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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 smiles, subjectid=nil
Compound.new RestClientWrapper.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 inchi, subjectid=nil
Compound.new RestClientWrapper.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 sdf, subjectid=nil
Compound.new RestClientWrapper.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 name, subjectid=nil
@inchi = RestClientWrapper.get File.join(CACTUS_URI,URI.escape(name),"stdinchi")
Compound.new RestClientWrapper.post(service_uri, @inchi, {:content_type => 'chemical/x-inchi', :subjectid => subjectid})
end
# Get InChI
# @return [String] InChI string
def inchi
@inchi ||= RestClientWrapper.get(@uri,{},{:accept => 'chemical/x-inchi'}).chomp
end
# Get InChIKey
# @return [String] InChI string
def inchikey
@inchikey ||= RestClientWrapper.get(@uri,{},{:accept => 'chemical/x-inchikey'}).chomp
end
# Get (canonical) smiles
# @return [String] Smiles string
def smiles
@smiles ||= RestClientWrapper.get(@uri,{},{:accept => 'chemical/x-daylight-smiles'}).chomp
end
# Get sdf
# @return [String] SDF string
def sdf
RestClientWrapper.get(@uri,{},{:accept => 'chemical/x-mdl-sdfile'}).chomp
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
RestClientWrapper.get(File.join @uri, "image")
end
# Get URI of compound image
# @return [String] Compound image URI
def image_uri
File.join @uri, "image"
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
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
def chebi
end
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
=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
# Match an array of smarts strings, returns hash
# Keys: matching smarts, values: number of non-unique hits, or 1
# @param [Array] smarts_array Array with Smarts strings
# @param [Boolean] Whether non-unique hits or 1 should be produced
# @return [Array] Array with matching Smarts strings
# @example {
# compound = Compound.from_name("Benzene")
# compound.match(['cc','cN']) # returns { 'cc' => 12, 'cN' => 0 }
# }
def match_hits(smarts_array, use_hits=true)
obconversion = OpenBabel::OBConversion.new
obmol = OpenBabel::OBMol.new
obconversion.set_in_format('inchi')
obconversion.read_string(obmol,inchi)
smarts_pattern = OpenBabel::OBSmartsPattern.new
smarts_hits = {}
smarts_array.collect do |smarts|
smarts_pattern.init(smarts)
if smarts_pattern.match(obmol)
if use_hits
hits = smarts_pattern.get_map_list
smarts_hits[smarts] = hits.to_a.size
else
smarts_hits[smarts] = 1
end
end
end
smarts_hits
end
# Provided for backward compatibility
def match(smarts_array)
match_hits(smarts_array,false)
end
end
end
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