1 files changed, 0 insertions, 96 deletions
diff --git a/pubchem.rb b/pubchem.rb
deleted file mode 100644
index d16f4b4..0000000
--- a/pubchem.rb
+++ /dev/null
@@ -1,96 +0,0 @@
-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