smiles generation and smarts matching with openbabel, canonical smiles as identifier, rake task for installation

1 files changed, 58 insertions, 0 deletions

diff --git a/application.rb b/application.rb
new file mode 100644
index 0000000..845895d
--- /dev/null
+++ b/application.rb
@@ -0,0 +1,58 @@
+[ 'rubygems', 'sinatra', 'rest_client', 'sinatra/url_for', 'sinatra/respond_to', 'openbabel' ].each do |lib|
+	require lib
+end
+
+mime :smiles, "chemical/x-daylight-smiles"
+mime :inchi, "chemical/x-inchi"
+mime :sdf, "chemical/x-mdl-sdfile"
+mime :image, "image/gif"
+mime :names, "text/plain"
+
+CACTUS_URI="http://cactus.nci.nih.gov/chemical/structure/"
+
+get '/*/match/*' do
+	smiles = URI.decode(params[:splat][0])
+	smarts = URI.decode(params[:splat][1])
+	smi2mol = OpenBabel::OBConversion.new
+	smi2mol.set_in_format('smi')
+	obmol = OpenBabel::OBMol.new
+	smi2mol.read_string(obmol,smiles) 
+	obmol.add_hydrogens
+	smarts_pattern = OpenBabel::OBSmartsPattern.new
+	smarts_pattern.init(smarts)
+	if smarts_pattern.match(obmol)
+		'true'
+	else
+		'false'
+	end
+end
+
+get %r{/(.+)} do |cansmi| # catches all remaining get requests
+	respond_to do |format|
+		format.html   { URI.unescape(cansmi).chomp }
+		format.text   { URI.unescape(cansmi).chomp }
+		format.smiles { URI.unescape(cansmi).chomp }
+		format.names  { RestClient.get "#{CACTUS_URI}#{cansmi}/names" }
+		format.inchi  { RestClient.get "#{CACTUS_URI}#{cansmi}/stdinchi" }
+		format.sdf    { RestClient.get "#{CACTUS_URI}#{cansmi}/sdf" }
+		format.image  { "#{CACTUS_URI}#{cansmi}/image" }
+	end
+end
+
+post '/' do 
+	if params[:smiles]
+		cansmi = canonical_smiles(URI.unescape(params[:smiles]),'smi').gsub(/\s+/,'')
+	elsif params[:name]
+		cansmi = RestClient.get "#{CACTUS_URI}#{params[:name]}/smiles"
+	end
+	url_for("/", :full) + URI.escape(cansmi, /[^\w]/)
+end
+
+def canonical_smiles(identifier,format)
+	conversion = OpenBabel::OBConversion.new
+	conversion.set_in_and_out_formats format, 'can'
+	mol = OpenBabel::OBMol.new
+	conversion.read_string mol, identifier
+	conversion.write_string mol
+end
+