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authorChristoph Helma <helma@in-silico.ch>2015-08-19 12:57:23 +0200
committerChristoph Helma <helma@in-silico.ch>2015-08-19 12:57:23 +0200
commit36e10aa98a3d19a78a1889857262abe338a05eef (patch)
tree38ac1c2e03ade553ea3402d79934c295e76ce6c9 /lib
parent4067d78c78c1f503b5f21d043ece8042260a3d78 (diff)
libfminer rpath fixed, installation instructions
Diffstat (limited to 'lib')
-rw-r--r--lib/compound.rb13
-rw-r--r--lib/lazar.rb3
2 files changed, 12 insertions, 4 deletions
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'