lib/compound.rb in opentox-ruby-0.0.1 vs lib/compound.rb in opentox-ruby-0.0.2
- old
+ new
@@ -1,119 +1,184 @@
@@cactus_uri="http://cactus.nci.nih.gov/chemical/structure/"
@@ambit_uri="http://ambit.uni-plovdiv.bg:8080/ambit2/depict/cdk?search="
module OpenTox
- class Compound #< OpenTox
+ # Ruby wrapper for OpenTox Compound Webservices (http://opentox.org/dev/apis/api-1.2/structure).
+ class Compound
- attr_reader :inchi, :uri
+ attr_accessor :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
- end
+ # 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
- # Get the (canonical) smiles
- def smiles
- obconversion(@inchi,'inchi','can')
+ # 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 (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
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
+ # 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
- def sdf2inchi(sdf)
- obconversion(sdf,'sdf','inchi')
+
+ private
+
+ # 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
obconversion.read_string obmol, identifier
case output_format