From 59509099257225b068a13626d3a42eac2f4244ab Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Tue, 13 Oct 2020 11:25:51 +0200
Subject: mutagenicity downloads moved, PaDEL metadata

---
 lib/compound.rb | 11 +++++------
 lib/dataset.rb  | 24 ------------------------
 2 files changed, 5 insertions(+), 30 deletions(-)

(limited to 'lib')

diff --git a/lib/compound.rb b/lib/compound.rb
index 4436e9d..4f0a924 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -111,16 +111,16 @@ class Compound
   # @return [Lazar::Compound]
   def self.from_smiles smiles
     return nil if smiles.match(/\s/) # spaces seem to confuse obconversion and may lead to invalid smiles
-    @smiles = obconversion(smiles,"smi","can") # test if SMILES is correct and return canonical smiles (for compound comparisons)
-    @smiles.empty? ? nil : @smiles
+    smiles = obconversion(smiles,"smi","can") # test if SMILES is correct and return canonical smiles (for compound comparisons)
+    smiles.empty? ? nil : self.new(smiles)
   end
 
   # Create a compound from InChI string
   # @param [String] InChI 
   # @return [OpenTox::Compound] 
   def self.from_inchi inchi
-    @smiles = obconversion(inchi,"inchi","can")
-    @smiles.empty? ? nil : @smiles
+    smiles = obconversion(inchi,"inchi","can")
+    smiles.empty? ? nil : self.new(smiles)
   end
 
   # Create a compound from SDF 
@@ -137,7 +137,7 @@ class Compound
   # @param [String] name, can be also an InChI/InChiKey, CAS number, etc
   # @return [OpenTox::Compound]
   def self.from_name name
-    Compound.from_smiles RestClientWrapper.get(File.join(PUBCHEM_URI,"compound","name",URI.escape(name),"property","CanonicalSMILES","TXT")).chomp
+    self.from_smiles RestClientWrapper.get(File.join(PUBCHEM_URI,"compound","name",URI.escape(name),"property","CanonicalSMILES","TXT")).chomp
   end
 
   # Get InChI
@@ -224,7 +224,6 @@ class Compound
       builder.build(obmol)
 
       sdf = obconversion.write_string(obmol)
-print sdf
       if sdf.match(/.nan/)
         
         #warn "3D generation failed for compound #{identifier}, trying to calculate 2D structure"
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 87e7fef..e30f000 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -114,30 +114,6 @@ end
       dataset
     end
 
-
-    # Convert dataset to SDF format
-    # @return [String] SDF string
-    def to_sdf
-
-      export_features = merged_features
-      export_features = transformed_bioactivity_features if export_features.empty? 
-      export_features = bioactivity_features if export_features.empty? 
-      export_feature = export_features.first
-
-      sdf = ""
-      compounds.each do |compound|
-        sdf_lines = compound.sdf.sub(/\$\$\$\$\n/,"").split("\n")
-        sdf_lines[0] = compound.smiles
-        sdf += sdf_lines.join("\n")
-        sdf += "\n> <#{export_feature.name}>\n"
-        sdf += values(compound,export_feature).uniq.join ","
-        sdf += "\n"
-        sdf += "\n$$$$\n"
-      end
-      sdf
-    end
-
-
     # Merge an array of datasets 
     # @param [Array<OpenTox::Dataset>] datasets Datasets to be merged
     # @param [Array<OpenTox::Feature>] features Features to be merged (same size as datasets)
-- 
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