fix storing feature datasets for dataset with duplicate compounds, preserve feature order

1 files changed, 33 insertions, 14 deletions

diff --git a/lib/descriptor.rb b/lib/descriptor.rb
index 36fb1a5..7403ebf 100644
--- a/lib/descriptor.rb
+++ b/lib/descriptor.rb
@@ -1,5 +1,8 @@
 require 'digest/md5'
 ENV["JAVA_HOME"] ||= "/usr/lib/jvm/java-7-openjdk" 
+
+BABEL_3D_CACHE_DIR = File.join(Dir.pwd,'/babel_3d_cache')
+
 module OpenTox
 
   module Algorithm 
@@ -118,7 +121,7 @@ module OpenTox
             $logger.debug "> #{line.chomp}"
           end
           io.close
-          raise "external cmd failed '#{cmd}' (error should be logged)" unless $?.to_i == 0
+          raise "external cmd failed '#{cmd}' (see log file for error msg)" unless $?.to_i == 0
         end
       end
 
@@ -172,7 +175,7 @@ module OpenTox
         obconversion.set_out_format 'sdf'
 
         digest = Digest::MD5.hexdigest compounds.collect{|c| c.uri}.inspect
-        sdf_file = "/tmp/#{digest}.sdf"
+        sdf_file = File.join(BABEL_3D_CACHE_DIR,"#{digest}.sdf")
         if File.exists? sdf_file # do not recreate existing 3d sdfs
           $logger.debug "re-using cached 3d structures from #{sdf_file}"
         else
@@ -185,20 +188,36 @@ module OpenTox
           c = 0
           compounds.each do |compound|
             c += 1
-            $logger.debug "compute 3d structures for compound #{c}/#{compounds.size}"
-            obconversion.read_string obmol, compound.inchi
-            sdf_2d = obconversion.write_string(obmol)  
-            OpenBabel::OBOp.find_type("Gen3D").do(obmol) 
-            sdf_3d = obconversion.write_string(obmol)  
-            if sdf_3d.match(/.nan/)
-              warning = "3D generation failed for compound #{compound.uri}, trying to calculate descriptors from 2D structure."
-              $logger.warn warning
-              # TODO
-              #@feature_dataset[RDF::OT.Warnings] ? @feature_dataset[RDF::OT.Warnings] << warning : @feature_dataset[RDF::OT.Warnings] = warning
-              tmp_file.write sdf_2d
+            cmp_file = File.join(BABEL_3D_CACHE_DIR,Digest::MD5.hexdigest(compound.inchi)+".sdf")
+            cmp_sdf = nil
+            if File.exists? cmp_file
+              $logger.debug "read cached 3d structure for compound #{c}/#{compounds.size}"
+              cmp_sdf = File.read(cmp_file)
             else
-              tmp_file.write sdf_3d
+              $logger.debug "compute 3d structure for compound #{c}/#{compounds.size}"
+              obconversion.read_string obmol, compound.inchi
+              sdf_2d = obconversion.write_string(obmol)  
+              error = nil
+              if compound.inchi.include?(";") # component includes multiple compounds (; in inchi, . in smiles)
+                error = "OpenBabel 3D generation failed for multi-compound #{compound.uri}, trying to calculate descriptors from 2D structure."
+              else
+                OpenBabel::OBOp.find_type("Gen3D").do(obmol) 
+                sdf_3d = obconversion.write_string(obmol)  
+                error = "3D generation failed for compound #{compound.uri}, trying to calculate descriptors from 2D structure." if sdf_3d.match(/.nan/)
+              end
+              if error
+                $logger.warn error
+                # TODO
+                # @feature_dataset[RDF::OT.Warnings] ? @feature_dataset[RDF::OT.Warnings] << error : @feature_dataset[RDF::OT.Warnings] = error
+                cmp_sdf = sdf_2d
+              else
+                cmp_sdf = sdf_3d
+              end
+              File.open(cmp_file,"w") do |f|
+                f.write(cmp_sdf)
+              end
             end
+            tmp_file.write cmp_sdf
           end
           tmp_file.close
           File.rename(tmp_file, sdf_file)