openbabel requirement removed. initial descriptor classes.

1 files changed, 22 insertions, 1 deletions

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')