openbabel-ruby 3.1.1.2-arm64-darwin

data/ext/openbabel/patches/CMakeLists.txt

@@ -0,0 +1,739 @@
+# Patched for CMake 4.x compatibility
+if(NOT EMBED_OPENBABEL)
+  cmake_minimum_required(VERSION 3.5...3.31)
+endif()
+
+project(openbabel)
+set(CMAKE_MODULE_PATH ${openbabel_SOURCE_DIR}/cmake/modules)
+
+set (CMAKE_CXX_STANDARD 11)
+
+if(COMMAND cmake_policy)
+  cmake_policy(SET CMP0003 NEW)
+endif()
+
+include (CheckCXXCompilerFlag)
+
+#include (MacroEnsureVersion)
+
+# Version numbering - should be bumped for each release
+# Note that for "beta" releases, we should start at x.90.0 -- we've
+# had too many 1.100.1 releases. :-)
+set(BABEL_MAJ_VER   3)
+set(BABEL_MIN_VER   1)
+set(BABEL_PATCH_VER 1)
+
+# This should be phased out in preference for just using the target name
+set(BABEL_LIBRARY openbabel)
+
+# This would be better handled with external projects...
+if(EMBED_OPENBABEL)
+  set(BABEL_VERSION  "${BABEL_MAJ_VER}.${BABEL_MIN_VER}.${BABEL_PATCH_VER}" PARENT_SCOPE)
+else()
+  set(BABEL_VERSION  "${BABEL_MAJ_VER}.${BABEL_MIN_VER}.${BABEL_PATCH_VER}")
+endif()
+set(BABEL_DATADIR  "${CMAKE_INSTALL_PREFIX}/share/openbabel")
+
+option(ENABLE_VERSIONED_FORMATS
+  "Enable versioning of the format plugin directory" ON)
+
+# Set up our path handling, inspired by the path handling used in KDE
+set(BIN_INSTALL_DIR      "bin"
+  CACHE PATH "Install dir for binaries")
+set(LIB_SUFFIX "" CACHE STRING "Suffix of the directory name, e.g. 64 for lib64")
+if(UNIX)
+  set(LIB_INSTALL_DIR    "lib${LIB_SUFFIX}"
+    CACHE PATH "Install dir for libraries")
+  if(ENABLE_VERSIONED_FORMATS)
+    set(OB_PLUGIN_INSTALL_DIR "${LIB_INSTALL_DIR}/openbabel/${BABEL_VERSION}"
+      CACHE PATH "Install dir for plugins")
+  else()
+    set(OB_PLUGIN_INSTALL_DIR "${LIB_INSTALL_DIR}/openbabel"
+      CACHE PATH "Install dir for plugins")
+  endif()
+else() # Windows - bin dir = lib dir to load libraries
+  set(LIB_INSTALL_DIR "${BIN_INSTALL_DIR}"
+      CACHE PATH "Install dir for libraries")
+  if(MSVC)
+    set(OB_PLUGIN_INSTALL_DIR "${BIN_INSTALL_DIR}"
+      CACHE PATH "Install dir for plugins")
+  else()
+    if(ENABLE_VERSIONED_FORMATS)
+      set(OB_PLUGIN_INSTALL_DIR "lib${LIB_SUFFIX}/openbabel/${BABEL_VERSION}"
+        CACHE PATH "Install dir for plugins")
+    else(ENABLE_VERSIONED_FORMATS)
+      set(OB_PLUGIN_INSTALL_DIR "lib${LIB_SUFFIX}/openbabel"
+        CACHE PATH "Install dir for plugins")
+    endif(ENABLE_VERSIONED_FORMATS)
+  endif()
+endif()
+if(NOT DEFINED OB_INCLUDE_DIRS)
+  set(OB_INCLUDE_DIRS "include/openbabel${BABEL_MAJ_VER}")
+endif()
+set(OB_EXPORTS_FILE "${openbabel_BINARY_DIR}/OpenBabel3_EXPORTS.cmake")
+# Ensure a fresh file is made each time CMake is run
+file(REMOVE "${OB_EXPORTS_FILE}")
+
+# Place binaries and libraries in the root of the build directory
+if(NOT CMAKE_RUNTIME_OUTPUT_DIRECTORY)
+  set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin"
+    CACHE STRING "Binary build output directory")
+endif()
+if(NOT CMAKE_LIBRARY_OUTPUT_DIRECTORY)
+  if(UNIX)
+    set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}"
+      CACHE STRING "Library build output directory")
+  else() # This is preferable on WIndows for example - bin = lib directory.
+    set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin"
+      CACHE STRING "Library build output directory")
+  endif()
+endif()
+
+mark_as_advanced(CMAKE_LIBRARY_OUTPUT_DIRECTORY
+  CMAKE_RUNTIME_OUTPUT_DIRECTORY)
+
+#GLIBC_2.4
+option(GLIBC_24_COMPATIBLE "Build project compatible with GLIBC 2.4" OFF)
+if(GLIBC_24_COMPATIBLE AND UNIX)
+  set(WRAP_MEMCPY_SRC memcpy.c)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wl,--wrap=memcpy")
+endif()
+
+option(BUILD_SHARED "enable shared build support" ON)
+option(BUILD_MIXED "enable linux relocatable binaries support" OFF)
+option(WITH_STATIC_INCHI "enable static inchi and related plugins" OFF)
+option(WITH_STATIC_LIBXML "enable static libxml and xml file format plugins" OFF)
+# Static building
+if(BUILD_SHARED)
+  set(BUILD_TYPE SHARED)
+  set(PLUGIN_TYPE MODULE)
+  add_definitions(-DUSING_DYNAMIC_LIBS)
+  set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+else()
+  set(BUILD_TYPE STATIC)
+  set(PLUGIN_TYPE STATIC)
+
+  if(WITH_STATIC_INCHI)
+    add_definitions(-DHAVE_STATIC_INCHI)
+  endif()
+  if(WITH_STATIC_LIBXML)
+    add_definitions(-DHAVE_STATIC_LIBXML)
+  endif()
+
+  if(MSVC)
+    # set cl flags for static compiling
+    set(CMAKE_CXX_FLAGS_DEBUG "/MTd")
+    set(CMAKE_C_FLAGS_DEBUG "/MTd")
+    set(CMAKE_EXE_LINKER_FLAGS_DEBUG "/INCREMENTAL:NO /NODEFAULTLIB:MSVCRT")
+    set(CMAKE_CXX_FLAGS_RELEASE	"/MT /O2 /Ob2 /D NDEBUG")
+    set(CMAKE_C_FLAGS_RELEASE	"/MT /O2 /Ob2 /D NDEBUG")
+    set(CMAKE_EXE_LINKER_FLAGS_RELEASE "/INCREMENTAL:NO /NODEFAULTLIB:MSVCRT")
+    # note: static libraries are specified when running cmake
+  else()
+    set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+  endif()
+endif()
+
+# Should we attempt to use the system inchi library?
+option(WITH_INCHI   "Build inchi support" ON)
+option(OPENBABEL_USE_SYSTEM_INCHI
+  "Use the system inchi library." OFF)
+if(OPENBABEL_USE_SYSTEM_INCHI)
+  find_package(Inchi REQUIRED)
+  if (NOT INCHI_FOUND)
+    message(FATAL_ERROR "Inchi library not found.")
+  endif()
+else()
+  message(STATUS "Using included inchi library.")
+  set(INCHI_LIBRARY inchi)
+endif()
+
+if(WIN32)
+  # FIXME: not used on windows... - inconsistency
+  set(MODULE_EXTENSION ".obf")
+else()
+  set(MODULE_EXTENSION ".so")
+endif()
+
+# configure checks
+find_package(LibXml2)
+if(NOT LIBXML2_FOUND)
+  message(WARNING "libxml2 not found - disabling CML support!")
+endif()
+
+find_package(ZLIB)
+if(ZLIB_FOUND)
+  add_definitions(-DHAVE_LIBZ)
+  include_directories(${ZLIB_INCLUDE_DIR})
+  # Longstanding unsolved problem with compression under Windows
+  if(WIN32)
+    add_definitions(-DDISABLE_WRITE_COMPRESSION)
+  endif()
+endif()
+
+# wxWidgets instructions based on http://wiki.wxwidgets.org/CMake
+#find_package(wxWidgets COMPONENTS base core REQUIRED)
+find_package(wxWidgets COMPONENTS base core adv)
+if(wxWidgets_FOUND)
+  include(${wxWidgets_USE_FILE})
+  add_definitions(-DHAVE_WXWIDGETS)
+  include_directories(${wxWidgets_INCLUDE_DIRS})
+endif()
+
+if(MSVC)
+  # Ensure that CharacterSet="0" in the project files
+  add_definitions(-D_SBCS) # Single-Byte Character Set (requires CMake 2.8.8)
+endif()
+
+if(MSVC)
+  option(OB_USE_PREBUILT_BINARIES
+    "Should Windows Open Babel builds use prebuilt binaries?" ON)
+	# dlhandler_win32.cpp assumes multibyte character set
+	remove_definitions(-DUNICODE -D_UNICODE)
+  include_directories(${openbabel_SOURCE_DIR}/windows-msvc/include)
+endif()
+
+if(MSVC AND OB_USE_PREBUILT_BINARIES)
+  include_directories(${XDR_INCLUDE_DIR})
+  # The following line is required for check_include_file(rpc/xdr.h ...) below
+  set(CMAKE_REQUIRED_INCLUDES ${XDR_INCLUDE_DIR})
+  # Force OPENBABEL_USE_SYSTEM_INCHI to ON, as this should be using the binary
+  set(OPENBABEL_USE_SYSTEM_INCHI ON CACHE BOOL
+    "Forced to ON for prebuilt binaries" FORCE)
+endif()
+
+include(CheckIncludeFile)
+include(CheckIncludeFileCXX)
+include(CheckSymbolExists)
+include(CheckLibraryExists)
+include(CheckTypeSize)
+include(CheckCSourceCompiles)
+
+check_include_file(conio.h      HAVE_CONIO_H)
+check_include_file(sys/time.h   HAVE_SYS_TIME_H)
+check_include_file(time.h       HAVE_TIME_H)
+check_include_file(strings.h    HAVE_STRINGS_H)
+check_include_file(regex.h      HAVE_REGEX_H)
+check_include_file_cxx(sstream  HAVE_SSTREAM)
+
+check_symbol_exists(rint             "math.h"     HAVE_RINT)
+check_symbol_exists(snprintf         "stdio.h"    HAVE_SNPRINTF)
+check_symbol_exists(sranddev         "stdlib.h"   HAVE_SRANDDEV)
+check_symbol_exists(strcasecmp       "string.h"   HAVE_STRCASECMP)
+check_symbol_exists(strncasecmp      "string.h"   HAVE_STRNCASECMP)
+check_symbol_exists(xdrstdio_create  "rpc/xdr.h"  HAVE_RPC_XDR_H)
+
+# BSDs don't link against libdl, but rather libc
+check_library_exists(dl dlopen "" HAVE_LIBDL)
+
+set(CMAKE_EXTRA_INCLUDE_FILES time.h)
+check_type_size(clock_t CLOCK_T)
+
+# Cygwin may be missing an XDR function: https://www.gnu.org/software/gnulib/manual/html_node/xdrstdio_005fcreate.html
+if(CYGWIN)
+  set(HAVE_RPC_XDR_H FALSE)
+  message(STATUS "Disabling rpc/xdr.h for Cygwin")
+endif()
+
+# Get the GCC version - from KDE4 cmake files
+if(CMAKE_COMPILER_IS_GNUCXX)
+  if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.0.0))
+    set(GCC_IS_NEWER_THAN_4_0 TRUE)
+  else()
+    set(GCC_IS_NEWER_THAN_4_0 FALSE)
+  endif()
+  if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.1.0))
+    set(GCC_IS_NEWER_THAN_4_1 TRUE)
+  else()
+    set(GCC_IS_NEWER_THAN_4_1 FALSE)
+  endif()
+  if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.2.0))
+    set(GCC_IS_NEWER_THAN_4_2 TRUE)
+  else()
+    set(GCC_IS_NEWER_THAN_4_2 FALSE)
+  endif()
+endif()
+
+if(UNIX)
+  option(ENABLE_SYMBOL_VISIBILITY
+    "Enable support for compiler symbol visibility. WARNING: Some issues reported"
+    OFF)
+endif()
+
+if(NOT MSVC)
+  SET(CMAKE_REQUIRED_FLAGS -Werror)
+  check_c_source_compiles("
+   #include <sys/types.h>
+   #include <dirent.h>
+    int main(){
+     extern int matchFiles (struct dirent *entry_p);
+     struct dirent **entries_pp;
+     int count = scandir (\"./\", &entries_pp, matchFiles, 0);
+     return count;
+    }
+   " SCANDIR_NEEDS_CONST)
+
+  set(OB_MODULE_PATH "${CMAKE_INSTALL_PREFIX}/${OB_PLUGIN_INSTALL_DIR}")
+
+  # Add some visibility support when using GCC
+  # note: Altough MinGW g++ 4.4 passes this test, visibility can't be used
+  if(CMAKE_COMPILER_IS_GNUCXX AND NOT APPLE)
+    if(CMAKE_SYSTEM_NAME MATCHES Linux)
+      set (CMAKE_SHARED_LINKER_FLAGS "-Wl,--fatal-warnings -Wl,--no-undefined -lc ${CMAKE_SHARED_LINKER_FLAGS}")
+      set (CMAKE_SHARED_LINKER_FLAGS "-Wl,--enable-new-dtags ${CMAKE_SHARED_LINKER_FLAGS}")
+      set (CMAKE_MODULE_LINKER_FLAGS "-Wl,--fatal-warnings -Wl,--no-undefined -lc ${CMAKE_SHARED_LINKER_FLAGS}")
+      set (CMAKE_MODULE_LINKER_FLAGS "-Wl,--enable-new-dtags ${CMAKE_SHARED_LINKER_FLAGS}")
+      if(BUILD_SHARED)
+        set (CMAKE_EXE_LINKER_FLAGS "-Wl,--fatal-warnings -Wl,--no-undefined -lc ${CMAKE_SHARED_LINKER_FLAGS}")
+        set (CMAKE_EXE_LINKER_FLAGS "-Wl,--enable-new-dtags ${CMAKE_EXE_LINKER_FLAGS}")
+      endif()
+    endif ()
+    # Now check if we can use visibility to selectively export symbols
+    check_cxx_compiler_flag(-fvisibility=hidden HAVE_GCC_VISIBILITY)
+    set(HAVE_GCC_VISIBILITY ${HAVE_GCC_VISIBILITY} CACHE BOOL "GCC support for hidden visibility")
+    set(_GCC_COMPILED_WITH_BAD_ALLOCATOR FALSE)
+    if(GCC_IS_NEWER_THAN_4_1)
+      execute_process(COMMAND ${CMAKE_C_COMPILER} -v OUTPUT_VARIABLE _gcc_alloc_info)
+      string(REGEX MATCH "(--enable-libstdcxx-allocator=mt)" _GCC_COMPILED_WITH_BAD_ALLOCATOR "${_gcc_alloc_info}")
+    endif()
+    if(HAVE_GCC_VISIBILITY AND GCC_IS_NEWER_THAN_4_2 AND ENABLE_SYMBOL_VISIBILITY
+       AND NOT _GCC_COMPILED_WITH_BAD_ALLOCATOR)
+      # We have all the parts necessary - use visibility support
+      add_definitions(-DHAVE_GCC_VISIBILITY)
+      set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fvisibility=hidden")
+      set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fvisibility-inlines-hidden")
+    endif()
+  endif()
+endif()
+
+# To avoid warnings when linking the plugins and exes
+if(MINGW)
+  set (CMAKE_MODULE_LINKER_FLAGS "-Wl,--enable-auto-import ${CMAKE_MODULE_LINKER_FLAGS}")
+  set (CMAKE_EXE_LINKER_FLAGS "-Wl,--enable-auto-import ${CMAKE_EXE_LINKER_FLAGS}")
+endif()
+
+find_package(Boost COMPONENTS program_options iostreams)
+  if(Boost_FOUND)
+    include_directories(${Boost_INCLUDE_DIRS} ${Boost_INCLUDE_DIR})
+ endif()
+
+# Intel C++ Compiler
+# Note: Windows version uses different options!
+if(${CMAKE_CXX_COMPILER_ID} MATCHES Intel AND UNIX)
+  add_definitions (-D_BSD_SOURCE)
+  # Set some linker flags
+  if(CMAKE_SYSTEM_NAME MATCHES Linux)
+    set(CMAKE_SHARED_LINKER_FLAGS
+      "-lc ${CMAKE_SHARED_LINKER_FLAGS}")
+    set(CMAKE_MODULE_LINKER_FLAGS
+      "-lc ${CMAKE_MODULE_LINKER_FLAGS}")
+    set (CMAKE_EXE_LINKER_FLAGS
+      "-lc ${CMAKE_EXE_LINKER_FLAGS}")
+  endif (CMAKE_SYSTEM_NAME MATCHES Linux)
+  check_cxx_compiler_flag(-fvisibility=hidden HAVE_INTEL_VISIBILITY)
+  set(HAVE_INTEL_VISIBILITY ${HAVE_INTEL_VISIBILITY} CACHE BOOL
+    "Intel Compiler support for hidden visibility")
+  if(HAVE_INTEL_VISIBILITY AND ENABLE_SYMBOL_VISIBILITY)
+    add_definitions(-DHAVE_GCC_VISIBILITY)
+#    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fvisibility=hidden")
+    check_cxx_compiler_flag(-fvisibility-inlines-hidden HAVE_INTEL_VISIBILITY_INLINES)
+    set(HAVE_INTEL_VISIBILITY_INLINES ${HAVE_INTEL_VISIBILITY_INLINES} CACHE BOOL
+      "Intel Compiler support for -fvisibility-inlines-hidden")
+    if(HAVE_INTEL_VISIBILITY_INLINES)
+      set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fvisibility-inlines-hidden")
+    endif()
+  endif()
+
+  if(POLICY CMP0069)
+    cmake_policy(SET CMP0069 NEW)
+    if("${CMAKE_BUILD_TYPE}" STREQUAL Release)
+      set(CMAKE_INTERPROCEDURAL_OPTIMIZATION ON)
+    endif()
+  endif()
+  set(CMAKE_EXE_LINKER_FLAGS_RELEASE "-Wl,-s")
+
+  # define WITH_SSE2 to enable the SSE2 instruction set.
+  # Available on Pentium 4, Athlon 64, and newer CPUs.
+  # TODO: Remove this? Should be handled by -march=native and only enabled if OPTIMIZE_NATIVE is ON
+  if(CMAKE_SIZEOF_VOID_P EQUAL 8 OR WITH_SSE2)
+    message(STATUS "Enabling the SSE2 instruction set")
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -msse2")
+  endif(CMAKE_SIZEOF_VOID_P EQUAL 8 OR WITH_SSE2)
+endif(${CMAKE_CXX_COMPILER_ID} MATCHES Intel AND UNIX)
+
+#Find if OpenMP support is enabled
+
+option(ENABLE_OPENMP
+    "Enable support for OpenMP compilation of forcefield code"
+    OFF)
+if(ENABLE_OPENMP)
+  find_package(OpenMP)
+  if(OPENMP_FOUND)
+   set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+   set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
+  endif()
+endif()
+
+# Some rpath handling for Linux and Mac
+if(UNIX AND BUILD_SHARED)
+  if(APPLE)
+    set(CMAKE_INSTALL_NAME_DIR ${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR})
+  else()
+    set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}")
+    set(CMAKE_SKIP_BUILD_RPATH FALSE)
+    set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+    set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+  endif()
+endif()
+
+# Three build types are available: Release, Debug, RelWithDebInfo.
+# We default to Release.
+if(NOT CMAKE_BUILD_TYPE)
+   set(CMAKE_BUILD_TYPE Release)
+endif()
+
+#define various build types
+if(CMAKE_COMPILER_IS_GNUCXX)
+  set (CMAKE_CXX_FLAGS_RELEASE        "${CMAKE_CXX_FLAGS_RELEASE} -O3 -DNDEBUG")
+  set (CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} -O2 -g")
+  set (CMAKE_CXX_FLAGS_DEBUG          "${CMAKE_CXX_FLAGS_DEBUG} -D_GLIBCXX_DEBUG -g3 -fno-inline")
+endif()
+
+file(GLOB_RECURSE headers include/openbabel/*.h)
+configure_file(${openbabel_SOURCE_DIR}/src/config.h.cmake
+  ${openbabel_BINARY_DIR}/include/openbabel/babelconfig.h)
+install(FILES ${openbabel_BINARY_DIR}/include/openbabel/babelconfig.h
+  DESTINATION ${OB_INCLUDE_DIRS}/openbabel)
+if(NOT MSVC)
+  configure_file(${openbabel_SOURCE_DIR}/openbabel-3.pc.cmake
+    ${openbabel_BINARY_DIR}/openbabel-3.pc @ONLY)
+  install(FILES ${openbabel_BINARY_DIR}/openbabel-3.pc
+    DESTINATION ${LIB_INSTALL_DIR}/pkgconfig)
+endif()
+
+include_directories(${openbabel_BINARY_DIR}/include
+  ${openbabel_SOURCE_DIR}/data
+  ${openbabel_BINARY_DIR}/data
+  ${openbabel_SOURCE_DIR}/include
+)
+
+#cjh
+find_package(Eigen3)
+if(EIGEN3_FOUND)
+  add_definitions(-DHAVE_EIGEN -DHAVE_EIGEN3)
+  include_directories(${EIGEN3_INCLUDE_DIR})
+else()
+  find_package(Eigen2) # find and setup Eigen2
+  if(EIGEN2_FOUND)
+    add_definitions (-DHAVE_EIGEN)
+    include_directories(${EIGEN2_INCLUDE_DIR})
+  endif()
+endif()
+#cjh
+
+
+find_package(Boost COMPONENTS filesystem iostreams unit_test_framework)
+if(Boost_FOUND)
+  include_directories(${Boost_INCLUDE_DIRS} ${Boost_INCLUDE_DIR})
+  option(WITH_MAEPARSER "Build Maestro support" ON)
+  if(BUILD_SHARED)
+    option(WITH_COORDGEN "Build Coordgen support" ON)
+  else()
+    option(WITH_COORDGEN "Build Coordgen support" OFF)
+  endif()
+else()
+  option(WITH_COORDGEN "Build Coordgen support" OFF)
+endif()
+
+if(WITH_MAEPARSER)
+
+    find_package(maeparser MODULE QUIET)
+
+    if (maeparser_FOUND)
+
+      message(STATUS "Maestro formats will be supported. Using MaeParser libraries at ${maeparser_LIBRARIES}.")
+
+    else()
+
+      set(MAEPARSER_VERSION "v1.2.3" CACHE STRING "Maeparser fallback version to download")
+
+      set(MAEPARSER_DIR "${openbabel_SOURCE_DIR}/external/maeparser-${MAEPARSER_VERSION}")
+
+      option(MAEPARSER_BUILD_SHARED_LIBS "Build maeparser as a shared library" ${BUILD_SHARED})
+
+      # Do not build the test, as it will be put into the bin dir, where it won't be found by the test runner.
+      set(MAEPARSER_BUILD_TESTS OFF CACHE BOOL "Disable Maeparser tests")
+
+      if(EXISTS "${MAEPARSER_DIR}/maeparser/CMakeLists.txt")
+
+        message(STATUS "Building existing MaeParser '${MAEPARSER_VERSION}' source at ${MAEPARSER_DIR}.")
+
+      else()
+
+          file(DOWNLOAD "https://github.com/schrodinger/maeparser/archive/${MAEPARSER_VERSION}.tar.gz"
+              "${MAEPARSER_DIR}/maeparser-${MAEPARSER_VERSION}.tar.gz")
+
+          execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf "maeparser-${MAEPARSER_VERSION}.tar.gz"
+              WORKING_DIRECTORY "${MAEPARSER_DIR}")
+
+          find_path(MAEPARSER_UNPACK_DIR "CMakeLists.txt" PATH "${MAEPARSER_DIR}/*" NO_DEFAULT_PATH)
+
+          if(MAEPARSER_UNPACK_DIR)
+            file(RENAME "${MAEPARSER_UNPACK_DIR}" "${MAEPARSER_DIR}/maeparser")
+            message(STATUS "Downloaded MaeParser '${MAEPARSER_VERSION}' to ${MAEPARSER_DIR}.")
+          else()
+            message(FATAL_ERROR "Failed getting or unpacking Maeparser '${MAEPARSER_VERSION}'.")
+          endif()
+
+      endif()
+
+      add_subdirectory("${MAEPARSER_DIR}/maeparser")
+
+      set(maeparser_INCLUDE_DIRS "${MAEPARSER_DIR}")
+      set(maeparser_LIBRARIES maeparser)
+
+      message(STATUS "Maestro formats will be supported. Using MaeParser '${MAEPARSER_VERSION}' at ${MAEPARSER_DIR}")
+
+    endif()
+
+    include_directories(${maeparser_INCLUDE_DIRS})
+    set(libs ${libs} ${maeparser_LIBRARIES})
+
+else()
+    message(STATUS "Maestro formats will NOT be supported. Please install Boost to enable Maestro formats.")
+endif()
+
+
+if(WITH_COORDGEN)
+
+    find_package(coordgen MODULE QUIET)
+
+    if (coordgen_FOUND)
+
+      message(STATUS "Coordinate generation with Coordgen will be supported. Using Coordgen libraries at ${coordgen_LIBRARIES}.")
+
+    else()
+
+      set(COORDGEN_VERSION "master" CACHE STRING "Coordgen fallback version to download")
+
+      set(COORDGEN_DIR "${openbabel_SOURCE_DIR}/external/coordgen-${COORDGEN_VERSION}")
+
+      # These won't work, since openbabel relocates them to the "bin" dir
+      set(COORDGEN_BUILD_TESTS OFF CACHE BOOL "Disable building Coordgen tests")
+      set(COORDGEN_BUILD_EXAMPLE OFF CACHE BOOL "Disable building Coordgen example")
+
+      if(EXISTS "${COORDGEN_DIR}/coordgen/CMakeLists.txt")
+
+        message(STATUS "Building existing Coordgen '${COORDGEN_VERSION}' source at ${COORDGEN_DIR}.")
+
+      else()
+
+          file(DOWNLOAD "https://github.com/schrodinger/coordgenlibs/archive/${COORDGEN_VERSION}.tar.gz"
+              "${COORDGEN_DIR}/coordgenlibs-${COORDGEN_VERSION}.tar.gz")
+
+          execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf "coordgenlibs-${COORDGEN_VERSION}.tar.gz"
+              WORKING_DIRECTORY "${COORDGEN_DIR}")
+
+          find_path(COORDGEN_UNPACK_DIR "CMakeLists.txt" PATH "${COORDGEN_DIR}/*" NO_DEFAULT_PATH)
+
+          if(COORDGEN_UNPACK_DIR)
+            file(RENAME "${COORDGEN_UNPACK_DIR}" "${COORDGEN_DIR}/coordgen")
+            message(STATUS "Downloaded Coordgen '${COORDGEN_VERSION}' to ${COORDGEN_DIR}.")
+          else()
+            message(FATAL_ERROR "Failed getting or unpacking Coordgen '${COORDGEN_VERSION}'.")
+          endif()
+
+      endif()
+
+      add_subdirectory("${COORDGEN_DIR}/coordgen")
+
+      set(coordgen_INCLUDE_DIRS "${COORDGEN_DIR}")
+      set(coordgen_LIBRARIES coordgen)
+
+
+      message(STATUS "Coordinate generation with Coordgen will be supported Using Coordgen '${COORDGEN_VERSION}' at ${COORDGEN_DIR}")
+
+    endif()
+
+    include_directories(${coordgen_INCLUDE_DIRS})
+    set(libs ${libs} ${coordgen_LIBRARIES})
+
+else()
+    message(STATUS "Coordinate generation with Coordgen will NOT be supported. Please install Boost to enable Maestro formats.")
+endif()
+
+option(WITH_JSON "Build JSON support" ON)
+option(OPENBABEL_USE_SYSTEM_RAPIDJSON "Use the system rapidjson if available." ON)
+if(WITH_JSON)
+  set(RAPIDJSON_VERSION_MIN 1.1.0)
+  # First try find system rapidjson
+  if(OPENBABEL_USE_SYSTEM_RAPIDJSON)
+    find_package(RapidJSON ${RAPIDJSON_VERSION_MIN})
+  endif()
+  # Otherwise download rapidjson to openbabel source directory
+  if (NOT RAPIDJSON_FOUND OR RAPIDJSON_VERSION VERSION_LESS ${RAPIDJSON_VERSION_MIN})
+    set(RAPIDJSON_VERSION "7c73dd7de7c4f14379b781418c6e947ad464c818")
+    if(NOT EXISTS "${openbabel_SOURCE_DIR}/external/rapidjson-${RAPIDJSON_VERSION}")
+      file(DOWNLOAD "https://github.com/Tencent/rapidjson/archive/${RAPIDJSON_VERSION}.tar.gz"
+        "${openbabel_SOURCE_DIR}/external/rapidjson-${RAPIDJSON_VERSION}.tar.gz" STATUS status)
+      execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
+        ${openbabel_SOURCE_DIR}/external/rapidjson-${RAPIDJSON_VERSION}.tar.gz
+        WORKING_DIRECTORY ${openbabel_SOURCE_DIR}/external)
+      message(STATUS "Downloaded RapidJSON to ${openbabel_SOURCE_DIR}/external/rapidjson-${RAPIDJSON_VERSION}.")
+    endif()
+    set(RAPIDJSON_FOUND TRUE)
+    set(RAPIDJSON_INCLUDE_DIRS ${openbabel_SOURCE_DIR}/external/rapidjson-${RAPIDJSON_VERSION}/include)
+  endif()
+  if(RAPIDJSON_FOUND)
+    message(STATUS "JSON formats will be supported. Using RapidJSON ${RAPIDJSON_VERSION} at ${RAPIDJSON_INCLUDE_DIRS}")
+    add_definitions(-DHAVE_RAPIDJSON)
+    include_directories(${RAPIDJSON_INCLUDE_DIRS})
+  endif()
+endif()
+
+find_package(Cairo)
+if(CAIRO_FOUND)
+  message(STATUS "Cairo found. PNG output will be supported.")
+else(CAIRO_FOUND)
+  message(STATUS "Could NOT find Cairo. PNG output will NOT be supported.")
+endif(CAIRO_FOUND)
+
+# Should we enable optimizations for the native CPU architecture?
+# (this will speed up JSON handling, similarity calculations and maybe those involving Eigen)
+option(OPTIMIZE_NATIVE "Optimize for native CPU architecture. Turn off if compiling for distribution/reuse on other machines." OFF)
+if(OPTIMIZE_NATIVE)
+  include(OptimizeNative)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${NATIVE_FLAGS}")
+  # Tell rapidjson which extensions are available
+  if(HAVE_SSE2)
+    add_definitions(-DRAPIDJSON_SSE2)
+  endif()
+  if(HAVE_SSE4_2)
+    add_definitions(-DRAPIDJSON_SSE42)
+  endif()
+  if(HAVE_NEON)
+    add_definitions(-DRAPIDJSON_NEON)
+  endif()
+  add_definitions(-DOPTIMIZE_NATIVE)
+  message(STATUS "Optimizing code for this machine's CPU architecture. Use -DOPTIMIZE_NATIVE=OFF if compiling for distribution/reuse on other machines.")
+endif()
+
+add_subdirectory(include)
+add_subdirectory(data)
+add_subdirectory(doc)
+add_subdirectory(src)
+add_subdirectory(tools)
+
+# Should we build the GUI? Default is yes on Linux or Windows, not Mac.
+if (APPLE OR NOT BUILD_SHARED)
+  option(BUILD_GUI "Build the GUI" OFF)
+else ()
+  option(BUILD_GUI "Build the GUI" ON)
+endif()
+
+if(BUILD_GUI)
+  message(STATUS "Attempting to build the GUI")
+  if(wxWidgets_FOUND)
+    message(STATUS "   wxWidgets found => GUI will be built")
+    add_subdirectory(src/GUI)
+  else()
+    message(STATUS "   wxWidgets not found => GUI will not be built")
+  endif()
+else()
+  message(STATUS "GUI will not be built")
+endif()
+
+# Do we want to build the tests?
+option(ENABLE_TESTS "Enable unit tests" ON)
+if(ENABLE_TESTS)
+  include(CTest)
+  enable_testing()
+  add_subdirectory(test)
+endif()
+
+# Should the language bindings be regenereted?
+option(RUN_SWIG "Generate language bindings with SWIG" OFF)
+
+# Build bindings only
+option(BINDINGS_ONLY "Build bindings only" OFF)
+
+# Point to library if building bindings only
+set(BABEL_SYSTEM_LIBRARY ${BABEL_LIBRARY}
+    CACHE PATH "Point to openbabel library if building bindings only")
+
+# Should all bindings be built?
+option(ALL_BINDINGS "Build all languages bindings" OFF)
+
+# Should PHP bindings be built
+option(PHP_BINDINGS "Build PHP bindings" OFF)
+
+# Should Python bindings be built?
+option(PYTHON_BINDINGS "Build Python bindings" OFF)
+
+# Should Ruby bindings be built?
+option(RUBY_BINDINGS "Build Ruby bindings" OFF)
+
+# Should Perl bindings be built?
+option(PERL_BINDINGS "Build Perl bindings" OFF)
+
+# Should Java bindings be built?
+option(JAVA_BINDINGS "Build Java bindings" OFF)
+
+# Should R bindings be built?
+option(R_BINDINGS "Build R bindings" OFF)
+
+# Should CSharp bindings be built?
+option(CSHARP_BINDINGS "Build Csharp bindings" OFF)
+
+if(ALL_BINDINGS)
+  set(PYTHON_BINDINGS ON)
+  set(RUBY_BINDINGS ON)
+  set(PHP_BINDINGS ON)
+  set(PERL_BINDINGS ON)
+  set(JAVA_BINDINGS ON)
+  set(CSHARP_BINDINGS ON)
+  set(R_BINDINGS ON)
+endif()
+
+add_subdirectory(scripts)
+
+# A minimal build with just two formats (SMI, SDF) useful for developers
+option(MINIMAL_BUILD "Disable full build" OFF)
+
+# Create the Config and ConfigVersion files in the build directory, useful to
+# build against an uninstalled OpenBabel build. Simply set OpenBabel3_DIR to
+# point at the build directory and call find_package(OpenBabel3)
+include(CMakePackageConfigHelpers)
+include(GNUInstallDirs)
+set(OB_CONFIG_DIR "${CMAKE_INSTALL_LIBDIR}/cmake/openbabel3")
+set(OpenBabel3_INCLUDE_DIRS "${OB_INCLUDE_DIRS}")
+set(OpenBabel3_LIBRARIES "openbabel")
+set(OB_EXPORTS_FILE "OpenBabel3_EXPORTS.cmake")
+write_basic_package_version_file("${openbabel_BINARY_DIR}/OpenBabel3ConfigVersion.cmake"
+  VERSION ${BABEL_VERSION}
+  COMPATIBILITY AnyNewerVersion)
+configure_package_config_file("${openbabel_SOURCE_DIR}/OpenBabel3Config.cmake.in"
+  "${openbabel_BINARY_DIR}/OpenBabel3Config.cmake"
+  INSTALL_DESTINATION "${OB_CONFIG_DIR}")
+
+install(EXPORT openbabel-targets
+  DESTINATION "${OB_CONFIG_DIR}"
+  FILE "${OB_EXPORTS_FILE}"
+  COMPONENT Development)
+install(FILES
+  "${openbabel_BINARY_DIR}/OpenBabel3Config.cmake"
+  "${openbabel_BINARY_DIR}/OpenBabel3ConfigVersion.cmake"
+  DESTINATION ${OB_CONFIG_DIR}
+  COMPONENT Development)
+
+# from https://cmake.org/Wiki/RecipeAddUninstallTarget
+########### Add uninstall target ###############
+if (NOT DEFINED EMBED_OPENBABEL)
+CONFIGURE_FILE(
+  "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
+  "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
+  IMMEDIATE @ONLY)
+ADD_CUSTOM_TARGET(uninstall
+  "${CMAKE_COMMAND}" -P "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
+endif()