api separated into individual components, adapted for new webservice versions

1 files changed, 67 insertions, 0 deletions

diff --git a/lib/compound.rb b/lib/compound.rb
new file mode 100644
index 0000000..4652770
--- /dev/null
+++ b/lib/compound.rb
@@ -0,0 +1,67 @@
+module OpenTox
+
+	# uri: /compound/:inchi
+	class Compound < OpenTox
+
+		attr_reader :inchi
+
+		# Initialize with <tt>:uri => uri</tt>, <tt>:smiles => smiles</tt> or <tt>:name => name</tt> (name can be also an InChI/InChiKey, CAS number, etc)
+		def initialize(params)
+			@@cactus_uri="http://cactus.nci.nih.gov/chemical/structure/"
+			if params[:smiles]
+				@inchi = smiles2inchi(params[:smiles])
+				@uri = File.join(@@config[:services]["opentox-dataset"],"compound",@inchi)
+			elsif params[:inchi]
+				@inchi = inchi
+				@uri = File.join(@@config[:services]["opentox-dataset"],"compound",@inchi)
+			elsif params[:name]
+				@inchi = RestClient.get "#{@@cactus_uri}#{params[:name]}/stdinchi"
+				@uri = File.join(@@config[:services]["opentox-dataset"],"compound",@inchi)
+			elsif params[:uri]
+				@inchi = params[:uri].sub(/^.*InChI/, 'InChI')
+				@uri = params[:uri]
+			end
+		end
+
+		# Get the (canonical) smiles
+		def smiles
+			obconversion(@inchi,'inchi','can')
+		end
+
+		def sdf
+			obconversion(@inchi,'inchi','sdf')
+		end
+
+		# Matchs a 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 features, returns matching features
+		def match(smarts_features)
+			smarts_features.all_features.collect{ |smarts| smarts if self.match?(smarts.name) }.compact
+		end
+
+		def smiles2inchi(smiles)
+			obconversion(smiles,'smi','inchi')
+		end
+
+		def smiles2cansmi(smiles)
+			obconversion(smiles,'smi','can')
+		end
+
+		def 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
+			obconversion.write_string(obmol).gsub(/\s/,'').chomp
+		end
+	end
+end