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-rw-r--r--lib/compound.rb21
1 files changed, 7 insertions, 14 deletions
diff --git a/lib/compound.rb b/lib/compound.rb
index a85507b..189db7b 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -29,30 +29,21 @@ module OpenTox
# @param [String] smiles Smiles string
# @return [OpenTox::Compound] Compound
def self.from_smiles(smiles)
- c = Compound.new
- c.inchi = Compound.smiles2inchi(smiles)
- c.uri = File.join(CONFIG[:services]["opentox-compound"],URI.escape(c.inchi))
- c
+ Compound.new RestClientWrapper.post(CONFIG[:services]["opentox-compound"], smiles, :content_type => 'chemical/x-daylight-smiles').to_s.chomp
end
# Create a compound from inchi string
# @param [String] smiles InChI string
# @return [OpenTox::Compound] Compound
def self.from_inchi(inchi)
- c = Compound.new
- c.inchi = inchi
- c.uri = File.join(CONFIG[:services]["opentox-compound"],URI.escape(c.inchi))
- c
+ Compound.new RestClientWrapper.post(CONFIG[:services]["opentox-compound"], inchi, :content_type => 'chemical/x-inchi').to_s.chomp
end
# Create a compound from sdf string
# @param [String] smiles SDF string
# @return [OpenTox::Compound] Compound
def self.from_sdf(sdf)
- c = Compound.new
- c.inchi = Compound.sdf2inchi(sdf)
- c.uri = File.join(CONFIG[:services]["opentox-compound"],URI.escape(c.inchi))
- c
+ Compound.new RestClientWrapper.post(CONFIG[:services]["opentox-compound"], sdf, :content_type => 'chemical/x-mdl-sdfile').to_s.chomp
end
# Create a compound from name. Relies on an external service for name lookups.
@@ -77,13 +68,13 @@ module OpenTox
# Get (canonical) smiles
# @return [String] Smiles string
def to_smiles
- Compound.obconversion(@inchi,'inchi','can')
+ RestClientWrapper.get(@uri, :accept => 'chemical/x-daylight-smiles').chomp
end
# Get sdf
# @return [String] SDF string
def to_sdf
- Compound.obconversion(@inchi,'inchi','sdf')
+ RestClientWrapper.get(@uri, :accept => 'chemical/x-mdl-sdfile').chomp
end
# Get gif image
@@ -118,6 +109,7 @@ module OpenTox
end
end
+=begin
# Match a smarts string
# @example
# compound = OpenTox::Compound.from_name("Benzene")
@@ -195,5 +187,6 @@ module OpenTox
obconversion.write_string(obmol)
end
end
+=end
end
end