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[ 'rubygems', 'sinatra', 'rest_client', 'sinatra/url_for', 'sinatra/respond_to', 'openbabel' ].each do |lib|
require lib
end
mime :uid, "text/plain"
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/"
set :default_content, :smiles
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.uid { URI.escape(cansmi, /[^#{URI::PATTERN::UNRESERVED}]/) }
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')
elsif params[:name]
cansmi = RestClient.get "#{CACTUS_URI}#{params[:name]}/smiles"
end
url_for("/", :full) + URI.escape(cansmi.gsub(/\s+/,''), /[^#{URI::PATTERN::UNRESERVED}]/)
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
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