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libcifpp
Commit b36988e6 by Maarten L. Hekkelman
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update changelog

parent 393aefce
Showing with 416 additions and 415 deletions
CMakeLists.txt
......@@ -6,10 +6,10 @@
# modification, are permitted provided that the following conditions are met:
# 1. Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer
# list of conditions and the following disclaimer
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
......@@ -26,9 +26,9 @@ cmake_minimum_required(VERSION 3.16)
# set the project name
project(
libcifpp
VERSION 6.0.1
LANGUAGES CXX)
libcifpp
VERSION 6.0.1
LANGUAGES CXX)
list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
......@@ -48,16 +48,16 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
# When building with ninja-multiconfig, build both debug and release by default
if(CMAKE_GENERATOR STREQUAL "Ninja Multi-Config")
set(CMAKE_CROSS_CONFIGS "Debug;Release")
set(CMAKE_DEFAULT_CONFIGS "Debug;Release")
set(CMAKE_CROSS_CONFIGS "Debug;Release")
set(CMAKE_DEFAULT_CONFIGS "Debug;Release")
endif()
if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
set(CMAKE_CXX_FLAGS
"${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers"
)
set(CMAKE_CXX_FLAGS
"${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers"
)
elseif(MSVC)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4")
endif()
# Build documentation?
......@@ -67,81 +67,81 @@ option(BUILD_DOCUMENTATION "Build the documentation" OFF)
option(BUILD_FOR_CCP4 "Build a version to be installed in CCP4")
# Building shared libraries?
if(NOT (BUILD_FOR_CCP4 AND WIN32))
option(BUILD_SHARED_LIBS "Build a shared library instead of a static one" OFF)
if(NOT(BUILD_FOR_CCP4 AND WIN32))
option(BUILD_SHARED_LIBS "Build a shared library instead of a static one" OFF)
endif()
if(BUILD_FOR_CCP4)
unset(CIFPP_DOWNLOAD_CCD)
unset(CIFPP_INSTALL_UPDATE_SCRIPT)
unset(CIFPP_DOWNLOAD_CCD)
unset(CIFPP_INSTALL_UPDATE_SCRIPT)
else()
# Lots of code depend on the availability of the components.cif file
option(CIFPP_DOWNLOAD_CCD
"Download the CCD file components.cif during installation" ON)
# An optional cron script can be installed to keep the data files up-to-date
if(UNIX AND NOT APPLE)
option(CIFPP_INSTALL_UPDATE_SCRIPT
"Install the script to update CCD and dictionary files" ON)
endif()
# Lots of code depend on the availability of the components.cif file
option(CIFPP_DOWNLOAD_CCD
"Download the CCD file components.cif during installation" ON)
# An optional cron script can be installed to keep the data files up-to-date
if(UNIX AND NOT APPLE)
option(CIFPP_INSTALL_UPDATE_SCRIPT
"Install the script to update CCD and dictionary files" ON)
endif()
endif()
# When CCP4 is sourced in the environment, we can recreate the symmetry
# operations table
if(EXISTS "$ENV{CCP4}/lib/data/syminfo.lib")
option(CIFPP_RECREATE_SYMOP_DATA
"Recreate SymOp data table in case it is out of date" ON)
option(CIFPP_RECREATE_SYMOP_DATA
"Recreate SymOp data table in case it is out of date" ON)
endif()
# CCP4 build
if(BUILD_FOR_CCP4)
if("$ENV{CCP4}" STREQUAL "" OR NOT EXISTS $ENV{CCP4})
message(FATAL_ERROR "A CCP4 built was requested but CCP4 was not sourced")
else()
list(PREPEND CMAKE_MODULE_PATH "$ENV{CCP4}")
list(PREPEND CMAKE_PREFIX_PATH "$ENV{CCP4}")
set(CMAKE_INSTALL_PREFIX "$ENV{CCP4}")
if(WIN32)
set(BUILD_SHARED_LIBS ON)
endif()
endif()
if("$ENV{CCP4}" STREQUAL "" OR NOT EXISTS $ENV{CCP4})
message(FATAL_ERROR "A CCP4 built was requested but CCP4 was not sourced")
else()
list(PREPEND CMAKE_MODULE_PATH "$ENV{CCP4}")
list(PREPEND CMAKE_PREFIX_PATH "$ENV{CCP4}")
set(CMAKE_INSTALL_PREFIX "$ENV{CCP4}")
if(WIN32)
set(BUILD_SHARED_LIBS ON)
endif()
endif()
endif()
# Now include the GNUInstallDirs module
include(GNUInstallDirs)
if(WIN32)
if(${CMAKE_SYSTEM_VERSION} GREATER_EQUAL 10) # Windows 10
add_definitions(-D _WIN32_WINNT=0x0A00)
elseif(${CMAKE_SYSTEM_VERSION} EQUAL 6.3) # Windows 8.1
add_definitions(-D _WIN32_WINNT=0x0603)
elseif(${CMAKE_SYSTEM_VERSION} EQUAL 6.2) # Windows 8
add_definitions(-D _WIN32_WINNT=0x0602)
elseif(${CMAKE_SYSTEM_VERSION} EQUAL 6.1) # Windows 7
add_definitions(-D _WIN32_WINNT=0x0601)
elseif(${CMAKE_SYSTEM_VERSION} EQUAL 6.0) # Windows Vista
add_definitions(-D _WIN32_WINNT=0x0600)
else() # Windows XP (5.1)
add_definitions(-D _WIN32_WINNT=0x0501)
endif()
add_definitions(-DNOMINMAX)
# We do not want to write an export file for all our symbols...
set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
if(${CMAKE_SYSTEM_VERSION} GREATER_EQUAL 10) # Windows 10
add_definitions(-D _WIN32_WINNT=0x0A00)
elseif(${CMAKE_SYSTEM_VERSION} EQUAL 6.3) # Windows 8.1
add_definitions(-D _WIN32_WINNT=0x0603)
elseif(${CMAKE_SYSTEM_VERSION} EQUAL 6.2) # Windows 8
add_definitions(-D _WIN32_WINNT=0x0602)
elseif(${CMAKE_SYSTEM_VERSION} EQUAL 6.1) # Windows 7
add_definitions(-D _WIN32_WINNT=0x0601)
elseif(${CMAKE_SYSTEM_VERSION} EQUAL 6.0) # Windows Vista
add_definitions(-D _WIN32_WINNT=0x0600)
else() # Windows XP (5.1)
add_definitions(-D _WIN32_WINNT=0x0501)
endif()
add_definitions(-DNOMINMAX)
# We do not want to write an export file for all our symbols...
set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
endif()
if(MSVC)
# make msvc standards compliant...
add_compile_options(/permissive- /bigobj)
add_link_options(/NODEFAULTLIB:library)
if(BUILD_SHARED_LIBS)
set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>DLL")
else()
set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
endif()
# make msvc standards compliant...
add_compile_options(/permissive- /bigobj)
add_link_options(/NODEFAULTLIB:library)
if(BUILD_SHARED_LIBS)
set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>DLL")
else()
set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
endif()
endif()
# Libraries
......@@ -150,43 +150,43 @@ endif()
# implementation in GCC is not acceptable, it crashes on long lines. The
# implementation in libc++ (clang) and MSVC seem to be OK.
check_cxx_source_compiles(
"
"
#include <iostream>
#ifndef __GLIBCXX__
#error
#endif
int main(int argc, char *argv[]) { return 0; }"
GXX_LIBSTDCPP)
GXX_LIBSTDCPP)
if(GXX_LIBSTDCPP)
message(
STATUS "Testing for known regex bug, since you're using GNU libstdc++")
message(
STATUS "Testing for known regex bug, since you're using GNU libstdc++")
try_run(STD_REGEX_RUNNING STD_REGEX_COMPILING
${CMAKE_CURRENT_BINARY_DIR}/test
${PROJECT_SOURCE_DIR}/cmake/test-rx.cpp)
try_run(STD_REGEX_RUNNING STD_REGEX_COMPILING
${CMAKE_CURRENT_BINARY_DIR}/test
${PROJECT_SOURCE_DIR}/cmake/test-rx.cpp)
if(STD_REGEX_RUNNING STREQUAL FAILED_TO_RUN)
message(
STATUS
"You are probably trying to compile using the g++ standard library which contains a crashing std::regex implementation. Will use boost::regex instead"
)
if(STD_REGEX_RUNNING STREQUAL FAILED_TO_RUN)
message(
STATUS
"You are probably trying to compile using the g++ standard library which contains a crashing std::regex implementation. Will use boost::regex instead"
)
find_package(Boost 1.80 QUIET COMPONENTS regex)
find_package(Boost 1.80 QUIET COMPONENTS regex)
if(NOT Boost_FOUND)
set(BOOST_REGEX_STANDALONE ON)
if(NOT Boost_FOUND)
set(BOOST_REGEX_STANDALONE ON)
FetchContent_Declare(
boost-rx
GIT_REPOSITORY https://github.com/boostorg/regex
GIT_TAG boost-1.83.0)
FetchContent_Declare(
boost-rx
GIT_REPOSITORY https://github.com/boostorg/regex
GIT_TAG boost-1.83.0)
FetchContent_MakeAvailable(boost-rx)
endif()
FetchContent_MakeAvailable(boost-rx)
endif()
set(BOOST_REGEX ON)
endif()
set(BOOST_REGEX ON)
endif()
endif()
set(CMAKE_THREAD_PREFER_PTHREAD)
......@@ -194,31 +194,31 @@ set(THREADS_PREFER_PTHREAD_FLAG)
find_package(Threads)
if(MSVC)
# Avoid linking the shared library of zlib Search ZLIB_ROOT first if it is
# set.
if(ZLIB_ROOT)
set(_ZLIB_SEARCH_ROOT PATHS ${ZLIB_ROOT} NO_DEFAULT_PATH)
list(APPEND _ZLIB_SEARCHES _ZLIB_SEARCH_ROOT)
endif()
# Normal search.
set(_ZLIB_x86 "(x86)")
set(_ZLIB_SEARCH_NORMAL
PATHS "[HKEY_LOCAL_MACHINE\\SOFTWARE\\GnuWin32\\Zlib;InstallPath]"
"$ENV{ProgramFiles}/zlib" "$ENV{ProgramFiles${_ZLIB_x86}}/zlib")
unset(_ZLIB_x86)
list(APPEND _ZLIB_SEARCHES _ZLIB_SEARCH_NORMAL)
if(BUILD_FOR_CCP4)
list(PREPEND _ZLIB_SEARCHES "$ENV{CCP4}/lib")
endif()
foreach(search ${_ZLIB_SEARCHES})
find_library(
ZLIB_LIBRARY
NAMES zlibstatic NAMES_PER_DIR ${${search}}
PATH_SUFFIXES lib)
endforeach()
# Avoid linking the shared library of zlib Search ZLIB_ROOT first if it is
# set.
if(ZLIB_ROOT)
set(_ZLIB_SEARCH_ROOT PATHS ${ZLIB_ROOT} NO_DEFAULT_PATH)
list(APPEND _ZLIB_SEARCHES _ZLIB_SEARCH_ROOT)
endif()
# Normal search.
set(_ZLIB_x86 "(x86)")
set(_ZLIB_SEARCH_NORMAL
PATHS "[HKEY_LOCAL_MACHINE\\SOFTWARE\\GnuWin32\\Zlib;InstallPath]"
"$ENV{ProgramFiles}/zlib" "$ENV{ProgramFiles${_ZLIB_x86}}/zlib")
unset(_ZLIB_x86)
list(APPEND _ZLIB_SEARCHES _ZLIB_SEARCH_NORMAL)
if(BUILD_FOR_CCP4)
list(PREPEND _ZLIB_SEARCHES "$ENV{CCP4}/lib")
endif()
foreach(search ${_ZLIB_SEARCHES})
find_library(
ZLIB_LIBRARY
NAMES zlibstatic NAMES_PER_DIR ${${search}}
PATH_SUFFIXES lib)
endforeach()
endif()
find_package(ZLIB REQUIRED)
......@@ -229,22 +229,22 @@ find_package(ZLIB REQUIRED)
find_package(Eigen3 3.4 QUIET)
if(Eigen3_FOUND AND TARGET Eigen3::Eigen)
get_target_property(EIGEN_INCLUDE_DIR Eigen3::Eigen
INTERFACE_INCLUDE_DIRECTORIES)
get_target_property(EIGEN_INCLUDE_DIR Eigen3::Eigen
INTERFACE_INCLUDE_DIRECTORIES)
else()
# Create a private copy of eigen3 and populate it only, no need to build
FetchContent_Declare(
my-eigen3
GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
GIT_TAG 3.4.0)
# Create a private copy of eigen3 and populate it only, no need to build
FetchContent_Declare(
my-eigen3
GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
GIT_TAG 3.4.0)
FetchContent_GetProperties(my-eigen3)
FetchContent_GetProperties(my-eigen3)
if(NOT my-eigen3_POPULATED)
FetchContent_Populate(my-eigen3)
endif()
if(NOT my-eigen3_POPULATED)
FetchContent_Populate(my-eigen3)
endif()
set(EIGEN_INCLUDE_DIR ${my-eigen3_SOURCE_DIR})
set(EIGEN_INCLUDE_DIR ${my-eigen3_SOURCE_DIR})
endif()
include(FindFilesystem)
......@@ -259,286 +259,286 @@ write_version_header(${PROJECT_SOURCE_DIR}/src/ LIB_NAME "LibCIFPP")
# SymOp data table
if(CIFPP_RECREATE_SYMOP_DATA)
# The tool to create the table
add_executable(symop-map-generator
"${PROJECT_SOURCE_DIR}/src/symop-map-generator.cpp")
add_custom_command(
OUTPUT ${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp
COMMAND
$<TARGET_FILE:symop-map-generator> $ENV{CLIBD}/syminfo.lib
$ENV{CLIBD}/symop.lib ${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp)
add_custom_target(
OUTPUT
${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp
DEPENDS symop-map-generator "$ENV{CLIBD}/syminfo.lib"
"$ENV{CLIBD}/symop.lib")
# The tool to create the table
add_executable(symop-map-generator
"${PROJECT_SOURCE_DIR}/src/symop-map-generator.cpp")
add_custom_command(
OUTPUT ${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp
COMMAND
$<TARGET_FILE:symop-map-generator> $ENV{CLIBD}/syminfo.lib
$ENV{CLIBD}/symop.lib ${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp)
add_custom_target(
OUTPUT
${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp
DEPENDS symop-map-generator "$ENV{CLIBD}/syminfo.lib"
"$ENV{CLIBD}/symop.lib")
endif()
# Sources
set(project_sources
${PROJECT_SOURCE_DIR}/src/category.cpp
${PROJECT_SOURCE_DIR}/src/condition.cpp
${PROJECT_SOURCE_DIR}/src/datablock.cpp
${PROJECT_SOURCE_DIR}/src/dictionary_parser.cpp
${PROJECT_SOURCE_DIR}/src/file.cpp
${PROJECT_SOURCE_DIR}/src/item.cpp
${PROJECT_SOURCE_DIR}/src/parser.cpp
${PROJECT_SOURCE_DIR}/src/row.cpp
${PROJECT_SOURCE_DIR}/src/validate.cpp
${PROJECT_SOURCE_DIR}/src/text.cpp
${PROJECT_SOURCE_DIR}/src/utilities.cpp
${PROJECT_SOURCE_DIR}/src/atom_type.cpp
${PROJECT_SOURCE_DIR}/src/compound.cpp
${PROJECT_SOURCE_DIR}/src/point.cpp
${PROJECT_SOURCE_DIR}/src/symmetry.cpp
${PROJECT_SOURCE_DIR}/src/model.cpp
${PROJECT_SOURCE_DIR}/src/pdb/cif2pdb.cpp
${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif.cpp
${PROJECT_SOURCE_DIR}/src/pdb/pdb_record.hpp
${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif_remark_3.hpp
${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif_remark_3.cpp
${PROJECT_SOURCE_DIR}/src/category.cpp
${PROJECT_SOURCE_DIR}/src/condition.cpp
${PROJECT_SOURCE_DIR}/src/datablock.cpp
${PROJECT_SOURCE_DIR}/src/dictionary_parser.cpp
${PROJECT_SOURCE_DIR}/src/file.cpp
${PROJECT_SOURCE_DIR}/src/item.cpp
${PROJECT_SOURCE_DIR}/src/parser.cpp
${PROJECT_SOURCE_DIR}/src/row.cpp
${PROJECT_SOURCE_DIR}/src/validate.cpp
${PROJECT_SOURCE_DIR}/src/text.cpp
${PROJECT_SOURCE_DIR}/src/utilities.cpp
${PROJECT_SOURCE_DIR}/src/atom_type.cpp
${PROJECT_SOURCE_DIR}/src/compound.cpp
${PROJECT_SOURCE_DIR}/src/point.cpp
${PROJECT_SOURCE_DIR}/src/symmetry.cpp
${PROJECT_SOURCE_DIR}/src/model.cpp
${PROJECT_SOURCE_DIR}/src/pdb/cif2pdb.cpp
${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif.cpp
${PROJECT_SOURCE_DIR}/src/pdb/pdb_record.hpp
${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif_remark_3.hpp
${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif_remark_3.cpp
${PROJECT_SOURCE_DIR}/src/pdb/reconstruct.cpp
${PROJECT_SOURCE_DIR}/src/pdb/validate-pdbx.cpp
)
)
set(project_headers
${PROJECT_SOURCE_DIR}/include/cif++.hpp
${PROJECT_SOURCE_DIR}/include/cif++/utilities.hpp
${PROJECT_SOURCE_DIR}/include/cif++/item.hpp
${PROJECT_SOURCE_DIR}/include/cif++/datablock.hpp
${PROJECT_SOURCE_DIR}/include/cif++/file.hpp
${PROJECT_SOURCE_DIR}/include/cif++/validate.hpp
${PROJECT_SOURCE_DIR}/include/cif++/iterator.hpp
${PROJECT_SOURCE_DIR}/include/cif++/parser.hpp
${PROJECT_SOURCE_DIR}/include/cif++/forward_decl.hpp
${PROJECT_SOURCE_DIR}/include/cif++/dictionary_parser.hpp
${PROJECT_SOURCE_DIR}/include/cif++/condition.hpp
${PROJECT_SOURCE_DIR}/include/cif++/category.hpp
${PROJECT_SOURCE_DIR}/include/cif++/row.hpp
${PROJECT_SOURCE_DIR}/include/cif++/atom_type.hpp
${PROJECT_SOURCE_DIR}/include/cif++/compound.hpp
${PROJECT_SOURCE_DIR}/include/cif++/point.hpp
${PROJECT_SOURCE_DIR}/include/cif++/symmetry.hpp
${PROJECT_SOURCE_DIR}/include/cif++/model.hpp
${PROJECT_SOURCE_DIR}/include/cif++/pdb.hpp
${PROJECT_SOURCE_DIR}/include/cif++/pdb/cif2pdb.hpp
${PROJECT_SOURCE_DIR}/include/cif++/pdb/io.hpp
${PROJECT_SOURCE_DIR}/include/cif++/pdb/pdb2cif.hpp
${PROJECT_SOURCE_DIR}/include/cif++/pdb/tls.hpp)
${PROJECT_SOURCE_DIR}/include/cif++.hpp
${PROJECT_SOURCE_DIR}/include/cif++/utilities.hpp
${PROJECT_SOURCE_DIR}/include/cif++/item.hpp
${PROJECT_SOURCE_DIR}/include/cif++/datablock.hpp
${PROJECT_SOURCE_DIR}/include/cif++/file.hpp
${PROJECT_SOURCE_DIR}/include/cif++/validate.hpp
${PROJECT_SOURCE_DIR}/include/cif++/iterator.hpp
${PROJECT_SOURCE_DIR}/include/cif++/parser.hpp
${PROJECT_SOURCE_DIR}/include/cif++/forward_decl.hpp
${PROJECT_SOURCE_DIR}/include/cif++/dictionary_parser.hpp
${PROJECT_SOURCE_DIR}/include/cif++/condition.hpp
${PROJECT_SOURCE_DIR}/include/cif++/category.hpp
${PROJECT_SOURCE_DIR}/include/cif++/row.hpp
${PROJECT_SOURCE_DIR}/include/cif++/atom_type.hpp
${PROJECT_SOURCE_DIR}/include/cif++/compound.hpp
${PROJECT_SOURCE_DIR}/include/cif++/point.hpp
${PROJECT_SOURCE_DIR}/include/cif++/symmetry.hpp
${PROJECT_SOURCE_DIR}/include/cif++/model.hpp
${PROJECT_SOURCE_DIR}/include/cif++/pdb.hpp
${PROJECT_SOURCE_DIR}/include/cif++/pdb/cif2pdb.hpp
${PROJECT_SOURCE_DIR}/include/cif++/pdb/io.hpp
${PROJECT_SOURCE_DIR}/include/cif++/pdb/pdb2cif.hpp
${PROJECT_SOURCE_DIR}/include/cif++/pdb/tls.hpp)
add_library(cifpp ${project_sources} ${project_headers}
${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp)
${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp)
add_library(cifpp::cifpp ALIAS cifpp)
set(CMAKE_DEBUG_POSTFIX d)
set_target_properties(cifpp PROPERTIES DEBUG_POSTFIX "d")
generate_export_header(cifpp EXPORT_FILE_NAME
${PROJECT_SOURCE_DIR}/include/cif++/exports.hpp)
${PROJECT_SOURCE_DIR}/include/cif++/exports.hpp)
if(BOOST_REGEX)
target_compile_definitions(cifpp PRIVATE USE_BOOST_REGEX=1
BOOST_REGEX_STANDALONE=1)
get_target_property(BOOST_REGEX_INCLUDE_DIR Boost::regex
INTERFACE_INCLUDE_DIRECTORIES)
target_compile_definitions(cifpp PRIVATE USE_BOOST_REGEX=1
BOOST_REGEX_STANDALONE=1)
get_target_property(BOOST_REGEX_INCLUDE_DIR Boost::regex
INTERFACE_INCLUDE_DIRECTORIES)
endif()
if(MSVC)
target_compile_definitions(cifpp PUBLIC NOMINMAX=1)
target_compile_definitions(cifpp PUBLIC NOMINMAX=1)
endif()
set_target_properties(cifpp PROPERTIES POSITION_INDEPENDENT_CODE ON)
target_include_directories(
cifpp
PUBLIC "$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>"
"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
PRIVATE "${BOOST_REGEX_INCLUDE_DIR}" "${EIGEN_INCLUDE_DIR}")
cifpp
PUBLIC "$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>"
"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
PRIVATE "${BOOST_REGEX_INCLUDE_DIR}" "${EIGEN_INCLUDE_DIR}")
target_link_libraries(cifpp PUBLIC Threads::Threads ZLIB::ZLIB
${CIFPP_REQUIRED_LIBRARIES})
${CIFPP_REQUIRED_LIBRARIES})
if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
endif(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
if(CIFPP_DOWNLOAD_CCD)
# download the components.cif file from CCD
set(COMPONENTS_CIF ${PROJECT_SOURCE_DIR}/rsrc/components.cif)
if(EXISTS ${COMPONENTS_CIF})
file(SIZE ${COMPONENTS_CIF} CCD_FILE_SIZE)
if(CCD_FILE_SIZE EQUAL 0)
message(STATUS "Removing empty ${COMPONENTS_CIF} file")
file(REMOVE "${COMPONENTS_CIF}")
endif()
endif()
if(NOT EXISTS ${COMPONENTS_CIF})
# Since the file(DOWNLOAD) command in cmake does not use compression, we try
# to download the gzipped version and decompress it ourselves.
find_program(GUNZIP gunzip)
if(WIN32 OR GUNZIP STREQUAL "GUNZIP-NOTFOUND")
file(
DOWNLOAD https://files.wwpdb.org/pub/pdb/data/monomers/components.cif
${COMPONENTS_CIF}
SHOW_PROGRESS
STATUS CCD_FETCH_STATUS)
else()
if(NOT EXISTS "${COMPONENTS_CIF}.gz")
file(
DOWNLOAD
https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
${COMPONENTS_CIF}.gz
SHOW_PROGRESS
STATUS CCD_FETCH_STATUS)
endif()
add_custom_command(
OUTPUT ${COMPONENTS_CIF}
COMMAND "${GUNZIP}" ${COMPONENTS_CIF}.gz
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/rsrc/)
add_custom_target(COMPONENTS ALL DEPENDS ${COMPONENTS_CIF})
endif()
# Do not continue if downloading went wrong
list(POP_FRONT CCD_FETCH_STATUS CCD_FETCH_STATUS_CODE)
if(CCD_FETCH_STATUS_CODE)
message(
FATAL_ERROR "Error trying to download CCD file: ${CCD_FETCH_STATUS}")
endif()
endif()
# download the components.cif file from CCD
set(COMPONENTS_CIF ${PROJECT_SOURCE_DIR}/rsrc/components.cif)
if(EXISTS ${COMPONENTS_CIF})
file(SIZE ${COMPONENTS_CIF} CCD_FILE_SIZE)
if(CCD_FILE_SIZE EQUAL 0)
message(STATUS "Removing empty ${COMPONENTS_CIF} file")
file(REMOVE "${COMPONENTS_CIF}")
endif()
endif()
if(NOT EXISTS ${COMPONENTS_CIF})
# Since the file(DOWNLOAD) command in cmake does not use compression, we try
# to download the gzipped version and decompress it ourselves.
find_program(GUNZIP gunzip)
if(WIN32 OR GUNZIP STREQUAL "GUNZIP-NOTFOUND")
file(
DOWNLOAD https://files.wwpdb.org/pub/pdb/data/monomers/components.cif
${COMPONENTS_CIF}
SHOW_PROGRESS
STATUS CCD_FETCH_STATUS)
else()
if(NOT EXISTS "${COMPONENTS_CIF}.gz")
file(
DOWNLOAD
https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
${COMPONENTS_CIF}.gz
SHOW_PROGRESS
STATUS CCD_FETCH_STATUS)
endif()
add_custom_command(
OUTPUT ${COMPONENTS_CIF}
COMMAND "${GUNZIP}" ${COMPONENTS_CIF}.gz
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/rsrc/)
add_custom_target(COMPONENTS ALL DEPENDS ${COMPONENTS_CIF})
endif()
# Do not continue if downloading went wrong
list(POP_FRONT CCD_FETCH_STATUS CCD_FETCH_STATUS_CODE)
if(CCD_FETCH_STATUS_CODE)
message(
FATAL_ERROR "Error trying to download CCD file: ${CCD_FETCH_STATUS}")
endif()
endif()
endif()
# Installation directories
if(BUILD_FOR_CCP4)
set(CIFPP_DATA_DIR
"$ENV{CCP4}/share/libcifpp"
CACHE PATH "Directory where dictionary and other static data is stored")
set(CIFPP_DATA_DIR
"$ENV{CCP4}/share/libcifpp"
CACHE PATH "Directory where dictionary and other static data is stored")
else()
set(CIFPP_DATA_DIR
"${CMAKE_INSTALL_FULL_DATADIR}/libcifpp"
CACHE PATH "Directory where dictionary and other static data is stored")
set(CIFPP_DATA_DIR
"${CMAKE_INSTALL_FULL_DATADIR}/libcifpp"
CACHE PATH "Directory where dictionary and other static data is stored")
endif()
if(CIFPP_DATA_DIR)
target_compile_definitions(cifpp PUBLIC DATA_DIR="${CIFPP_DATA_DIR}")
target_compile_definitions(cifpp PUBLIC DATA_DIR="${CIFPP_DATA_DIR}")
endif()
if(UNIX AND NOT BUILD_FOR_CCP4)
if("${CMAKE_INSTALL_PREFIX}" STREQUAL "/usr/local")
set(CIFPP_CACHE_DIR
"/var/cache/libcifpp"
CACHE PATH "The directory where downloaded data files are stored")
else()
set(CIFPP_CACHE_DIR
"${CMAKE_INSTALL_FULL_LOCALSTATEDIR}/cache/libcifpp"
CACHE PATH "The directory where downloaded data files are stored")
endif()
target_compile_definitions(cifpp PUBLIC CACHE_DIR="${CIFPP_CACHE_DIR}")
set(CIFPP_ETC_DIR
"${CMAKE_INSTALL_FULL_SYSCONFDIR}"
CACHE PATH "The directory where the update configuration file is stored")
if("${CMAKE_INSTALL_PREFIX}" STREQUAL "/usr/local")
set(CIFPP_CACHE_DIR
"/var/cache/libcifpp"
CACHE PATH "The directory where downloaded data files are stored")
else()
set(CIFPP_CACHE_DIR
"${CMAKE_INSTALL_FULL_LOCALSTATEDIR}/cache/libcifpp"
CACHE PATH "The directory where downloaded data files are stored")
endif()
target_compile_definitions(cifpp PUBLIC CACHE_DIR="${CIFPP_CACHE_DIR}")
set(CIFPP_ETC_DIR
"${CMAKE_INSTALL_FULL_SYSCONFDIR}"
CACHE PATH "The directory where the update configuration file is stored")
else()
unset(CIFPP_CACHE_DIR)
unset(CIFPP_CACHE_DIR)
endif()
# Install rules
install(
TARGETS cifpp
EXPORT cifpp-targets
ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
INCLUDES
DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
TARGETS cifpp
EXPORT cifpp-targets
ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
INCLUDES
DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
if(MSVC AND BUILD_SHARED_LIBS)
install(
FILES $<TARGET_PDB_FILE:cifpp>
DESTINATION ${CMAKE_INSTALL_LIBDIR}
OPTIONAL)
install(
FILES $<TARGET_PDB_FILE:cifpp>
DESTINATION ${CMAKE_INSTALL_LIBDIR}
OPTIONAL)
endif()
# Clean up old config files (with old names)
file(GLOB OLD_CONFIG_FILES
${CMAKE_INSTALL_FULL_LIBDIR}/cmake/cifpp/cifppConfig*.cmake
${CMAKE_INSTALL_FULL_LIBDIR}/cmake/cifpp/cifppTargets*.cmake)
${CMAKE_INSTALL_FULL_LIBDIR}/cmake/cifpp/cifppConfig*.cmake
${CMAKE_INSTALL_FULL_LIBDIR}/cmake/cifpp/cifppTargets*.cmake)
if(OLD_CONFIG_FILES)
message(
STATUS "Installation will remove old config files: ${OLD_CONFIG_FILES}")
install(CODE "file(REMOVE ${OLD_CONFIG_FILES})")
message(
STATUS "Installation will remove old config files: ${OLD_CONFIG_FILES}")
install(CODE "file(REMOVE ${OLD_CONFIG_FILES})")
endif()
install(
EXPORT cifpp-targets
FILE "cifpp-targets.cmake"
NAMESPACE cifpp::
DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cifpp)
EXPORT cifpp-targets
FILE "cifpp-targets.cmake"
NAMESPACE cifpp::
DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cifpp)
install(
DIRECTORY include/cif++
DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
COMPONENT Devel)
DIRECTORY include/cif++
DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
COMPONENT Devel)
install(
FILES include/cif++.hpp
DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
COMPONENT Devel)
FILES include/cif++.hpp
DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
COMPONENT Devel)
if(CIFPP_DATA_DIR)
install(
FILES ${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx.dic
${PROJECT_SOURCE_DIR}/rsrc/mmcif_ma.dic ${COMPONENTS_CIF}
DESTINATION ${CIFPP_DATA_DIR})
install(
FILES ${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx.dic
${PROJECT_SOURCE_DIR}/rsrc/mmcif_ma.dic ${COMPONENTS_CIF}
DESTINATION ${CIFPP_DATA_DIR})
endif()
if(CIFPP_CACHE_DIR)
install(
FILES ${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx.dic
${PROJECT_SOURCE_DIR}/rsrc/mmcif_ma.dic ${COMPONENTS_CIF}
DESTINATION ${CIFPP_CACHE_DIR})
install(
FILES ${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx.dic
${PROJECT_SOURCE_DIR}/rsrc/mmcif_ma.dic ${COMPONENTS_CIF}
DESTINATION ${CIFPP_CACHE_DIR})
endif()
set(CONFIG_TEMPLATE_FILE ${PROJECT_SOURCE_DIR}/cmake/cifpp-config.cmake.in)
configure_package_config_file(
${CONFIG_TEMPLATE_FILE} ${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config.cmake
INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cifpp
PATH_VARS CIFPP_DATA_DIR)
${CONFIG_TEMPLATE_FILE} ${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config.cmake
INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cifpp
PATH_VARS CIFPP_DATA_DIR)
install(
FILES "${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config.cmake"
"${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config-version.cmake"
DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cifpp
COMPONENT Devel)
FILES "${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config.cmake"
"${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config-version.cmake"
DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cifpp
COMPONENT Devel)
set_target_properties(
cifpp
PROPERTIES VERSION ${PROJECT_VERSION}
SOVERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}"
INTERFACE_cifpp_MAJOR_VERSION ${PROJECT_VERSION_MAJOR})
cifpp
PROPERTIES VERSION ${PROJECT_VERSION}
SOVERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}"
INTERFACE_cifpp_MAJOR_VERSION ${PROJECT_VERSION_MAJOR})
set_property(
TARGET cifpp
APPEND
PROPERTY COMPATIBLE_INTERFACE_STRING cifpp_MAJOR_VERSION)
TARGET cifpp
APPEND
PROPERTY COMPATIBLE_INTERFACE_STRING cifpp_MAJOR_VERSION)
write_basic_package_version_file(
"${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config-version.cmake"
VERSION ${PROJECT_VERSION}
COMPATIBILITY AnyNewerVersion)
"${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config-version.cmake"
VERSION ${PROJECT_VERSION}
COMPATIBILITY AnyNewerVersion)
# In case we're included as sub_directory:
if(NOT PROJECT_IS_TOP_LEVEL)
......@@ -546,109 +546,109 @@ if(NOT PROJECT_IS_TOP_LEVEL)
endif()
if(BUILD_TESTING)
# We're using the older version 2 of Catch2
FetchContent_Declare(
Catch2
GIT_REPOSITORY https://github.com/catchorg/Catch2.git
GIT_TAG v2.13.9)
FetchContent_MakeAvailable(Catch2)
list(
APPEND
CIFPP_tests
unit-v2
unit-3d
format
model
rename-compound
sugar
spinner
validate-pdbx)
foreach(CIFPP_TEST IN LISTS CIFPP_tests)
set(CIFPP_TEST "${CIFPP_TEST}-test")
set(CIFPP_TEST_SOURCE "${CMAKE_CURRENT_SOURCE_DIR}/test/${CIFPP_TEST}.cpp")
add_executable(
${CIFPP_TEST} ${CIFPP_TEST_SOURCE}
"${CMAKE_CURRENT_SOURCE_DIR}/test/test-main.cpp")
target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp::cifpp
Catch2::Catch2)
target_include_directories(${CIFPP_TEST} PRIVATE "${EIGEN_INCLUDE_DIR}")
if(MSVC)
# Specify unwind semantics so that MSVC knowns how to handle exceptions
target_compile_options(${CIFPP_TEST} PRIVATE /EHsc)
endif()
add_custom_target(
"run-${CIFPP_TEST}"
DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch ${CIFPP_TEST})
add_custom_command(
OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch
COMMAND $<TARGET_FILE:${CIFPP_TEST}> --data-dir
${CMAKE_CURRENT_SOURCE_DIR}/test)
add_test(NAME ${CIFPP_TEST} COMMAND $<TARGET_FILE:${CIFPP_TEST}> --data-dir
${CMAKE_CURRENT_SOURCE_DIR}/test)
endforeach()
# We're using the older version 2 of Catch2
FetchContent_Declare(
Catch2
GIT_REPOSITORY https://github.com/catchorg/Catch2.git
GIT_TAG v2.13.9)
FetchContent_MakeAvailable(Catch2)
list(
APPEND
CIFPP_tests
unit-v2
unit-3d
format
model
rename-compound
sugar
spinner
validate-pdbx)
foreach(CIFPP_TEST IN LISTS CIFPP_tests)
set(CIFPP_TEST "${CIFPP_TEST}-test")
set(CIFPP_TEST_SOURCE "${CMAKE_CURRENT_SOURCE_DIR}/test/${CIFPP_TEST}.cpp")
add_executable(
${CIFPP_TEST} ${CIFPP_TEST_SOURCE}
"${CMAKE_CURRENT_SOURCE_DIR}/test/test-main.cpp")
target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp::cifpp
Catch2::Catch2)
target_include_directories(${CIFPP_TEST} PRIVATE "${EIGEN_INCLUDE_DIR}")
if(MSVC)
# Specify unwind semantics so that MSVC knowns how to handle exceptions
target_compile_options(${CIFPP_TEST} PRIVATE /EHsc)
endif()
add_custom_target(
"run-${CIFPP_TEST}"
DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch ${CIFPP_TEST})
add_custom_command(
OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch
COMMAND $<TARGET_FILE:${CIFPP_TEST}> --data-dir
${CMAKE_CURRENT_SOURCE_DIR}/test)
add_test(NAME ${CIFPP_TEST} COMMAND $<TARGET_FILE:${CIFPP_TEST}> --data-dir
${CMAKE_CURRENT_SOURCE_DIR}/test)
endforeach()
endif()
# Optionally install the update scripts for CCD and dictionary files
if(CIFPP_INSTALL_UPDATE_SCRIPT)
if(${CMAKE_SYSTEM_NAME} STREQUAL "Linux" OR ${CMAKE_SYSTEM_NAME} STREQUAL
"GNU")
if("${CMAKE_INSTALL_PREFIX}" STREQUAL "/usr/local")
set(CIFPP_CRON_DIR
"/etc/cron.weekly"
CACHE PATH "The cron directory, for the update script")
else()
set(CIFPP_CRON_DIR
"${CIFPP_ETC_DIR}/cron.weekly"
CACHE PATH "The cron directory, for the update script")
endif()
elseif(${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD")
set(CIFPP_CRON_DIR
"${CIFPP_ETC_DIR}/periodic/weekly"
CACHE PATH "The cron directory, for the update script")
else()
message(FATAL_ERROR "Don't know where to install the update script")
endif()
configure_file(${PROJECT_SOURCE_DIR}/tools/update-libcifpp-data.in
update-libcifpp-data @ONLY)
install(
FILES ${CMAKE_CURRENT_BINARY_DIR}/update-libcifpp-data
DESTINATION ${CIFPP_CRON_DIR}
PERMISSIONS OWNER_EXECUTE OWNER_READ GROUP_EXECUTE GROUP_READ WORLD_EXECUTE
WORLD_READ)
install(DIRECTORY DESTINATION ${CIFPP_CACHE_DIR})
# a config file, to make it complete
if(NOT EXISTS "${CIFPP_ETC_DIR}/libcifpp.conf")
file(
WRITE ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf
[[# Uncomment the next line to enable automatic updates
if(${CMAKE_SYSTEM_NAME} STREQUAL "Linux" OR ${CMAKE_SYSTEM_NAME} STREQUAL
"GNU")
if("${CMAKE_INSTALL_PREFIX}" STREQUAL "/usr/local")
set(CIFPP_CRON_DIR
"/etc/cron.weekly"
CACHE PATH "The cron directory, for the update script")
else()
set(CIFPP_CRON_DIR
"${CIFPP_ETC_DIR}/cron.weekly"
CACHE PATH "The cron directory, for the update script")
endif()
elseif(${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD")
set(CIFPP_CRON_DIR
"${CIFPP_ETC_DIR}/periodic/weekly"
CACHE PATH "The cron directory, for the update script")
else()
message(FATAL_ERROR "Don't know where to install the update script")
endif()
configure_file(${PROJECT_SOURCE_DIR}/tools/update-libcifpp-data.in
update-libcifpp-data @ONLY)
install(
FILES ${CMAKE_CURRENT_BINARY_DIR}/update-libcifpp-data
DESTINATION ${CIFPP_CRON_DIR}
PERMISSIONS OWNER_EXECUTE OWNER_READ GROUP_EXECUTE GROUP_READ WORLD_EXECUTE
WORLD_READ)
install(DIRECTORY DESTINATION ${CIFPP_CACHE_DIR})
# a config file, to make it complete
if(NOT EXISTS "${CIFPP_ETC_DIR}/libcifpp.conf")
file(
WRITE ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf
[[# Uncomment the next line to enable automatic updates
# update=true
]])
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf
DESTINATION "${CIFPP_ETC_DIR}")
install(
CODE "message(\"A configuration file has been written to ${CIFPP_ETC_DIR}/libcifpp.conf, please edit this file to enable automatic updates\")"
)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf
DESTINATION "${CIFPP_ETC_DIR}")
install(
CODE "message(\"A configuration file has been written to ${CIFPP_ETC_DIR}/libcifpp.conf, please edit this file to enable automatic updates\")"
)
install(DIRECTORY DESTINATION "${CIFPP_ETC_DIR}/libcifpp/cache-update.d")
endif()
install(DIRECTORY DESTINATION "${CIFPP_ETC_DIR}/libcifpp/cache-update.d")
endif()
target_compile_definitions(cifpp PUBLIC CACHE_DIR="${CIFPP_CACHE_DIR}")
target_compile_definitions(cifpp PUBLIC CACHE_DIR="${CIFPP_CACHE_DIR}")
endif()
if(BUILD_DOCUMENTATION)
add_subdirectory(docs)
add_subdirectory(docs)
endif()
set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")
......
changelog
......@@ -3,6 +3,7 @@ Version 6.0.1
- Change order of categories inside a datablock to match order in file
- Change default order to write out categories in a file based on
parent/child relationship
- Added validate_pdbx and recover_pdbx
Version 6.0.0
- Drop the use of CCP4's monomer library for compound information
......
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