From 3262e3cf2ed1ce896dcd11d9c1bde5222ea720ce Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 4 Jul 2013 18:17:56 +0200
Subject: Algorithm::Generic and Model::Generic classes.

---
 lib/compound.rb | 139 --------------------------------------------------------
 1 file changed, 139 deletions(-)

(limited to 'lib/compound.rb')

diff --git a/lib/compound.rb b/lib/compound.rb
index 9bd2066..82f0d73 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -112,144 +112,5 @@ module OpenTox
       uri = "http://www.ebi.ac.uk/chemblws/compounds/smiles/#{smiles}.json"
       @chemblid = JSON.parse(RestClientWrapper.get(uri))["compounds"].first["chemblId"]
     end
-
-=begin
-    # Match a smarts string
-    # @example
-    #   compound = OpenTox::Compound.from_name("Benzene")
-    #   compound.match?("cN") # returns false
-    # @param [String] smarts Smarts string
-    def match?(smarts)
-      matcher = Algorithm.new File.join($algorithm[:uri],"descriptor","smarts")
-      matcher.run :compound_uri => @uri, :smarts => smarts, :count => false
-    end
-
-    # Match an array of smarts strings, returns array with matching smarts
-    # @example
-    #   compound = OpenTox::Compound.from_name("Benzene")
-    #   compound.match(['cc','cN']) # returns ['cc']
-    # @param [Array] smarts_array Array with Smarts strings
-    # @return [Array] Array with matching Smarts strings
-    def match(smarts_array)
-      matcher = Algorithm.new File.join($algorithm[:uri],"descriptor","smarts")
-      matcher.run :compound_uri => @uri, :smarts => smarts_array, :count => false
-    end
-
-    # Match a smarts string
-    # @example
-    #   compound = OpenTox::Compound.from_name("Benzene")
-    #   compound.match?("cN") # returns false
-    # @param [String] smarts Smarts string
-    def match?(smarts)
-      obconversion = OpenBabel::OBConversion.new
-      obmol = OpenBabel::OBMol.new
-      obconversion.set_in_format('inchi')
-      obconversion.read_string(obmol,@inchi)
-      smarts_pattern = OpenBabel::OBSmartsPattern.new
-      smarts_pattern.init(smarts)
-      smarts_pattern.match(obmol)
-    end
-
-    # Match an array of smarts strings, returns array with matching smarts
-    # @example
-    #   compound = OpenTox::Compound.from_name("Benzene")
-    #   compound.match(['cc','cN']) # returns ['cc']
-    # @param [Array] smarts_array Array with Smarts strings
-    # @return [Array] Array with matching Smarts strings
-    def match(smarts_array)
-      # avoid recreation of OpenBabel objects
-      obconversion = OpenBabel::OBConversion.new
-      obmol = OpenBabel::OBMol.new
-      obconversion.set_in_format('inchi')
-      obconversion.read_string(obmol,@inchi)
-      smarts_pattern = OpenBabel::OBSmartsPattern.new
-      smarts_array.collect do |smarts|
-        smarts_pattern.init(smarts)
-        smarts if smarts_pattern.match(obmol)
-      end.compact
-      #smarts_array.collect { |s| s if match?(s)}.compact
-    end
-
-    # Get URI of compound image with highlighted fragments
-    #
-    # @param [Array] activating Array with activating Smarts strings
-    # @param [Array] deactivating Array with deactivating Smarts strings
-    # @return [String] URI for compound image with highlighted fragments
-    def matching_smarts_image_uri(activating, deactivating)
-      activating_smarts = URI.encode "\"#{activating.join("\"/\"")}\""
-      deactivating_smarts = URI.encode "\"#{deactivating.join("\"/\"")}\""
-      File.join @uri, "smarts/activating", URI.encode(activating_smarts),"deactivating", URI.encode(deactivating_smarts)
-    end
-
-
-    private
-
-    # Convert sdf to inchi
-    def self.sdf2inchi(sdf)
-      Compound.obconversion(sdf,'sdf','inchi')
-    end
-
-    # Convert smiles to inchi
-    def self.smiles2inchi(smiles)
-      Compound.obconversion(smiles,'smi','inchi')
-    end
-
-    # Convert smiles to canonical smiles
-    def self.smiles2cansmi(smiles)
-      Compound.obconversion(smiles,'smi','can')
-    end
-
-    # Convert identifier from OpenBabel input_format to OpenBabel output_format
-		def self.obconversion(identifier,input_format,output_format)
-			obconversion = OpenBabel::OBConversion.new
-			obmol = OpenBabel::OBMol.new
-			obconversion.set_in_and_out_formats input_format, output_format
-			obconversion.read_string obmol, identifier
-			case output_format
-			when /smi|can|inchi/
-				obconversion.write_string(obmol).gsub(/\s/,'').chomp
-			else
-				obconversion.write_string(obmol)
-			end
-		end
-
-
-
-    # Match an array of smarts strings, returns hash
-    # Keys: matching smarts, values: number of non-unique hits, or 1
-    # @param [Array] smarts_array Array with Smarts strings
-    # @param use_hits [Boolean] Whether non-unique hits or 1 should be produced
-    # @return [Hash] Hash with matching Smarts as keys, nr-of-hits/1 as values
-    # @example
-    #   compound = Compound.from_name("Benzene")
-    #   compound.match(['cc','cN'],true) # returns { 'cc' => 12 }, 'cN' is not included because it does not match
-    #   compound.match(['cc','cN'],false) # returns { 'cc' => 1 }
-    def match_hits(smarts_array, use_hits=true)
-      obconversion = OpenBabel::OBConversion.new
-      obmol = OpenBabel::OBMol.new
-      obconversion.set_in_format('inchi')
-      obconversion.read_string(obmol,inchi)
-      smarts_pattern = OpenBabel::OBSmartsPattern.new
-      smarts_hits = {}
-      smarts_array.collect do |smarts|
-        smarts_pattern.init(smarts)
-        if smarts_pattern.match(obmol)
-          if use_hits
-            hits = smarts_pattern.get_map_list
-            smarts_hits[smarts] = hits.to_a.size
-          else
-            smarts_hits[smarts] = 1
-          end
-        end
-      end
-      smarts_hits
-    end
-
-    # Provided for backward compatibility
-    def match(smarts_array)
-      match_hits(smarts_array,false)
-    end
-=end
-
   end
 end
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