batch prediction of openbabel parameters added

2 files changed, 120 insertions, 18 deletions

diff --git a/fminer.rb b/fminer.rb
index df91701..d74f183 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -195,7 +195,6 @@ post '/fminer/bbrc/?' do
               ]
             }
             feature_dataset.add_feature feature_uri, metadata
-            #feature_dataset.add_feature_parameters feature_uri, feature_dataset.parameters
           end
           ids.each { |id| feature_dataset.add(compounds[id], feature_uri, true)}
         end
@@ -207,10 +206,8 @@ post '/fminer/bbrc/?' do
     halt 503,task.uri+"\n" if task.status == "Cancelled"
     halt 202,task.uri.to_s+"\n"
   end
-#end
 
 # Run last algorithm on a dataset
-#
 # @param [String] dataset_uri URI of the training dataset
 # @param [String] prediction_feature URI of the prediction feature (i.e. dependent variable)
 # @param [optional] parameters LAST parameters, accepted parameters are
diff --git a/openbabel.rb b/openbabel.rb
index a5a8841..3a873c0 100644
--- a/openbabel.rb
+++ b/openbabel.rb
@@ -1,3 +1,58 @@
+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
@@ -5,39 +60,89 @@
 #   - 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
+#   - 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
+#   - MW             Molecular weight
+#   - nF             Number of fluorine atoms
 #   - nHal           Number of halogen atoms
-#   - spinMult       Total Spin Multiplicity
+#   - spinMult       Total spin multiplicity
 #   - TPSA           Topological polar surface area
-# @param [URI] compound_uri Compound URI
-# @return [Sting] descriptor value
+# @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
-  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
+  if OBMOL_METHODS.keys.include? params[:property]
     eval("obmol.#{params[:property].underscore}").to_s
-  elsif descriptor_methods.include? params[:property]
+  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