diff options
Diffstat (limited to 'lib/compound.rb')
| -rw-r--r-- | lib/compound.rb | 67 |
1 files changed, 65 insertions, 2 deletions
diff --git a/lib/compound.rb b/lib/compound.rb index 6adf3c0..7abd913 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -19,8 +19,11 @@ module OpenTox field :png_id, type: BSON::ObjectId field :svg_id, type: BSON::ObjectId field :sdf_id, type: BSON::ObjectId + field :fp2, type: Array + field :fp3, type: Array field :fp4, type: Array field :fp4_size, type: Integer + field :maccs, type: Array index({smiles: 1}, {unique: true}) @@ -42,6 +45,38 @@ module OpenTox compound end + def openbabel_fingerprint type="FP2" + unless self.send(type.downcase.to_sym) # stored fingerprint + fp = OpenBabel::OBFingerprint.find_fingerprint(type) + obmol = OpenBabel::OBMol.new + obconversion = OpenBabel::OBConversion.new + obconversion.set_in_format "smi" + obconversion.read_string obmol, smiles + result = OpenBabel::VectorUnsignedInt.new + fp.get_fingerprint(obmol,result) + # TODO: %ignore *::DescribeBits @ line 163 openbabel/scripts/openbabel-ruby.i + #p OpenBabel::OBFingerprint.describe_bits(result) + # convert result to a list of the bits that are set + # from openbabel/scripts/python/pybel.py line 830 + # see also http://openbabel.org/docs/dev/UseTheLibrary/Python_Pybel.html#fingerprints + result = result.to_a + bitsperint = OpenBabel::OBFingerprint.getbitsperint() + bits_set = [] + start = 1 + result.each do |x| + i = start + while x > 0 do + bits_set << i if (x % 2) == 1 + x >>= 1 + i += 1 + end + start += bitsperint + end + update type.downcase.to_sym, bits_set + end + self.send(type.downcase.to_sym) + end + # Create a compound from smiles string # @example # compound = OpenTox::Compound.from_smiles("c1ccccc1") @@ -177,6 +212,36 @@ module OpenTox self["chemblid"] end + def fingerprint_neighbors params + bad_request_error "Incorrect parameters '#{params}' for Compound#fingerprint_neighbors. Please provide :type, :training_dataset_id, :min_sim." unless params[:type] and params[:training_dataset_id] and params[:min_sim] + neighbors = [] + query_fingerprint = self.openbabel_fingerprint params[:type] + training_dataset = Dataset.find(params[:training_dataset_id]).compounds.each do |compound| + unless self == compound + fingerprint = compound.openbabel_fingerprint params[:type] + sim = (query_fingerprint & fingerprint).size/(query_fingerprint | fingerprint).size.to_f + neighbors << [compound.id, sim] if sim >= params[:min_sim] + end + end + neighbors.sort{|a,b| b.last <=> a.last} + end + + def fminer_neighbors params + bad_request_error "Incorrect parameters for Compound#fminer_neighbors. Please provide :feature_dataset_id, :min_sim." unless params[:feature_dataset_id] and params[:min_sim] + feature_dataset = Dataset.find params[:feature_dataset_id] + query_fingerprint = Algorithm::Descriptor.smarts_match(self, feature_dataset.features) + neighbors = [] + + # find neighbors + feature_dataset.data_entries.each_with_index do |fingerprint, i| + sim = Algorithm::Similarity.tanimoto fingerprint, query_fingerprint + 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 @@ -202,8 +267,6 @@ module OpenTox $mongo["compounds"].aggregate(aggregate).collect{ |r| [r["_id"], r["tanimoto"]] } end -=begin -=end private |