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|
@@cactus_uri="http://cactus.nci.nih.gov/chemical/structure/"
@@ambit_uri="http://ambit.uni-plovdiv.bg:8080/ambit2/depict/cdk?search="
module OpenTox
# Ruby wrapper for OpenTox Compound Webservices (http://opentox.org/dev/apis/api-1.2/structure).
#
# Examples:
# require "opentox-ruby-api-wrapper"
#
# # Creating compounds
#
# # from smiles string
# compound = OpenTox::Compound.from_smiles("c1ccccc1")
# # from name
# compound = OpenTox::Compound.from_name("Benzene")
# # from uri
# compound = OpenTox::Compound.new("http://webservices.in-silico.ch/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"")
#
# # Getting compound representations
#
# # get InChI
# inchi = compound.inchi
# # get all compound names
# names = compound.names
# # get png image
# image = compound.png
# # get uri
# uri = compound.uri
#
# # SMARTS matching
#
# # match a smarts string
# compound.match?("cN") # returns false
# # match an array of smarts strings
# compound.match(['cc','cN']) # returns ['cc']
class Compound
attr_accessor :inchi, :uri
# Create compound with optional uri
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
# Create a compound from smiles string
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
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
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 (name can be also an InChI/InChiKey, CAS number, etc)
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
def smiles
Compound.obconversion(@inchi,'inchi','can')
end
# Get sdf
def sdf
Compound.obconversion(@inchi,'inchi','sdf')
end
# Get gif image
def gif
RestClientWrapper.get("#{@@cactus_uri}#{@inchi}/image")
end
# Get png image
def png
RestClientWrapper.get(File.join @uri, "image")
end
# Get URI of compound image
def image_uri
File.join @uri, "image"
end
# Get all known compound names
def names
begin
RestClientWrapper.get("#{@@cactus_uri}#{@inchi}/names").split("\n")
rescue
"not available"
end
end
# Match a 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
def match(smarts_array)
smarts_array.collect{|s| s if match?(s)}.compact
end
# Get URI of compound image with highlighted fragments
def matching_smarts_image_uri(activating, deactivating, highlight = 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
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
|
