local inchi conversion, url_for removed, gem dependencies in gemspec

1 files changed, 58 insertions, 0 deletions

diff --git a/compound.rb b/compound.rb
new file mode 100644
index 0000000..cb194ff
--- /dev/null
+++ b/compound.rb
@@ -0,0 +1,58 @@
+require "openbabel"
+module OpenTox
+
+  # Perform OpenBabel conversions locally in order to prevent net overhead
+	class Compound 
+
+    attr_writer :smiles, :inchi
+
+    # Create a compound from smiles string
+    # @example
+    #   compound = OpenTox::Compound.from_smiles("c1ccccc1")
+    # @param [String] smiles Smiles string
+    # @return [OpenTox::Compound] Compound
+    def self.from_smiles service_uri, smiles, subjectid=nil
+			inchi = obconversion(smiles,'smi','inchi')
+      compound = Compound.new(File.join service_uri, inchi)
+      compound.inchi = inchi
+      compound.smiles = smiles
+      compound
+    end
+
+    # Create a compound from inchi string
+    # @param [String] smiles InChI string
+    # @return [OpenTox::Compound] Compound
+    def self.from_inchi service_uri, inchi, subjectid=nil
+      compound = Compound.new(File.join service_uri, inchi)
+      compound.inchi = inchi
+      compound
+    end
+
+    # Create a compound from sdf string
+    # @param [String] smiles SDF string
+    # @return [OpenTox::Compound] Compound
+    def self.from_sdf service_uri, sdf, subjectid=nil
+			inchi = obconversion(sdf,'sdf','inchi')
+      compound = Compound.new(File.join service_uri, inchi)
+      compound.inchi = inchi
+      compound
+    end
+
+    private
+    
+    # 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
+  end
+
+end