Merge pull request #375 from stuartjamesmcnicholas/64-bit

64 bit

README.md

@@ -69,6 +69,13 @@ Binaries are available on the releases page. Please read the instructions there
 <br/>After first checkout you should run the following script to build:  
 `./initial_build.sh`  
 This should build all dependencies and then `Moorhen`. 
+\
+\
+It is also possible to build a 64-bit version of Moorhen which (currently) can address up to 8GB memory:  
+`./initial_build.sh --64bit`  
+Note that you need a 64-bit WASM capable web browser to use this. Most browsers are not 64-bit capable by default. Some have
+64-bit capability available as an option or in development versions.  
+See the `MEMORY64` feature at [https://webassembly.org/features/](https://webassembly.org/features/)
 
 6. To run the Moorhen molecular graphics application:  
 `cd baby-gru`  

get_sources

@@ -113,7 +113,7 @@ echo
 echo "Attempting to get emsdk zlib/png ports"
 echo
 echo "" > silly.c
-emcc silly.c -s USE_ZLIB=1 -s USE_LIBPNG=1 -s USE_FREETYPE=1
+emcc silly.c -s USE_ZLIB=1 -s USE_LIBPNG=1 -s USE_FREETYPE=1 -s USE_PTHREADS=1 -pthread -sMEMORY64=1
 rm -f silly.c
 rm -f a.out.js
 rm -f a.out.wasm
@@ -135,3 +135,11 @@ mkdir -p include
 cd include
 ln -s ../checkout/glm-$glm_release/glm glm
 cd ..
+
+cd checkout/coot-1.0
+patch -p1 < ../../patches/coot-emscripten-64.patch
+cd ../..
+
+cd checkout/gemmi
+patch -p1 < ../../patches/gemmi-emscripten-64.patch
+cd ../..

include/igraph_f2c_arith_64.h

@@ -0,0 +1,9 @@
+#define IEEE_8087
+#define Arith_Kind_ASL 1
+#define Long int
+#define Intcast (int)(long)
+#define Double_Align
+#define X64_bit_pointers
+#define NANCHECK
+#define QNaN0 0x0
+#define QNaN1 0xfff80000

initial_build.sh

@@ -24,77 +24,101 @@ echo "Sources are in ${SOURCE_DIR}"
 echo "Building in ${BUILD_DIR}"
 echo "Installing in ${INSTALL_DIR}"
 
+MEMORY64=0
+
+optspec=":-"
+while getopts ':-:' OPT; do
+  case $OPT in
+    -) #long option
+       case $OPTARG in
+         64bit) MEMORY64=1;;
+         *) echo unknown long option: $OPTARG;;
+       esac;;
+    *) echo unknown short option: $OPTARG;;
+  esac
+done
+
+if test x"${MEMORY64}" = x"1"; then
+    echo "#######################################################"
+    echo "#######################################################"
+    echo "Building ** 64-bit ** (large memory) version of Moorhen"
+    echo "#######################################################"
+    echo "#######################################################"
+    echo
+    echo
+    MOORHEN_CMAKE_FLAGS="-sMEMORY64=1 -pthread"
+else
+    echo "########################################"
+    echo "########################################"
+    echo "Building ** 32-bit ** version of Moorhen"
+    echo "########################################"
+    echo "########################################"
+    echo
+    echo
+    MOORHEN_CMAKE_FLAGS="-pthread"
+fi
+
 mkdir -p ${INSTALL_DIR}
 
 #gsl
 mkdir -p ${BUILD_DIR}/gsl_build
 cd ${BUILD_DIR}/gsl_build
 emconfigure ${SOURCE_DIR}/gsl-2.7.1/configure --prefix=${INSTALL_DIR}
-emmake make LDFLAGS=-all-static -j ${NUMPROCS}
+emmake make LDFLAGS=-all-static -j ${NUMPROCS} CXXFLAGS="${MOORHEN_CMAKE_FLAGS}" CFLAGS="${MOORHEN_CMAKE_FLAGS}"
 emmake make install
 cd ${BUILD_DIR}
 
-#Boost (has to be built in source tree as far as I am aware)
-cd ${SOURCE_DIR}/boost
-./bootstrap.sh --with-libraries=serialization,regex,chrono,date_time,filesystem,iostreams,program_options,thread,math,random,system
-./b2 toolset=emscripten link=static variant=release cxxflags="-pthread" linkflags="-pthread" threading=multi runtime-link=static thread system filesystem regex serialization chrono date_time program_options random -j ${NUMPROCS}
-./b2 toolset=emscripten link=static variant=release cxxflags="-pthread" linkflags="-pthread" threading=multi runtime-link=static install --prefix=${INSTALL_DIR}
+#boost with cmake
+mkdir -p ${BUILD_DIR}/boost
+cd ${BUILD_DIR}/boost
+emcmake cmake -DCMAKE_C_FLAGS="${MOORHEN_CMAKE_FLAGS}" -DCMAKE_CXX_FLAGS="${MOORHEN_CMAKE_FLAGS}" -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} ${SOURCE_DIR}/checkout/boost-1.83.0 -DBOOST_EXCLUDE_LIBRARIES="context;fiber;fiber_numa;asio;log;coroutine;cobalt;nowide"
+emmake make -j ${NUMPROCS}
+emmake make install
 cd ${BUILD_DIR}
 
-emar q ${INSTALL_DIR}/lib/libboost_chrono.a ${INSTALL_DIR}/lib/libboost_chrono.bc
-emar q ${INSTALL_DIR}/lib/libboost_date_time.a ${INSTALL_DIR}/lib/libboost_date_time.bc
-emar q ${INSTALL_DIR}/lib/libboost_filesystem.a ${INSTALL_DIR}/lib/libboost_filesystem.bc
-emar q ${INSTALL_DIR}/lib/libboost_iostreams.a ${INSTALL_DIR}/lib/libboost_iostreams.bc
-emar q ${INSTALL_DIR}/lib/libboost_math_c99.a ${INSTALL_DIR}/lib/libboost_math_c99.bc
-emar q ${INSTALL_DIR}/lib/libboost_math_c99f.a ${INSTALL_DIR}/lib/libboost_math_c99f.bc
-emar q ${INSTALL_DIR}/lib/libboost_math_c99l.a ${INSTALL_DIR}/lib/libboost_math_c99l.bc
-emar q ${INSTALL_DIR}/lib/libboost_math_tr1.a ${INSTALL_DIR}/lib/libboost_math_tr1.bc
-emar q ${INSTALL_DIR}/lib/libboost_math_tr1f.a ${INSTALL_DIR}/lib/libboost_math_tr1f.bc
-emar q ${INSTALL_DIR}/lib/libboost_math_tr1l.a ${INSTALL_DIR}/lib/libboost_math_tr1l.bc
-emar q ${INSTALL_DIR}/lib/libboost_program_options.a ${INSTALL_DIR}/lib/libboost_program_options.bc
-emar q ${INSTALL_DIR}/lib/libboost_random.a ${INSTALL_DIR}/lib/libboost_random.bc
-emar q ${INSTALL_DIR}/lib/libboost_regex.a ${INSTALL_DIR}/lib/libboost_regex.bc
-emar q ${INSTALL_DIR}/lib/libboost_serialization.a ${INSTALL_DIR}/lib/libboost_serialization.bc
-emar q ${INSTALL_DIR}/lib/libboost_system.a ${INSTALL_DIR}/lib/libboost_system.bc
-emar q ${INSTALL_DIR}/lib/libboost_wserialization.a ${INSTALL_DIR}/lib/libboost_wserialization.bc
-emar q ${INSTALL_DIR}/lib/libboost_thread.a ${INSTALL_DIR}/lib/libboost_thread.bc
-
 #RDKit
+BOOST_CMAKE_STUFF=`for i in ${INSTALL_DIR}/lib/cmake/boost*; do j=${i%-1.83.0}; k=${j#${INSTALL_DIR}/lib/cmake/boost_}; echo -Dboost_${k}_DIR=$i; done`
 mkdir -p ${BUILD_DIR}/rdkit_build
 cd ${BUILD_DIR}/rdkit_build
-emcmake cmake -Dboost_iostreams_DIR=${INSTALL_DIR}/lib/cmake/boost_iostreams-1.83.0/ -Dboost_system_DIR=${INSTALL_DIR}/lib/cmake/boost_system-1.83.0/  -Dboost_headers_DIR=${INSTALL_DIR}/lib/cmake/boost_headers-1.83.0/ -DBoost_DIR=${INSTALL_DIR}/lib/cmake/Boost-1.83.0 -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_INSTALL_STATIC_LIBS=ON -DRDK_INSTALL_INTREE=OFF -DRDK_BUILD_SLN_SUPPORT=OFF -DRDK_TEST_MMFF_COMPLIANCE=OFF -DRDK_BUILD_CPP_TESTS=OFF -DRDK_USE_BOOST_SERIALIZATION=ON -DRDK_BUILD_THREADSAFE_SSS=OFF -DBoost_INCLUDE_DIR=${INSTALL_DIR}/include -DBoost_USE_STATIC_LIBS=ON -DBoost_USE_STATIC_RUNTIME=ON -DBoost_DEBUG=TRUE -DCMAKE_CXX_FLAGS="-s USE_PTHREADS=1 -pthread -Wno-enum-constexpr-conversion -D_HAS_AUTO_PTR_ETC=0" -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} ${SOURCE_DIR}/rdkit -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_INSTALL_COMIC_FONTS=OFF
+emcmake cmake -DBoost_DIR=${INSTALL_DIR}/lib/cmake/Boost-1.83.0 ${BOOST_CMAKE_STUFF} -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_INSTALL_STATIC_LIBS=ON -DRDK_INSTALL_INTREE=OFF -DRDK_BUILD_SLN_SUPPORT=OFF -DRDK_TEST_MMFF_COMPLIANCE=OFF -DRDK_BUILD_CPP_TESTS=OFF -DRDK_USE_BOOST_SERIALIZATION=ON -DRDK_BUILD_THREADSAFE_SSS=OFF -DBoost_INCLUDE_DIR=${INSTALL_DIR}/include -DBoost_USE_STATIC_LIBS=ON -DBoost_USE_STATIC_RUNTIME=ON -DBoost_DEBUG=TRUE -DCMAKE_CXX_FLAGS="${MOORHEN_CMAKE_FLAGS} -Wno-enum-constexpr-conversion -D_HAS_AUTO_PTR_ETC=0" -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} ${SOURCE_DIR}/rdkit -DRDK_OPTIMIZE_POPCNT=OFF -DRDK_INSTALL_COMIC_FONTS=OFF -DCMAKE_C_FLAGS="${MOORHEN_CMAKE_FLAGS}" -DCMAKE_MODULE_PATH=${INSTALL_DIR}/lib/cmake
 emmake make -j ${NUMPROCS}
 emmake make install
 cd ${BUILD_DIR}
 
 #gemmi
 mkdir -p ${BUILD_DIR}/gemmi_build
 cd ${BUILD_DIR}/gemmi_build
-emcmake cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} ${SOURCE_DIR}/gemmi
+emcmake cmake  -DCMAKE_EXE_LINKER_FLAGS="${MOORHEN_CMAKE_FLAGS}" -DCMAKE_C_FLAGS="${MOORHEN_CMAKE_FLAGS}" -DCMAKE_CXX_FLAGS="${MOORHEN_CMAKE_FLAGS}" -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} ${SOURCE_DIR}/gemmi
 emmake make -j ${NUMPROCS}
 emmake make install
 cd ${BUILD_DIR}
 
 #jsoncpp
 mkdir -p ${BUILD_DIR}/jsoncpp_build
 cd ${BUILD_DIR}/jsoncpp_build
-emcmake cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} ${SOURCE_DIR}/checkout/jsoncpp -DJSONCPP_WITH_TESTS=OFF
+emcmake cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} ${SOURCE_DIR}/checkout/jsoncpp -DJSONCPP_WITH_TESTS=OFF -DCMAKE_C_FLAGS="${MOORHEN_CMAKE_FLAGS}" -DCMAKE_CXX_FLAGS="${MOORHEN_CMAKE_FLAGS}"
 emmake make -j ${NUMPROCS}
 emmake make install
 cd ${BUILD_DIR}
 
 #igraph
 mkdir -p ${BUILD_DIR}/igraph_build
 cd ${BUILD_DIR}/igraph_build
-emcmake cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} ${SOURCE_DIR}/checkout/igraph -DCMAKE_CXX_FLAGS="-pthread" -DCMAKE_C_FLAGS="-pthread"
-emmake make -j ${NUMPROCS}
+if test x"${MEMORY64}" = x"1"; then
+#There is some hoop-jumping to make igraph compile with "-sMEMORY64=1 -pthread"
+    emcmake cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} ${SOURCE_DIR}/checkout/igraph -DCMAKE_C_FLAGS="${MOORHEN_CMAKE_FLAGS}" -DCMAKE_CXX_FLAGS="${MOORHEN_CMAKE_FLAGS}" -DIEEE754_DOUBLE_ENDIANNESS_MATCHES=ON -DF2C_EXTERNAL_ARITH_HEADER=${SOURCE_DIR}/include/igraph_f2c_arith_64.h
+    emmake make -j ${NUMPROCS} C_FLAGS="${MOORHEN_CMAKE_FLAGS} -Wno-error=experimental" CXX_FLAGS="${MOORHEN_CMAKE_FLAGS} -Wno-error=experimental"
+else
+    emcmake cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} ${SOURCE_DIR}/checkout/igraph -DCMAKE_C_FLAGS="${MOORHEN_CMAKE_FLAGS}" -DCMAKE_CXX_FLAGS="${MOORHEN_CMAKE_FLAGS}"
+    emmake make -j ${NUMPROCS}
+fi
 emmake make install
 cd ${BUILD_DIR}
 
 #Moorhen
 mkdir -p ${BUILD_DIR}/moorhen_build
 cd ${BUILD_DIR}/moorhen_build
-emcmake cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} ${SOURCE_DIR}
+emcmake cmake -DMEMORY64=${MEMORY64} -DCMAKE_EXE_LINKER_FLAGS="${MOORHEN_CMAKE_FLAGS}" -DCMAKE_C_FLAGS="${MOORHEN_CMAKE_FLAGS}" -DCMAKE_CXX_FLAGS="${MOORHEN_CMAKE_FLAGS}" -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} ${SOURCE_DIR}
 emmake make -j ${NUMPROCS}
 emmake make install
 cd ${BUILD_DIR}
@@ -103,7 +127,5 @@ cd ${SOURCE_DIR}/baby-gru/
 npm install
 cd ${BUILD_DIR}
 
-#*This link must be removed before building electron app!*
-#Links cause confusion in Linux/Mac, and are followed on Windows making huge packages that take forever to build.
 cd ${SOURCE_DIR}/baby-gru/public/baby-gru
 ln -s ${SOURCE_DIR}/checkout/monomers

patches/coot-emscripten-64.patch

@@ -0,0 +1,29 @@
+diff --git a/coot-utils/slurp-map.cc b/coot-utils/slurp-map.cc
+index a432676fc..f1b60b823 100644
+--- a/coot-utils/slurp-map.cc
++++ b/coot-utils/slurp-map.cc
+@@ -110,12 +110,14 @@ coot::util::slurp_fill_xmap_from_map_file(const std::string &file_name,
+
+       bool is_gzip = false;
+       std::string ext = file_name_extension(file_name);
++#if !((__POINTER_WIDTH__==64) && __EMSCRIPTEN__)
+       if (ext == ".gz") is_gzip = true;
+
+       if (is_gzip) {
+          // this can fail (at the moment) if the axes are not in X,Y,Z order
+          status = slurp_fill_xmap_from_gz_map_file(file_name, xmap_p, check_only);
+       } else {
++#endif
+          // 20231006-PE as it used to be.
+          struct stat s;
+          int fstat = stat(file_name.c_str(), &s);
+@@ -139,7 +141,9 @@ coot::util::slurp_fill_xmap_from_map_file(const std::string &file_name,
+             }
+             delete [] space;
+          }
++#if !((__POINTER_WIDTH__==64) && __EMSCRIPTEN__)
+       }
++#endif
+    } else {
+       std::cout << "WARNING:: file does not exist " << file_name << std::endl;
+    }

patches/gemmi-emscripten-64.patch

@@ -0,0 +1,13 @@
+diff --git a/third_party/stb_sprintf.h b/third_party/stb_sprintf.h
+index 28e9d64b..27429a8c 100644
+--- a/third_party/stb_sprintf.h
++++ b/third_party/stb_sprintf.h
+@@ -230,7 +230,7 @@ STBSP__PUBLICDEC void STB_SPRINTF_DECORATE(set_separators)(char comma, char peri
+ #define stbsp__uint16 unsigned short
+
+ #ifndef stbsp__uintptr
+-#if defined(__ppc64__) || defined(__powerpc64__) || defined(__aarch64__) || defined(_M_X64) || defined(__x86_64__) || defined(__x86_64) || defined(__s390x__)
++#if defined(__ppc64__) || defined(__powerpc64__) || defined(__aarch64__) || defined(_M_X64) || defined(__x86_64__) || defined(__x86_64) || defined(__s390x__) || ((__POINTER_WIDTH__==64) && defined(__EMSCRIPTEN__))
+ #define stbsp__uintptr stbsp__uint64
+ #else
+ #define stbsp__uintptr stbsp__uint32

slicendice_cpp/CMakeLists.txt

@@ -1,6 +1,5 @@
 project(slicendice)
 
-
 add_library(slicendice_cpp STATIC 
 ${CMAKE_SOURCE_DIR}/checkout/slicendice_cpp/prog/extmath.cpp
 ${CMAKE_SOURCE_DIR}/checkout/slicendice_cpp/prog/dist_metrics.cpp

wasm_src/CMakeLists.txt

@@ -437,7 +437,7 @@ ${coot_src}/ideal/write-png.cc
 
 target_include_directories(coot PRIVATE ${coot_src} ${coot_src}/coords ${coot_src}/ccp4mg-utils ${coot_src}/utils ${coot_src}/src ../include ../checkout/ssm ../checkout/mmdb2 ../checkout/clipper ../checkout/fftw-2.1.5/fftw ../checkout/fftw-2.1.5/rfftw ../checkout/libccp4/ccp4 ../boost  ../checkout/gemmi/include )
 
-set_target_properties(coot PROPERTIES COMPILE_FLAGS "-DHAVE_BOOST_BASED_THREAD_POOL_LIBRARY -Wno-deprecated-declarations -Wno-deprecated-builtins -pthread -DHAVE_CXX11=1 -DHAVE_SSMLIB -DHAVE_BOOST -DNODERAWFS -DFFTW_ENABLE_FLOAT -s USE_LIBPNG=1 -s USE_ZLIB=1 -s USE_PTHREADS=1" LINK_FLAGS "-fexceptions -pthread -s USE_LIBPNG=1 -s USE_ZLIB=1 -s USE_PTHREADS=1 -sDEMANGLE_SUPPORT=1 -sASSERTIONS=2")
+set_target_properties(coot PROPERTIES COMPILE_FLAGS "-DHAVE_BOOST_BASED_THREAD_POOL_LIBRARY -Wno-deprecated-declarations -Wno-deprecated-builtins -pthread -DHAVE_CXX11=1 -DHAVE_SSMLIB -DHAVE_BOOST -DNODERAWFS -DFFTW_ENABLE_FLOAT -s USE_LIBPNG=1 -s USE_ZLIB=1 -s USE_PTHREADS=1" LINK_FLAGS "-fexceptions -pthread -s USE_LIBPNG=1 -s USE_ZLIB=1 -s USE_PTHREADS=1 -sASSERTIONS=2")
 
 set_source_files_properties(${coot_exception_srcs} PROPERTIES COMPILE_FLAGS "-DHAVE_BOOST_BASED_THREAD_POOL_LIBRARY -fexceptions -pthread -DHAVE_SSMLIB -DHAVE_BOOST -DNODERAWFS -DFFTW_ENABLE_FLOAT -s USE_LIBPNG=1 -s USE_ZLIB=1 -s USE_PTHREADS=1" )
 
@@ -518,7 +518,11 @@ FILE(COPY ${CMAKE_INSTALL_PREFIX}/share/RDKit/Data/BaseFeatures.fdef DESTINATION
 
 #-sALLOW_MEMORY_GROWTH=1 -sINITIAL_MEMORY=512MB -sMAXIMUM_MEMORY=4092MB -sTOTAL_MEMORY=4092MB
 add_executable(moorhen moorhen-wrappers.cc gemmi-wrappers.cc smilestopdb.cc)
-target_link_options(moorhen PRIVATE -sDEMANGLE_SUPPORT=1 -sASSERTIONS=2 -fexceptions -pthread -sPTHREAD_POOL_SIZE=32 -sPTHREAD_POOL_SIZE_STRICT=32 -sUSE_PTHREADS=1 -sALLOW_MEMORY_GROWTH=1 --bind -sFORCE_FILESYSTEM=1 -sMODULARIZE=1 -sEXPORT_NAME=createRSRModule -sEXPORTED_RUNTIME_METHODS=['FS','readFile'] --preload-file data  --pre-js ${CMAKE_CURRENT_SOURCE_DIR}/coot_env_web.js)
+if(${MEMORY64} MATCHES "1")
+target_link_options(moorhen PRIVATE -sASSERTIONS=2 -fexceptions -pthread -sPTHREAD_POOL_SIZE=32 -sPTHREAD_POOL_SIZE_STRICT=32 -sUSE_PTHREADS=1 -sALLOW_MEMORY_GROWTH=1 -sINITIAL_MEMORY=4096MB -sMAXIMUM_MEMORY=8192MB --bind -sFORCE_FILESYSTEM=1 -sMODULARIZE=1 -sEXPORT_NAME=createRSRModule -sEXPORTED_RUNTIME_METHODS=['FS','readFile'] --preload-file data  --pre-js ${CMAKE_CURRENT_SOURCE_DIR}/coot_env_web.js)
+else()
+target_link_options(moorhen PRIVATE -sASSERTIONS=2 -fexceptions -pthread -sPTHREAD_POOL_SIZE=32 -sPTHREAD_POOL_SIZE_STRICT=32 -sUSE_PTHREADS=1 -sALLOW_MEMORY_GROWTH=1 --bind -sFORCE_FILESYSTEM=1 -sMODULARIZE=1 -sEXPORT_NAME=createRSRModule -sEXPORTED_RUNTIME_METHODS=['FS','readFile'] --preload-file data  --pre-js ${CMAKE_CURRENT_SOURCE_DIR}/coot_env_web.js)
+endif()
 target_link_directories(moorhen PUBLIC ../ssm ../mmdb2 ../clipper/cif ../clipper/mmdb ../clipper/core ../clipper/contrib ../clipper/ccp4 ../clipper/gemmi ../fftw ../rfftw ../ccp4 ../lib ../install/lib ../privateer)
 target_link_libraries(moorhen ssm mmdb2 clipper-minimol clipper-phs clipper-mmdb clipper-cif clipper-core clipper-contrib clipper-ccp4 clipper-gemmi fftw rfftw ccp4  coot gsl gslcblas RDKitMolDraw2D RDKitForceFieldHelpers RDKitDescriptors RDKitForceField RDKitSubstructMatch RDKitOptimizer RDKitDistGeomHelpers RDKitDistGeometry RDKitChemReactions RDKitAlignment RDKitEigenSolvers RDKitDepictor RDKitcoordgen RDKitMolChemicalFeatures RDKitPartialCharges RDKitFileParsers RDKitRDGeometryLib RDKitGraphMol RDKitShapeHelpers RDKitFingerprints RDKitMolAlign RDKitMolTransforms RDKitChemTransforms RDKitSmilesParse RDKitFilterCatalog RDKitCatalogs RDKitSubgraphs RDKitRDGeneral RDKitDataStructs RDKitGenericGroups boost_thread boost_serialization gemmi_cpp privateer freetype slicendice_cpp jsoncpp igraph m z idbfs.js)
 target_include_directories(moorhen PRIVATE ${coot_src} ${coot_src}/ccp4mg-utils ${coot_src}/src ../checkout/boost_1_80_0 ../checkout/clipper/ ../checkout/mmdb2 ../checkout/mmdb2/mmdb2 ../checkout/ssm ../checkout/libccp4/ccp4 ../fftw ../rfftw ../include ../checkout/gemmi/include ../checkout/privateer-wasm/src/privateer/cpp ../checkout/privateer-wasm/src/privateer/cpp/pybind11 ../checkout/privateer-wasm/src/privateer/cpp/third-party/simdjson ../checkout/slicendice_cpp/prog/ ../checkout/rdkit-Release_2023_09_1/External/Eigen/eigen/ )