diff options
Diffstat (limited to 'lib/descriptor.rb')
| -rw-r--r-- | lib/descriptor.rb | 10 |
1 files changed, 8 insertions, 2 deletions
diff --git a/lib/descriptor.rb b/lib/descriptor.rb index 1d43d7d..8ec7480 100644 --- a/lib/descriptor.rb +++ b/lib/descriptor.rb @@ -1,7 +1,6 @@ require 'digest/md5' ENV["JAVA_HOME"] ||= "/usr/lib/jvm/java-7-openjdk" BABEL_3D_CACHE_DIR = File.join(File.dirname(__FILE__),"..",'/babel_3d_cache') -# TODO store 3D structures in mongodb # TODO store descriptors in mongodb module OpenTox @@ -59,6 +58,7 @@ module OpenTox bad_request_error "Compounds for smarts_match are empty" unless compounds bad_request_error "Smarts for smarts_match are empty" unless smarts parse compounds + @count = count obconversion = OpenBabel::OBConversion.new obmol = OpenBabel::OBMol.new obconversion.set_in_format('inchi') @@ -100,13 +100,19 @@ module OpenTox @data_entries end when "OpenTox::Dataset" - dataset = OpenTox::Dataset.new(:compound_ids => @compounds.collect{|c| c.id}) + dataset = OpenTox::DescriptorDataset.new(:compound_ids => @compounds.collect{|c| c.id}) if @smarts dataset.feature_ids = @smarts.collect{|smart| Smarts.find_or_create_by(:smarts => smart).id} + @count ? algo = "count" : algo = "match" + dataset.feature_calculation_algorithm = "#{self}.smarts_#{algo}" + elsif @physchem_descriptors dataset.feature_ids = @physchem_descriptors.collect{|d| PhysChemDescriptor.find_or_create_by(:name => d, :creator => __FILE__).id} dataset.data_entries = @data_entries + dataset.feature_calculation_algorithm = "#{self}.physchem" + #TODO params? end + dataset.save_all dataset end end |