diff options
Diffstat (limited to 'lib/compound.rb')
| -rw-r--r-- | lib/compound.rb | 171 |
1 files changed, 95 insertions, 76 deletions
diff --git a/lib/compound.rb b/lib/compound.rb index d3df125..7a3dc5c 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -9,6 +9,8 @@ module OpenTox class Compound include OpenTox + DEFAULT_FINGERPRINT = "MP2D" + field :inchi, type: String field :smiles, type: String field :inchikey, type: String @@ -19,77 +21,64 @@ 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 + field :fingerprints, type: Hash, default: {} + field :default_fingerprint_size, type: Integer index({smiles: 1}, {unique: true}) # Overwrites standard Mongoid method to create fingerprints before database insertion def self.find_or_create_by params compound = self.find_or_initialize_by params - unless compound.fp4 and !compound.fp4.empty? - compound.fp4_size = 0 - compound.fp4 = [] - fingerprint = FingerprintSmarts.fingerprint - Algorithm::Descriptor.smarts_match(compound, fingerprint).each_with_index do |m,i| - if m > 0 - compound.fp4 << fingerprint[i].id - compound.fp4_size += 1 - end - end - end + compound.default_fingerprint_size = compound.fingerprint(DEFAULT_FINGERPRINT) 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 - 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 + def fingerprint type="MP2D" + unless fingerprints[type] + return [] unless self.smiles + #http://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html#molprint2d-format + if type == "MP2D" + fp = obconversion(smiles,"smi","mpd").strip.split("\t") + name = fp.shift # remove Title + fingerprints[type] = fp + #http://openbabel.org/docs/dev/FileFormats/Multilevel_Neighborhoods_of_Atoms_(MNA).html + elsif type== "MNA" + level = 2 # TODO: level as parameter, evaluate level 1, see paper + fp = obconversion(smiles,"smi","mna","xL\"#{level}\"").split("\n") + fp.shift # remove Title + fingerprints[type] = fp + else # standard fingerprints + fp = OpenBabel::OBFingerprint.find_fingerprint(type) + obmol = OpenBabel::OBMol.new + obconversion = OpenBabel::OBConversion.new + obconversion.set_in_format "smi" + obconversion.read_string obmol, self.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 - start += bitsperint + fingerprints[type] = bits_set end - update_attribute type.downcase.to_sym, bits_set + save end - self.send(type.downcase.to_sym) + fingerprints[type] end # Create a compound from smiles string @@ -100,7 +89,8 @@ module OpenTox def self.from_smiles smiles smiles = obconversion(smiles,"smi","can") if smiles.empty? - Compound.find_or_create_by(:warning => "SMILES parsing failed for '#{smiles}', this may be caused by an incorrect SMILES string.") + return nil + #Compound.find_or_create_by(:warning => "SMILES parsing failed for '#{smiles}', this may be caused by an incorrect SMILES string.") else Compound.find_or_create_by :smiles => obconversion(smiles,"smi","can") end @@ -146,7 +136,7 @@ module OpenTox result = obconversion(smiles,"smi","inchi") #result = `echo "#{self.smiles}" | "#{File.join(File.dirname(__FILE__),"..","openbabel","bin","babel")}" -ismi - -oinchi`.chomp - update(:inchi => result.chomp) unless result.empty? + update(:inchi => result.chomp) if result and !result.empty? end self["inchi"] end @@ -227,20 +217,47 @@ 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] + def fingerprint_count_neighbors params + # TODO fix neighbors = [] - query_fingerprint = self.openbabel_fingerprint params[:type] + query_fingerprint = self.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] + candidate_fingerprint = compound.fingerprint params[:type] + features = (query_fingerprint + candidate_fingerprint).uniq + min_sum = 0 + max_sum = 0 + features.each do |f| + min,max = [query_fingerprint.count(f),candidate_fingerprint.count(f)].minmax + min_sum += min + max_sum += max + end + max_sum == 0 ? sim = 0 : sim = min_sum/max_sum.to_f + neighbors << [compound.id, sim] if sim and sim >= params[:min_sim] end end neighbors.sort{|a,b| b.last <=> a.last} 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 = [] + #if params[:type] == DEFAULT_FINGERPRINT + #neighbors = db_neighbors params + #p neighbors + #else + query_fingerprint = self.fingerprint params[:type] + training_dataset = Dataset.find(params[:training_dataset_id]).compounds.each do |compound| + unless self == compound + candidate_fingerprint = compound.fingerprint params[:type] + sim = (query_fingerprint & candidate_fingerprint).size/(query_fingerprint | candidate_fingerprint).size.to_f + neighbors << [compound.id, sim] if sim >= params[:min_sim] + end + 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] @@ -248,8 +265,8 @@ module OpenTox neighbors = [] # find neighbors - feature_dataset.data_entries.each_with_index do |fingerprint, i| - sim = Algorithm::Similarity.tanimoto fingerprint, query_fingerprint + feature_dataset.data_entries.each_with_index do |candidate_fingerprint, i| + sim = Algorithm::Similarity.tanimoto candidate_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 @@ -261,10 +278,10 @@ module OpenTox 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| + feature_dataset.data_entries.each_with_index do |candidate_fingerprint, i| # TODO implement pearson and cosine similarity separatly R.assign "x", query_fingerprint - R.assign "y", fingerprint + R.assign "y", candidate_fingerprint # pearson r #sim = R.eval("cor(x,y,use='complete.obs',method='pearson')").to_ruby #p "pearson" @@ -279,10 +296,12 @@ module OpenTox neighbors end - def neighbors threshold=0.7 + def db_neighbors params + p "DB NEIGHBORS" + p params # TODO restrict to dataset # from http://blog.matt-swain.com/post/87093745652/chemical-similarity-search-in-mongodb - qn = fp4.size + qn = fingerprint(params[:type]).size #qmin = qn * threshold #qmax = qn / threshold #not sure if it is worth the effort of keeping feature counts up to date (compound deletions, additions, ...) @@ -292,12 +311,12 @@ module OpenTox {'$match' => {'_id' => {'$ne' => self.id}}}, # remove self {'$project' => { 'tanimoto' => {'$let' => { - 'vars' => {'common' => {'$size' => {'$setIntersection' => ['$fp4', fp4]}}}, - 'in' => {'$divide' => ['$$common', {'$subtract' => [{'$add' => [qn, '$fp4_size']}, '$$common']}]} + 'vars' => {'common' => {'$size' => {'$setIntersection' => ["'$#{DEFAULT_FINGERPRINT}'", DEFAULT_FINGERPRINT]}}}, + 'in' => {'$divide' => ['$$common', {'$subtract' => [{'$add' => [qn, '$default_fingerprint_size']}, '$$common']}]} }}, '_id' => 1 }}, - {'$match' => {'tanimoto' => {'$gte' => threshold}}}, + {'$match' => {'tanimoto' => {'$gte' => params[:min_sim]}}}, {'$sort' => {'tanimoto' => -1}} ] @@ -312,12 +331,12 @@ module OpenTox obconversion.set_options(option, OpenBabel::OBConversion::OUTOPTIONS) if option obmol = OpenBabel::OBMol.new obconversion.set_in_and_out_formats input_format, output_format + return nil if identifier.nil? obconversion.read_string obmol, identifier case output_format when /smi|can|inchi/ obconversion.write_string(obmol).gsub(/\s/,'').chomp when /sdf/ -p "SDF conversion" # TODO: find disconnected structures # strip_salts # separate |