openbabel-heroku 2.3.2.0

data/Rakefile

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+require "bundler/gem_tasks"
+require 'rake/testtask'
+
+Rake::TestTask.new do |t|
+  t.libs << 'test'
+end
+
+desc "Run tests"
+task :default => :test

data/ext/openbabel/extconf.rb

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+require 'fileutils'
+require 'mkmf'
+require 'rbconfig'
+$:.unshift File.expand_path('../../../lib', __FILE__)
+require 'openbabel/version'
+
+ob_num_ver = OpenBabel::VERSION
+ob_ver     = "openbabel-"+ob_num_ver
+
+RUBY=File.join(RbConfig::CONFIG['bindir'], RbConfig::CONFIG['ruby_install_name'])
+
+main_dir = File.expand_path(File.join(File.dirname(__FILE__),"..",".."))
+src_dir = File.join main_dir, ob_ver
+build_dir = File.join main_dir, "build"
+install_dir = main_dir 
+install_lib_dir = File.join install_dir, "lib"
+lib_dir = File.join main_dir, "lib", "openbabel"
+ruby_src_dir = File.join src_dir, "scripts", "ruby"
+cmake_dir = File.join main_dir, "cmake-2.8.11.2"
+
+begin
+  nr_processors = `grep processor /proc/cpuinfo | wc -l` # speed up compilation, Linux only
+rescue
+  nr_processors = 1
+end
+
+begin
+  Dir.chdir main_dir do
+    FileUtils.rm_rf src_dir
+    system "curl -L 'http://www.cmake.org/files/v2.8/cmake-2.8.11.2.tar.gz' | tar xz"
+    
+    Dir.chdir cmake_dir do
+      system "./bootstrap"
+      system "make"
+    end
+    
+  end
+    
+  Dir.chdir main_dir do  
+    puts "Downloading OpenBabel sources"
+    system "curl -L -d use_mirror=netcologne 'http://downloads.sourceforge.net/project/openbabel/openbabel/#{ob_num_ver}/openbabel-#{ob_num_ver}.tar.gz' | tar xz"
+    system "sed -i -e 's/-Wl,-flat_namespace//;s/-flat_namespace//' #{File.join ruby_src_dir, "extconf.rb"}" # remove unrecognized compiler option
+    system "sed -i -e 's/Init_OpenBabel/Init_openbabel/g' #{File.join ruby_src_dir,"*cpp"}" # fix swig bindings
+  end
+  FileUtils.mkdir_p build_dir
+  FileUtils.mkdir_p install_dir
+  Dir.chdir build_dir do
+    puts "Configuring OpenBabel"
+    
+    
+    cmake = "#{cmake_dir}/bin/cmake #{src_dir} -DCMAKE_INSTALL_PREFIX=#{install_dir} -DBUILD_GUI=OFF -DENABLE_TESTS=OFF -DRUBY_BINDINGS=ON"
+    # set rpath for local installations
+    # http://www.cmake.org/Wiki/CMake_RPATH_handling
+    # http://vtk.1045678.n5.nabble.com/How-to-force-cmake-not-to-remove-install-rpath-td5721193.html
+    cmake += " -DCMAKE_INSTALL_RPATH:STRING=\"#{install_lib_dir}\"" unless have_library('openbabel')
+    system cmake
+  end
+  unless have_library('openbabel')
+    # local installation in gem directory
+    Dir.chdir build_dir do
+      puts "OpenBabel not installed. Compiling sources."
+      system "make -j#{nr_processors}"
+      system "make install"
+      ENV["PKG_CONFIG_PATH"] = File.dirname(File.expand_path(Dir["#{install_dir}/**/openbabel*pc"].first))
+    end
+  end
+  # compile ruby bindings
+  puts "Compiling and installing OpenBabel Ruby bindings."
+  Dir.chdir ruby_src_dir do
+    # fix rpath
+    system "sed -i 's|with_ldflags.*$|with_ldflags(\"#\$LDFLAGS -dynamic -Wl,-rpath,#{install_lib_dir}\") do|' #{File.join(ruby_src_dir,'extconf.rb')}" unless have_library('openbabel')
+    # get include and lib from pkg-config
+    ob_include=`pkg-config openbabel-2.0 --cflags-only-I`.sub(/\s+/,'').sub(/-I/,'')
+    ob_lib=`pkg-config openbabel-2.0 --libs-only-L`.sub(/\s+/,'').sub(/-L/,'')
+    system "#{RUBY} extconf.rb --with-openbabel-include=#{ob_include} --with-openbabel-lib=#{ob_lib}"
+    system "make -j#{nr_processors}"
+  end
+  FileUtils.cp(ruby_src_dir+"/openbabel.#{RbConfig::CONFIG["DLEXT"]}", "./")
+	File.open('Makefile', 'w') do |makefile|
+		makefile.write <<"EOF"
+.PHONY: openbabel.#{RbConfig::CONFIG["DLEXT"]}
+openbabel.#{RbConfig::CONFIG["DLEXT"]}:
+	chmod 755 openbabel.#{RbConfig::CONFIG["DLEXT"]}
+
+.PHONY: install
+install:
+	mkdir -p #{lib_dir}
+	mv openbabel.#{RbConfig::CONFIG["DLEXT"]} #{lib_dir}
+EOF
+	end
+ensure
+  FileUtils.remove_entry_secure src_dir, build_dir
+end

data/lib/openbabel.rb

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+require 'openbabel/openbabel'
+require 'openbabel/version'
+# http://sourceforge.net/mailarchive/message.php?msg_id=31065700
+OpenBabel::OBConversion.new # required to load plugins

data/lib/openbabel/version.rb

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+module OpenBabel
+  VERSION = '2.3.2'
+  GEMVERSION = VERSION + '.0'
+end

data/test/test_openbabel.rb

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+require 'test/unit'
+
+$:.unshift File.expand_path('../../lib', __FILE__)
+$:.unshift File.expand_path('../../ext', __FILE__)
+require 'openbabel'
+include OpenBabel
+
+class OBTest < Test::Unit::TestCase
+  def test_obmol
+    # Code from http://goo.gl/9H1LZ
+
+    smi2mol = OBConversion.new
+    smi2mol.set_in_format("smi")
+
+    mol = OBMol.new
+    smi2mol.read_string(mol, 'CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C') # cholesterol, no chirality
+    mol.add_hydrogens
+
+    assert_equal(mol.num_atoms, 74)
+    assert_in_delta(mol.get_mol_wt, 386.65, 0.1)
+    assert_equal(mol.get_formula, "C27H46O")
+
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: openbabel-heroku
+version: !ruby/object:Gem::Version
+  version: 2.3.2.0
+  prerelease: 
+platform: ruby
+authors:
+- Dominic Lütjohann
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-04-03 00:00:00.000000000 Z
+dependencies: []
+description: OpenBabel as a GEM
+email: 
+executables: []
+extensions:
+- ext/openbabel/extconf.rb
+extra_rdoc_files: []
+files:
+- Rakefile
+- lib/openbabel.rb
+- lib/openbabel/version.rb
+- test/test_openbabel.rb
+- ext/openbabel/extconf.rb
+homepage: http://github.com/cominch/openbabel-heroku-gem
+licenses:
+- GPL-3
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.25
+signing_key: 
+specification_version: 3
+summary: OpenBabel!
+test_files:
+- test/test_openbabel.rb