diff options
Diffstat (limited to 'lib/compound.rb')
| -rw-r--r-- | lib/compound.rb | 41 |
1 files changed, 39 insertions, 2 deletions
diff --git a/lib/compound.rb b/lib/compound.rb index 7abd913..d3df125 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -44,6 +44,21 @@ module OpenTox compound.save compound end + + #http://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html#molprint2d-format + def mpd + smarts = obconversion(smiles,"smi","mpd").strip.split("\t") + smarts.shift # remove Title + smarts + + end + + #http://openbabel.org/docs/dev/FileFormats/Multilevel_Neighborhoods_of_Atoms_(MNA).html + def mna level=2 + smarts = obconversion(smiles,"smi","mna","xL\"#{level}\"").split("\n") + smarts.shift # remove Title + smarts + end def openbabel_fingerprint type="FP2" unless self.send(type.downcase.to_sym) # stored fingerprint @@ -72,7 +87,7 @@ module OpenTox end start += bitsperint end - update type.downcase.to_sym, bits_set + update_attribute type.downcase.to_sym, bits_set end self.send(type.downcase.to_sym) end @@ -242,6 +257,28 @@ module OpenTox neighbors end + def physchem_neighbors params + feature_dataset = Dataset.find params[:feature_dataset_id] + query_fingerprint = Algorithm.run params[:feature_calculation_algorithm], self, params[:descriptors] + neighbors = [] + feature_dataset.data_entries.each_with_index do |fingerprint, i| + # TODO implement pearson and cosine similarity separatly + R.assign "x", query_fingerprint + R.assign "y", fingerprint + # pearson r + #sim = R.eval("cor(x,y,use='complete.obs',method='pearson')").to_ruby + #p "pearson" + #p sim + #p "cosine" + sim = R.eval("x %*% y / sqrt(x%*%x * y%*%y)").to_ruby.first + #p sim + if sim >= params[:min_sim] + neighbors << [feature_dataset.compound_ids[i],sim] # use compound_ids, instantiation of Compounds is too time consuming + end + end + neighbors + end + def neighbors threshold=0.7 # TODO restrict to dataset # from http://blog.matt-swain.com/post/87093745652/chemical-similarity-search-in-mongodb @@ -308,7 +345,7 @@ print sdf end def obconversion(identifier,input_format,output_format,option=nil) - self.class.obconversion(identifier,input_format,output_format,option=nil) + self.class.obconversion(identifier,input_format,output_format,option) end end end |