openbabel requirement removed. initial descriptor classes.

1 files changed, 28 insertions, 1 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 8576681..1ffc883 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -5,11 +5,38 @@ module OpenTox
 
     # 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 true if method should wait for task result
+    # @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