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require "openbabel"
module OpenTox
# Perform OpenBabel conversions locally in order to prevent net overhead
class Compound
attr_writer :smiles, :inchi
# 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
inchi = obconversion(smiles,'smi','inchi')
compound = Compound.new(File.join service_uri, inchi)
compound.inchi = inchi
compound.smiles = smiles
compound
end
# Create a compound from inchi string
# @param [String] smiles InChI string
# @return [OpenTox::Compound] Compound
def self.from_inchi inchi
compound = Compound.new(File.join service_uri, inchi)
compound.inchi = inchi
compound
end
# Create a compound from sdf string
# @param [String] smiles SDF string
# @return [OpenTox::Compound] Compound
def self.from_sdf sdf
inchi = obconversion(sdf,'sdf','inchi')
compound = Compound.new(File.join service_uri, inchi)
compound.inchi = inchi
compound
end
private
# 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
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