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-rw-r--r--lib/compound.rb104
1 files changed, 19 insertions, 85 deletions
diff --git a/lib/compound.rb b/lib/compound.rb
index e002305..8a1143b 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -1,11 +1,9 @@
-CACTUS_URI="http://cactus.nci.nih.gov/chemical/structure/"
+CACTUS_URI="https://cactus.nci.nih.gov/chemical/structure/"
module OpenTox
- class Compound
+ class Compound < Substance
require_relative "unique_descriptors.rb"
- include OpenTox
-
DEFAULT_FINGERPRINT = "MP2D"
field :inchi, type: String
@@ -19,9 +17,6 @@ module OpenTox
field :sdf_id, type: BSON::ObjectId
field :fingerprints, type: Hash, default: {}
field :default_fingerprint_size, type: Integer
- field :physchem_descriptors, type: Hash, default: {}
- field :dataset_ids, type: Array, default: []
- field :features, type: Hash, default: {}
index({smiles: 1}, {unique: true})
@@ -80,9 +75,8 @@ module OpenTox
fingerprints[type]
end
- def physchem descriptors=PhysChem.openbabel_descriptors
- # TODO: speedup java descriptors
- calculated_ids = physchem_descriptors.keys
+ def calculate_properties descriptors=PhysChem::OPENBABEL
+ calculated_ids = properties.keys
# BSON::ObjectId instances are not allowed as keys in a BSON document.
new_ids = descriptors.collect{|d| d.id.to_s} - calculated_ids
descs = {}
@@ -95,11 +89,11 @@ module OpenTox
# avoid recalculating Cdk features with multiple values
descs.keys.uniq.each do |k|
descs[k].send(k[0].downcase,k[1],self).each do |n,v|
- physchem_descriptors[algos[n].id.to_s] = v # BSON::ObjectId instances are not allowed as keys in a BSON document.
+ properties[algos[n].id.to_s] = v # BSON::ObjectId instances are not allowed as keys in a BSON document.
end
end
save
- physchem_descriptors.select{|id,v| descriptors.collect{|d| d.id.to_s}.include? id}
+ descriptors.collect{|d| properties[d.id.to_s]}
end
def smarts_match smarts, count=false
@@ -142,9 +136,6 @@ module OpenTox
# @param inchi [String] smiles InChI string
# @return [OpenTox::Compound] Compound
def self.from_inchi inchi
- # Temporary workaround for OpenBabels Inchi bug
- # http://sourceforge.net/p/openbabel/bugs/957/
- # bug has not been fixed in latest git/development version
#smiles = `echo "#{inchi}" | "#{File.join(File.dirname(__FILE__),"..","openbabel","bin","babel")}" -iinchi - -ocan`.chomp.strip
smiles = obconversion(inchi,"inchi","can")
if smiles.empty?
@@ -246,7 +237,7 @@ module OpenTox
# @return [String] PubChem Compound Identifier (CID), derieved via restcall to pubchem
def cid
- pug_uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/"
+ pug_uri = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/"
update(:cid => RestClientWrapper.post(File.join(pug_uri, "compound", "inchi", "cids", "TXT"),{:inchi => inchi}).strip) unless self["cid"]
self["cid"]
end
@@ -254,70 +245,13 @@ module OpenTox
# @return [String] ChEMBL database compound id, derieved via restcall to chembl
def chemblid
# https://www.ebi.ac.uk/chembldb/ws#individualCompoundByInChiKey
- uri = "http://www.ebi.ac.uk/chemblws/compounds/smiles/#{smiles}.json"
+ uri = "https://www.ebi.ac.uk/chemblws/compounds/smiles/#{smiles}.json"
update(:chemblid => JSON.parse(RestClientWrapper.get(uri))["compounds"].first["chemblId"]) unless self["chemblid"]
self["chemblid"]
end
- def fingerprint_count_neighbors params
- # TODO fix
- neighbors = []
- 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]
- 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
- else
- query_fingerprint = self.fingerprint params[:type]
- training_dataset = Dataset.find(params[:training_dataset_id])
- prediction_feature = training_dataset.features.first
- training_dataset.compounds.each do |compound|
- candidate_fingerprint = compound.fingerprint params[:type]
- sim = (query_fingerprint & candidate_fingerprint).size/(query_fingerprint | candidate_fingerprint).size.to_f
- feature_values = training_dataset.values(compound,prediction_feature)
- neighbors << {"_id" => compound.id, "features" => {prediction_feature.id.to_s => feature_values}, "tanimoto" => sim} if sim >= params[:min_sim]
- end
- neighbors.sort!{|a,b| b["tanimoto"] <=> a["tanimoto"]}
- end
- 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 |candidate_fingerprint, i|
- # TODO implement pearson and cosine similarity separatly
- R.assign "x", query_fingerprint
- R.assign "y", candidate_fingerprint
- sim = R.eval("x %*% y / sqrt(x%*%x * y%*%y)").to_ruby.first
- 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 db_neighbors params
+ def db_neighbors min_sim: 0.1, dataset_id:
+ #p fingerprints[DEFAULT_FINGERPRINT]
# from http://blog.matt-swain.com/post/87093745652/chemical-similarity-search-in-mongodb
#qn = default_fingerprint_size
@@ -329,20 +263,20 @@ module OpenTox
#{'$match': {'mfp.count': {'$gte': qmin, '$lte': qmax}, 'mfp.bits': {'$in': reqbits}}},
#{'$match' => {'_id' => {'$ne' => self.id}}}, # remove self
{'$project' => {
- 'tanimoto' => {'$let' => {
+ 'similarity' => {'$let' => {
'vars' => {'common' => {'$size' => {'$setIntersection' => ["$fingerprints.#{DEFAULT_FINGERPRINT}", fingerprints[DEFAULT_FINGERPRINT]]}}},
- #'vars' => {'common' => {'$size' => {'$setIntersection' => ["$default_fingerprint", default_fingerprint]}}},
'in' => {'$divide' => ['$$common', {'$subtract' => [{'$add' => [default_fingerprint_size, '$default_fingerprint_size']}, '$$common']}]}
}},
'_id' => 1,
- 'features' => 1,
+ #'measurements' => 1,
'dataset_ids' => 1
}},
- {'$match' => {'tanimoto' => {'$gte' => params[:min_sim]}}},
- {'$sort' => {'tanimoto' => -1}}
+ {'$match' => {'similarity' => {'$gte' => min_sim}}},
+ {'$sort' => {'similarity' => -1}}
]
-
- $mongo["compounds"].aggregate(aggregate).select{|r| r["dataset_ids"].include? params[:training_dataset_id]}
+
+ # TODO move into aggregate pipeline, see http://stackoverflow.com/questions/30537317/mongodb-aggregation-match-if-value-in-array
+ $mongo["substances"].aggregate(aggregate).select{|r| r["dataset_ids"].include? dataset_id}
end
@@ -353,7 +287,7 @@ module OpenTox
end
# Convert mg to mmol
- # @return [Float] value in mg
+ # @return [Float] value in mmol
def mg_to_mmol mg
mg.to_f/molecular_weight
end
@@ -362,7 +296,7 @@ module OpenTox
# @return [Float] molecular weight
def molecular_weight
mw_feature = PhysChem.find_or_create_by(:name => "Openbabel.MW")
- physchem([mw_feature])[mw_feature.id.to_s]
+ calculate_properties([mw_feature]).first
end
private
generated by cgit v1.2.3 (git 2.25.1) at 2024-04-27 01:43:21 +0000