rdkit_chem 2019.03.3.1 → 2025.09.3.1

data/Rakefile

@@ -1,9 +1,130 @@
-require "bundler/gem_tasks"
+# frozen_string_literal: true
+
 require 'rake/testtask'
+require 'fileutils'
+
+# Load version
+$LOAD_PATH.unshift File.expand_path('lib', __dir__)
+require 'rdkit_chem/version'
 
-Rake::TestTask.new do |t|
+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
 
-desc "Run tests"
-task :default => :test
+task default: :test

data/ext/rdkit_chem/CMakeLists.txt

@@ -0,0 +1,69 @@
+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

@@ -0,0 +1,5 @@
+all:
+	true
+
+install:
+	true

data/ext/rdkit_chem/extconf.rb

@@ -1,16 +1,14 @@
+# frozen_string_literal: true
+
 require 'fileutils'
 require 'rbconfig'
 require 'mkmf'
 
-main_dir = File.expand_path(File.join(File.dirname(__FILE__),"..",".."))
-
-# install OpenBabel
-
-rdkit_dir = File.join main_dir, 'rdkit'
+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'
-install_dir = rdkit_dir
+build_dir = File.join(src_dir, 'build')
 
 begin
   nr_processors = `getconf _NPROCESSORS_ONLN`.to_i # should be POSIX compatible
@@ -22,32 +20,64 @@ 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/CamAnNguyen/rdkit.git \
-          --branch 'ruby-binding'"
+  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
-FileUtils.mkdir_p install_dir
 Dir.chdir build_dir do
   puts 'Configuring RDKit'
 
-  cmake = "cmake #{src_dir} -DCMAKE_INSTALL_PREFIX=#{install_dir} " \
+  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=ON ' \
-          '-DBOOST_ROOT=/usr/include/'
+          '-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 "make -j#{nr_processors}"
-  system 'make install'
+  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|
+File.open(File.join(File.dirname(__FILE__), 'Makefile'), 'w+') do |makefile|
   makefile.puts "all:\n\ttrue\n\ninstall:\n\ttrue\n"
 end
 

data/lib/rdkit_chem/version.rb

@@ -1,4 +1,4 @@
 module RDKitChem
-  VERSION = '2019.03.3'.freeze
+  VERSION = '2025.09.3'.freeze
   GEMVERSION = VERSION + '.1'
 end

data/lib/rdkit_chem.rb

@@ -1,2 +1,32 @@
-require_relative '../rdkit/Code/lib/RDKitChem'
+# frozen_string_literal: true
+
 require 'rdkit_chem/version'
+
+# Try to load the native extension from multiple possible locations:
+# 1. Pre-compiled gem: lib/rdkit_chem/<ruby_version>/RDKitChem.so
+# 2. Source-compiled gem: rdkit_chem/lib/RDKitChem.so (legacy location)
+
+def find_rdkit_native_extension
+  ruby_version = "#{RUBY_VERSION.split('.')[0..1].join('.')}.0"
+
+  # Location 1: Pre-compiled gem (platform-specific)
+  precompiled_path = File.expand_path("rdkit_chem/#{ruby_version}", __dir__)
+  if File.directory?(precompiled_path)
+    return precompiled_path
+  end
+
+  # Location 2: Source-compiled gem (legacy rdkit_chem/lib/)
+  source_compiled_path = File.expand_path('../rdkit_chem/lib', __dir__)
+  if File.exist?(File.join(source_compiled_path, 'RDKitChem.so')) ||
+     File.exist?(File.join(source_compiled_path, 'RDKitChem.bundle'))
+    return source_compiled_path
+  end
+
+  raise LoadError, "Cannot find RDKitChem native extension. " \
+                   "Searched in:\n  - #{precompiled_path}\n  - #{source_compiled_path}"
+end
+
+native_path = find_rdkit_native_extension
+$LOAD_PATH.unshift(native_path) unless $LOAD_PATH.include?(native_path)
+
+require 'RDKitChem'

data/test/test_rdkit_chem.rb

@@ -1,19 +1,47 @@
 require 'test/unit'
 
 require 'rdkit_chem'
-include RDKit
 
 class RDKitTest < Test::Unit::TestCase
-  def test_ROMol
-    # smi2mol = OBConversion.new
-    # smi2mol.set_in_format("smi")
+  def test_mol_from_smiles
+    smiles = 'CCO'  # ethanol
+    rw_mol = RDKitChem::RWMol.mol_from_smiles(smiles)
+    assert_not_nil(rw_mol)
+    assert_equal(3, rw_mol.get_num_atoms)
+  end
+
+  def test_mol_to_mol_block
+    smiles = 'CCO'  # ethanol
+    rw_mol = RDKitChem::RWMol.mol_from_smiles(smiles)
+    mdl = rw_mol.mol_to_mol_block(true, -1, false)
+    assert_not_nil(mdl)
+    assert(mdl.include?('V2000') || mdl.include?('V3000'))
+  end
+
+  def test_mol_from_mol_block
+    smiles = 'c1ccccc1'  # benzene
+    rw_mol = RDKitChem::RWMol.mol_from_smiles(smiles)
+    mdl = rw_mol.mol_to_mol_block(true, -1, false)
 
-    # 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
+    # Round-trip: mol block back to molecule
+    mol_from_block = RDKitChem::RWMol.mol_from_mol_block(mdl)
+    assert_not_nil(mol_from_block)
+    assert_equal(6, mol_from_block.get_num_atoms)
+  end
+
+  def test_mol_to_smiles
+    smiles = 'CCO'
+    rw_mol = RDKitChem::RWMol.mol_from_smiles(smiles)
+    output_smiles = RDKitChem.mol_to_smiles(rw_mol)
+    assert_not_nil(output_smiles)
+    assert_equal('CCO', output_smiles)
+  end
 
-    # assert_equal(mol.num_atoms, 74)
-    # assert_in_delta(mol.get_mol_wt, 386.65, 0.1)
-    # assert_equal(mol.get_formula, "C27H46O")
+  def test_cholesterol
+    # Cholesterol without chirality
+    smiles = 'CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C'
+    rw_mol = RDKitChem::RWMol.mol_from_smiles(smiles)
+    assert_not_nil(rw_mol)
+    assert_equal(28, rw_mol.get_num_atoms)  # C27H46O has 28 heavy atoms (27 C + 1 O)
   end
 end

metadata

@@ -1,33 +1,141 @@
 --- !ruby/object:Gem::Specification
 name: rdkit_chem
 version: !ruby/object:Gem::Version
-  version: 2019.03.3.1
+  version: 2025.09.3.1
 platform: ruby
 authors:
 - An Nguyen
-autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-07-15 00:00:00.000000000 Z
-dependencies: []
-description: RDKit as a GEM
+date: 1980-01-02 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '13.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '13.0'
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+description: Ruby bindings for RDKit cheminformatics library
 email:
-- annguyen@kit.edu
+- caman.nguyenthanh@gmail.com
 executables: []
 extensions:
 - ext/rdkit_chem/extconf.rb
 extra_rdoc_files: []
 files:
+- CMakeLists.txt
+- Code/CMakeLists.txt
+- Code/RubyWrappers/Abbreviations.i
+- Code/RubyWrappers/AddHs.i
+- Code/RubyWrappers/Atom.i
+- Code/RubyWrappers/AtomIterators.i
+- Code/RubyWrappers/AtomPairs.i
+- Code/RubyWrappers/AvalonLib.i
+- Code/RubyWrappers/BitOps.i
+- Code/RubyWrappers/Bond.i
+- Code/RubyWrappers/BondIterators.i
+- Code/RubyWrappers/CMakeLists.txt
+- Code/RubyWrappers/Canon.i
+- Code/RubyWrappers/ChemDraw.i
+- Code/RubyWrappers/ChemReactions.i
+- Code/RubyWrappers/ChemTransforms.i
+- Code/RubyWrappers/Conformer.i
+- Code/RubyWrappers/Descriptors.i
+- Code/RubyWrappers/Dict.i
+- Code/RubyWrappers/DistGeom.i
+- Code/RubyWrappers/DiversityPick.h
+- Code/RubyWrappers/DiversityPick.i
+- Code/RubyWrappers/ErrorGenerator.i
+- Code/RubyWrappers/ExplicitBitVect.i
+- Code/RubyWrappers/FMCS.i
+- Code/RubyWrappers/FilterCatalog.i
+- Code/RubyWrappers/Fingerprints.i
+- Code/RubyWrappers/ForceField.i
+- Code/RubyWrappers/GeneralizedSubstruct.i
+- Code/RubyWrappers/GenericRDKitException.h
+- Code/RubyWrappers/Inchi.i
+- Code/RubyWrappers/MolBundle.i
+- Code/RubyWrappers/MolDraw2D.i
+- Code/RubyWrappers/MolEnumerator.i
+- Code/RubyWrappers/MolHash.i
+- Code/RubyWrappers/MolOps.i
+- Code/RubyWrappers/MolStandardize.i
+- Code/RubyWrappers/MolSupplier.i
+- Code/RubyWrappers/MolTransforms.i
+- Code/RubyWrappers/MolWriters.i
+- Code/RubyWrappers/MonomerInfo.i
+- Code/RubyWrappers/MorganFingerprints.h
+- Code/RubyWrappers/MorganFingerprints.i
+- Code/RubyWrappers/PeriodicTable.i
+- Code/RubyWrappers/Queries.i
+- Code/RubyWrappers/QueryAtom.i
+- Code/RubyWrappers/QueryBond.i
+- Code/RubyWrappers/QueryOps.i
+- Code/RubyWrappers/RDKitExceptions.i
+- Code/RubyWrappers/RDLogger.i
+- Code/RubyWrappers/RDProps.i
+- Code/RubyWrappers/RGroupDecomposition.i
+- Code/RubyWrappers/ROMol.i
+- Code/RubyWrappers/RWMol.i
+- Code/RubyWrappers/RascalMCES.i
+- Code/RubyWrappers/ReactionFingerprints.i
+- Code/RubyWrappers/RingInfo.i
+- Code/RubyWrappers/Rings.i
+- Code/RubyWrappers/SanitException.i
+- Code/RubyWrappers/ScaffoldNetwork.i
+- Code/RubyWrappers/SmartsWrite.i
+- Code/RubyWrappers/SmilesParse.i
+- Code/RubyWrappers/SmilesWrite.i
+- Code/RubyWrappers/StereoGroup.i
+- Code/RubyWrappers/Streams.i
+- Code/RubyWrappers/Subgraphs.i
+- Code/RubyWrappers/Subset.i
+- Code/RubyWrappers/SubstanceGroup.i
+- Code/RubyWrappers/SubstructLibrary.i
+- Code/RubyWrappers/TautomerQuery.i
+- Code/RubyWrappers/Trajectory.i
+- Code/RubyWrappers/boost_tuple.i
+- Code/RubyWrappers/extend_std_vector.i
+- Code/RubyWrappers/gmwrapper/CMakeLists.txt
+- Code/RubyWrappers/gmwrapper/GraphMolRuby.i
+- Code/RubyWrappers/gmwrapper/std_list.i
+- Code/RubyWrappers/point.i
+- Code/RubyWrappers/transforms.i
+- Code/RubyWrappers/types.i
+- README.md
 - Rakefile
+- ext/rdkit_chem/CMakeLists.txt
+- ext/rdkit_chem/Makefile
 - ext/rdkit_chem/extconf.rb
 - lib/rdkit_chem.rb
 - lib/rdkit_chem/version.rb
 - test/test_rdkit_chem.rb
 homepage: https://github.com/CamAnNguyen/rdkit-chem
 licenses:
-- BSD
+- BSD-3-Clause
 metadata: {}
-post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -35,17 +143,15 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 2.7.0
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.9
-signing_key: 
+rubygems_version: 4.0.1
 specification_version: 4
-summary: Ruby gem for RDKit !
+summary: Ruby gem for RDKit
 test_files:
 - test/test_rdkit_chem.rb