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Diffstat (limited to 'openbabel.rb')
| -rw-r--r-- | openbabel.rb | 148 |
1 files changed, 0 insertions, 148 deletions
diff --git a/openbabel.rb b/openbabel.rb deleted file mode 100644 index 463663e..0000000 --- a/openbabel.rb +++ /dev/null @@ -1,148 +0,0 @@ -OBMOL_METHODS = { - "NumAtoms" => "Number of atoms", - "NumBonds" => "Number of bonds", - "NumHvyAtoms" => "Number of heavy atoms", - "NumResidues" => "Number of residues", - "NumRotors" => "Number of rotatable bonds", - "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", -} - -OBDESCRIPTOR_METHODS = { - "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", -} - -# Get a list of OpenBabel algorithms -# @return [text/uri-list] URIs of OpenBabel algorithms -get '/openbabel' do - algorithms = OBMOL_METHODS.collect{|name,description| url_for("/openbabel/#{name}",:full)} - algorithms << OBDESCRIPTOR_METHODS.collect{|name,description| url_for("/openbabel/#{name}",:full)} - response['Content-Type'] = 'text/uri-list' - algorithms.join("\n") -end - -# Get RDF/XML representation of OpenBabel algorithm -# @return [application/rdf+xml] OWL-DL representation of OpenBabel algorithm -get '/openbabel/:property' do - description = OBMOL_METHODS[params[:property]] if OBMOL_METHODS.include? params[:property] - description = OBDESCRIPTOR_METHODS[params[:property]] if OBDESCRIPTOR_METHODS.include? params[:property] - if description - algorithm = OpenTox::Algorithm::Generic.new(url_for("/openbabel/#{params[:property]}",:full)) - algorithm.metadata = { - DC.title => params[:property], - DC.creator => "helma@in-silico.ch", - DC.description => description, - RDF.type => [OTA.DescriptorCalculation], - } - response['Content-Type'] = 'application/rdf+xml' - algorithm.to_rdfxml - else - raise OpenTox::NotFoundError.new "Unknown OpenBabel descriptor #{params[:property]}." - end -end - -# 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 -# - 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 [String] compound_uri Compound URI -# @return [String] 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 - if OBMOL_METHODS.keys.include? params[:property] - eval("obmol.#{params[:property].underscore}").to_s - elsif OBDESCRIPTOR_METHODS.keys.include? params[:property] - descriptor = OpenBabel::OBDescriptor.find_type(params[:property]) - descriptor.predict(obmol).to_s - else - raise OpenTox::NotFoundError.new "Cannot calculate property #{params[:property]} with OpenBabel" - end -end - -# Calculate all OpenBabel descriptors for a dataset -# @param [String] dataset_uri Dataset URI -# @return [text/uri-list] Task URI -post '/openbabel' do - task = OpenTox::Task.create("Calculating OpenBabel descriptors for #{params[:dataset_uri]}", url_for('/openbabel',:full)) do - - dataset = OpenTox::Dataset.find(params[:dataset_uri]) - result_dataset = OpenTox::Dataset.create - result_dataset.add_metadata({ - DC.title => "OpenBabel descriptors for " + dataset.metadata[DC.title].to_s, - DC.creator => url_for('/openbabel',:full), - OT.hasSource => url_for('/openbabel', :full), - OT.parameters => [ - { DC.title => "dataset_uri", OT.paramValue => params[:dataset_uri] }, - ] - }) - - obconversion = OpenBabel::OBConversion.new - obmol = OpenBabel::OBMol.new - obconversion.set_in_and_out_formats 'inchi', 'can' - - OBMOL_METHODS.merge(OBDESCRIPTOR_METHODS).each do |name,description| - feature_uri = File.join result_dataset.uri, "feature", "openbabel", name - metadata = { - OT.hasSource => url_for("/openbabel/#{name}", :full), - DC.description => description, - DC.title => name, - } - result_dataset.add_feature feature_uri, metadata - end - - dataset.compounds.each do |compound_uri| - compound = OpenTox::Compound.new(compound_uri) - obconversion.read_string obmol, compound.to_inchi - #result_dataset.add_compound compound_uri - OBMOL_METHODS.keys.each do |name| - feature_uri = File.join result_dataset.uri, "feature", "openbabel", name - value = eval("obmol.#{name.underscore}").to_f - result_dataset.add compound_uri, feature_uri, value - end - OBDESCRIPTOR_METHODS.keys.each do |name| - feature_uri = File.join result_dataset.uri, "feature", "openbabel", name - value = OpenBabel::OBDescriptor.find_type(params[:property]).predict(obmol).to_f - result_dataset.add compound_uri, feature_uri, value - end - end - result_dataset.save - result_dataset.uri - end - response['Content-Type'] = 'text/uri-list' - raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled" - halt 202,task.uri.to_s+"\n" -end |