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# Calculate OpenBabel descriptors
# Supports the following OpenBabel methods (see OpenBabel API http://openbabel.org/api/2.2.0/)
# - NumAtoms Number of atoms
# - NumBonds Number of bonds
# - NumHvyAtoms Number of heavy atoms
# - NumResidues Number of residues
# - NumRotors Number of rotatable bonds
# - GetFormula Stochoimetric formula
# - GetEnergy Heat of formation for this molecule (in kcal/mol)
# - GetMolWt Standard molar mass given by IUPAC atomic masses (amu)
# - GetExactMass Mass given by isotopes (or most abundant isotope, if not specified)
# - GetTotalCharge Total charge
# - HBA1 Number of Hydrogen Bond Acceptors 1 (JoelLib)
# - HBA2 Number of Hydrogen Bond Acceptors 2 (JoelLib)
# - HBD Number of Hydrogen Bond Donors (JoelLib)
# - L5 Lipinski Rule of Five
# - logP Octanol/water partition coefficient
# - MR Molar refractivity
# - MW Molecular Weight
# - nF Number of Fluorine Atoms
# - nHal Number of halogen atoms
# - spinMult Total Spin Multiplicity
# - TPSA Topological polar surface area
# @param [URI] compound_uri Compound URI
# @return [Sting] descriptor value
post '/openbabel/:property' do
obconversion = OpenBabel::OBConversion.new
obmol = OpenBabel::OBMol.new
compound = OpenTox::Compound.new params[:compound_uri]
obconversion.set_in_and_out_formats 'inchi', 'can'
obconversion.read_string obmol, compound.to_inchi
obmol_methods = ["num_atoms", "num_bonds", "num_hvy_atoms", "num_residues", "num_rotors", "get_formula", "get_energy", "get_mol_wt", "get_exact_mass", "get_total_charge", "get_total_spin_multiplicity"]
descriptor_methods = [ "HBA1", "HBA2", "HBD", "L5", "logP", "MR", "MW", "nF", "nHal", "spinMult", "TPSA" ]
if obmol_methods.include? params[:property].underscore
eval("obmol.#{params[:property].underscore}").to_s
elsif descriptor_methods.include? params[:property]
descriptor = OpenBabel::OBDescriptor.find_type(params[:property])
descriptor.predict(obmol).to_s
else
halt 404, "Cannot calculate property #{params[:property]} with OpenBabel"
end
end
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