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module OpenTox
class Compound #< OpenTox
attr_reader :inchi, :uri
# Initialize with <tt>:uri => uri</tt>, <tt>:smiles => smiles</tt> or <tt>:name => name</tt> (name can be also an InChI/InChiKey, CAS number, etc)
def initialize(params)
@@cactus_uri="http://cactus.nci.nih.gov/chemical/structure/"
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]
@inchi = RestClient.get("#{@@cactus_uri}#{params[:name]}/stdinchi").chomp
@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
elsif params[:uri]
@inchi = params[:uri].sub(/^.*InChI/, 'InChI')
@uri = params[:uri]
end
end
# Get the (canonical) smiles
def smiles
obconversion(@inchi,'inchi','can')
end
def sdf
obconversion(@inchi,'inchi','sdf')
end
def image
RestClient.get("#{@@cactus_uri}#{@inchi}/image")
end
def image_uri
"#{@@cactus_uri}#{@inchi}/image"
end
# Matchs 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 features, returns matching features
def match(smarts_array)
smarts_array.collect{|s| s if match?(s)}.compact
end
def sdf2inchi(sdf)
obconversion(sdf,'sdf','inchi')
end
def smiles2inchi(smiles)
obconversion(smiles,'smi','inchi')
end
def smiles2cansmi(smiles)
obconversion(smiles,'smi','can')
end
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
end
end
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