diff options
Diffstat (limited to 'lib/compound.rb')
| -rw-r--r-- | lib/compound.rb | 54 |
1 files changed, 40 insertions, 14 deletions
diff --git a/lib/compound.rb b/lib/compound.rb index 3418fcc..5343aa0 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -10,13 +10,13 @@ module OpenTox include OpenTox field :inchi, type: String - attr_readonly :inchi field :smiles, type: String field :inchikey, type: String field :names, type: Array field :cid, type: String field :chemblid, type: String - field :image_id, type: BSON::ObjectId + field :png_id, type: BSON::ObjectId + field :svg_id, type: BSON::ObjectId field :sdf_id, type: BSON::ObjectId field :fp4, type: Array field :fp4_size, type: Integer @@ -46,14 +46,18 @@ module OpenTox # @return [OpenTox::Compound] Compound def self.from_smiles smiles # do not store smiles because it might be noncanonical - Compound.find_or_create_by :inchi => obconversion(smiles,"smi","inchi") + Compound.find_or_create_by :smiles => obconversion(smiles,"smi","can") end # Create a compound from inchi string # @param inchi [String] smiles InChI string # @return [OpenTox::Compound] Compound def self.from_inchi inchi - Compound.find_or_create_by :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}" | babel -iinchi - -ocan`.chomp.strip + smiles.empty? ? nil : Compound.find_or_create_by(:smiles => smiles, :inchi => inchi) end # Create a compound from sdf string @@ -61,7 +65,7 @@ module OpenTox # @return [OpenTox::Compound] Compound def self.from_sdf sdf # do not store sdf because it might be 2D - Compound.find_or_create_by :inchi => obconversion(sdf,"sdf","inchi") + Compound.find_or_create_by :smiles => obconversion(sdf,"sdf","can") end # Create a compound from name. Relies on an external service for name lookups. @@ -70,20 +74,30 @@ module OpenTox # @param name [String] can be also an InChI/InChiKey, CAS number, etc # @return [OpenTox::Compound] Compound def self.from_name name - Compound.find_or_create_by :inchi => RestClientWrapper.get(File.join(CACTUS_URI,URI.escape(name),"stdinchi")) + Compound.find_or_create_by :smiles => RestClientWrapper.get(File.join(CACTUS_URI,URI.escape(name),"smiles")) end - # Get InChIKey + # Get InChI # @return [String] InChI string + def inchi + unless self["inchi"] + result = `echo "#{self.smiles}" | babel -ismi - -oinchi`.chomp + update(:inchi => result.chomp) unless result.empty? + end + self["inchi"] + end + + # Get InChIKey + # @return [String] InChIKey string def inchikey - update(:inchikey => obconversion(inchi,"inchi","inchikey")) unless self["inchikey"] + update(:inchikey => obconversion(smiles,"smi","inchikey")) unless self["inchikey"] self["inchikey"] end # Get (canonical) smiles # @return [String] Smiles string def smiles - update(:smiles => obconversion(inchi,"inchi","smi")) unless self["smiles"] # should give canonical smiles, "can" seems to give incorrect results + update(:smiles => obconversion(self["smiles"],"smi","can")) #unless self["smiles"] # should give canonical smiles, "can" seems to give incorrect results self["smiles"] end @@ -91,7 +105,7 @@ module OpenTox # @return [String] SDF string def sdf if self.sdf_id.nil? - sdf = obconversion(inchi,"inchi","sdf") + sdf = obconversion(smiles,"smi","sdf") file = Mongo::Grid::File.new(sdf, :filename => "#{id}.sdf",:content_type => "chemical/x-mdl-sdfile") sdf_id = $gridfs.insert_one file update :sdf_id => sdf_id @@ -99,17 +113,29 @@ module OpenTox $gridfs.find_one(_id: self.sdf_id).data end + # Get SVG image + # @return [image/svg] Image data + def svg + if self.svg_id.nil? + svg = obconversion(smiles,"smi","svg") + file = Mongo::Grid::File.new(svg, :filename => "#{id}.svg", :content_type => "image/svg") + update(:image_id => $gridfs.insert_one(file)) + end + $gridfs.find_one(_id: self.svg_id).data + + end + # Get png image # @example # image = compound.png # @return [image/png] Image data def png - if self.image_id.nil? - png = obconversion(inchi,"inchi","_png2") + if self.png_id.nil? + png = obconversion(smiles,"smi","_png2") file = Mongo::Grid::File.new(Base64.encode64(png), :filename => "#{id}.png", :content_type => "image/png") - update(:image_id => $gridfs.insert_one(file)) + update(:png_id => $gridfs.insert_one(file)) end - Base64.decode64($gridfs.find_one(_id: self.image_id).data) + Base64.decode64($gridfs.find_one(_id: self.png_id).data) end |