diff options
Diffstat (limited to 'lib/compound.rb')
| -rw-r--r-- | lib/compound.rb | 15 |
1 files changed, 10 insertions, 5 deletions
diff --git a/lib/compound.rb b/lib/compound.rb index fdec019..6d755da 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -46,7 +46,6 @@ module OpenTox # @param [String] smiles Smiles string # @return [OpenTox::Compound] Compound def self.from_smiles smiles - # do not store smiles because it might be noncanonical 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.") @@ -62,7 +61,8 @@ module OpenTox # 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 = `echo "#{inchi}" | "#{File.join(File.dirname(__FILE__),"..","openbabel","bin","babel")}" -iinchi - -ocan`.chomp.strip + smiles = obconversion(inchi,"inchi","can") 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 @@ -92,7 +92,8 @@ module OpenTox def inchi unless self["inchi"] - result = `echo "#{self.smiles}" | "#{File.join(File.dirname(__FILE__),"..","openbabel","bin","babel")}" -ismi - -oinchi`.chomp + 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? end self["inchi"] @@ -108,7 +109,7 @@ module OpenTox # Get (canonical) smiles # @return [String] Smiles string def smiles - update(:smiles => obconversion(self["smiles"],"smi","can")) #unless self["smiles"] # should give canonical smiles, "can" seems to give incorrect results + update(:smiles => obconversion(self["smiles"],"smi","can")) unless self["smiles"] self["smiles"] end @@ -219,8 +220,12 @@ p "SDF conversion" # segfaults with openbabel git master #OpenBabel::OBOp.find_type("Gen3D").do(obmol) + # TODO: find disconnected structures + # strip_salts + # separate + obmol.add_hydrogens builder = OpenBabel::OBBuilder.new - builder.build(obmol); + builder.build(obmol) sdf = obconversion.write_string(obmol) print sdf |