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libcifpp
Commit f1ca916d by Maarten L. Hekkelman
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Merge remote-tracking branch 'origin/develop' into develop-cif2fasta

parents 4782a4e0 6aae012a
Showing with 539 additions and 178 deletions
CMakeLists.txt
......@@ -11,21 +11,24 @@
# 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 IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
cmake_minimum_required(VERSION 3.16)
# set the project name
project(libcifpp VERSION 6.0.0 LANGUAGES CXX)
project(
libcifpp
VERSION 6.0.1
LANGUAGES CXX)
list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
......@@ -50,7 +53,9 @@ if(CMAKE_GENERATOR STREQUAL "Ninja Multi-Config")
endif()
if("${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 "${CMAKE_CXX_FLAGS} /W4")
endif()
......@@ -62,7 +67,7 @@ option(BUILD_DOCUMENTATION "Build the documentation" OFF)
option(BUILD_FOR_CCP4 "Build a version to be installed in CCP4")
# Building shared libraries?
if(NOT(BUILD_FOR_CCP4 AND WIN32))
if(NOT (BUILD_FOR_CCP4 AND WIN32))
option(BUILD_SHARED_LIBS "Build a shared library instead of a static one" OFF)
endif()
......@@ -71,17 +76,21 @@ if(BUILD_FOR_CCP4)
unset(CIFPP_INSTALL_UPDATE_SCRIPT)
else()
# Lots of code depend on the availability of the components.cif file
option(CIFPP_DOWNLOAD_CCD "Download the CCD file components.cif during installation" ON)
option(CIFPP_DOWNLOAD_CCD
"Download the CCD file components.cif during installation" ON)
# An optional cron script can be installed to keep the data files up-to-date
if(UNIX AND NOT APPLE)
option(CIFPP_INSTALL_UPDATE_SCRIPT "Install the script to update CCD and dictionary files" ON)
option(CIFPP_INSTALL_UPDATE_SCRIPT
"Install the script to update CCD and dictionary files" ON)
endif()
endif()
# When CCP4 is sourced in the environment, we can recreate the symmetry operations table
# When CCP4 is sourced in the environment, we can recreate the symmetry
# operations table
if(EXISTS "$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
......@@ -138,23 +147,30 @@ endif()
# Libraries
# Start by finding out if std:regex is usable. Note that the current
# 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("
# 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)
int main(int argc, char *argv[]) { return 0; }"
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)
${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")
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)
......@@ -164,8 +180,7 @@ if(GXX_LIBSTDCPP)
FetchContent_Declare(
boost-rx
GIT_REPOSITORY https://github.com/boostorg/regex
GIT_TAG boost-1.83.0
)
GIT_TAG boost-1.83.0)
FetchContent_MakeAvailable(boost-rx)
endif()
......@@ -179,8 +194,8 @@ 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.
# Avoid linking the shared library of zlib Search ZLIB_ROOT first if it is
# set.
if(ZLIB_ROOT)
set(_ZLIB_SEARCH_ROOT PATHS ${ZLIB_ROOT} NO_DEFAULT_PATH)
list(APPEND _ZLIB_SEARCHES _ZLIB_SEARCH_ROOT)
......@@ -190,8 +205,7 @@ if(MSVC)
set(_ZLIB_x86 "(x86)")
set(_ZLIB_SEARCH_NORMAL
PATHS "[HKEY_LOCAL_MACHINE\\SOFTWARE\\GnuWin32\\Zlib;InstallPath]"
"$ENV{ProgramFiles}/zlib"
"$ENV{ProgramFiles${_ZLIB_x86}}/zlib")
"$ENV{ProgramFiles}/zlib" "$ENV{ProgramFiles${_ZLIB_x86}}/zlib")
unset(_ZLIB_x86)
list(APPEND _ZLIB_SEARCHES _ZLIB_SEARCH_NORMAL)
......@@ -200,26 +214,29 @@ if(MSVC)
endif()
foreach(search ${_ZLIB_SEARCHES})
find_library(ZLIB_LIBRARY NAMES zlibstatic NAMES_PER_DIR ${${search}} PATH_SUFFIXES lib)
find_library(
ZLIB_LIBRARY
NAMES zlibstatic NAMES_PER_DIR ${${search}}
PATH_SUFFIXES lib)
endforeach()
endif()
find_package(ZLIB REQUIRED)
# Using Eigen3 is a bit of a thing. We don't want to build it completely since we
# only need a couple of header files. Nothing special. But often, eigen3 is already
# installed and then we prefer that.
# Using Eigen3 is a bit of a thing. We don't want to build it completely since
# we only need a couple of header files. Nothing special. But often, eigen3 is
# already installed and then we prefer that.
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
)
GIT_TAG 3.4.0)
FetchContent_GetProperties(my-eigen3)
......@@ -243,17 +260,20 @@ 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_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
)
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"
)
OUTPUT
${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp
DEPENDS symop-map-generator "$ENV{CLIBD}/syminfo.lib"
"$ENV{CLIBD}/symop.lib")
endif()
# Sources
......@@ -269,20 +289,16 @@ set(project_sources
${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/pdb2cif_remark_3.cpp)
set(project_headers
${PROJECT_SOURCE_DIR}/include/cif++.hpp
......@@ -298,33 +314,32 @@ set(project_headers
${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++/pdb/tls.hpp)
add_library(cifpp ${project_sources} ${project_headers} ${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp)
add_library(cifpp ${project_sources} ${project_headers}
${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)
generate_export_header(cifpp EXPORT_FILE_NAME
${PROJECT_SOURCE_DIR}/include/cif++/exports.hpp)
if(BOOST_REGEX)
target_compile_definitions(cifpp PRIVATE USE_BOOST_REGEX=1 BOOST_REGEX_STANDALONE=1)
get_target_property(BOOST_REGEX_INCLUDE_DIR Boost::regex INTERFACE_INCLUDE_DIRECTORIES)
target_compile_definitions(cifpp PRIVATE USE_BOOST_REGEX=1
BOOST_REGEX_STANDALONE=1)
get_target_property(BOOST_REGEX_INCLUDE_DIR Boost::regex
INTERFACE_INCLUDE_DIRECTORIES)
endif()
if(MSVC)
......@@ -333,17 +348,14 @@ endif()
set_target_properties(cifpp PROPERTIES POSITION_INDEPENDENT_CODE ON)
target_include_directories(cifpp
PUBLIC
"$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>"
target_include_directories(
cifpp
PUBLIC "$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>"
"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
PRIVATE
"${BOOST_REGEX_INCLUDE_DIR}"
"${EIGEN_INCLUDE_DIR}"
)
PRIVATE "${BOOST_REGEX_INCLUDE_DIR}" "${EIGEN_INCLUDE_DIR}")
target_link_libraries(cifpp
PUBLIC Threads::Threads ZLIB::ZLIB ${CIFPP_REQUIRED_LIBRARIES})
target_link_libraries(cifpp PUBLIC Threads::Threads ZLIB::ZLIB
${CIFPP_REQUIRED_LIBRARIES})
if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
......@@ -363,21 +375,28 @@ if(CIFPP_DOWNLOAD_CCD)
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.
# 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)
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)
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}
add_custom_command(
OUTPUT ${COMPONENTS_CIF}
COMMAND "${GUNZIP}" ${COMPONENTS_CIF}.gz
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/rsrc/)
......@@ -388,41 +407,56 @@ if(CIFPP_DOWNLOAD_CCD)
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}")
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
"${CMAKE_INSTALL_FULL_DATADIR}/libcifpp"
CACHE PATH "Directory where dictionary and other static data is stored")
endif()
target_compile_definitions(cifpp PUBLIC DATA_DIR="${CIFPP_DATA_DIR}")
if(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")
set(CIFPP_CACHE_DIR
"/var/cache/libcifpp"
CACHE PATH "The directory where downloaded data files are stored")
else()
set(CIFPP_CACHE_DIR "${CMAKE_INSTALL_FULL_LOCALSTATEDIR}/cache/libcifpp" CACHE PATH "The directory where downloaded data files are stored")
set(CIFPP_CACHE_DIR
"${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")
set(CIFPP_ETC_DIR
"${CMAKE_INSTALL_FULL_SYSCONFDIR}"
CACHE PATH "The directory where the update configuration file is stored")
else()
unset(CIFPP_CACHE_DIR)
endif()
# Install rules
install(TARGETS cifpp
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})
INCLUDES
DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
if(MSVC AND BUILD_SHARED_LIBS)
install(
......@@ -437,104 +471,102 @@ file(GLOB OLD_CONFIG_FILES
${CMAKE_INSTALL_FULL_LIBDIR}/cmake/cifpp/cifppTargets*.cmake)
if(OLD_CONFIG_FILES)
message(STATUS "Installation will remove old config files: ${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
install(
EXPORT cifpp-targets
FILE "cifpp-targets.cmake"
NAMESPACE cifpp::
DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cifpp
)
DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cifpp)
install(
DIRECTORY include/cif++
DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
COMPONENT Devel
)
COMPONENT Devel)
install(
FILES include/cif++.hpp
DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
COMPONENT Devel
)
COMPONENT Devel)
install(FILES
${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
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}
)
${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
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}
)
${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
${CONFIG_TEMPLATE_FILE} ${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config.cmake
INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cifpp
PATH_VARS CIFPP_DATA_DIR
)
PATH_VARS CIFPP_DATA_DIR)
install(FILES
"${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config.cmake"
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
)
COMPONENT Devel)
set_target_properties(cifpp PROPERTIES
VERSION ${PROJECT_VERSION}
set_target_properties(
cifpp
PROPERTIES VERSION ${PROJECT_VERSION}
SOVERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}"
INTERFACE_cifpp_MAJOR_VERSION ${PROJECT_VERSION_MAJOR})
set_property(TARGET cifpp APPEND PROPERTY
COMPATIBLE_INTERFACE_STRING cifpp_MAJOR_VERSION
)
set_property(
TARGET cifpp
APPEND
PROPERTY COMPATIBLE_INTERFACE_STRING cifpp_MAJOR_VERSION)
write_basic_package_version_file(
"${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config-version.cmake"
VERSION ${PROJECT_VERSION}
COMPATIBILITY AnyNewerVersion
)
COMPATIBILITY AnyNewerVersion)
if(BUILD_TESTING)
# We're using the older version 2 of Catch2
FetchContent_Declare(
Catch2
GIT_REPOSITORY https://github.com/catchorg/Catch2.git
GIT_TAG v2.13.9
)
GIT_TAG v2.13.9)
FetchContent_MakeAvailable(Catch2)
list(APPEND CIFPP_tests
list(
APPEND
CIFPP_tests
unit-v2
unit-3d
format
model
rename-compound
sugar
spinner
)
spinner)
foreach(CIFPP_TEST IN LISTS CIFPP_tests)
set(CIFPP_TEST "${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")
add_executable(
${CIFPP_TEST} ${CIFPP_TEST_SOURCE}
"${CMAKE_CURRENT_SOURCE_DIR}/test/test-main.cpp")
target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp::cifpp Catch2::Catch2)
target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp::cifpp
Catch2::Catch2)
target_include_directories(${CIFPP_TEST} PRIVATE "${EIGEN_INCLUDE_DIR}")
if(MSVC)
......@@ -542,47 +574,63 @@ if(BUILD_TESTING)
target_compile_options(${CIFPP_TEST} PRIVATE /EHsc)
endif()
add_custom_target("run-${CIFPP_TEST}" DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch ${CIFPP_TEST})
add_custom_target(
"run-${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)
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)
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_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")
set(CIFPP_CRON_DIR
"/etc/cron.weekly"
CACHE PATH "The cron directory, for the update script")
else()
set(CIFPP_CRON_DIR "${CIFPP_ETC_DIR}/cron.weekly" CACHE PATH "The cron directory, for the update script")
set(CIFPP_CRON_DIR
"${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")
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)
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
)
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
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()
......
changelog
Version 6.0.1
- Add formula weight to entity in pdb2cif
- 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
Version 6.0.0
- Drop the use of CCP4's monomer library for compound information
......
docs/resources.rst
......@@ -18,7 +18,7 @@ Loading Resources
No matter where the resource is located, you should always use the single libcifpp API call :cpp:func:`cif::load_resource` to load them. This function returns a *std::istream* wrapped inside a *std::unique_ptr*.
The order in which resources are search for is:
The order in which resources are searched for is:
* Use the resource that was defined by calling :cpp:func:`cif::add_file_resource`
for this name.
......
include/cif++/compound.hpp
......@@ -168,14 +168,18 @@ class compound
private:
friend class compound_factory_impl;
friend class local_compound_factory_impl;
compound(cif::datablock &db);
compound(cif::datablock &db, const std::string &id, const std::string &name, const std::string &type, const std::string &group);
compound(cif::datablock &db, int);
std::string m_id;
std::string m_name;
std::string m_type;
std::string m_group;
/// @cond
// m_group is no longer used
std::string __m_group;
/// @endcond
std::string m_formula;
float m_formula_weight = 0;
int m_formal_charge = 0;
......@@ -214,6 +218,20 @@ class compound_factory
/// Override any previously loaded dictionary with @a inDictFile
void push_dictionary(const std::filesystem::path &inDictFile);
/** @brief Override any previously loaded dictionary with the data in @a file
*
* @note experimental feature
*
* Load the file @a file as a source for compound information. This may
* be e.g. a regular mmCIF file with extra files containing compound
* information.
*
* Be carefull to remove the block again, best use @ref cif::compound_source
* as a stack based object.
*/
void push_dictionary(const file &file);
/// Remove the last pushed dictionary
void pop_dictionary();
......@@ -251,4 +269,35 @@ class compound_factory
std::shared_ptr<compound_factory_impl> m_impl;
};
// --------------------------------------------------------------------
/**
* @brief Stack based source for compound info.
*
* Use this class to temporarily add a compound source to the
* compound_factory.
*
* @code{.cpp}
* cif::file f("1cbs-with-custom-rea.cif");
* cif::compound_source cs(f);
*
* auto &cf = cif::compound_factory::instance();
* auto rea_compound = cf.create("REA");
* @endcode
*/
class compound_source
{
public:
compound_source(const cif::file &file)
{
cif::compound_factory::instance().push_dictionary(file);
}
~compound_source()
{
cif::compound_factory::instance().pop_dictionary();
}
};
} // namespace cif
include/cif++/row.hpp
......@@ -290,6 +290,13 @@ class row_handle
return operator[](get_column_ix(column)).template as<T>();
}
/// \brief Get the value of column @a column cast to type @a T
template <typename T>
T get(std::string_view column) const
{
return operator[](get_column_ix(column)).template as<T>();
}
/// \brief assign each of the columns named in @a values to their respective value
void assign(const std::vector<item> &values)
{
......
src/compound.cpp
......@@ -142,8 +142,6 @@ compound::compound(cif::datablock &db)
// The name should not contain newline characters since that triggers validation errors later on
cif::replace_all(m_name, "\n", "");
m_group = "non-polymer";
auto &chemCompAtom = db["chem_comp_atom"];
for (auto row : chemCompAtom)
{
......@@ -153,6 +151,9 @@ compound::compound(cif::datablock &db)
row.get("atom_id", "type_symbol", "charge", "pdbx_aromatic_flag", "pdbx_leaving_atom_flag", "pdbx_stereo_config",
"model_Cartn_x", "model_Cartn_y", "model_Cartn_z");
atom.type_symbol = atom_type_traits(type_symbol).type();
if (stereo_config.empty())
atom.stereo_config = stereo_config_type::N;
else
atom.stereo_config = parse_stereo_config_from_string(stereo_config);
m_atoms.push_back(std::move(atom));
}
......@@ -163,17 +164,28 @@ compound::compound(cif::datablock &db)
compound_bond bond;
std::string valueOrder;
cif::tie(bond.atom_id[0], bond.atom_id[1], valueOrder, bond.aromatic, bond.stereo_config) = row.get("atom_id_1", "atom_id_2", "value_order", "pdbx_aromatic_flag", "pdbx_stereo_config");
if (valueOrder.empty())
bond.type = bond_type::sing;
else
bond.type = parse_bond_type_from_string(valueOrder);
m_bonds.push_back(std::move(bond));
}
}
compound::compound(cif::datablock &db, const std::string &id, const std::string &name, const std::string &type, const std::string &group)
: m_id(id)
, m_name(name)
, m_type(type)
, m_group(group)
compound::compound(cif::datablock &db, int)
{
auto &chemComp = db["chem_comp"];
if (chemComp.size() != 1)
throw std::runtime_error("Invalid compound file, chem_comp should contain a single row");
cif::tie(m_id, m_name) =
chemComp.front().get("id", "name");
cif::trim(m_name);
m_type = "NON-POLYMER";
auto &chemCompAtom = db["chem_comp_atom"];
for (auto row : chemCompAtom)
{
......@@ -184,7 +196,6 @@ compound::compound(cif::datablock &db, const std::string &id, const std::string
atom.type_symbol = atom_type_traits(type_symbol).type();
m_formal_charge += atom.charge;
m_formula_weight += atom_type_traits(atom.type_symbol).weight();
m_atoms.push_back(std::move(atom));
}
......@@ -209,11 +220,39 @@ compound::compound(cif::datablock &db, const std::string &id, const std::string
else
{
if (cif::VERBOSE > 0)
std::cerr << "Unimplemented chem_comp_bond.type " << btype << " in " << id << '\n';
std::cerr << "Unimplemented chem_comp_bond.type " << btype << " in " << db.name() << '\n';
bond.type = bond_type::sing;
}
m_bonds.push_back(std::move(bond));
}
// reconstruct a formula and weight
m_formula_weight = 0;
std::map<atom_type, int> f;
for (auto &atom : m_atoms)
f[atom.type_symbol] += 1;
if (f.count(atom_type::C))
{
atom_type_traits att(atom_type::C);
m_formula += att.symbol() + std::to_string(f[atom_type::C]) + ' ';
m_formula_weight += att.weight() * f[atom_type::C];
}
for (const auto &[type, count] : f)
{
if (type == atom_type::C)
continue;
atom_type_traits att(type);
m_formula += att.symbol() + std::to_string(count) + ' ';
m_formula_weight += att.weight() * count;
}
if (not m_formula.empty())
m_formula.pop_back();
}
compound_atom compound::get_atom_by_atom_id(const std::string &atom_id) const
......@@ -260,13 +299,12 @@ float compound::bond_length(const std::string &atomId_1, const std::string &atom
auto a = get_atom_by_atom_id(atomId_1);
auto b = get_atom_by_atom_id(atomId_2);
result = distance(point{a.x, a.y, a.z}, point{b.x, b.y, b.z});
result = distance(point{ a.x, a.y, a.z }, point{ b.x, b.y, b.z });
}
return result;
}
// --------------------------------------------------------------------
// known amino acids and bases
......@@ -316,7 +354,7 @@ class compound_factory_impl : public std::enable_shared_from_this<compound_facto
compound_factory_impl();
compound_factory_impl(const fs::path &file, std::shared_ptr<compound_factory_impl> next);
~compound_factory_impl()
virtual ~compound_factory_impl()
{
for (auto c : m_compounds)
delete c;
......@@ -378,8 +416,10 @@ class compound_factory_impl : public std::enable_shared_from_this<compound_facto
m_next->describe(os);
}
private:
compound *create(const std::string &id);
protected:
compound_factory_impl(std::shared_ptr<compound_factory_impl> next);
virtual compound *create(const std::string &id);
std::shared_timed_mutex mMutex;
......@@ -395,10 +435,15 @@ compound_factory_impl::compound_factory_impl()
{
}
compound_factory_impl::compound_factory_impl(std::shared_ptr<compound_factory_impl> next)
: m_next(next)
{
}
compound_factory_impl::compound_factory_impl(const fs::path &file, std::shared_ptr<compound_factory_impl> next)
: m_file(file)
, m_next(next)
: compound_factory_impl(next)
{
m_file = file;
}
compound *compound_factory_impl::create(const std::string &id)
......@@ -476,6 +521,45 @@ compound *compound_factory_impl::create(const std::string &id)
// --------------------------------------------------------------------
class local_compound_factory_impl : public compound_factory_impl
{
public:
local_compound_factory_impl(const cif::file &file, std::shared_ptr<compound_factory_impl> next)
: compound_factory_impl(next)
, m_local_file(file)
{
}
compound *create(const std::string &id) override;
private:
const cif::file &m_local_file;
};
compound *local_compound_factory_impl::create(const std::string &id)
{
compound *result = nullptr;
for (auto &db : m_local_file)
{
if (db.name() == "comp_" + id)
{
cif::datablock db_copy(db);
result = new compound(db_copy, 1);
std::shared_lock lock(mMutex);
m_compounds.push_back(result);
break;
}
}
return result;
}
// --------------------------------------------------------------------
std::unique_ptr<compound_factory> compound_factory::s_instance;
thread_local std::unique_ptr<compound_factory> compound_factory::tl_instance;
bool compound_factory::s_use_thread_local_instance;
......@@ -553,6 +637,18 @@ void compound_factory::push_dictionary(const fs::path &inDictFile)
}
}
void compound_factory::push_dictionary(const cif::file &inDictFile)
{
try
{
m_impl.reset(new local_compound_factory_impl(inDictFile, m_impl));
}
catch (const std::exception &)
{
std::throw_with_nested(std::runtime_error("Error loading dictionary from local mmCIF file"));
}
}
void compound_factory::pop_dictionary()
{
if (m_impl)
......@@ -584,7 +680,8 @@ void compound_factory::report_missing_compound(const std::string &compound_id)
{
using namespace cif::colour;
std::clog << "\n" << cif::coloured("Configuration error:", white, red) << "\n\n"
std::clog << "\n"
<< cif::coloured("Configuration error:", white, red) << "\n\n"
<< "The attempt to retrieve compound information for " << std::quoted(compound_id) << " failed.\n\n"
<< "This information is searched for in a CCD file called components.cif or\n"
<< "components.cif.gz which should be located in one of the following directories:\n\n";
......@@ -601,7 +698,7 @@ void compound_factory::report_missing_compound(const std::string &compound_id)
<< "update=true\n\n"
<< "If you do not have a working cron script, you can manually update the files\n"
<< "in /var/cache/libcifpp using the following commands:\n\n"
<< "curl -o " << CACHE_DIR << "/components.cif https://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz\n"
<< "curl -o " << CACHE_DIR << "/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz\n"
<< "curl -o " << CACHE_DIR << "/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz\n"
<< "curl -o " << CACHE_DIR << "/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic\n\n";
#endif
......
src/datablock.cpp
......@@ -158,11 +158,12 @@ std::tuple<datablock::iterator, bool> datablock::emplace(std::string_view name)
if (is_new)
{
auto &c = emplace_front(name);
auto &c = emplace_back(name);
c.set_validator(m_validator, *this);
}
return std::make_tuple(begin(), is_new);
assert(end() != begin());
return std::make_tuple(std::prev(end()), is_new);
}
std::vector<std::string> datablock::get_tag_order() const
......@@ -171,14 +172,16 @@ std::vector<std::string> datablock::get_tag_order() const
// for entry and audit_conform on top
auto ci = find_if(begin(), end(), [](const category &cat) { return cat.name() == "entry"; });
auto ci = find_if(begin(), end(), [](const category &cat)
{ return cat.name() == "entry"; });
if (ci != end())
{
auto cto = ci->get_tag_order();
result.insert(result.end(), cto.begin(), cto.end());
}
ci = find_if(begin(), end(), [](const category &cat) { return cat.name() == "audit_conform"; });
ci = find_if(begin(), end(), [](const category &cat)
{ return cat.name() == "audit_conform"; });
if (ci != end())
{
auto cto = ci->get_tag_order();
......@@ -196,11 +199,107 @@ std::vector<std::string> datablock::get_tag_order() const
return result;
}
namespace
{
using elem_t = std::tuple<std::string, int, bool>;
using cat_order_t = std::vector<elem_t>;
using iter_t = cat_order_t::iterator;
constexpr inline int get_count(iter_t i)
{
return std::get<1>(*i);
}
constexpr inline bool is_on_stack(iter_t i)
{
return std::get<2>(*i);
}
void calculate_cat_order(cat_order_t &cat_order, iter_t i, const validator &validator)
{
if (i == cat_order.end() or get_count(i) >= 0)
return;
auto &&[cat, count, on_stack] = *i;
on_stack = true;
int parent_count = 0;
for (auto link : validator.get_links_for_child(cat))
{
auto ei = std::find_if(cat_order.begin(), cat_order.end(), [parent = link->m_parent_category](elem_t &a)
{ return std::get<0>(a) == parent; });
if (ei == cat_order.end())
continue;
if (not is_on_stack(ei))
calculate_cat_order(cat_order, ei, validator);
parent_count += get_count(ei);
}
count = parent_count + 1;
}
}
void datablock::write(std::ostream &os) const
{
os << "data_" << m_name << '\n'
<< "# \n";
if (m_validator and size() > 0)
{
// If the dictionary declares an audit_conform category, put it in,
// but only if it does not exist already!
if (get("audit_conform") == nullptr and m_validator->get_validator_for_category("audit_conform") != nullptr)
{
category auditConform("audit_conform");
auditConform.emplace({ { "dict_name", m_validator->name() },
{ "dict_version", m_validator->version() } });
auditConform.write(os);
}
// base order on parent child relationships, parents first
cat_order_t cat_order;
for (auto &cat : *this)
cat_order.emplace_back(cat.name(), -1, false);
for (auto i = cat_order.begin(); i != cat_order.end(); ++i)
calculate_cat_order(cat_order, i, *m_validator);
std::sort(cat_order.begin(), cat_order.end(), [](const elem_t &a, const elem_t &b)
{
const auto &[cat_a, count_a, on_stack_a] = a;
const auto &[cat_b, count_b, on_stack_b] = b;
int d = 0;
if (cat_a == "audit_conform")
d = -1;
else if (cat_b == "audit_conform")
d = 1;
else if (cat_a == "entry")
d = -1;
else if (cat_b == "entry")
d = 1;
else
{
d = std::get<1>(a) - std::get<1>(b);
if (d == 0)
d = cat_b.compare(cat_a);
}
return d < 0; });
for (auto &&[cat, count, on_stack] : cat_order)
get(cat)->write(os);
}
else
{
// mmcif support, sort of. First write the 'entry' Category
// and if it exists, _AND_ we have a Validator, write out the
// audit_conform record.
......@@ -219,20 +318,13 @@ void datablock::write(std::ostream &os) const
// but only if it does not exist already!
if (get("audit_conform"))
get("audit_conform")->write(os);
else if (m_validator != nullptr and m_validator->get_validator_for_category("audit_conform") != nullptr)
{
category auditConform("audit_conform");
auditConform.emplace({
{"dict_name", m_validator->name()},
{"dict_version", m_validator->version()}});
auditConform.write(os);
}
for (auto &cat : *this)
{
if (cat.name() != "entry" and cat.name() != "audit_conform")
cat.write(os);
}
}
}
void datablock::write(std::ostream &os, const std::vector<std::string> &tag_order)
......@@ -337,7 +429,7 @@ bool datablock::operator==(const datablock &rhs) const
++catA_i;
else
{
if (not (*dbA.get(*catA_i) == *dbB.get(*catB_i)))
if (not(*dbA.get(*catA_i) == *dbB.get(*catB_i)))
return false;
++catA_i;
++catB_i;
......@@ -347,4 +439,4 @@ bool datablock::operator==(const datablock &rhs) const
return true;
}
} // namespace cif::cif
\ No newline at end of file
} // namespace cif
\ No newline at end of file
src/file.cpp
......@@ -173,11 +173,12 @@ std::tuple<file::iterator, bool> file::emplace(std::string_view name)
if (is_new)
{
auto &db = emplace_front(name);
auto &db = emplace_back(name);
db.set_validator(m_validator);
}
return std::make_tuple(begin(), is_new);
assert(begin() != end());
return std::make_tuple(std::prev(end()), is_new);
}
void file::load(const std::filesystem::path &p)
......
src/pdb/pdb2cif.cpp
......@@ -4511,6 +4511,47 @@ void PDBFileParser::ConstructEntities()
}
}
}
// Finish by calculating the formula_weight for each entity
for (auto entity : *getCategory("entity"))
{
auto entity_id = entity["id"].as<std::string>();
float formula_weight = 0;
if (entity["type"] == "polymer")
{
int n = 0;
for (std::string comp_id : getCategory("pdbx_poly_seq_scheme")->find<std::string>(cif::key("entity_id") == entity_id, "mon_id"))
{
auto compound = cif::compound_factory::instance().create(comp_id);
assert(compound);
if (not compound)
throw std::runtime_error("missing information for compound " + comp_id);
formula_weight += compound->formula_weight();
++n;
}
formula_weight -= (n - 1) * 18.015;
}
else if (entity["type"] == "water")
formula_weight = 18.015;
else
{
auto comp_id = getCategory("pdbx_nonpoly_scheme")->find_first<std::optional<std::string>>(cif::key("entity_id") == entity_id, "mon_id");
if (comp_id.has_value())
{
auto compound = cif::compound_factory::instance().create(*comp_id);
assert(compound);
if (not compound)
throw std::runtime_error("missing information for compound " + *comp_id);
formula_weight = compound->formula_weight();
}
}
if (formula_weight > 0)
entity["formula_weight"] = formula_weight;
}
}
void PDBFileParser::ConstructSugarTrees(int &asymNr)
......
test/unit-v2-test.cpp
......@@ -3468,3 +3468,22 @@ TEST_CASE("compound_not_found_test_1")
auto cmp = cif::compound_factory::instance().create("&&&");
REQUIRE(cmp == nullptr);
}
// --------------------------------------------------------------------
// PDB2CIF tests
TEST_CASE("pdb2cif_formula_weight")
{
cif::compound_factory::instance().push_dictionary(gTestDir / "REA.cif");
cif::file a = cif::pdb::read(gTestDir / "pdb1cbs.ent.gz");
auto fw = a.front()["entity"].find1<float>(cif::key("id") == 1, "formula_weight");
CHECK(std::abs(fw - 15581.802f) < 0.1f);
fw = a.front()["entity"].find1<float>(cif::key("id") == 2, "formula_weight");
CHECK(fw == 300.435f);
fw = a.front()["entity"].find1<float>(cif::key("id") == 3, "formula_weight");
CHECK(fw == 18.015f);
}
\ No newline at end of file
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