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CACTUS_URI="http://cactus.nci.nih.gov/chemical/structure/"
module OpenTox
# Ruby wrapper for OpenTox Compound Webservices (http://opentox.org/dev/apis/api-1.2/structure).
class Compound
# 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 service_uri, smiles, subjectid=nil
Compound.new RestClient.post(service_uri, smiles, {:content_type => 'chemical/x-daylight-smiles', :subjectid => subjectid})
end
# Create a compound from inchi string
# @param [String] smiles InChI string
# @return [OpenTox::Compound] Compound
def self.from_inchi service_uri, inchi, subjectid=nil
Compound.new RestClient.post(service_uri, inchi, {:content_type => 'chemical/x-inchi', :subjectid => subjectid})
end
# Create a compound from sdf string
# @param [String] smiles SDF string
# @return [OpenTox::Compound] Compound
def self.from_sdf service_uri, sdf, subjectid=nil
Compound.new RestClient.post(service_uri, sdf, {:content_type => 'chemical/x-mdl-sdfile', :subjectid => subjectid})
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 service_uri, name, subjectid=nil
Compound.new RestClient.post(service_uri, name, {:content_type => 'text/plain', :subjectid => subjectid})
end
# Get InChI
# @return [String] InChI string
def to_inchi
get(:accept => 'chemical/x-inchi').to_s.chomp if @uri
end
# Get (canonical) smiles
# @return [String] Smiles string
def to_smiles
get(:accept => 'chemical/x-daylight-smiles').chomp
end
# Get sdf
# @return [String] SDF string
def to_sdf
get(:accept => 'chemical/x-mdl-sdfile').chomp
end
# Get gif image
# @return [image/gif] Image data
def to_gif
get("#{CACTUS_URI}#{to_inchi}/image")
end
# Get png image
# @example
# image = compound.to_png
# @return [image/png] Image data
def to_png
get(File.join @uri, "image")
end
# 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
get("#{CACTUS_URI}#{to_inchi}/names").split("\n")
rescue
"not available"
end
end
=begin
# 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 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)
# 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
# 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
# Convert sdf to inchi
def self.sdf2inchi(sdf)
Compound.obconversion(sdf,'sdf','inchi')
end
# Convert smiles to inchi
def self.smiles2inchi(smiles)
Compound.obconversion(smiles,'smi','inchi')
end
# Convert smiles to canonical smiles
def self.smiles2cansmi(smiles)
Compound.obconversion(smiles,'smi','can')
end
# 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
when /smi|can|inchi/
obconversion.write_string(obmol).gsub(/\s/,'').chomp
else
obconversion.write_string(obmol)
end
end
=end
end
end
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