From 57bb9c2c691d350dce8c30b862030973043818cc Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Wed, 19 Aug 2015 14:00:55 +0200
Subject: hydrogens added for 3d generation

---
 README.md            | 25 ++++++++++---------------
 ext/lazar/extconf.rb |  1 -
 lib/compound.rb      | 15 ++++++++++-----
 3 files changed, 20 insertions(+), 21 deletions(-)

diff --git a/README.md b/README.md
index ac40156..e0b17d1 100644
--- a/README.md
+++ b/README.md
@@ -12,33 +12,28 @@ Dependencies
   
   You will also need at least mongodb version 3.0, but Debian "Wheezy" provides version 2.4. Please follow the instructions at http://docs.mongodb.org/manual/tutorial/install-mongodb-on-debian/:
 
-```
-   sudo apt-key adv --keyserver keyserver.ubuntu.com --recv 7F0CEB10
-   echo "deb http://repo.mongodb.org/apt/debian wheezy/mongodb-org/3.0 main" | sudo tee /etc/apt/sources.list.d/mongodb-org-3.0.list
-   sudo apt-get update
-   sudo apt-get install -y mongodb-org
-```
+  ```
+  sudo apt-key adv --keyserver keyserver.ubuntu.com --recv 7F0CEB10
+  echo "deb http://repo.mongodb.org/apt/debian wheezy/mongodb-org/3.0 main" | sudo tee /etc/apt/sources.list.d/mongodb-org-3.0.list
+  sudo apt-get update
+  sudo apt-get install -y mongodb-org
+  ```
 
 Installation
 ------------
 
   `gem install lazar`
 
-  Please be patient, the compilation of OpenBabel and Fminer libraries can be very time consuming. If installation fails you can try a
+  Please be patient, the compilation of OpenBabel and Fminer libraries can be very time consuming. If installation fails you can try to install manually:
 
-  Manual installation
-  ...................
-
-```
+  ```
   git clone https://github.com/opentox/lazar.git
   cd lazar
   ruby ext/lazar/extconf.rb
   bundle install
-```
-
-  This should give you more verbose information that can help in debugging (e.g. to identify missing libraries).
+  ```
 
-  This should
+  The output should give you more verbose information that can help in debugging (e.g. to identify missing libraries).
 
 Documentation
 -------------
diff --git a/ext/lazar/extconf.rb b/ext/lazar/extconf.rb
index b9db3f0..0ee5e93 100644
--- a/ext/lazar/extconf.rb
+++ b/ext/lazar/extconf.rb
@@ -49,7 +49,6 @@ Dir.chdir build_dir do
   ENV["PKG_CONFIG_PATH"] = File.dirname(File.expand_path(Dir["#{install_dir}/**/openbabel*pc"].first))
 end
 
-# get include and lib from pkg-config
 ob_include= File.expand_path File.join(File.dirname(__FILE__),"../../openbabel/include/openbabel-2.0")
 ob_lib= File.expand_path File.join(File.dirname(__FILE__),"../../openbabel/lib")
 
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
-- 
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