Class: OpenTox::Compound

Inherits:
Object
  • Object
show all
Defined in:
lib/compound.rb

Overview

< OpenTox

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(params) ⇒ Compound

Initialize with :uri => uri, :smiles => smiles or :name => name (name can be also an InChI/InChiKey, CAS number, etc)



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# File 'lib/compound.rb', line 11

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

Instance Attribute Details

#inchi ⇒ Object (readonly)

Returns the value of attribute inchi.



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# File 'lib/compound.rb', line 8

def inchi
  @inchi
end

#uri ⇒ Object (readonly)

Returns the value of attribute uri.



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# File 'lib/compound.rb', line 8

def uri
  @uri
end

Instance Method Details

#display_smarts_uri(activating, deactivating, highlight = nil) ⇒ Object 



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# File 'lib/compound.rb', line 66

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

#gif ⇒ Object 



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# File 'lib/compound.rb', line 50

def gif
	RestClientWrapper.get("#{@@cactus_uri}#{@inchi}/image")
end

#image_uri ⇒ Object 



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# File 'lib/compound.rb', line 77

def image_uri
    File.join @uri, "image"
end

#match(smarts_array) ⇒ Object

Match an array of smarts features, returns matching features



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# File 'lib/compound.rb', line 93

def match(smarts_array)
	smarts_array.collect{|s| s if match?(s)}.compact
end

#match?(smarts) ⇒ Boolean

Matchs a smarts string

Returns:

  • (Boolean) 


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# File 'lib/compound.rb', line 82

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_all(smarts_array) ⇒ Object

AM Match an array of smarts features, returns (0)1 for (non)matching features at each pos



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# File 'lib/compound.rb', line 99

def match_all(smarts_array)
	smarts_array.collect{|s| match?(s) ? 1 : 0 }
end

#names ⇒ Object 



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# File 'lib/compound.rb', line 58

def names
    begin
      RestClientWrapper.get("#{@@cactus_uri}#{@inchi}/names")
    rescue
      "not available"
    end
end

#obconversion(identifier, input_format, output_format) ⇒ Object 



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# File 'lib/compound.rb', line 115

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

#png ⇒ Object 



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# File 'lib/compound.rb', line 54

def png
    RestClientWrapper.get(File.join @uri, "image")
end

#sdf ⇒ Object 



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# File 'lib/compound.rb', line 46

def sdf
	obconversion(@inchi,'inchi','sdf')
end

#sdf2inchi(sdf) ⇒ Object 



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# File 'lib/compound.rb', line 103

def sdf2inchi(sdf)
	obconversion(sdf,'sdf','inchi')
end

#smiles ⇒ Object

Get the (canonical) smiles



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# File 'lib/compound.rb', line 42

def smiles
	obconversion(@inchi,'inchi','can')
end

#smiles2cansmi(smiles) ⇒ Object 



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# File 'lib/compound.rb', line 111

def smiles2cansmi(smiles)
	obconversion(smiles,'smi','can')
end

#smiles2inchi(smiles) ⇒ Object 



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# File 'lib/compound.rb', line 107

def smiles2inchi(smiles)
	obconversion(smiles,'smi','inchi')
end