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CACTUS_URI="http://cactus.nci.nih.gov/chemical/structure/"
require 'openbabel'
module OpenTox
# Ruby wrapper for OpenTox Compound Webservices (http://opentox.org/dev/apis/api-1.2/structure).
class Compound
attr_reader :inchi
def initialize inchi
@inchi = inchi
end
def == compound
self.inchi == compound.inchi
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
OpenTox::Compound.new obconversion(smiles,"smi","inchi")
end
# Create a compound from inchi string
# @param inchi [String] smiles InChI string
# @return [OpenTox::Compound] Compound
def self.from_inchi inchi
OpenTox::Compound.new inchi
end
# Create a compound from sdf string
# @param sdf [String] smiles SDF string
# @return [OpenTox::Compound] Compound
def self.from_sdf sdf
OpenTox::Compound.new obconversion(sdf,"sdf","inchi")
end
# Create a compound from name. Relies on an external service for name lookups.
# @example
# compound = OpenTox::Compound.from_name("Benzene")
# @param name [String] can be also an InChI/InChiKey, CAS number, etc
# @return [OpenTox::Compound] Compound
def self.from_name name
OpenTox::Compound.new RestClientWrapper.get File.join(CACTUS_URI,URI.escape(name),"stdinchi")
end
# Get InChIKey
# @return [String] InChI string
def inchikey
obconversion(@inchi,"inchi","inchikey")
end
# Get (canonical) smiles
# @return [String] Smiles string
def smiles
obconversion(@inchi,"inchi","smi") # "can" gives nonn-canonical smiles??
end
# Get sdf
# @return [String] SDF string
def sdf
obconversion(@inchi,"inchi","sdf")
end
# Get gif image
# @return [image/gif] Image data
def gif
RestClientWrapper.get File.join(CACTUS_URI,inchi,"image")
end
# Get png image
# @example
# image = compound.png
# @return [image/png] Image data
def png
obconversion(@inchi,"inchi","_png2")
end
=begin
# Get URI of compound image
# @return [String] Compound image URI
def image_uri
File.join @data["uri"], "image"
end
=end
# Get all known compound names. Relies on an external service for name lookups.
# @example
# names = compound.names
# @return [String] Compound names
def names
RestClientWrapper.get("#{CACTUS_URI}#{inchi}/names").split("\n")
end
# @return [String] PubChem Compound Identifier (CID), derieved via restcall to pubchem
def cid
pug_uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/"
@cid ||= RestClientWrapper.post(File.join(pug_uri, "compound", "inchi", "cids", "TXT"),{:inchi => inchi}).strip
end
# @todo
def chebi
internal_server_error "not yet implemented"
end
# @return [String] ChEMBL database compound id, derieved via restcall to chembl
def chemblid
# https://www.ebi.ac.uk/chembldb/ws#individualCompoundByInChiKey
uri = "http://www.ebi.ac.uk/chemblws/compounds/smiles/#{smiles}.json"
@chemblid = JSON.parse(RestClientWrapper.get(uri))["compounds"].first["chemblId"]
end
private
def self.obconversion(identifier,input_format,output_format,option=nil)
obconversion = OpenBabel::OBConversion.new
obconversion.set_options(option, OpenBabel::OBConversion::OUTOPTIONS) if option
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
def obconversion(identifier,input_format,output_format,option=nil)
self.class.obconversion(identifier,input_format,output_format,option=nil)
end
end
end
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