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require '../opentox-client/lib/opentox-client.rb'
require 'json'
require 'base64'
def Math.gauss(x, sigma = 0.3)
d = 1.0 - x.to_f
Math.exp(-(d*d)/(2*sigma*sigma))
end
module OpenTox
class PubChemCompound < Compound
attr_accessor :cid
@@pug_proxy = "http://localhost:8081/"
def initialize cid
@cid = cid.to_s
end
def fingerprint
JSON.parse RestClient.get(File.join(@@pug_proxy,"cid",@cid,"fingerprint"))
end
def self.from_name name
cids = JSON.parse(RestClient.get(File.join(@@pug_proxy,"name",CGI.escape(name))))
if cids.size == 1
PubChemCompound.new cids.first
elsif cids.empty?
nil
else
cids.collect{|cid| PubChemCompound.new cid}
end
end
def name
RestClient.get(File.join(@@pug_proxy,"cid",cid,"name")).chomp.sub(/^"/,'').sub(/"$/,'')
end
def neighbors
JSON.parse(RestClient.get(File.join(@@pug_proxy,"cid",@cid,"neighbors"))).collect{|n| PubChemCompound.new(n) }
end
def assays
JSON.parse RestClient.get(File.join(@@pug_proxy,"cid",cid,"assays"))
end
def active_assays
assays.select{|a| a["Activity Outcome"] == "active"} if assays
end
def inactive_assays
assays.select{|a| a["Activity Outcome"] == "inactive"} if assays
end
def targets
active_assays.select{|a| a["Target GI"]} if assays
end
def non_targets
inactive_assays.select{|a| a["Target GI"]} if assays
end
def predicted_assays
JSON.parse RestClient.get(File.join(@@pug_proxy,"cid",cid,"predictions"))
end
def predicted_active_assays
predicted_assays.select{|a| a["p_active"] > a["p_inactive"]} if predicted_assays
end
def predicted_inactive_assays
predicted_assays.select{|a| a["p_active"] < a["p_inactive"]} if predicted_assays
end
def predicted_targets
predicted_active_assays.select{|a| a["Target GI"]} if predicted_assays
end
def predicted_non_targets
predicted_inactive_assays.select{|a| a["Target GI"]} if predicted_assays
end
def image_uri
File.join @@pug_proxy, "cid", @cid, "image"
end
def similarity compound
cosine compound
end
def cosine compound
RestClient.get(File.join(@@pug_proxy,"cid",@cid,"cosine",compound.cid)).to_f
end
end
end
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