Remove CMake code for downloading and builing bundled dependencies: They are packaged separately as rapidjson, avalon-toolkit, freesasa, ringdecomposerlib and yaehmop. diff --git a/Code/GraphMol/MolInterchange/CMakeLists.txt b/Code/GraphMol/MolInterchange/CMakeLists.txt index 1673386a4..c3504e6f1 100644 --- a/Code/GraphMol/MolInterchange/CMakeLists.txt +++ b/Code/GraphMol/MolInterchange/CMakeLists.txt @@ -1,18 +1,3 @@ - -if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0") - downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz" - "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz" - "badd12c511e081fec6c89c43a7027bce") - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf - ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz - WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External) -else() - message("-- Found RapidJSON source in ${CMAKE_SOURCE_DIR}/External") -endif() - -include_directories(${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include) - - rdkit_library(MolInterchange Parser.cpp Writer.cpp LINK_LIBRARIES GraphMol) diff --git a/External/AvalonTools/AvalonTools.cpp b/External/AvalonTools/AvalonTools.cpp index e6c382123..d83d80668 100644 --- a/External/AvalonTools/AvalonTools.cpp +++ b/External/AvalonTools/AvalonTools.cpp @@ -24,15 +24,15 @@ #include "AvalonTools.h" extern "C" { -#include "local.h" -#include "reaccs.h" -#include "reaccsio.h" -#include "utilities.h" -#include "ssmatch.h" -#include "smi2mol.h" -#include "canonizer.h" -#include "layout.h" -#include "struchk.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include extern int RunStruchk(struct reaccs_molecule_t **mpp, struct data_line_t *data_list); diff --git a/External/AvalonTools/CMakeLists.txt b/External/AvalonTools/CMakeLists.txt index 3e31195fc..314ba35b5 100644 --- a/External/AvalonTools/CMakeLists.txt +++ b/External/AvalonTools/CMakeLists.txt @@ -2,90 +2,8 @@ if(NOT RDK_BUILD_AVALON_SUPPORT) return() endif(NOT RDK_BUILD_AVALON_SUPPORT) -set(AVALON_VERSION "2.0.5-pre.3") -if(NOT DEFINED AVALONTOOLS_DIR) - set(AVALONTOOLS_DIR "${CMAKE_CURRENT_SOURCE_DIR}/ava-formake-AvalonToolkit_${AVALON_VERSION}") - set(fileToCheck "${AVALONTOOLS_DIR}/src/main/C/common/reaccsio.c") - set(needDownload "TRUE") - if(EXISTS "${fileToCheck}") - set(needDownload "FALSE") - endif() -else() - string(REGEX REPLACE "\\\\" "/" AVALONTOOLS_DIR ${AVALONTOOLS_DIR}) - set(needDownload "FALSE") -endif() - -set(AVALON_SRC_PATH "${AVALONTOOLS_DIR}/src/main/C") -set(AVALON_COMMON_PATH "${AVALON_SRC_PATH}/common") -set(AVALON_INCLUDE_PATH "${AVALON_SRC_PATH}/include") -set(AVALON_PROGRAMS_PATH "${AVALON_SRC_PATH}/programs") - -if(needDownload) - if(NOT DEFINED AVALONTOOLS_URL) - set(AVALONTOOLS_URL "https://github.com/rdkit/ava-formake/archive/refs/tags/AvalonToolkit_${AVALON_VERSION}.tar.gz") - endif() - if(NOT DEFINED AVALONTOOLS_MD5SUM) - set(AVALONTOOLS_MD5SUM "7a20c25a7e79f3344e0f9f49afa03351") - endif() - if(NOT DEFINED AVALONTOOLS_BASE) - string(REGEX REPLACE "^.*/" "" AVALONTOOLS_BASE "${AVALONTOOLS_URL}") - endif() - downloadAndCheckMD5(${AVALONTOOLS_URL} "${CMAKE_CURRENT_SOURCE_DIR}/${AVALONTOOLS_BASE}" ${AVALONTOOLS_MD5SUM}) - execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf - ${CMAKE_CURRENT_SOURCE_DIR}/AvalonToolkit_${AVALON_VERSION}.tar.gz - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) -endif() - -if(CMAKE_C_COMPILER_ID STREQUAL "GNU") - add_compile_options(-Wno-format-security -Wformat=0 -Wstringop-overflow=0 -Wformat-overflow=0 -Wno-unused-result ) -endif() -if(CMAKE_C_COMPILER_ID STREQUAL "Clang") - add_compile_options(-Wno-absolute-value -Wno-return-type -Wno-tautological-overlap-compare) -endif() -if (MSVC) - add_definitions("/D_CRT_SECURE_NO_WARNINGS") - add_compile_options(/wd4018 /wd4101 /wd4146 /wd4334 /wd4477 /wd4715 /wd4716 /wd4996 /nologo) -endif(MSVC) - -set(avalon_clib_srcs ${AVALON_COMMON_PATH}/layout.c - ${AVALON_COMMON_PATH}/symboltable.c - ${AVALON_COMMON_PATH}/patclean.c - ${AVALON_COMMON_PATH}/utilities.c - ${AVALON_COMMON_PATH}/symbol_lists.c - ${AVALON_COMMON_PATH}/stereo.c - ${AVALON_COMMON_PATH}/set.c - ${AVALON_COMMON_PATH}/perceive.c - ${AVALON_COMMON_PATH}/local.c - ${AVALON_COMMON_PATH}/graph.c - ${AVALON_COMMON_PATH}/geometry.c - ${AVALON_COMMON_PATH}/forio.c - ${AVALON_COMMON_PATH}/depictutil.c - ${AVALON_COMMON_PATH}/denormal.c - ${AVALON_COMMON_PATH}/casutils.c - ${AVALON_COMMON_PATH}/ssmatch.c - ${AVALON_COMMON_PATH}/rtutils.c - ${AVALON_COMMON_PATH}/smi2mol.c - ${AVALON_COMMON_PATH}/didepict.c - ${AVALON_COMMON_PATH}/pattern.c - ${AVALON_COMMON_PATH}/canonizer.c - ${AVALON_COMMON_PATH}/aacheck.c - ${AVALON_COMMON_PATH}/fixcharges.c - ${AVALON_PROGRAMS_PATH}/struchk.c - ${AVALON_COMMON_PATH}/reaccsio.c - ${AVALON_COMMON_PATH}/hashcode.c - ) - -rdkit_library(avalon_clib ${avalon_clib_srcs}) -target_compile_definitions(avalon_clib PRIVATE RDKIT_AVALONLIB_BUILD) -if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32)) - set_target_properties(avalon_clib PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE) -endif() - -include_directories(${CMAKE_CURRENT_SOURCE_DIR}) -include_directories(${AVALON_INCLUDE_PATH}) - rdkit_library(AvalonLib AvalonTools.cpp SHARED - LINK_LIBRARIES avalon_clib SubstructMatch FileParsers SmilesParse GraphMol DataStructs ) + LINK_LIBRARIES -lavalon4rdkit SubstructMatch FileParsers SmilesParse GraphMol DataStructs ) target_compile_definitions(AvalonLib PRIVATE RDKIT_AVALONLIB_BUILD) rdkit_headers(AvalonTools.h DEST GraphMol) rdkit_test(testAvalonLib1 test1.cpp diff --git a/External/AvalonTools/Wrap/pyAvalonTools.cpp b/External/AvalonTools/Wrap/pyAvalonTools.cpp index fb24c497e..31997bc0a 100644 --- a/External/AvalonTools/Wrap/pyAvalonTools.cpp +++ b/External/AvalonTools/Wrap/pyAvalonTools.cpp @@ -12,7 +12,7 @@ #include extern "C" { -#include "struchk.h" +#include } namespace python = boost::python; diff --git a/External/FreeSASA/CMakeLists.txt b/External/FreeSASA/CMakeLists.txt index 43dfbdc40..81165a143 100644 --- a/External/FreeSASA/CMakeLists.txt +++ b/External/FreeSASA/CMakeLists.txt @@ -2,88 +2,8 @@ if(NOT RDK_BUILD_FREESASA_SUPPORT) return() endif(NOT RDK_BUILD_FREESASA_SUPPORT) -if(NOT DEFINED FREESASA_DIR) - set(FREESASA_DIR "${CMAKE_CURRENT_SOURCE_DIR}/freesasa") - set(needDownload "TRUE") - if(EXISTS "${FREESASA_DIR}/src/freesasa.h") - set(needDownload "FALSE") - endif() -endif() - -if(needDownload) - # don't actually use the md5 here - set(FREESASA_VERSION "2.0.3") - set(FREESASA_SRC_DIR "${CMAKE_CURRENT_SOURCE_DIR}/freesasa-${FREESASA_VERSION}") - if(NOT EXISTS "${FREESASA_SRC_DIR}/src") - downloadAndCheckMD5("https://github.com/mittinatten/freesasa/releases/download/${FREESASA_VERSION}/freesasa-${FREESASA_VERSION}.tar.gz" - "${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz" - "") - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf - ${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) - message("Copying freesasa2.c to ${FREESASA_SRC_DIR}/src/freesasa2.c") - file(COPY freesasa2.c DESTINATION ${FREESASA_SRC_DIR}/src/) - else() - message("FreeSASA found in ${FREESASA_SRC_DIR}, no download required") - endif() -endif() - -set(CMAKE_C_STANDARD 99) - -set (freesasa_clib_srcs - ${FREESASA_SRC_DIR}/src/classifier.c - ${FREESASA_SRC_DIR}/src/classifier_naccess.c - ${FREESASA_SRC_DIR}/src/classifier_oons.c - ${FREESASA_SRC_DIR}/src/classifier_protor.c - ${FREESASA_SRC_DIR}/src/coord.c - ${FREESASA_SRC_DIR}/src/freesasa2.c - ${FREESASA_SRC_DIR}/src/lexer.c - ${FREESASA_SRC_DIR}/src/log.c - ${FREESASA_SRC_DIR}/src/nb.c - ${FREESASA_SRC_DIR}/src/node.c - ${FREESASA_SRC_DIR}/src/parser.c - ${FREESASA_SRC_DIR}/src/pdb.c - ${FREESASA_SRC_DIR}/src/rsa.c - ${FREESASA_SRC_DIR}/src/sasa_lr.c - ${FREESASA_SRC_DIR}/src/sasa_sr.c - ${FREESASA_SRC_DIR}/src/selection.c - ${FREESASA_SRC_DIR}/src/structure.c - ${FREESASA_SRC_DIR}/src/util.c - ) -if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32)) - set(freesasa_additional_exports ${CMAKE_CURRENT_SOURCE_DIR}/additional_exports.def) - file(WRITE ${freesasa_additional_exports} - "EXPORTS\n" - "freesasa_default_parameters DATA\n" - "freesasa_protor_classifier DATA\n" - "freesasa_naccess_classifier DATA\n" - "freesasa_oons_classifier DATA\n" - ) - set (freesasa_clib_srcs - ${freesasa_clib_srcs} - ${freesasa_additional_exports} - ) -endif() - -set (freesasa_h ${FREESASA_SRC_DIR}/src/freesasa.h) -file(READ ${freesasa_h} freesasa_h_data) -string(REGEX REPLACE "(#include )" "\\1\n#include " freesasa_h_data "${freesasa_h_data}") -string(REGEX REPLACE "([^R][^D][^K][^I][^T][^_][^F][^R][^E][^E][^S][^A][^S][^A][^_][^C][^L][^I][^B][^_][^E][^X][^P][^O][^R][^T][^ ])(extern const)" "\\1RDKIT_FREESASA_CLIB_EXPORT \\2" freesasa_h_data "${freesasa_h_data}") -file(WRITE ${freesasa_h} "${freesasa_h_data}") - -add_definitions(-DUSE_THREADS=0) -add_definitions(-DUSE_JSON=0) -add_definitions(-DUSE_XML=0) -rdkit_library(freesasa_clib ${freesasa_clib_srcs}) -target_compile_definitions(freesasa_clib PRIVATE RDKIT_FREESASALIB_BUILD) - -if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32)) - set_target_properties(freesasa_clib PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE) -endif() -include_directories("${FREESASA_SRC_DIR}/src") - rdkit_library(FreeSASALib RDFreeSASA.cpp SHARED - LINK_LIBRARIES freesasa_clib GraphMol ) + LINK_LIBRARIES -lfreesasa GraphMol ) target_compile_definitions(FreeSASALib PRIVATE RDKIT_FREESASALIB_BUILD) rdkit_headers(RDFreeSASA.h DEST GraphMol) diff --git a/External/RingFamilies/CMakeLists.txt b/External/RingFamilies/CMakeLists.txt index 08dd1fe04..66ecd5834 100644 --- a/External/RingFamilies/CMakeLists.txt +++ b/External/RingFamilies/CMakeLists.txt @@ -1,47 +1,7 @@ -add_custom_target(ringdecomposerlib_support ALL) - if(NOT RDK_USE_URF) return() endif(NOT RDK_USE_URF) -if(NOT DEFINED URFLIB_DIR) - set(URFLIB_DIR "${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib/src/RingDecomposerLib") -endif() - -if(NOT EXISTS "${URFLIB_DIR}/RingDecomposerLib.h") - set(RELEASE_NO "1.1.3_rdkit") - set(MD5 "e9a0bcdda8b921a35e812b9888a9a874") - downloadAndCheckMD5("https://github.com/rareylab/RingDecomposerLib/archive/v${RELEASE_NO}.tar.gz" - "${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib-v${RELEASE_NO}.tar.gz" ${MD5}) - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf - ${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib-v${RELEASE_NO}.tar.gz - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) - file(RENAME "RingDecomposerLib-${RELEASE_NO}" "RingDecomposerLib") -else() - message("-- Found RingDecomposerLib source in ${URFLIB_DIR}") -endif() - -set(urflib_INCLUDE_DIRS ${URFLIB_DIR} - CACHE STRING "RingDecomposerLib Include Dir" FORCE) -file(GLOB URFSOURCES "${URFLIB_DIR}/*.c") - -#if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32 AND (NOT RDK_INSTALL_STATIC_LIBS))) -if(WIN32) - set (ringdecomposerlib_h ${URFLIB_DIR}/RingDecomposerLib.h) - file(READ ${ringdecomposerlib_h} ringdecomposerlib_h_data) - if (NOT "${ringdecomposerlib_h_data}" MATCHES "RDKIT_URFLIB_BUILD") - string(REGEX REPLACE "(#if[ ]+\\([ ]*defined[ ]*\\([ ]*_WIN32[ ]*\\)[ ]*&&[ ]*)(defined\\([ ]*_MSC_VER[ ]*\\))" "\\1!defined( RDL_WIN_STATIC )" ringdecomposerlib_h_data "${ringdecomposerlib_h_data}") - string(REGEX REPLACE "([ ]*)(#define[ ]+RDL_API[ ]+__declspec)(\\([ ]*dllexport[ ]*\\))" "\\1#ifdef RDKIT_URFLIB_BUILD\n\\1\\1\\2\\3\n\\1#else\n\\1\\1\\2(dllimport)\n\\1#endif" ringdecomposerlib_h_data "${ringdecomposerlib_h_data}") - file(WRITE ${ringdecomposerlib_h} "${ringdecomposerlib_h_data}") - endif() -endif() -rdkit_library(RingDecomposerLib ${URFSOURCES} SHARED) -if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32 AND (NOT RDK_INSTALL_STATIC_LIBS))) - target_compile_definitions(RingDecomposerLib PRIVATE RDKIT_URFLIB_BUILD) -endif() -install(TARGETS RingDecomposerLib DESTINATION ${RDKit_LibDir}) -rdkit_headers(${URFLIB_DIR}/RingDecomposerLib.h DEST "") - - +rdkit_library(RingDecomposerLib dummy.cpp SHARED LINK_LIBRARIES -lRingDecomposerLib) set(RDK_URF_LIBS RingDecomposerLib CACHE STRING "the libraries for the URF calculation" FORCE) diff --git a/External/RingFamilies/dummy.cpp b/External/RingFamilies/dummy.cpp new file mode 100644 index 000000000..e69de29bb diff --git a/External/YAeHMOP/CMakeLists.txt b/External/YAeHMOP/CMakeLists.txt index f1027b3bd..8bee2f910 100644 --- a/External/YAeHMOP/CMakeLists.txt +++ b/External/YAeHMOP/CMakeLists.txt @@ -4,52 +4,7 @@ endif(NOT RDK_BUILD_YAEHMOP_SUPPORT) add_definitions(-DRDK_BUILD_YAEHMOP_SUPPORT) -if(NOT DEFINED YAEHMOP_DIR) - set(YAEHMOP_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop") -endif() - -if(NOT EXISTS "${YAEHMOP_DIR}/tightbind/bind.h") - set(RELEASE_NO "2023.03.1") - set(MD5 "e6450f13e02c54d024233b993c3c7ff6") - downloadAndCheckMD5("https://github.com/greglandrum/yaehmop/archive/refs/tags/v${RELEASE_NO}.tar.gz" - "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz" ${MD5}) - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf - ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) - - file(RENAME "yaehmop-${RELEASE_NO}" "${YAEHMOP_DIR}") -else() - message("-- Found YAeHMOP source in ${YAEHMOP_DIR}") -endif() - -set(yaehmop_INCLUDE_DIRS ${YAEHMOP_DIR}/.. - CACHE STRING "yaehmop Include File" FORCE) -include_directories(${yaehmop_INCLUDE_DIRS}) - -if(CMAKE_COMPILER_IS_GNUCXX AND NOT CYGWIN) - SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC") -endif() -if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang") - SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC") -endif() - -# bring in the eHT code, but skip the targets (we'll get yaehmop_eht anyway because it's a dependency) -add_subdirectory(yaehmop/tightbind EXCLUDE_FROM_ALL True) - -# set install dir for the yaehmop library: -INSTALL(TARGETS yaehmop_eht EXPORT rdkit-targets - DESTINATION ${RDKit_LibDir}/${RDKLIB_DEST} - COMPONENT runtime ) - - - - -set(EHT_PARAM_FILE ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat ) -install(FILES ${EHT_PARAM_FILE} - DESTINATION ${RDKit_ShareDir}/Data - COMPONENT data) - -rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES yaehmop_eht GraphMol ) +rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES -lyaehmop_eht GraphMol ) target_compile_definitions(EHTLib PRIVATE RDKIT_EHTLIB_BUILD) rdkit_headers(EHTTools.h DEST GraphMol) rdkit_catch_test(testEHTLib1 test1.cpp diff --git a/External/YAeHMOP/EHTTools.cpp b/External/YAeHMOP/EHTTools.cpp index 7a229f51f..71033dc5c 100644 --- a/External/YAeHMOP/EHTTools.cpp +++ b/External/YAeHMOP/EHTTools.cpp @@ -10,7 +10,7 @@ #include extern "C" { -#include +#include } namespace RDKit { @@ -160,4 +160,4 @@ bool runMol(const ROMol &mol, EHTResults &results, int confId, } } // end of namespace EHTTools -} // end of namespace RDKit \ No newline at end of file +} // end of namespace RDKit diff --git a/External/YAeHMOP/Wrap/CMakeLists.txt b/External/YAeHMOP/Wrap/CMakeLists.txt index 759a9f360..114d24532 100644 --- a/External/YAeHMOP/Wrap/CMakeLists.txt +++ b/External/YAeHMOP/Wrap/CMakeLists.txt @@ -4,6 +4,8 @@ rdkit_python_extension(rdEHTTools DEST Chem LINK_LIBRARIES EHTLib ) + +target_include_directories(rdEHTTools PRIVATE ${RDKit_ExternalDir}/YAeHMOP) add_pytest(pyEHTTools ${CMAKE_CURRENT_SOURCE_DIR}/testEHTTools.py)