diff options
Diffstat (limited to 'openbabel.rb')
| -rw-r--r-- | openbabel.rb | 170 |
1 files changed, 145 insertions, 25 deletions
diff --git a/openbabel.rb b/openbabel.rb index a261866..3a873c0 100644 --- a/openbabel.rb +++ b/openbabel.rb @@ -1,28 +1,148 @@ -get '/openbabel/:smiles/:property/?' do +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, + OT.isA => OTA.DescriptorCalculation, + } + response['Content-Type'] = 'application/rdf+xml' + algorithm.to_rdfxml + else + halt 404, "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 - obconversion.set_in_and_out_formats 'smi', 'can' - case params[:property] - when 'logP' - #logP = OpenBabel::OBLogP.new - #logP.predict(obmol) - "not yet implemented" - when 'psa' - #psa = OpenBabel::OBPSA.new - "not yet implemented" - when 'mr' - #mr = OpenBabel::OBMR.new - "not yet implemented" - else - begin - obconversion.read_string obmol, params[:smiles] - rescue - halt 404, "Incorrect Smiles string #{params[:smiles]}" - end - begin - eval("obmol.#{params[:property]}").to_s - rescue - halt 404, "Could not calculate property #{params[:property]}" - end - end + 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 + halt 404, "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' + halt 503,task.uri+"\n" if task.status == "Cancelled" + halt 202,task.uri.to_s+"\n" end |