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module OpenTox
module Algorithm
class Neighbor
def self.fingerprint_similarity compound, params={}
compound.neighbors params[:min_sim]
end
def self.fminer_similarity compound, params
feature_dataset = Dataset.find params[:feature_dataset_id]
query_fingerprint = Algorithm::Descriptor.smarts_match(compound, feature_dataset.features.collect{|f| f.smarts} )
neighbors = []
# find neighbors
feature_dataset.data_entries.each_with_index do |fingerprint, i|
sim = Algorithm::Similarity.tanimoto fingerprint, query_fingerprint
if sim > params[:min_sim]
neighbors << [feature_dataset.compound_ids[i],sim] # use compound_ids, instantiation of Compounds is too time consuming
end
end
neighbors
end
end
end
end
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