OpenBabel descriptors added

3 files changed, 40 insertions, 27 deletions

diff --git a/fminer.rb b/fminer.rb
index 06d66fb..df91701 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -6,7 +6,6 @@ ENV['FMINER_PVALUES'] = 'true'
 @@last = Last::Last.new 
 
 # Get list of fminer algorithms
-#
 # @return [text/uri-list] URIs of fminer algorithms
 get '/fminer/?' do
 	response['Content-Type'] = 'text/uri-list'
@@ -56,7 +55,6 @@ get "/fminer/last/?" do
 end
 
 # Run bbrc algorithm on 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 BBRC parameters, accepted parameters are
diff --git a/libfminer b/libfminer
-Subproject e0eee431ecb954328ff64e3cc48840c7003a276
+Subproject 6e35cacd8da45f21c4039591d339a74af9a44a6
diff --git a/openbabel.rb b/openbabel.rb
index a261866..a5a8841 100644
--- a/openbabel.rb
+++ b/openbabel.rb
@@ -1,28 +1,43 @@
-get '/openbabel/:smiles/:property/?' do 
+# 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
-	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
+  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