diff options
Diffstat (limited to 'lib/compound.rb')
| -rw-r--r-- | lib/compound.rb | 215 |
1 files changed, 143 insertions, 72 deletions
diff --git a/lib/compound.rb b/lib/compound.rb index 49c166f..a85507b 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -3,82 +3,126 @@ module OpenTox - class Compound #< OpenTox - - attr_reader :inchi, :uri - - # 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) - if params[:smiles] - @inchi = smiles2inchi(params[:smiles]) - @uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi)) - elsif params[:inchi] - @inchi = params[:inchi] - @uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi)) - elsif params[:sdf] - @inchi = sdf2inchi(params[:sdf]) - @uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi)) - elsif params[:name] - # paranoid URI encoding to keep SMILES charges and brackets - @inchi = RestClient.get("#{@@cactus_uri}#{URI.encode(params[:name], Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))}/stdinchi").body.chomp - # this was too hard for me to debug and leads to additional errors (ch) - #@inchi = RestClientWrapper.get("#{@@cactus_uri}#{URI.encode(params[:name], Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))}/stdinchi").chomp - @uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi)) - elsif params[:uri] - @uri = params[:uri] - case params[:uri] - when /ambit/ # Ambit does not deliver InChIs reliably - smiles = RestClientWrapper.get @uri, :accept => 'chemical/x-daylight-smiles' - @inchi = obconversion(smiles,'smi','inchi') - when /InChI/ # shortcut for IST services - @inchi = params[:uri].sub(/^.*InChI/, 'InChI') - else - @inchi = RestClientWrapper.get @uri, :accept => 'chemical/x-inchi' - end - end + # Ruby wrapper for OpenTox Compound Webservices (http://opentox.org/dev/apis/api-1.2/structure). + class Compound + + attr_accessor :inchi, :uri + + # Create compound with optional uri + # @example + # compound = OpenTox::Compound.new("http://webservices.in-silico.ch/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"") + # @param [optional, String] uri Compound URI + # @return [OpenTox::Compound] Compound + def initialize(uri=nil) + @uri = uri + case @uri + when /InChI/ # shortcut for IST services + @inchi = @uri.sub(/^.*InChI/, 'InChI') + else + @inchi = RestClientWrapper.get(@uri, :accept => 'chemical/x-inchi').to_s.chomp if @uri + end + end + + # 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(smiles) + c = Compound.new + c.inchi = Compound.smiles2inchi(smiles) + c.uri = File.join(CONFIG[:services]["opentox-compound"],URI.escape(c.inchi)) + c + end + + # Create a compound from inchi string + # @param [String] smiles InChI string + # @return [OpenTox::Compound] Compound + def self.from_inchi(inchi) + c = Compound.new + c.inchi = inchi + c.uri = File.join(CONFIG[:services]["opentox-compound"],URI.escape(c.inchi)) + c + end + + # Create a compound from sdf string + # @param [String] smiles SDF string + # @return [OpenTox::Compound] Compound + def self.from_sdf(sdf) + c = Compound.new + c.inchi = Compound.sdf2inchi(sdf) + c.uri = File.join(CONFIG[:services]["opentox-compound"],URI.escape(c.inchi)) + c + end + + # Create a compound from name. Relies on an external service for name lookups. + # @example + # compound = OpenTox::Compound.from_name("Benzene") + # @param [String] name name can be also an InChI/InChiKey, CAS number, etc + # @return [OpenTox::Compound] Compound + def self.from_name(name) + c = Compound.new + # paranoid URI encoding to keep SMILES charges and brackets + c.inchi = RestClientWrapper.get("#{@@cactus_uri}#{URI.encode(name, Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))}/stdinchi").to_s.chomp + c.uri = File.join(CONFIG[:services]["opentox-compound"],URI.escape(c.inchi)) + c + end + + # Get InChI + # @return [String] InChI string + def to_inchi + @inchi end - # Get the (canonical) smiles - def smiles - obconversion(@inchi,'inchi','can') + # Get (canonical) smiles + # @return [String] Smiles string + def to_smiles + Compound.obconversion(@inchi,'inchi','can') end - def sdf - obconversion(@inchi,'inchi','sdf') + # Get sdf + # @return [String] SDF string + def to_sdf + Compound.obconversion(@inchi,'inchi','sdf') end - def gif + # Get gif image + # @return [image/gif] Image data + def to_gif RestClientWrapper.get("#{@@cactus_uri}#{@inchi}/image") end - def png + # Get png image + # @example + # image = compound.to_png + # @return [image/png] Image data + def to_png RestClientWrapper.get(File.join @uri, "image") end - def names + # Get URI of compound image + # @return [String] Compound image URI + def to_image_uri + File.join @uri, "image" + end + + # Get all known compound names. Relies on an external service for name lookups. + # @example + # names = compound.to_names + # @return [String] Compound names + def to_names begin - RestClientWrapper.get("#{@@cactus_uri}#{@inchi}/names") + RestClientWrapper.get("#{@@cactus_uri}#{@inchi}/names").split("\n") rescue "not available" end end - def display_smarts_uri(activating, deactivating, highlight = nil) - LOGGER.debug activating.to_yaml unless activating.nil? - activating_smarts = URI.encode "\"#{activating.join("\"/\"")}\"" - deactivating_smarts = URI.encode "\"#{deactivating.join("\"/\"")}\"" - if highlight.nil? - File.join @@config[:services]["opentox-compound"], "smiles", URI.encode(smiles), "smarts/activating", URI.encode(activating_smarts),"deactivating", URI.encode(deactivating_smarts) - else - File.join @@config[:services]["opentox-compound"], "smiles", URI.encode(smiles), "smarts/activating", URI.encode(activating_smarts),"deactivating", URI.encode(deactivating_smarts), "highlight", URI.encode(highlight) - end - end - - def image_uri - File.join @uri, "image" - end - - # Matchs a smarts string + # Match a smarts string + # @example + # compound = OpenTox::Compound.from_name("Benzene") + # compound.match?("cN") # returns false + # @param [String] smarts Smarts string def match?(smarts) obconversion = OpenBabel::OBConversion.new obmol = OpenBabel::OBMol.new @@ -89,30 +133,57 @@ module OpenTox smarts_pattern.match(obmol) end - # Match an array of smarts features, returns matching features + # Match an array of smarts strings, returns array with matching smarts + # @example + # compound = OpenTox::Compound.from_name("Benzene") + # compound.match(['cc','cN']) # returns ['cc'] + # @param [Array] smarts_array Array with Smarts strings + # @return [Array] Array with matching Smarts strings def match(smarts_array) - smarts_array.collect{|s| s if match?(s)}.compact + # avoid recreation of OpenBabel objects + obconversion = OpenBabel::OBConversion.new + obmol = OpenBabel::OBMol.new + obconversion.set_in_format('inchi') + obconversion.read_string(obmol,@inchi) + smarts_pattern = OpenBabel::OBSmartsPattern.new + smarts_array.collect do |smarts| + smarts_pattern.init(smarts) + smarts if smarts_pattern.match(obmol) + end.compact + #smarts_array.collect { |s| s if match?(s)}.compact end - # AM - # Match an array of smarts features, returns (0)1 for (non)matching features at each pos - def match_all(smarts_array) - smarts_array.collect{|s| match?(s) ? 1 : 0 } - end + # Get URI of compound image with highlighted fragments + # + # @param [Array] activating Array with activating Smarts strings + # @param [Array] deactivating Array with deactivating Smarts strings + # @return [String] URI for compound image with highlighted fragments + def matching_smarts_image_uri(activating, deactivating) + activating_smarts = URI.encode "\"#{activating.join("\"/\"")}\"" + deactivating_smarts = URI.encode "\"#{deactivating.join("\"/\"")}\"" + File.join @uri, "smarts/activating", URI.encode(activating_smarts),"deactivating", URI.encode(deactivating_smarts) + end + + + private - def sdf2inchi(sdf) - obconversion(sdf,'sdf','inchi') + # Convert sdf to inchi + def self.sdf2inchi(sdf) + Compound.obconversion(sdf,'sdf','inchi') end - def smiles2inchi(smiles) - obconversion(smiles,'smi','inchi') + # Convert smiles to inchi + def self.smiles2inchi(smiles) + Compound.obconversion(smiles,'smi','inchi') end - def smiles2cansmi(smiles) - obconversion(smiles,'smi','can') + # Convert smiles to canonical smiles + def self.smiles2cansmi(smiles) + Compound.obconversion(smiles,'smi','can') end - def obconversion(identifier,input_format,output_format) + # 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 |