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require 'openbabel'
module OpenTox
class Application < Service
FORMATS = {
"chemical/x-daylight-smiles" => "smi",
"chemical/x-inchi" => "inchi",
#"chemical/x-inchikey" => "inchikey",
# OpenBabel segfaults randomly durng inchikey calculation
"chemical/x-mdl-sdfile" => "sdf",
"chemical/x-mdl-molfile" => "sdf",
"image/png" => 'png',
}
helpers do
# Convert identifier from OpenBabel input_format to OpenBabel output_format
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
case output_format
when /smi|can|inchi/
obconversion.write_string(obmol).gsub(/\s/,'').chomp
else
obconversion.write_string(obmol)
end
end
end
before do
@inchi = URI.unescape request.env['REQUEST_URI'].sub(/^\//,'').sub(/.*compound\//,'').sub(/\/smarts.*$/,'').sub(/\/image/,'').sub(/\?.*$/,'') # hack to avoid sinatra's URI/CGI unescaping, splitting, ..."
end
get "/compound/?" do
not_implemented_error "Object listing not implemented, because compounds are not stored at the server.", to("/compound")
end
get %r{/compound/(.+)/image} do |inchi| # catches all remaining get requests
obconversion @inchi, "inchi", "png"
end
# Get compound representation
# @param [optinal, HEADER] Accept one of `chemical/x-daylight-smiles, chemical/x-inchi, chemical/x-mdl-sdfile, chemical/x-mdl-molfile, text/plain, image/gif, image/png`, defaults to chemical/x-daylight-smiles
# @example Get smiles
# curl http://webservices.in-silico.ch/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
# @example Get all known names
# curl -H "Accept:text/plain" http://webservices.in-silico.ch/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
# @return [chemical/x-daylight-smiles, chemical/x-inchi, chemical/x-mdl-sdfile, chemical/x-mdl-molfile, text/plain, image/gif, image/png] Compound representation
get %r{/compound/(.+)} do |inchi| # catches all remaining get requests
bad_request_error "Unsupported MIME type '#{@accept}.", uri unless FORMATS.keys.include? @accept
return @inchi if @accept == "chemical/x-inchi"
obconversion @inchi, "inchi", FORMATS[@accept]
end
# Create a new compound URI (compounds are not saved at the compound service)
# @param [HEADER] Content-type one of `chemical/x-daylight-smiles, chemical/x-inchi, chemical/x-mdl-sdfile, chemical/x-mdl-molfile, text/plain`
# @example Create compound from Smiles string
# curl -X POST -H "Content-type:chemical/x-daylight-smiles" --data "c1ccccc1" http://webservices.in-silico.ch/compound
# @example Create compound from name, uses an external lookup service and should work also with trade names, CAS numbers, ...
# curl -X POST -H "Content-type:text/plain" --data "Benzene" http://webservices.in-silico.ch/compound
# @param [BODY] - string with identifier/data in selected Content-type
# @return [text/uri-list] compound URI
post '/compound/?' do
response['Content-Type'] = 'text/uri-list'
bad_request_error "Unsupported MIME type '#{@content_type}.", uri unless FORMATS.keys.include? @content_type
return to(File.join("/compound",@body)) if @content_type == "chemical/x-inchi"
to(File.join("compound",obconversion(@body, FORMATS[@content_type], "inchi")))
end
end
end
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