diff options
Diffstat (limited to 'lib/descriptor.rb')
| -rw-r--r-- | lib/descriptor.rb | 39 |
1 files changed, 27 insertions, 12 deletions
diff --git a/lib/descriptor.rb b/lib/descriptor.rb index d862a41..f556df7 100644 --- a/lib/descriptor.rb +++ b/lib/descriptor.rb @@ -63,7 +63,6 @@ module OpenTox obmol = OpenBabel::OBMol.new obconversion.set_in_format('inchi') smarts_pattern = OpenBabel::OBSmartsPattern.new - #fingerprint = {} smarts = [smarts] unless smarts.is_a? Array fingerprint = Array.new(compounds.size){Array.new(smarts.size,false)} compounds.each_with_index do |compound,c| @@ -87,6 +86,8 @@ module OpenTox def self.physchem compounds, descriptors=UNIQUEDESCRIPTORS compounds = parse compounds + dataset = OpenTox::CalculatedDataset.new + dataset.compounds = compounds des = {} descriptors.each do |d| lib, descriptor = d.split(".",2) @@ -95,13 +96,27 @@ module OpenTox des[lib] << descriptor end result = {} - des.each do |lib,d| - send(lib, compounds, d).each do |compound,values| - result[compound] ||= {} - result[compound].merge! values - end + features = [] + data_entries = Array.new(compounds.size){Array.new(des.size)} + n = 0 + des.each do |lib,descriptors| + features += descriptors.collect do |d| + OpenTox::Feature.find_or_create_by( + :title => "#{lib}.#{d}", + :creator => __FILE__ + ) + end + r = send(lib, compounds, descriptors) + #p r + r.each_with_index do |values,i| + data_entries[i][n] = values + end + n += 1 end - result + #dataset.features = features + #dataset.data_entries = data_entries + #dataset + data_entries end def self.openbabel compounds, descriptors @@ -111,12 +126,11 @@ module OpenTox obmol = OpenBabel::OBMol.new obconversion = OpenBabel::OBConversion.new obconversion.set_in_format 'inchi' - fingerprint = {} - compounds.each do |compound| + fingerprint = Array.new(compounds.size){Array.new(obdescriptors.size)} + compounds.each_with_index do |compound,c| obconversion.read_string obmol, compound.inchi - fingerprint[compound] = {} - obdescriptors.each_with_index do |descriptor,i| - fingerprint[compound]["Openbabel."+descriptors[i]] = fix_value(descriptor.predict(obmol)) + obdescriptors.each_with_index do |descriptor,d| + fingerprint[c][d] = fix_value(descriptor.predict(obmol)) end end fingerprint @@ -238,6 +252,7 @@ module OpenTox end def self.parse compounds + p compounds case compounds.class.to_s when "OpenTox::Compound" compounds = [compounds] |