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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
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)
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]
# paranoid URI encoding to keep SMILES charges and brackets
@inchi = RestClient.get("#{@@cactus_uri}#{URI.encode(params[:name], Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))}/stdinchi").body.chomp
# this was too hard for me to debug and leads to additional errors (ch)
#@inchi = RestClientWrapper.get("#{@@cactus_uri}#{URI.encode(params[:name], Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))}/stdinchi").chomp
@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
elsif params[:uri]
@uri = params[:uri]
case params[:uri]
when /ambit/ # Ambit does not deliver InChIs reliably
smiles = RestClientWrapper.get @uri, :accept => 'chemical/x-daylight-smiles'
@inchi = obconversion(smiles,'smi','inchi')
when /InChI/ # shortcut for IST services
@inchi = params[:uri].sub(/^.*InChI/, 'InChI')
else
@inchi = RestClientWrapper.get @uri, :accept => 'chemical/x-inchi'
end
end
end
# Get the (canonical) smiles
def smiles
obconversion(@inchi,'inchi','can')
end
def sdf
obconversion(@inchi,'inchi','sdf')
end
def gif
RestClientWrapper.get("#{@@cactus_uri}#{@inchi}/image")
end
def png
RestClientWrapper.get(File.join @uri, "image")
end
def names
begin
RestClientWrapper.get("#{@@cactus_uri}#{@inchi}/names")
rescue
"not available"
end
end
def display_smarts_uri(activating, deactivating, highlight = nil)
LOGGER.debug activating.to_yaml unless activating.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
def image_uri
File.join @uri, "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
# AM
# Match an array of smarts features, returns (0)1 for (non)matching features at each pos
def match_all(smarts_array)
smarts_array.collect{|s| match?(s) ? 1 : 0 }
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
|
