From 36e10aa98a3d19a78a1889857262abe338a05eef Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Wed, 19 Aug 2015 12:57:23 +0200
Subject: libfminer rpath fixed, installation instructions

---
 lib/compound.rb | 13 ++++++++++++-
 lib/lazar.rb    |  3 ---
 2 files changed, 12 insertions(+), 4 deletions(-)

(limited to 'lib')

diff --git a/lib/compound.rb b/lib/compound.rb
index e51e9ad..fdec019 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -213,11 +213,22 @@ module OpenTox
       when /smi|can|inchi/
         obconversion.write_string(obmol).gsub(/\s/,'').chomp
       when /sdf/
-# TODO set 3D
+p "SDF conversion"
+        # has no effect
+	#obconversion.add_option("gen3D", OpenBabel::OBConversion::GENOPTIONS)
+        # segfaults with openbabel git master 
         #OpenBabel::OBOp.find_type("Gen3D").do(obmol) 
+
+        builder = OpenBabel::OBBuilder.new
+        builder.build(obmol);
+
         sdf = obconversion.write_string(obmol)
+print sdf
         if sdf.match(/.nan/)
+          
+# TODO: fix or eliminate 2d generation
           $logger.warn "3D generation failed for compound #{identifier}, trying to calculate 2D structure"
+          obconversion.set_options("gen2D", OpenBabel::OBConversion::GENOPTIONS)
           #OpenBabel::OBOp.find_type("Gen2D").do(obmol) 
           sdf = obconversion.write_string(obmol)
           if sdf.match(/.nan/)
diff --git a/lib/lazar.rb b/lib/lazar.rb
index 9e2363c..2ea8cba 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -31,9 +31,6 @@ Mongo::Logger.level = Logger::WARN
 #Mongoid.logger = $logger
 
 # Require sub-Repositories
-# TODO: set 
-ENV["LD_LIBRARY_PATH"] = "#{File.join File.dirname(__FILE__),'..','openbabel','lib'}"
-p ENV["LD_LIBRARY_PATH"] 
 require_relative '../libfminer/libbbrc/bbrc' # include before openbabel
 require_relative '../libfminer/liblast/last' # 
 require_relative '../last-utils/lu.rb'
-- 
cgit v1.2.3