openbabel requirement removed. initial descriptor classes.

3 files changed, 58 insertions, 2 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
diff --git a/lib/compound.rb b/lib/compound.rb
index 89bf840..daeabb9 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -1,4 +1,4 @@
-require "openbabel"
+#require "openbabel"
 CACTUS_URI="http://cactus.nci.nih.gov/chemical/structure/"
 
 module OpenTox
@@ -116,6 +116,27 @@ module OpenTox
     #   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')
diff --git a/lib/overwrite.rb b/lib/overwrite.rb
index 04de58d..b2382e0 100644
--- a/lib/overwrite.rb
+++ b/lib/overwrite.rb
@@ -28,6 +28,14 @@ class String
     downcase
   end
 
+  # convert strings to boolean values
+  # @return [TrueClass,FalseClass] true or false
+  def to_boolean
+    return true if self == true || self =~ (/(true|t|yes|y|1)$/i)
+    return false if self == false || self.nil? || self =~ (/(false|f|no|n|0)$/i)
+    bad_request_error "invalid value for Boolean: \"#{self}\""
+  end
+
   # encloses URI in text with with link tag
   # @return [String] new text with marked links
   def link_urls