diff options
Diffstat (limited to 'lib/compound.rb')
| -rw-r--r-- | lib/compound.rb | 14 |
1 files changed, 12 insertions, 2 deletions
diff --git a/lib/compound.rb b/lib/compound.rb index 5343aa0..10deabc 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -13,6 +13,7 @@ module OpenTox field :smiles, type: String field :inchikey, type: String field :names, type: Array + field :warning, type: String field :cid, type: String field :chemblid, type: String field :png_id, type: BSON::ObjectId @@ -46,7 +47,12 @@ 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 :smiles => obconversion(smiles,"smi","can") + 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.") + else + Compound.find_or_create_by :smiles => obconversion(smiles,"smi","can") + end end # Create a compound from inchi string @@ -57,7 +63,11 @@ module OpenTox # 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) + if smiles.empty? + Compound.find_or_create_by(:warning => "InChi parsing failed for #{inchi}, this may be caused by an incorrect InChi string or a bug in OpenBabel libraries.") + else + Compound.find_or_create_by(:smiles => smiles, :inchi => inchi) + end end # Create a compound from sdf string |