openbabel-ruby 3.1.1.0 → 3.1.1.2

data/ext/openbabel/patches/scripts/CMakeLists.txt

@@ -0,0 +1,239 @@
+# Patched for CMake 4.x compatibility
+cmake_minimum_required(VERSION 3.5...3.31)
+# Library versioning (used in Mac Python bindings)x
+set(SOVERSION 4)
+
+if (RUN_SWIG)
+  include(FindSWIG)
+  # This module finds an installed SWIG. It sets the following variables:
+  # SWIG_FOUND - set to true if SWIG is found
+  # SWIG_DIR - the directory where swig is installed
+  # SWIG_EXECUTABLE - the path to the swig executable
+  # SWIG_VERSION   - the version number of the swig executable
+
+  find_package(SWIG 2.0)
+  if (NOT SWIG_FOUND)
+    message(STATUS "SWIG 2.0 NOT found")
+    return()
+  else ()
+    if(SWIG_VERSION VERSION_GREATER_EQUAL 4.0)
+      set(doxygen_switch "-doxygen")
+    endif()
+  endif (NOT SWIG_FOUND)
+endif (RUN_SWIG)
+
+# The following needs to be kept in synch with ..\CMakeLists.txt
+if(EIGEN3_FOUND)
+  set (eigen_define "-DHAVE_EIGEN" "-DHAVE_EIGEN3")
+  include_directories(${EIGEN3_INCLUDE_DIR})
+  set (CPPFLAGS_VALUE "-I${EIGEN3_INCLUDE_DIR}")
+  set (CPPFLAGS_TEXT "CPPFLAGS=${CPPFLAGS_VALUE}")
+else()
+  if(EIGEN2_FOUND)
+    set (eigen_define "-DHAVE_EIGEN")
+    include_directories(${EIGEN2_INCLUDE_DIR})
+    set (CPPFLAGS_VALUE "-I${EIGEN2_INCLUDE_DIR}")
+    set (CPPFLAGS_TEXT "CPPFLAGS=${CPPFLAGS_VALUE}")
+  endif()
+endif()
+
+###################
+# Python
+###################
+
+if (PYTHON_BINDINGS)
+  if (EXISTS ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp OR RUN_SWIG)
+    find_package(PythonInterp)
+    if (NOT PYTHONINTERP_FOUND)
+      message(STATUS "Python interpreter NOT found")
+    endif (NOT PYTHONINTERP_FOUND)
+
+    if (PYTHONINTERP_FOUND AND NOT Python_ADDITIONAL_VERSIONS)
+      set(Python_ADDITIONAL_VERSIONS "${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}")
+    endif (PYTHONINTERP_FOUND AND NOT Python_ADDITIONAL_VERSIONS)
+
+    find_package(PythonLibs)
+    if (NOT PYTHONLIBS_FOUND)
+      message(STATUS "Python libraries NOT found")
+    endif (NOT PYTHONLIBS_FOUND)
+
+    if(PYTHONLIBS_FOUND AND PYTHONINTERP_FOUND)
+      set(DO_PYTHON_BINDINGS ON BOOL)
+      message(STATUS "Python bindings will be compiled")
+    endif(PYTHONLIBS_FOUND AND PYTHONINTERP_FOUND)
+
+  else ()
+    message(STATUS "Warning: Python bindings NOT found. Generate using -DRUN_SWIG=ON.")
+
+  endif ()
+endif (PYTHON_BINDINGS)
+
+if (DO_PYTHON_BINDINGS)
+
+    include_directories(
+        ${PYTHON_INCLUDE_PATH}
+    )
+
+    if(RUN_SWIG)
+      add_custom_command(OUTPUT ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel.py
+      COMMAND ${SWIG_EXECUTABLE} -python -c++ ${doxygen_switch} -small -O -templatereduce -naturalvar -I${openbabel_SOURCE_DIR}/include -I${openbabel_BINARY_DIR}/include -o ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp ${eigen_define} -outdir ${openbabel_SOURCE_DIR}/scripts/python/openbabel ${openbabel_SOURCE_DIR}/scripts/openbabel-python.i
+              MAIN_DEPENDENCY openbabel-python.i
+              VERBATIM
+              )
+    endif(RUN_SWIG)
+    
+    configure_file(${openbabel_SOURCE_DIR}/scripts/python/openbabel/__init__.py.in
+                   ${openbabel_SOURCE_DIR}/scripts/python/openbabel/__init__.py)
+    add_library(bindings_python MODULE ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp)
+
+    if(APPLE)
+      # Don't link against Python library on Mac
+      set_target_properties(bindings_python PROPERTIES LINK_FLAGS "-undefined dynamic_lookup")
+      if(BINDINGS_ONLY)
+        target_link_libraries(bindings_python ${BABEL_SYSTEM_LIBRARY})
+      else()
+        target_link_libraries(bindings_python ${BABEL_LIBRARY})
+      endif()
+    else()
+      # Link against Python library on Linux and Windows
+      if(BINDINGS_ONLY)
+        target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_SYSTEM_LIBRARY})
+      else()
+        target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_LIBRARY})
+      endif()
+    endif()
+
+    if(NOT WIN32)
+        set_target_properties(bindings_python PROPERTIES
+            OUTPUT_NAME _openbabel
+            PREFIX ""
+            LIBRARY_OUTPUT_DIRECTORY "${openbabel_SOURCE_DIR}/scripts/python/openbabel/"
+            SUFFIX .so )
+      if( "${PYTHON_INSTDIR}" STREQUAL "" )
+        execute_process(
+          COMMAND
+          ${PYTHON_EXECUTABLE} -c "from distutils import sysconfig; print(sysconfig.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
+          OUTPUT_VARIABLE PYTHON_INSTDIR
+          OUTPUT_STRIP_TRAILING_WHITESPACE
+        )
+	#workaround for https://bugs.launchpad.net/ubuntu/+source/python3-defaults/+bug/1814653
+	if(NOT ${PYTHON_INSTDIR} MATCHES "python[0-9].[0-9]")
+	  execute_process(
+           COMMAND
+           ${PYTHON_EXECUTABLE} -c "from distutils import sysconfig; print(sysconfig.get_python_lib(1,1,prefix='${CMAKE_INSTALL_PREFIX}'))"
+           OUTPUT_VARIABLE PYTHON_INSTDIR
+           OUTPUT_STRIP_TRAILING_WHITESPACE
+          )
+          set(PYTHON_INSTDIR "${PYTHON_INSTDIR}/dist-packages")
+	endif()
+      endif()
+        if(NOT BINDINGS_ONLY)
+            add_dependencies(bindings_python openbabel)
+        endif()
+
+        install(TARGETS bindings_python
+                LIBRARY DESTINATION ${PYTHON_INSTDIR}/openbabel
+                COMPONENT bindings_python)
+        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel/__init__.py
+                DESTINATION ${PYTHON_INSTDIR}/openbabel
+                COMPONENT bindings_python)
+        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel.py
+                DESTINATION ${PYTHON_INSTDIR}/openbabel
+                COMPONENT bindings_python)
+        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel/pybel.py
+                DESTINATION ${PYTHON_INSTDIR}/openbabel
+                COMPONENT bindings_python)
+    else(NOT WIN32)
+        set_target_properties(bindings_python PROPERTIES
+            OUTPUT_NAME _openbabel
+            PREFIX ""
+            SUFFIX .pyd )
+        execute_process(
+          COMMAND
+          ${PYTHON_EXECUTABLE} -c "from distutils import sysconfig; print(sysconfig.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
+          OUTPUT_VARIABLE PYTHON_INSTDIR
+          OUTPUT_STRIP_TRAILING_WHITESPACE
+        )
+        if(NOT BINDINGS_ONLY)
+            add_dependencies(bindings_python openbabel)
+        endif()
+
+        install(TARGETS bindings_python
+                LIBRARY DESTINATION ${PYTHON_INSTDIR}/openbabel
+                COMPONENT bindings_python)
+        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel/__init__.py
+                DESTINATION ${PYTHON_INSTDIR}/openbabel
+                COMPONENT bindings_python)
+        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel.py
+                DESTINATION ${PYTHON_INSTDIR}/openbabel
+                COMPONENT bindings_python)
+        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel/pybel.py
+                DESTINATION ${PYTHON_INSTDIR}/openbabel
+                COMPONENT bindings_python)
+        add_custom_command(TARGET bindings_python POST_BUILD
+          COMMAND ${CMAKE_COMMAND} -E copy ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel.py ${openbabel_BINARY_DIR}/bin/${CMAKE_CFG_INTDIR}
+          )
+    endif(NOT WIN32)
+endif (DO_PYTHON_BINDINGS)
+
+###################
+# Ruby
+###################
+
+if (RUBY_BINDINGS)
+  if (EXISTS ${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.cpp OR RUN_SWIG)
+    find_package(Ruby)
+    if (NOT RUBY_LIBRARY)
+      message(STATUS "Ruby library files NOT found. Ruby bindings will NOT be compiled.")
+    endif (NOT RUBY_LIBRARY)
+
+    if (RUBY_LIBRARY)
+      set(DO_RUBY_BINDINGS ON BOOL)
+      message(STATUS "Ruby bindings will be compiled")
+    endif (RUBY_LIBRARY)
+
+  else (EXISTS ${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.cpp OR RUN_SWIG)
+    message(STATUS "Warning: Ruby bindings NOT found. Generate using -DRUN_SWIG=ON.")
+
+  endif (EXISTS ${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.cpp OR RUN_SWIG)
+endif (RUBY_BINDINGS)
+
+if (DO_RUBY_BINDINGS)
+
+    if (RUN_SWIG)
+      set(WORKAROUND_CMAKE260_BUG "s/rb_define_module(\"Openbabel\")/rb_define_module(\"OpenBabel\")/")
+      add_custom_command(OUTPUT ${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.cpp
+          COMMAND ${SWIG_EXECUTABLE} -ruby -c++ -small -O -templatereduce -naturalvar -autorename -I${openbabel_SOURCE_DIR}/include -I${openbabel_BINARY_DIR}/include -o ${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.txt ${openbabel_SOURCE_DIR}/scripts/openbabel-ruby.i
+          COMMAND sed -e '${WORKAROUND_CMAKE_260_BUG}' -e's/void Init_OpenBabel/void Init_openbabel/' <${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.txt >${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.cpp
+          COMMAND ${CMAKE_COMMAND} -E remove ${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.txt
+          MAIN_DEPENDENCY openbabel-ruby.i
+      )
+    endif (RUN_SWIG)
+
+    include_directories(
+        ${RUBY_INCLUDE_PATH}
+    )
+
+    add_library(bindings_ruby MODULE ${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.cpp)
+    if(BINDINGS_ONLY)
+      target_link_libraries(bindings_ruby ${RUBY_LIBRARY} ${BABEL_SYSTEM_LIBRARY})
+    else()
+      target_link_libraries(bindings_ruby ${RUBY_LIBRARY} ${BABEL_LIBRARY})
+    endif()
+
+    set_target_properties(bindings_ruby PROPERTIES
+        OUTPUT_NAME openbabel
+        PREFIX "" )
+
+    if(NOT BINDINGS_ONLY)
+      add_dependencies(bindings_ruby openbabel)
+    endif()
+
+    if( "${RUBY_INSTDIR}" STREQUAL "" )
+      set( RUBY_INSTDIR "${LIB_INSTALL_DIR}" )
+    endif()
+    install(TARGETS bindings_ruby
+            LIBRARY DESTINATION ${RUBY_INSTDIR}
+            COMPONENT bindings_ruby)
+
+endif (DO_RUBY_BINDINGS)

data/lib/openbabel/version.rb

@@ -1,4 +1,4 @@
 module OpenBabel
   VERSION = '3.1.1'
-  GEMVERSION = VERSION + '.0'
+  GEMVERSION = VERSION + '.2'
 end

data/lib/openbabel.rb

@@ -1,4 +1,83 @@
-require_relative '../openbabel/lib/openbabel'
+# OpenBabel Ruby bindings loader
+# Supports both precompiled (fat gem) and source-compiled installations
+
 require 'openbabel/version'
+
+module OpenBabel
+  class << self
+    # Find the native extension directory
+    def find_native_extension_path
+      ruby_version = "#{RUBY_VERSION.split('.')[0..1].join('.')}.0"
+
+      # Check for precompiled fat gem location first
+      precompiled_path = File.join(__dir__, 'openbabel', ruby_version)
+      return precompiled_path if has_native_extension?(precompiled_path)
+
+      # Fallback to source-compiled location (relative to gem root)
+      source_path = File.expand_path('../openbabel/lib', __dir__)
+      return source_path if has_native_extension?(source_path)
+
+      # Legacy path (direct in openbabel/lib)
+      legacy_path = File.expand_path('../openbabel/lib/openbabel', __dir__)
+      return legacy_path if has_native_extension?(legacy_path)
+
+      nil
+    end
+
+    # Check if a directory contains the native extension
+    def has_native_extension?(path)
+      return false unless path && File.directory?(path)
+
+      # Look for .so (Linux) or .bundle (macOS)
+      Dir[File.join(path, 'openbabel.{so,bundle}')].any? ||
+        Dir[File.join(path, '*.so')].any? ||
+        Dir[File.join(path, '*.bundle')].any?
+    end
+
+    # Get the path to OpenBabel data files
+    def data_path
+      ruby_version = "#{RUBY_VERSION.split('.')[0..1].join('.')}.0"
+
+      # Check precompiled location
+      precompiled_data = File.join(__dir__, 'openbabel', ruby_version, 'data')
+      return precompiled_data if File.directory?(precompiled_data)
+
+      # Check source-compiled location
+      source_data = File.expand_path('../openbabel/share/openbabel', __dir__)
+      return source_data if File.directory?(source_data)
+
+      nil
+    end
+  end
+end
+
+# Find and load the native extension
+native_path = OpenBabel.find_native_extension_path
+
+if native_path.nil?
+  raise LoadError, <<~ERROR
+    Cannot find OpenBabel native extension.
+
+    If you installed from a precompiled gem, your Ruby version (#{RUBY_VERSION})#{' '}
+    may not be supported. Try installing the source gem instead:
+
+      gem install openbabel-ruby --platform ruby
+
+    If you installed from source, the compilation may have failed.
+    Check the installation logs for errors.
+  ERROR
+end
+
+# Add native path to load path
+$LOAD_PATH.unshift(native_path) unless $LOAD_PATH.include?(native_path)
+
+# Set BABEL_DATADIR environment variable if data files are bundled
+data_path = OpenBabel.data_path
+ENV['BABEL_DATADIR'] ||= data_path if data_path && File.directory?(data_path)
+
+# Load the native extension
+require 'openbabel'
+
+# Initialize OpenBabel plugins
 # http://sourceforge.net/mailarchive/message.php?msg_id=31065700
-OpenBabel::OBConversion.new # required to load plugins
+OpenBabel::OBConversion.new

metadata

@@ -1,15 +1,20 @@
 --- !ruby/object:Gem::Specification
 name: openbabel-ruby
 version: !ruby/object:Gem::Version
-  version: 3.1.1.0
+  version: 3.1.1.2
 platform: ruby
 authors:
 - An Nguyen
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2025-12-12 00:00:00.000000000 Z
+date: 2026-01-24 00:00:00.000000000 Z
 dependencies: []
-description: OpenBabel as a GEM
+description: Ruby bindings for OpenBabel, an open-source chemical toolbox for molecular
+  modeling, cheminformatics, and computational chemistry. Supports 110+ molecular
+  file formats (SMILES, SDF, MOL2, PDB, CIF, etc.), molecular fingerprints, 2D/3D
+  coordinate generation, and structure manipulation. The gem compiles OpenBabel 3.1.1
+  from source with SWIG bindings during installation.
 email:
 - caman.nguyenthanh@gmail.com
 executables: []
@@ -19,13 +24,18 @@ extra_rdoc_files: []
 files:
 - Rakefile
 - ext/openbabel/extconf.rb
+- ext/openbabel/patches/CMakeLists.txt
+- ext/openbabel/patches/scripts/CMakeLists.txt
 - lib/openbabel.rb
 - lib/openbabel/version.rb
-- test/test_openbabel.rb
 homepage: https://github.com/CamAnNguyen/openbabel-gem
 licenses:
 - GPL-3.0
-metadata: {}
+metadata:
+  source_code_uri: https://github.com/CamAnNguyen/openbabel-gem
+  documentation_uri: https://openbabel.org/index.html
+  bug_tracker_uri: https://github.com/CamAnNguyen/openbabel-gem/issues
+post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -40,8 +50,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 4.0.1
+rubygems_version: 3.5.22
+signing_key: 
 specification_version: 4
-summary: OpenBabel!
-test_files:
-- test/test_openbabel.rb
+summary: Ruby bindings for OpenBabel, the chemistry toolbox
+test_files: []

data/test/test_openbabel.rb

@@ -1,22 +0,0 @@
-require 'test/unit'
-
-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