diff options
Diffstat (limited to 'lib/lazar.rb')
| -rw-r--r-- | lib/lazar.rb | 21 |
1 files changed, 19 insertions, 2 deletions
diff --git a/lib/lazar.rb b/lib/lazar.rb index 6ce19d8..2416569 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -133,10 +133,27 @@ module OpenTox end @training_fingerprints = @feature_dataset.data_entries + # fill trailing missing values with nil + @training_fingerprints = @training_fingerprints.collect do |values| + values << nil while (values.size < @feature_dataset.features.size) + values + end @training_compounds = @training_dataset.compounds - query_fingerprints = OpenTox::Algorithm::Descriptor.send( @feature_calculation_algorithm, compounds, @feature_dataset.features.collect{ |f| f[RDF::DC.title] } )#.collect{|row| row.collect{|val| val ? val.to_f : 0.0 } } - + feature_names = @feature_dataset.features.collect{ |f| f[RDF::DC.title] } + # one Cdk descriptor may produce several features, e.g., Cdk.WienerNumbers produces Cdk.WienerNumbers.WPATH and Cdk.WienerNumbers.WPOL + # -> strip suffix and use the feature only once + feature_names = feature_names.collect do |f| + if f=~/Cdk/ and f.count(".")==2 + f[0..(f.rindex(".")-1)] + else + f + end + end + feature_names.uniq! + + query_fingerprints = OpenTox::Algorithm::Descriptor.send( @feature_calculation_algorithm, compounds, feature_names )#.collect{|row| row.collect{|val| val ? val.to_f : 0.0 } } + compounds.each do |compound| database_activities = @training_dataset.values(compound,@prediction_feature) |