algorithm result
# @return [String] URI of new resource (dataset, model, ...)
def run params=nil, wait=true
uri = RestClientWrapper.post @uri, params, { :content_type => "text/uri-list", :subjectid => @subjectid}
wait_for_task uri if wait
end
end
module Descriptor
class Smarts
def self.fingerprint compounds, smarts, count=false
matcher = Algorithm.new File.join($algorithm[:uri],"descriptor","smarts","fingerprint")
smarts = [smarts] unless smarts.is_a? Array
if compounds.is_a? OpenTox::Compound
json = matcher.run :compound_uri => compounds.uri, :smarts => smarts, :count => count
elsif compounds.is_a? OpenTox::Dataset
# TODO: add task and return dataset instead of result
json = matcher.run :dataset_uri => compounds.uri, :smarts => smarts, :count => count
else
bad_request_error "Cannot match smarts on #{compounds.class} objects."
end
JSON.parse json
end
def self.count compounds, smarts
fingerprint compounds,smarts,true
end
end
end
end
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