rdkit/CMakeLists.txt

cmake_minimum_required(VERSION 3.18)

project (RDKit)

IF(NOT CMAKE_BUILD_TYPE)
  SET(CMAKE_BUILD_TYPE Release CACHE STRING
      "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel."
      FORCE)
ENDIF(NOT CMAKE_BUILD_TYPE)

# Enable CTest
include(CTest)

set(CMAKE_CXX_STANDARD 20)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_C_STANDARD 99)
set(CMAKE_C_STANDARD_REQUIRED ON)

set(CMAKE_MODULE_PATH
    ${CMAKE_MODULE_PATH} "${CMAKE_CURRENT_SOURCE_DIR}/Code/cmake/Modules/")

add_library(rdkit_base INTERFACE)

option(RDK_BUILD_SWIG_WRAPPERS "build the SWIG wrappers" OFF )
option(RDK_BUILD_PYTHON_WRAPPERS "build the standard python wrappers" ON )
option(RDK_BUILD_COMPRESSED_SUPPLIERS "build in support for compressed MolSuppliers" OFF )
option(RDK_BUILD_INCHI_SUPPORT "build the rdkit inchi wrapper" OFF )
option(RDK_BUILD_AVALON_SUPPORT "install support for the avalon toolkit. Use the variable AVALONTOOLS_DIR to set the location of the source." OFF )
option(RDK_BUILD_PGSQL "build the PostgreSQL cartridge" OFF )
option(RDK_BUILD_RPATH_SUPPORT "build shared libraries using rpath" OFF)
option(RDK_PGSQL_STATIC "statically link rdkit libraries into the PostgreSQL cartridge" ON )
option(RDK_PGSQL_BFP_GIST_SORTSUPPORT "enable the sortsupport method in the PostgreSQL bfp gist index" OFF )
option(RDK_PGSQL_MOL_GIST_SORTSUPPORT "enable the sortsupport method in the PostgreSQL mol gist index" ON )
option(RDK_PGSQL_QMOL_GIST_SORTSUPPORT "enable the sortsupport method in the PostgreSQL qmol gist index" ON )
option(RDK_BUILD_CONTRIB "build the Contrib directory" OFF )
option(RDK_INSTALL_INTREE "install the rdkit in the source tree (former behavior)" ON )
option(RDK_INSTALL_DLLS_MSVC "install the rdkit DLLs when using MSVC" OFF)
option(RDK_INSTALL_STATIC_LIBS "install the rdkit static libraries" ON )
option(RDK_INSTALL_PYTHON_TESTS "install the rdkit Python tests with the wrappers" OFF )
option(RDK_BUILD_THREADSAFE_SSS "enable thread-safe substructure searching" ON )
option(RDK_BUILD_SLN_SUPPORT "include support for the SLN format" ON )
option(RDK_TEST_MULTITHREADED "run some tests of multithreading" ON )
option(RDK_BUILD_SWIG_JAVA_WRAPPER "build the SWIG JAVA wrappers (does nothing if RDK_BUILD_SWIG_WRAPPERS is not set)" ON )
option(RDK_BUILD_SWIG_CSHARP_WRAPPER "build the experimental SWIG C# wrappers (does nothing if RDK_BUILD_SWIG_WRAPPERS is not set)" OFF )
option(RDK_BUILD_DOTNET_CSHARP_TESTS "build the DotNet Core tests for C# wrappers on Linux (does nothing if RDK_BUILD_SWIG_CSHARP_WRAPPER is not set and is ignored on Windows)" OFF )
option(RDK_SWIG_STATIC "statically link rdkit libraries into the SWIG wrappers" ON )
option(RDK_TEST_MMFF_COMPLIANCE "run MMFF compliance tests (requires tar/gzip)" ON )
option(RDK_BUILD_CPP_TESTS "build the c++ tests (disabing can speed up builds" ON)
option(RDK_USE_FLEXBISON "use flex/bison, if available, to build the SMILES/SMARTS/SLN parsers" OFF)
option(RDK_TEST_COVERAGE "Use G(L)COV to compute test coverage" OFF)
option(RDK_USE_BOOST_SERIALIZATION "Use the boost serialization library if available" ON)
option(RDK_USE_BOOST_STACKTRACE "use boost::stacktrace to do more verbose invariant output (linux only)" ON)
option(RDK_BUILD_TEST_GZIP "Build the gzip'd stream test" OFF)
option(RDK_OPTIMIZE_POPCNT "Use SSE4.2 popcount instruction while compiling." ON)
option(RDK_USE_STRICT_ROTOR_DEFINITION "Use the most strict rotatable bond definition" ON)
option(RDK_BUILD_DESCRIPTORS3D "Build the 3D descriptors calculators, requires Eigen3 to be installed" ON)
option(RDK_BUILD_CHEMDRAW_SUPPORT "build support for the Revvity ChemDraw document format" ON )
option(RDK_BUILD_FREESASA_SUPPORT "build the rdkit freesasa wrapper" OFF )
option(RDK_BUILD_COORDGEN_SUPPORT "build the rdkit coordgen wrapper" ON )
option(RDK_BUILD_MAEPARSER_SUPPORT "build the rdkit MAE parser wrapper" ON )
option(RDK_BUILD_MOLINTERCHANGE_SUPPORT "build in support for CommonChem molecule interchange" ON )
option(RDK_BUILD_YAEHMOP_SUPPORT "build support for the YAeHMOP wrapper" OFF)
option(RDK_BUILD_XYZ2MOL_SUPPORT "build in support for the RDKit's implementation of xyz2mol (in the DetermineBonds library)" OFF )
option(RDK_BUILD_STRUCTCHECKER_SUPPORT "build in support for the StructChecker alpha (not recommended, use the MolVS integration instead)" OFF )
option(RDK_BUILD_PUBCHEMSHAPE_SUPPORT "build the rdkit wrapper around pubchem-align3d" ON )
option(RDK_USE_URF "Build support for Florian Flachsenberg's URF library" ON)
option(RDK_INSTALL_DEV_COMPONENT "install libraries and headers" ON)
option(RDK_USE_BOOST_IOSTREAMS "use boost::iostreams" ON)
option(RDK_BUILD_MINIMAL_LIB "build the minimal RDKit wrapper (for the JS bindings)" OFF)
option(RDK_MINIMAL_LIB_SUPPORT_LEGACY_BROWSERS "build the minimal RDKit JS wrapper such that it supports legacy browsers" OFF)
option(RDK_BUILD_CFFI_LIB "build the CFFI wrapper (for use in other programming languges)" OFF)
option(RDK_CFFI_STATIC "statically link rdkit libraries into the cffi wrapper" ON)
option(RDK_BUILD_FUZZ_TARGETS "build the fuzz targets" OFF)
option(RDK_BUILD_MINIMAL_LIB_RXN "build support for reactions into MinimalLib" ON )
option(RDK_BUILD_MINIMAL_LIB_SUBSTRUCTLIBRARY "build support for SubstructLibrary into MinimalLib" ON )
option(RDK_BUILD_MINIMAL_LIB_MCS "build support for MCS into MinimalLib" OFF )
option(RDK_BUILD_MINIMAL_LIB_MOLZIP "build support for molzip into MinimalLib" OFF )
option(RDK_BUILD_MINIMAL_LIB_MMPA "build support for MMPA into MinimalLib" OFF )
option(RDK_BUILD_LONG_RUNNING_TESTS "build longer running tests" OFF )

set(RDK_BOOST_VERSION "1.81.0")

if(NOT MSVC AND RDK_OPTIMIZE_POPCNT)
  if(CMAKE_SYSTEM_PROCESSOR MATCHES "^(ppc64|powerpc64)")
    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcntd")
  elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^(x86_64|i*86)")
    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcnt")
  else()
    message(STATUS "POPCNT hardware flag not supported or not required for ${CMAKE_SYSTEM_PROCESSOR} architecture")
  endif()
endif()

# Detect clang, which masquerades as gcc.  CMake 2.6 doesn't know how to
# detect it.
string(REGEX MATCH "clang" CMAKE_COMPILER_IS_CLANG "${CMAKE_C_COMPILER}")
# Detect emcc
string(REGEX MATCH "Emscripten" CMAKE_COMPILER_IS_EMCC "${CMAKE_SYSTEM_NAME}")

if(NOT UNIX OR APPLE OR CYGWIN OR CMAKE_COMPILER_IS_EMCC)
  if(RDK_USE_BOOST_STACKTRACE)
    MESSAGE("Disabling boost::stacktrace on non-linux and emscripten platforms")
    set(RDK_USE_BOOST_STACKTRACE OFF)
  endif(RDK_USE_BOOST_STACKTRACE)
endif()

if(NOT RDK_BUILD_SWIG_WRAPPERS)
  set(RDK_BUILD_SWIG_JAVA_WRAPPER OFF)
  set(RDK_BUILD_SWIG_CSHARP_WRAPPER OFF)
endif()

if(RDK_SWIG_STATIC AND RDK_BUILD_SWIG_WRAPPERS)
  if(NOT MSVC AND NOT RDK_INSTALL_STATIC_LIBS)
    message("Enabling RDK_INSTALL_STATIC_LIBS because RDK_SWIG_STATIC is set.")
    set(RDK_INSTALL_STATIC_LIBS ON CACHE BOOL "install the rdkit static libraries" FORCE)
  endif(NOT MSVC AND NOT RDK_INSTALL_STATIC_LIBS)
endif()
if ((MSVC AND (NOT RDK_INSTALL_DLLS_MSVC)) OR (WIN32 AND RDK_INSTALL_STATIC_LIBS) OR RDK_BUILD_MINIMAL_LIB)
  set(RDK_BUILD_STATIC_LIBS_ONLY ON)
else()
  set(RDK_BUILD_STATIC_LIBS_ONLY OFF)
endif()
if(NOT RDK_BUILD_STATIC_LIBS_ONLY)
  add_definitions(-DRDKIT_DYN_LINK)
endif()

if(RDK_PGSQL_STATIC AND RDK_BUILD_PGSQL)
  if(NOT MSVC AND NOT RDK_INSTALL_STATIC_LIBS)
    message("Enabling RDK_INSTALL_STATIC_LIBS because RDK_PGSQL_STATIC is set.")
    set(RDK_INSTALL_STATIC_LIBS ON CACHE BOOL "install the rdkit static libraries" FORCE)
  endif(NOT MSVC AND NOT RDK_INSTALL_STATIC_LIBS)
endif()

if(RDK_CFFI_STATIC AND RDK_BUILD_CFFI_LIB)
  if(NOT MSVC AND NOT RDK_INSTALL_STATIC_LIBS)
    message("Enabling RDK_INSTALL_STATIC_LIBS because RDK_CFFI_STATIC is set.")
    set(RDK_INSTALL_STATIC_LIBS ON CACHE BOOL "install the rdkit static libraries" FORCE)
  endif(NOT MSVC AND NOT RDK_INSTALL_STATIC_LIBS)
endif()


include(TestBigEndian)
TEST_BIG_ENDIAN(RDK_BIG_ENDIAN)

# At build time put runtime binaries in the bin subdirectory
set(RDK_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/bin")
set(RDK_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/lib")
set(RDK_ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/lib")
# Also place the python extension where the source tree would expect them
set(RDK_PYTHON_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/rdkit")

#-------
# Config variables:
set(RDKit_Year "2025")
set(RDKit_Month "09")
set(RDKit_Revision "6")
set(RDKit_RevisionModifier "")
set(RDKit_ABI "1")

# we need an integer version of the month later, so remove the zero padding
# if there is any
string(REGEX REPLACE "^0" "" RDKit_intMonth ${RDKit_Month} )

set(RDKit_CodeDir "${CMAKE_CURRENT_SOURCE_DIR}/Code")
set(RDKit_ExternalDir "${CMAKE_CURRENT_SOURCE_DIR}/External")
set(RDKit_DataDir "${CMAKE_CURRENT_SOURCE_DIR}/Data")

#include catch
find_package(Catch2 3 QUIET)
if(NOT Catch2_FOUND)
  Include(FetchContent)

  FetchContent_Declare(
    Catch2
    GIT_REPOSITORY https://github.com/catchorg/Catch2.git
    GIT_TAG        v3.4.0 # or a later release
  )

  FetchContent_MakeAvailable(Catch2)
endif()

# make sure we have better_enums
Include(FetchContent)

FetchContent_Declare(
  better_enums
  GIT_REPOSITORY https://github.com/aantron/better-enums.git
  GIT_TAG        c35576bed0295689540b39873126129adfa0b4c8 # 0.11.3
)

if(RDK_INSTALL_INTREE)
  set(RDKit_BinDir "${CMAKE_SOURCE_DIR}/bin")
  set(RDKit_LibDir "${CMAKE_SOURCE_DIR}/lib")
  set(RDKit_HdrDir "Code") # used in rdkit-config.cmake, path prefix not needed.
  set(RDKit_ShareDir "${CMAKE_SOURCE_DIR}")
else(RDK_INSTALL_INTREE)
  set(RDKit_BinDir "bin")
  set(RDKit_LibDir "lib${LIB_SUFFIX}")
  set(RDKit_HdrDir "include/rdkit")
  set(RDKit_ShareDir "share/RDKit")
endif(RDK_INSTALL_INTREE)

if(RDK_BUILD_RPATH_SUPPORT)
  # use, i.e. don't skip the full RPATH for the build tree
  SET(CMAKE_SKIP_BUILD_RPATH  FALSE)

  # when building, don't use the install RPATH already
  # (but later on when installing)
  SET(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)

  message("CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/lib")
  SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")

  # add the automatically determined parts of the RPATH
  # which point to directories outside the build tree to the install RPATH
  SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)

  # the RPATH to be used when installing, but only if it's not a system
  # directory
  LIST(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES
  "${CMAKE_INSTALL_PREFIX}/lib" isSystemDir)
  IF("${isSystemDir}" STREQUAL "-1")
     SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
  ENDIF("${isSystemDir}" STREQUAL "-1")
endif()



if(RDK_BUILD_SWIG_WRAPPERS)
  set(RDKit_JavaLibDir "${RDKit_ExternalDir}/java_lib")
endif(RDK_BUILD_SWIG_WRAPPERS)


if(RDK_BUILD_COORDGEN_SUPPORT)
    add_definitions(-DRDK_BUILD_COORDGEN_SUPPORT)
    include_directories(${RDKit_ExternalDir})
endif()

if(RDK_BUILD_MAEPARSER_SUPPORT)
    add_definitions(-DRDK_BUILD_MAEPARSER_SUPPORT)
    include_directories(${RDKit_ExternalDir})
endif()

if(RDK_USE_URF)
  add_definitions(-DRDK_USE_URF)
  if((MSVC AND (NOT RDK_INSTALL_DLLS_MSVC)) OR ((NOT MSVC) AND WIN32 AND RDK_INSTALL_STATIC_LIBS))
    add_definitions(-DRDL_WIN_STATIC)
  endif()
  include_directories(${RDKit_ExternalDir}/RingFamilies/RingDecomposerLib/src/RingDecomposerLib)
endif()

if(RDK_BUILD_XYZ2MOL_SUPPORT)
    add_definitions(-DRDK_BUILD_XYZ2MOL_SUPPORT)
    include_directories(${RDKit_ExternalDir})
endif()

if(RDK_BUILD_YAEHMOP_SUPPORT)
    add_definitions(-DRDK_BUILD_YAEHMOP_SUPPORT)
endif()

if(CMAKE_SIZEOF_VOID_P EQUAL 4)
  target_compile_definitions(rdkit_base INTERFACE "-DRDK_32BIT_BUILD")
else()
  target_compile_definitions(rdkit_base INTERFACE "-DRDK_64BIT_BUILD")
endif()

if(MINGW)
  target_compile_definitions(rdkit_base INTERFACE "-DBOOST_SYSTEM_NO_DEPRECATED")
endif(MINGW)
# fallback on match to "Clang" where CMAKE_C_COMPILER=/usr/bin/cc
if (CMAKE_COMPILER_IS_CLANG OR CMAKE_CXX_COMPILER_ID MATCHES "Clang" OR CMAKE_COMPILER_IS_EMCC)
  if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 15)
    target_compile_definitions(rdkit_base INTERFACE -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_NO_CXX98_FUNCTION_BASE -D_HAS_AUTO_PTR_ETC=0)
    target_compile_options(rdkit_base INTERFACE -Wno-deprecated-builtins -Wno-deprecated-non-prototype -Wno-unused-parameter)
  endif()
endif()

# defines macros: rdkit_python_extension, rdkit_test
include(RDKitUtils)

install(TARGETS rdkit_base EXPORT ${RDKit_EXPORTED_TARGETS}
        COMPONENT dev )

# disable some warnings that we don't care about
if(MSVC)
  # These should occasionally be enabled to check what's going on
  # 4267 conversion with possible loss of data.
  # 4305 truncation from 'double' to 'const float'
  # 4244 conversion from 'uint64_t' to 'unsigned int', possible loss of data
  target_compile_options(rdkit_base INTERFACE "/wd4267" "/wd4305" "/wd4244")
  target_compile_definitions(rdkit_base INTERFACE "_CRT_SECURE_NO_WARNINGS")
endif(MSVC)


# extra boost versions
if(MSVC)
  # FIX: do we still need this?
  target_compile_definitions(rdkit_base INTERFACE "-DBOOST_ALL_NO_LIB")
  if(RDK_INSTALL_DLLS_MSVC)
    target_compile_definitions(rdkit_base INTERFACE "-DBOOST_ALL_DYN_LINK")
  endif(RDK_INSTALL_DLLS_MSVC)
endif(MSVC)

if(RDK_BUILD_INCHI_SUPPORT)
  find_package(Inchi)
endif(RDK_BUILD_INCHI_SUPPORT)

if(RDK_BUILD_PYTHON_WRAPPERS)
  add_library(rdkit_py_base INTERFACE)

  #-------
  # pull in python:
  find_package(Python3 COMPONENTS Interpreter Development.Module NumPy)
  target_include_directories(rdkit_py_base INTERFACE ${Python3_INCLUDE_DIRS})
  target_include_directories(rdkit_py_base INTERFACE ${Python3_NumPy_INCLUDE_DIRS})

  # determine linkage of python
  execute_process(
      COMMAND
      ${Python3_EXECUTABLE} -c "import sysconfig; print(sysconfig.get_config_var('Py_ENABLE_SHARED'))"
      OUTPUT_VARIABLE Py_ENABLE_SHARED
      OUTPUT_STRIP_TRAILING_WHITESPACE
  )

  if(WIN32 OR "${Py_ENABLE_SHARED}" STREQUAL "1")
    target_link_libraries(rdkit_py_base INTERFACE ${Python3_LIBRARIES} )
  endif()


  find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS "python${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR}" "numpy${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR}" REQUIRED CONFIG)

  target_link_libraries(rdkit_py_base INTERFACE "Boost::python${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR}" "Boost::numpy${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR}")

  if(RDK_INSTALL_INTREE)
    set(RDKit_PythonDir "${CMAKE_SOURCE_DIR}/rdkit")
  else(RDK_INSTALL_INTREE)
    if (NOT PYTHON_INSTDIR)
      # Determine correct installation directory for Python bindings
      execute_process(
        COMMAND
        ${Python3_EXECUTABLE} -c "import sys; import sysconfig; \
          base_key = 'base' if sys.platform == 'win32' else 'platbase'; \
          schema = 'nt' if sys.platform == 'win32' else 'posix_prefix'; \
          print(sysconfig.get_path('platlib', schema, vars={base_key: '${CMAKE_INSTALL_PREFIX}'}))"
        OUTPUT_VARIABLE PYTHON_INSTDIR
        OUTPUT_STRIP_TRAILING_WHITESPACE
      )
    endif (NOT PYTHON_INSTDIR)
    string(REGEX REPLACE "\\\\" "/" PYTHON_INSTDIR ${PYTHON_INSTDIR})
    message("Python Install directory ${PYTHON_INSTDIR}")
    set(RDKit_PythonDir "${PYTHON_INSTDIR}/rdkit")
    if(RDK_INSTALL_PYTHON_TESTS)
      install(DIRECTORY rdkit DESTINATION ${PYTHON_INSTDIR}
        COMPONENT python
        PATTERN ".svn" EXCLUDE
        PATTERN "CMake*" EXCLUDE
        PATTERN "Basement" EXCLUDE
      )
    else(RDK_INSTALL_PYTHON_TESTS)
      install(DIRECTORY rdkit DESTINATION ${PYTHON_INSTDIR}
        COMPONENT python
        PATTERN ".svn" EXCLUDE
        PATTERN "test_data" EXCLUDE
        PATTERN "testData" EXCLUDE
        PATTERN "test_list*" EXCLUDE
        PATTERN "CMake*" EXCLUDE
        PATTERN "Basement" EXCLUDE
        PATTERN "UnitTest*" EXCLUDE
      )
    endif(RDK_INSTALL_PYTHON_TESTS)

  endif(RDK_INSTALL_INTREE)

  if(NOT WIN32)
    # See https://bugs.python.org/msg277944
    # The "command to create shared modules". Used as variable in the "Makefile (and similar) templates to build python modules"
    # for both in-python and third party modules. Initialized to hold the value which works for third party modules to link
    # against the _installed_ python.
    # We strip off the first word though (which will be the compiler name).
    execute_process(
        COMMAND
        ${Python3_EXECUTABLE} -c "import sysconfig; print(sysconfig.get_config_var('LDSHARED').lstrip().split(' ', 1)[1])"
        OUTPUT_VARIABLE PYTHON_LDSHARED
        OUTPUT_STRIP_TRAILING_WHITESPACE
     )
  endif()


  install(TARGETS rdkit_py_base EXPORT ${RDKitPython_EXPORTED_TARGETS}
          COMPONENT dev )

  # check to see if we can find nbval,
  execute_process(
    COMMAND
    ${Python3_EXECUTABLE} -c "import nbval"
    ERROR_VARIABLE nbvalERR
    OUTPUT_STRIP_TRAILING_WHITESPACE)
  if(NOT nbvalERR)
    set(RDK_NBVAL_AVAILABLE ON)
  else()
    message("nbval not found, disabling the jupyter tests")
  endif()

else(RDK_BUILD_PYTHON_WRAPPERS)
  find_package(Boost ${RDK_BOOST_VERSION} REQUIRED CONFIG)
endif(RDK_BUILD_PYTHON_WRAPPERS)

find_package(Eigen3)
if(RDK_BUILD_DESCRIPTORS3D)
  if(NOT EIGEN3_FOUND)
    add_subdirectory(External/Eigen)
  endif()
  target_compile_definitions(rdkit_base INTERFACE "-DRDK_BUILD_DESCRIPTORS3D")
endif()

if(TARGET Eigen3::Eigen)
  target_compile_definitions(rdkit_base INTERFACE "-DRDK_HAS_EIGEN3")
  target_link_libraries(rdkit_base INTERFACE Eigen3::Eigen)
  set(RDK_HAS_EIGEN ON)
endif()

if(RDK_BUILD_THREADSAFE_SSS)
  find_package (Threads)
  set(RDKit_THREAD_LIBS Threads::Threads)
  target_compile_definitions(rdkit_base INTERFACE -DRDK_BUILD_THREADSAFE_SSS)
  if(RDK_TEST_MULTITHREADED)
    target_compile_definitions(rdkit_base INTERFACE "-DRDK_TEST_MULTITHREADED")
  endif()
  target_link_libraries(rdkit_base INTERFACE Threads::Threads)
else()
  # otherwise boost flyweight links against pthreads and causes the
  # RDK_BUILD_THREADSAFE_SSS=OFF build to fail
  target_compile_definitions(rdkit_base INTERFACE "-DBOOST_DISABLE_THREADS")
  if(RDK_TEST_MULTITHREADED)
    message("RDK_TEST_MULTITHREADED does not make sense without RDK_BUILD_THREADSAFE_SSS, disabling it.")
    set(RDK_TEST_MULTITHREADED OFF)
  endif()
endif()

if(RDK_USE_BOOST_SERIALIZATION)
    find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS serialization iostreams REQUIRED CONFIG)
    target_link_libraries(rdkit_base INTERFACE ${Boost_LIBRARIES})
    target_compile_definitions(rdkit_base INTERFACE -DRDK_USE_BOOST_SERIALIZATION)
    if(NOT Boost_USE_STATIC_LIBS)
      target_compile_definitions(rdkit_base INTERFACE -DBOOST_SERIALIZATION_DYN_LINK)
    endif()
endif()

if(RDK_USE_BOOST_IOSTREAMS)
    target_compile_definitions(rdkit_base INTERFACE -DRDK_USE_BOOST_IOSTREAMS)
    find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS iostreams REQUIRED CONFIG)
    target_link_libraries(rdkit_base INTERFACE ${Boost_LIBRARIES})

    if (NOT Boost_USE_STATIC_LIBS)
      target_compile_definitions(rdkit_base INTERFACE -DBOOST_IOSTREAMS_DYN_LINK)
    endif()

    # deal with zlib
    if (WIN32)
      find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS zlib CONFIG)
      if(Boost_zlib_FOUND)
        set(zlib_lib Boost::zlib)
      endif()
    else()
      if(Boost_USE_STATIC_LIBS)
        # when we're doing static linkage of boost
        # to also link against zlib (due to iostreams)
        find_package(ZLIB)
        set(zlib_lib ${ZLIB_LIBRARIES})
     endif()
    endif()
    target_link_libraries(rdkit_base INTERFACE ${zlib_lib})
endif()


# set the boost include directories and linkage:
target_include_directories(rdkit_base INTERFACE
                           $<BUILD_INTERFACE:${RDKit_CodeDir}>
                           $<INSTALL_INTERFACE:${RDKit_HdrDir}>
                           )
# linking against Boost::boost will add Boost to the include directories without
# hard-coding Boost's path into the rdkit-targets.cmake that gets generated
target_link_libraries(rdkit_base INTERFACE ${BOOST_LIBRARIES} Boost::boost)


if(RDK_BUILD_PGSQL)
  find_package(PostgreSQL REQUIRED)
endif(RDK_BUILD_PGSQL)

# setup our compiler flags:
if (RDK_TEST_COVERAGE)
 if (NOT RDK_USE_FLEXBISON)
   message(FATAL_ERROR, "Test coverage doesn't current work unless FLEX and BISON are run.")
 endif(NOT RDK_USE_FLEXBISON)

 message("====== Installing test coverage support ======")
 message("  To run:")
 message("   make install")
 message("   make RDKit_coverage")
 message("")
 message(" open <build_dir>/coverage/index.html")
 message("")
 message(" If any of the RDKit tests fail, coverage will probably not be generated.")
 message("====== Installing test coverage support ======")
 message("")

 INCLUDE(CodeCoverage)
 SET(CMAKE_CXX_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
 SET(CMAKE_C_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
 message("== setup_target_for_coverage(${PROJECT_NAME}_coverage test coverage)")
 setup_target_for_coverage(${PROJECT_NAME}_coverage ctest coverage)

else(RDK_TEST_COVERAGE)
 if(CMAKE_COMPILER_IS_GNUCXX)
   # We don't on C_FLAGS warnings to keep Avalon compiling quiet
   SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-deprecated -Wno-unused-function -fno-strict-aliasing")
   SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra")
  if (NOT CYGWIN)
    SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
  endif()
 endif()
 if(CMAKE_CXX_COMPILER_ID MATCHES "Clang") # there's at least Clang and AppleClang
   # We don't on C_FLAGS warnings to keep Avalon compiling quiet
   SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-array-bounds -fPIC -Wno-parentheses -Wno-logical-op-parentheses -Wno-format")
   SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC")
   if(APPLE)
     SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
   endif()
 endif()
endif(RDK_TEST_COVERAGE)

if(NOT RDK_INSTALL_INTREE)
  install(DIRECTORY Data DESTINATION
      ${RDKit_ShareDir}
      COMPONENT data
      PATTERN ".svn" EXCLUDE
      )
  install(DIRECTORY Docs DESTINATION
      ${RDKit_ShareDir}
      COMPONENT docs
      PATTERN ".svn" EXCLUDE
      PATTERN "_build" EXCLUDE
      )
  install(DIRECTORY Contrib DESTINATION
      ${RDKit_ShareDir}
      COMPONENT extras
      PATTERN ".svn" EXCLUDE
      )
  if(RDK_BUILD_PYTHON_WRAPPERS)
    install(DIRECTORY Projects DESTINATION
        ${RDKit_ShareDir}
        COMPONENT extras
        PATTERN ".svn" EXCLUDE
        PATTERN "test_list*" EXCLUDE
        PATTERN "CMake*" EXCLUDE
        )
    if(RDK_INSTALL_PYTHON_TESTS)
      install(DIRECTORY Scripts DESTINATION
        ${RDKit_ShareDir}
        COMPONENT data
        PATTERN ".svn" EXCLUDE
        )
    else(RDK_INSTALL_PYTHON_TESTS)
      install(DIRECTORY Scripts DESTINATION
        ${RDKit_ShareDir}
        COMPONENT data
        PATTERN ".svn" EXCLUDE
        PATTERN "run_python_tests.py" EXCLUDE
        )
    endif(RDK_INSTALL_PYTHON_TESTS)


  endif(RDK_BUILD_PYTHON_WRAPPERS)
  install(FILES README.md license.txt
          DESTINATION ${RDKit_ShareDir}
          COMPONENT base
          )
endif(NOT RDK_INSTALL_INTREE)

if (RDK_SQUASH_MVC_SECURE_WARNINGS)
  MESSAGE("== Squashing MSVC Security warnings (do not use during development)")
  target_compile_definitions(rdkit_base INTERFACE "-D_SCL_SECURE_NO_WARNINGS")
  target_compile_definitions(rdkit_base INTERFACE "/wd4996")
endif(RDK_SQUASH_MVC_SECURE_WARNINGS)

if(RDK_USE_STRICT_ROTOR_DEFINITION)
    MESSAGE("== Using strict rotor definition")
    target_compile_definitions(rdkit_base INTERFACE "-DRDK_USE_STRICT_ROTOR_DEFINITION")
endif()

if (MSVC)
  # disable warnings:
  #  - 4267: conversion from 'size_t' to 'unsigned int', possible loss of data
  add_definitions( "/wd4267" )
endif(MSVC)

add_subdirectory(External)
add_subdirectory(Code)

if(RDK_BUILD_PYTHON_WRAPPERS)
  add_subdirectory(Projects)
  add_subdirectory(rdkit)
  add_subdirectory(rdkit-stubs)
endif(RDK_BUILD_PYTHON_WRAPPERS)

if(RDK_BUILD_CONTRIB)
  add_subdirectory(Contrib)
endif(RDK_BUILD_CONTRIB)

# export the project targets (to be included in the cmake package configuration)
include(CMakePackageConfigHelpers)

# first manage the targets for the base C++ toolkit
install(
  EXPORT ${RDKit_EXPORTED_TARGETS}
  FILE ${RDKit_EXPORTED_TARGETS}.cmake
  NAMESPACE RDKit::
  DESTINATION ${RDKit_LibDir}/cmake/rdkit
)

# create and install package configuration and version files
write_basic_package_version_file(
  "${RDKit_BINARY_DIR}/rdkit-config-version.cmake"
  VERSION ${RDKit_RELEASENAME}
  COMPATIBILITY AnyNewerVersion
)

configure_file (
    ${RDKit_SOURCE_DIR}/rdkit-config.cmake.in
    ${RDKit_BINARY_DIR}/rdkit-config.cmake @ONLY)

install(FILES
    ${RDKit_BINARY_DIR}/rdkit-config.cmake
    ${RDKit_BINARY_DIR}/rdkit-config-version.cmake
    DESTINATION ${RDKit_LibDir}/cmake/rdkit)

# then manage the targets for the python bindings
if(RDK_BUILD_PYTHON_WRAPPERS)
  install(
    EXPORT ${RDKitPython_EXPORTED_TARGETS}
    FILE ${RDKitPython_EXPORTED_TARGETS}.cmake
    NAMESPACE RDKit::
    DESTINATION ${RDKit_LibDir}/cmake/rdkitpython
  )

  write_basic_package_version_file(
    "${RDKit_BINARY_DIR}/rdkitpython-config-version.cmake"
    VERSION ${RDKit_RELEASENAME}
    COMPATIBILITY AnyNewerVersion
  )

  configure_file (
    ${RDKit_SOURCE_DIR}/rdkitpython-config.cmake.in
    ${RDKit_BINARY_DIR}/rdkitpython-config.cmake @ONLY)

  install(FILES
    ${RDKit_BINARY_DIR}/rdkitpython-config.cmake
    ${RDKit_BINARY_DIR}/rdkitpython-config-version.cmake
    DESTINATION ${RDKit_LibDir}/cmake/rdkitpython)
endif(RDK_BUILD_PYTHON_WRAPPERS)

# Memory testing setup
FIND_PROGRAM(MEMORYCHECK_COMMAND valgrind)
CONFIGURE_FILE(CTestCustom.ctest.in ${RDKit_BINARY_DIR}/CTestCustom.ctest)

# Packaging
SET(CPACK_GENERATOR "TGZ;DEB;RPM")
SET(CPACK_RPM_COMPONENT_INSTALL ON)
SET(CPACK_DEB_COMPONENT_INSTALL ON)
SET(CPACK_MONOLITHIC_INSTALL OFF)

SET(CPACK_COMPONENTS_ALL runtime base data docs dev python extras)
set(CPACK_COMPONENT_RUNTIME_GROUP "Runtime")
set(CPACK_COMPONENT_BASE_GROUP "Runtime")
set(CPACK_COMPONENT_DATA_GROUP "Runtime")
set(CPACK_COMPONENT_DOCS_GROUP "Runtime")
set(CPACK_COMPONENT_DEV_GROUP "Development")
set(CPACK_COMPONENT_PYTHON_GROUP "Python")
set(CPACK_COMPONENT_EXTRAS_GROUP "Extras")
if(RDK_BUILD_PGSQL)
  SET(CPACK_COMPONENTS_ALL ${CPACK_COMPONENTS_ALL} pgsql)
  set(CPACK_COMPONENT_PGSQL_GROUP "PgSQL")
endif()

SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "RDKit")
SET(CPACK_PACKAGE_VENDOR "rdkit.org")
SET(CPACK_PACKAGE_CONTACT "greg.landrum@gmail.com")
SET(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/README.md")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/license.txt")
SET(CPACK_PACKAGE_VERSION_MAJOR ${RDKit_Year})
SET(CPACK_PACKAGE_VERSION_MINOR ${RDKit_Month})
SET(CPACK_PACKAGE_VERSION_PATCH ${RDKit_Revision}${RDKit_RevisionModifier})
SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CMake ${CMake_VERSION_MAJOR}.${CMake_VERSION_MINOR}")
#IF(WIN32 AND NOT UNIX)
#  # There is a bug in NSI that does not handle full unix paths properly. Make
#  # sure there is at least one set of four (4) backlasshes.
#  SET(CPACK_PACKAGE_ICON "${CMake_SOURCE_DIR}/Utilities/Release\\\\InstallIcon.bmp")
#  SET(CPACK_NSIS_INSTALLED_ICON_NAME "bin\\\\MyExecutable.exe")
#  SET(CPACK_NSIS_DISPLAY_NAME "${CPACK_PACKAGE_INSTALL_DIRECTORY} My Famous Project")
#  SET(CPACK_NSIS_HELP_LINK "http:\\\\\\\\www.my-project-home-page.org")
#  SET(CPACK_NSIS_URL_INFO_ABOUT "http:\\\\\\\\www.my-personal-home-page.com")
#  SET(CPACK_NSIS_CONTACT "me@my-personal-home-page.com")
#  SET(CPACK_NSIS_MODIFY_PATH ON)
#ELSE(WIN32 AND NOT UNIX)
#  SET(CPACK_STRIP_FILES "bin/MyExecutable")
#  SET(CPACK_SOURCE_STRIP_FILES "")
#ENDIF(WIN32 AND NOT UNIX)
#SET(CPACK_PACKAGE_EXECUTABLES "MyExecutable" "My Executable")


SET(CPACK_SET_DESTDIR ON)

INCLUDE(CPack)