rdkit_chem 2025.09.3.1-x86_64-linux

data/Rakefile

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+# frozen_string_literal: true
+
+require 'rake/testtask'
+require 'fileutils'
+
+# Load version
+$LOAD_PATH.unshift File.expand_path('lib', __dir__)
+require 'rdkit_chem/version'
+
+VERSION = RDKitChem::GEMVERSION
+NATIVE_DIR = 'rdkit_chem/lib'
+
+desc 'Run tests'
+Rake::TestTask.new(:test) do |t|
+  t.libs << 'lib'
+  t.libs << 'test'
+  t.pattern = 'test/**/*_test.rb,test/**/test_*.rb'
+  t.verbose = true
+end
+
+desc 'Build source gem (requires compilation on install)'
+task :build do
+  sh 'gem build rdkit_chem.gemspec'
+end
+
+desc 'Build pre-compiled gem for current platform (x86_64-linux)'
+task :build_native do
+  # Check that native libraries exist
+  unless File.exist?(File.join(NATIVE_DIR, 'RDKitChem.so'))
+    abort "ERROR: Native extension not found at #{NATIVE_DIR}/RDKitChem.so\n" \
+          "Run 'gem install rdkit_chem' first to compile, or build manually."
+  end
+
+  # Get Ruby version for directory structure
+  ruby_version = "#{RUBY_VERSION.split('.')[0..1].join('.')}.0"
+  target_dir = "lib/rdkit_chem/#{ruby_version}"
+
+  puts "Packaging pre-compiled gem for Ruby #{ruby_version}..."
+
+  # Create target directory
+  FileUtils.mkdir_p(target_dir)
+
+  # Copy native extension and all shared libraries
+  Dir.glob("#{NATIVE_DIR}/*.so*").each do |lib|
+    # Skip symlinks, copy only real files
+    next if File.symlink?(lib)
+    dest = File.join(target_dir, File.basename(lib))
+    FileUtils.cp(lib, dest, verbose: true)
+  end
+
+  # Also copy symlinks (they're needed for library resolution)
+  # This includes both .so -> .so.1 and .so.1 -> .so.1.version symlinks
+  Dir.glob("#{NATIVE_DIR}/*.so*").each do |lib|
+    next unless File.symlink?(lib)
+    link_target = File.readlink(lib)
+    dest = File.join(target_dir, File.basename(lib))
+    FileUtils.rm_f(dest)
+    FileUtils.ln_s(link_target, dest, verbose: true)
+  end
+
+  # Build the platform-specific gem
+  ENV['RDKIT_PRECOMPILED'] = '1'
+  sh 'gem build rdkit_chem.gemspec'
+  ENV.delete('RDKIT_PRECOMPILED')
+
+  # Clean up
+  FileUtils.rm_rf(target_dir)
+
+  puts "\nBuilt: rdkit_chem-#{VERSION}-#{Gem::Platform.local}.gem"
+end
+
+desc 'Apply RPATH fix to existing native extension (no recompile needed)'
+task :fix_rpath do
+  so_file = File.join(NATIVE_DIR, 'RDKitChem.so')
+  unless File.exist?(so_file)
+    abort "ERROR: #{so_file} not found"
+  end
+
+  # Check if patchelf is available
+  unless system('which patchelf > /dev/null 2>&1')
+    abort "ERROR: patchelf not installed. Run: sudo apt install patchelf"
+  end
+
+  # Fix RPATH on all shared libraries (including versioned ones like *.so.1.2026.03.1pre)
+  puts "Setting RPATH to $ORIGIN on all shared libraries..."
+  count = 0
+  Dir.glob("#{NATIVE_DIR}/*.so*").each do |lib|
+    next if File.symlink?(lib)  # Skip symlinks
+    next if lib.end_with?('.a') # Skip static libraries
+    system("patchelf --set-rpath '$ORIGIN' '#{lib}' 2>/dev/null")
+    count += 1
+  end
+  puts "Fixed RPATH on #{count} libraries"
+
+  # Verify main extension
+  puts "\nVerifying RPATH on #{so_file}:"
+  sh "readelf -d #{so_file} | grep -E '(RPATH|RUNPATH)' || echo 'No RPATH found'"
+end
+
+desc 'Test that native extension loads without LD_LIBRARY_PATH'
+task :test_native do
+  so_dir = File.expand_path(NATIVE_DIR, __dir__)
+  puts "Testing native extension loading from #{so_dir}..."
+
+  # Test without LD_LIBRARY_PATH
+  result = system("ruby -I#{so_dir} -Ilib -e \"require 'rdkit_chem'; puts 'SUCCESS: RDKitChem loaded'\"")
+
+  if result
+    puts "\nNative extension loads correctly without LD_LIBRARY_PATH!"
+  else
+    puts "\nFAILED: Still requires LD_LIBRARY_PATH. Run 'rake fix_rpath' first."
+    exit 1
+  end
+end
+
+desc 'Install gem locally'
+task :install => :build do
+  sh "gem install rdkit_chem-#{VERSION}.gem"
+end
+
+desc 'Clean build artifacts'
+task :clean do
+  FileUtils.rm_f(Dir.glob('*.gem'))
+  FileUtils.rm_rf('lib/rdkit_chem/3.0')
+  FileUtils.rm_rf('lib/rdkit_chem/3.1')
+  FileUtils.rm_rf('lib/rdkit_chem/3.2')
+  FileUtils.rm_rf('lib/rdkit_chem/3.3')
+end
+
+task default: :test

data/ext/rdkit_chem/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.8)
+
+# Apple: Don't modify install_name when touching RPATH.
+if(POLICY CMP0068)
+  cmake_policy(SET CMP0068 NEW)
+endif()
+# target_sources: use absolute path for INTERFACE_SOURCES.
+if(POLICY CMP0076)
+  cmake_policy(SET CMP0076 NEW)
+endif()
+# SWIG: use standard target name.
+if(POLICY CMP0078)
+  cmake_policy(SET CMP0078 NEW)
+endif()
+# SWIG: use SWIG_MODULE_NAME property.
+if(POLICY CMP0086)
+  cmake_policy(SET CMP0086 NEW)
+endif()
+
+project (GraphMolRuby)
+
+include_directories( ${RDKit_ExternalDir} )
+
+find_package(Ruby REQUIRED)
+
+INCLUDE_DIRECTORIES(${RDKit_INCLUDE_DIR} ${RUBY_INCLUDE_PATH})
+
+SET_SOURCE_FILES_PROPERTIES(GraphMolRuby.i PROPERTIES CPLUSPLUS ON )
+
+SET(CMAKE_SWIG_OUTDIR ${CMAKE_CURRENT_SOURCE_DIR}/swig_ruby )
+
+if(RDK_BUILD_INCHI_SUPPORT)
+  SET(CMAKE_SWIG_FLAGS "-DRDK_BUILD_INCHI_SUPPORT" ${CMAKE_SWIG_FLAGS} )
+endif()
+if(RDK_BUILD_AVALON_SUPPORT)
+  SET(CMAKE_SWIG_FLAGS "-DRDK_BUILD_AVALON_SUPPORT" ${CMAKE_SWIG_FLAGS} )
+endif()
+if(RDK_USE_BOOST_IOSTREAMS)
+  SET(CMAKE_SWIG_FLAGS "-DRDK_USE_BOOST_IOSTREAMS" ${CMAKE_SWIG_FLAGS} )
+endif()
+
+FILE(GLOB SWIG_SRC_FILES "${CMAKE_CURRENT_SOURCE_DIR}/../*.i")
+
+# we added all source files, now remove the ones that we're not supporting in this build:
+if(NOT RDK_BUILD_AVALON_SUPPORT)
+LIST(REMOVE_ITEM SWIG_SRC_FILES "${CMAKE_CURRENT_SOURCE_DIR}/../AvalonLib.i")
+endif()
+
+if(NOT RDK_BUILD_INCHI_SUPPORT)
+LIST(REMOVE_ITEM SWIG_SRC_FILES "${CMAKE_CURRENT_SOURCE_DIR}/../Inchi.i")
+endif()
+
+SET(SWIG_MODULE_RDKitChem_EXTRA_DEPS ${SWIG_SRC_FILES} )
+SET(CMAKE_SWIG_FLAGS -small -naturalvar -autorename)
+
+SWIG_ADD_LIBRARY(RDKitChem TYPE MODULE LANGUAGE ruby SOURCES GraphMolRuby.i)
+
+# it doesnt seem like the threading libs should need to be here, but
+# as of Oct 2012 using boost 1.51 under at least ubuntu 12.04 we get a
+# link error if they aren't there.
+SWIG_LINK_LIBRARIES(RDKitChem
+  ${RDKit_Wrapper_Libs}
+  ${Boost_SERIALIZATION_LIBRARY}
+  ${RDKit_THREAD_LIBS})
+
+MESSAGE("serial: ${Boost_SERIALIZATION_LIBRARY}")
+MESSAGE("THREAD: ${RDKit_THREAD_LIBS}")
+
+INSTALL(TARGETS RDKitChem LIBRARY DESTINATION lib)

data/ext/rdkit_chem/Makefile

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+all:
+	true
+
+install:
+	true

data/ext/rdkit_chem/extconf.rb

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+# frozen_string_literal: true
+
+require 'fileutils'
+require 'rbconfig'
+require 'mkmf'
+
+main_dir = File.expand_path(File.join(File.dirname(__FILE__), '..', '..'))
+rdkit_dir = File.join(main_dir, 'rdkit')
+install_dir = File.join(main_dir, 'rdkit_chem')
+src_dir = rdkit_dir
+build_dir = File.join(src_dir, 'build')
+
+begin
+  nr_processors = `getconf _NPROCESSORS_ONLN`.to_i # should be POSIX compatible
+rescue StandardError
+  nr_processors = 1
+end
+
+FileUtils.mkdir_p rdkit_dir
+Dir.chdir main_dir do
+  FileUtils.rm_rf src_dir
+  puts 'Downloading RDKit sources'
+  git = 'git clone https://github.com/rdkit/rdkit.git'
+  system git
+end
+
+Dir.chdir(src_dir) do
+  checkout = 'git checkout c2e48f41d88ddc15c6e1f818d1c4ced70b7f20d1'
+  system checkout
+end
+
+FileUtils.cp_r(
+  File.join(main_dir, 'Code'),
+  File.join(rdkit_dir),
+  remove_destination: true
+)
+
+FileUtils.cp_r(
+  File.join(main_dir, 'CMakeLists.txt'),
+  File.join(rdkit_dir),
+  remove_destination: true
+)
+
+host_os = RbConfig::CONFIG['host_os']
+is_linux = host_os =~ /linux/
+is_mac = host_os =~ /darwin/
+ld_path = ''
+
+if is_linux || is_mac
+  ld_string = is_linux ? 'LD_LIBRARY_PATH' : 'DYLD_LIBRARY_PATH'
+  ld_path = "#{ld_string}=#{install_dir}/lib"
+  env_ld = ENV[ld_string] || ''
+
+  ld_path += ":#{env_ld}" unless env_ld.empty?
+end
+
+FileUtils.mkdir_p build_dir
+Dir.chdir build_dir do
+  puts 'Configuring RDKit'
+
+  cmake = "#{ld_path} cmake #{src_dir} -DRDK_INSTALL_INTREE=OFF " \
+          "-DCMAKE_INSTALL_PREFIX=#{install_dir} " \
+          '-DCMAKE_BUILD_TYPE=Release -DRDK_BUILD_PYTHON_WRAPPERS=OFF ' \
+          '-DRDK_BUILD_SWIG_WRAPPERS=ON -DRDK_BUILD_INCHI_SUPPORT=OFF ' \
+          '-DBoost_NO_BOOST_CMAKE=ON'
+  system cmake
+end
+
+# local installation in gem directory
+Dir.chdir build_dir do
+  puts 'Compiling RDKit sources.'
+  system "#{ld_path} make -j#{nr_processors}"
+  system "#{ld_path} make install"
+end
+
+# Remove compiled file, free spaces
+FileUtils.remove_dir(rdkit_dir)
+
+# create a fake Makefile
+File.open(File.join(File.dirname(__FILE__), 'Makefile'), 'w+') do |makefile|
+  makefile.puts "all:\n\ttrue\n\ninstall:\n\ttrue\n"
+end
+
+$makefile_created = true

data/lib/rdkit_chem/3.3.0/libRDKitAbbreviations.so

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data/lib/rdkit_chem/3.3.0/libRDKitAbbreviations.so.1

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data/lib/rdkit_chem/3.3.0/libRDKitAlignment.so

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data/lib/rdkit_chem/3.3.0/libRDKitAlignment.so.1

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data/lib/rdkit_chem/3.3.0/libRDKitCIPLabeler.so

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data/lib/rdkit_chem/3.3.0/libRDKitCIPLabeler.so.1

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data/lib/rdkit_chem/3.3.0/libRDKitCatalogs.so

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data/lib/rdkit_chem/3.3.0/libRDKitCatalogs.so.1

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data/lib/rdkit_chem/3.3.0/libRDKitChemDraw.so

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data/lib/rdkit_chem/3.3.0/libRDKitChemDraw.so.1

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data/lib/rdkit_chem/3.3.0/libRDKitChemReactions.so

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data/lib/rdkit_chem/3.3.0/libRDKitChemReactions.so.1

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data/lib/rdkit_chem/3.3.0/libRDKitChemTransforms.so

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data/lib/rdkit_chem/3.3.0/libRDKitChemTransforms.so.1

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data/lib/rdkit_chem/3.3.0/libRDKitChemicalFeatures.so

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data/lib/rdkit_chem/3.3.0/libRDKitDataStructs.so

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data/lib/rdkit_chem/3.3.0/libRDKitDepictor.so

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data/lib/rdkit_chem/3.3.0/libRDKitDeprotect.so

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data/lib/rdkit_chem/3.3.0/libRDKitDescriptors.so

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data/lib/rdkit_chem/3.3.0/libRDKitDistGeomHelpers.so

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data/lib/rdkit_chem/3.3.0/libRDKitDistGeometry.so

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data/lib/rdkit_chem/3.3.0/libRDKitDistGeometry.so.1

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data/lib/rdkit_chem/3.3.0/libRDKitEigenSolvers.so

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data/lib/rdkit_chem/3.3.0/libRDKitEnumerateStereoisomers.so

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data/lib/rdkit_chem/3.3.0/libRDKitFMCS.so

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data/lib/rdkit_chem/3.3.0/libRDKitFileParsers.so

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data/lib/rdkit_chem/3.3.0/libRDKitFilterCatalog.so

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data/lib/rdkit_chem/3.3.0/libRDKitFingerprints.so

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data/lib/rdkit_chem/3.3.0/libRDKitForceField.so

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data/lib/rdkit_chem/3.3.0/libRDKitForceFieldHelpers.so

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data/lib/rdkit_chem/3.3.0/libRDKitFragCatalog.so

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data/lib/rdkit_chem/3.3.0/libRDKitGeneralizedSubstruct.so

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data/lib/rdkit_chem/3.3.0/libRDKitGenericGroups.so

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data/lib/rdkit_chem/3.3.0/libRDKitGraphMol.so

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data/lib/rdkit_chem/3.3.0/libRDKitInfoTheory.so

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data/lib/rdkit_chem/3.3.0/libRDKitMolAlign.so

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data/lib/rdkit_chem/3.3.0/libRDKitMolCatalog.so

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data/lib/rdkit_chem/3.3.0/libRDKitMolChemicalFeatures.so

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data/lib/rdkit_chem/3.3.0/libRDKitMolDraw2D.so

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data/lib/rdkit_chem/3.3.0/libRDKitMolEnumerator.so

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data/lib/rdkit_chem/3.3.0/libRDKitMolHash.so

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data/lib/rdkit_chem/3.3.0/libRDKitMolHash.so.1

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data/lib/rdkit_chem/3.3.0/libRDKitMolInteractionFields.so

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