update changelog

* Use `find_package` for FastFloat prior to `FetchContent_Declare`

* Convert space to tab

.clang-format

@@ -0,0 +1,22 @@
+BasedOnStyle: LLVM
+UseTab: AlignWithSpaces
+IndentWidth: 4
+TabWidth: 4
+BreakBeforeBraces: Allman
+ColumnLimit: 0
+NamespaceIndentation: Inner
+FixNamespaceComments: true
+AccessModifierOffset: -2
+AllowShortCaseLabelsOnASingleLine: true
+IndentCaseLabels: true
+BreakConstructorInitializers: BeforeComma
+BraceWrapping:
+  BeforeLambdaBody: false
+AlignAfterOpenBracket: DontAlign
+Cpp11BracedListStyle: false
+IncludeBlocks: Regroup
+LambdaBodyIndentation: Signature
+AllowShortLambdasOnASingleLine: Inline
+EmptyLineBeforeAccessModifier: LogicalBlock
+IndentPPDirectives: AfterHash
+PPIndentWidth: 1

.github/workflows/build-documentation.yml

@@ -19,7 +19,7 @@ jobs:
   docs:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
 
     - name: Set reusable strings
       # Turn repeated input strings (such as the build output directory) into step outputs. These step outputs can be used throughout the workflow file.
@@ -47,7 +47,7 @@ jobs:
         ls -l ${{ steps.strings.outputs.build-output-dir }}/docs/sphinx
 
     - name: Upload artifact
-      uses: actions/upload-pages-artifact@v2
+      uses: actions/upload-pages-artifact@v3
       with:
         path: ${{ steps.strings.outputs.build-output-dir }}/docs/sphinx
 
@@ -62,4 +62,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v2
+        uses: actions/deploy-pages@v4

.github/workflows/cmake-multi-platform.yml

@@ -33,13 +33,18 @@ jobs:
 
     - name: Install dependencies Ubuntu
       if: matrix.os == 'ubuntu-latest'
-      run: sudo apt-get update && sudo apt-get install mrc
+      run: sudo apt-get update && sudo apt-get install mrc catch2
 
     - name: Install dependencies Window
       if: matrix.os == 'windows-latest'
       run: ./tools/depends.cmd
       shell: cmd
 
+    - name: Install Catch2 macOS
+      if: matrix.os == 'macos-latest'
+      run: >
+        brew install catch2
+
     - name: Configure CMake
       run: >
         cmake -B ${{ steps.strings.outputs.build-output-dir }}

.gitignore

@@ -13,3 +13,6 @@ docs/api
 docs/conf.py
 build_ci/
 data/components.cif
+perf.data*
+.cache/
+

CMakeLists.txt

@@ -22,29 +22,28 @@
 # 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)
+cmake_minimum_required(VERSION 3.23)
+
+if(CMAKE_SOURCE_DIR STREQUAL CMAKE_CURRENT_SOURCE_DIR AND NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+	set(CMAKE_BUILD_TYPE Release CACHE STRING "Build type" FORCE)
+	set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+endif()
 
 # set the project name
 project(
 	libcifpp
-	VERSION 7.0.1
-	LANGUAGES CXX)
+	VERSION 9.0.6
+	LANGUAGES CXX C)
 
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 
-include(CheckFunctionExists)
-include(CheckIncludeFiles)
-include(CheckLibraryExists)
+include(FindAtomic)
 include(CMakePackageConfigHelpers)
-include(CheckCXXSourceCompiles)
 include(GenerateExportHeader)
 include(CTest)
-include(FetchContent)
 include(ExternalProject)
-
-set(CXX_EXTENSIONS OFF)
-set(CMAKE_CXX_STANDARD 20)
-set(CMAKE_CXX_STANDARD_REQUIRED ON)
+include(FetchContent)
+include(VersionString)
 
 # When building with ninja-multiconfig, build both debug and release by default
 if(CMAKE_GENERATOR STREQUAL "Ninja Multi-Config")
@@ -61,42 +60,39 @@ elseif(MSVC)
 endif()
 
 # Build documentation?
-option(BUILD_DOCUMENTATION "Build the documentation" OFF)
+set(BUILD_DOCUMENTATION OFF CACHE BOOL "Build the documentation")
 
 # Optionally build a version to be installed inside CCP4
-option(BUILD_FOR_CCP4 "Build a version to be installed in CCP4")
+set(BUILD_FOR_CCP4 OFF CACHE BOOL "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)
+	set(BUILD_SHARED_LIBS OFF CACHE BOOL "Build a shared library instead of a static one")
 endif()
 
-if(BUILD_FOR_CCP4)
-	unset(CIFPP_DOWNLOAD_CCD)
-	unset(CIFPP_INSTALL_UPDATE_SCRIPT)
-else()
+if(PROJECT_IS_TOP_LEVEL AND NOT BUILD_FOR_CCP4)
 	# 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)
+	set(CIFPP_DOWNLOAD_CCD ON CACHE BOOL "Download the CCD file components.cif during installation")
 
 	# 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)
+		set(CIFPP_INSTALL_UPDATE_SCRIPT ON CACHE BOOL "Install the script to update CCD and dictionary files")
 	endif()
+else()
+	unset(CIFPP_DOWNLOAD_CCD)
+	unset(CIFPP_INSTALL_UPDATE_SCRIPT)
 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)
+	set(CIFPP_RECREATE_SYMOP_DATA ON CACHE BOOL "Recreate SymOp data table in case it is out of date")
 endif()
 
 # CCP4 build
 if(BUILD_FOR_CCP4)
 	if("$ENV{CCP4}" STREQUAL "" OR NOT EXISTS $ENV{CCP4})
-		message(FATAL_ERROR "A CCP4 built was requested but CCP4 was not sourced")
+		message(FATAL_ERROR "cifpp: A CCP4 built was requested but CCP4 was not sourced")
 	else()
 		list(PREPEND CMAKE_MODULE_PATH "$ENV{CCP4}")
 		list(PREPEND CMAKE_PREFIX_PATH "$ENV{CCP4}")
@@ -126,8 +122,6 @@ if(WIN32)
 		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()
@@ -136,65 +130,12 @@ 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()
 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(
-	"
-#include <iostream>
-#ifndef __GLIBCXX__
-#error
-#endif
-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++")
-
-	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"
-		)
-
-		find_package(Boost 1.80 QUIET COMPONENTS regex)
-
-		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_MakeAvailable(boost-rx)
-		endif()
-
-		set(BOOST_REGEX ON)
-	endif()
-endif()
-
-set(CMAKE_THREAD_PREFER_PTHREAD)
-set(THREADS_PREFER_PTHREAD_FLAG)
-find_package(Threads)
-
 if(MSVC)
-	# Avoid linking the shared library of zlib Search ZLIB_ROOT first if it is
+	# 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)
@@ -221,7 +162,41 @@ if(MSVC)
 	endforeach()
 endif()
 
-find_package(ZLIB REQUIRED)
+# Using fast_float for float parsing, but only if needed
+try_compile(STD_CHARCONV_COMPILING
+	SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/cmake/test-charconv.cpp
+	CXX_STANDARD 20
+	CXX_STANDARD_REQUIRED ON)
+
+if(NOT STD_CHARCONV_COMPILING)
+	message(NOTICE "libcifpp: Using fast_float for std::from_chars")
+	find_package(FastFloat 8.0 QUIET CONFIG)
+	if(NOT FastFloat_FOUND)
+		message(STATUS "FastFloat not found in system, fetching from GitHub")
+		FetchContent_Declare(fastfloat
+			GIT_REPOSITORY "https://github.com/fastfloat/fast_float"
+			GIT_TAG v8.0.2
+			EXCLUDE_FROM_ALL)
+		FetchContent_MakeAvailable(fastfloat)
+	endif()
+endif()
+
+find_package(Threads)
+find_package(ZLIB QUIET)
+
+if(NOT ZLIB_FOUND)
+	message(FATAL_ERROR "cifpp: The zlib development files were not found you this system, please install them and try again (hint: on debian/ubuntu use apt-get install zlib1g-dev)")
+endif()
+
+include(FindPkgConfig)
+
+if(PKG_CONFIG_FOUND)
+	pkg_check_modules(PCRE2 IMPORTED_TARGET libpcre2-8)
+endif()
+
+if(NOT PCRE2_FOUND)
+	add_subdirectory(pcre2-simple)
+endif()
 
 # 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
@@ -232,108 +207,110 @@ if(Eigen3_FOUND AND TARGET Eigen3::Eigen)
 	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)
+	# Use ExternalProject since FetchContent always tries to install the result...
+	ExternalProject_Add(my-eigen3
+		URL https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.zip
+		DOWNLOAD_EXTRACT_TIMESTAMP TRUE
+		CONFIGURE_COMMAND ""
+		BUILD_COMMAND ""
+		INSTALL_COMMAND "")
 
-	FetchContent_GetProperties(my-eigen3)
-
-	if(NOT my-eigen3_POPULATED)
-		FetchContent_Populate(my-eigen3)
-	endif()
-
-	set(EIGEN_INCLUDE_DIR ${my-eigen3_SOURCE_DIR})
+	ExternalProject_Get_Property(my-eigen3 SOURCE_DIR)
+	set(EIGEN_INCLUDE_DIR ${SOURCE_DIR})
 endif()
 
-include(FindFilesystem)
-list(APPEND CIFPP_REQUIRED_LIBRARIES ${STDCPPFS_LIBRARY})
-
-include(FindAtomic)
-list(APPEND CIFPP_REQUIRED_LIBRARIES ${STDCPPATOMIC_LIBRARY})
-
-# Create a revision file, containing the current git version info
-include(VersionString)
-write_version_header(${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
-		"${PROJECT_SOURCE_DIR}/src/symop-map-generator.cpp")
+		"${CMAKE_CURRENT_SOURCE_DIR}/src/symop-map-generator.cpp")
+
+	target_compile_features(symop-map-generator PUBLIC cxx_std_20)
 
 	add_custom_command(
-		OUTPUT ${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp
+		OUTPUT ${CMAKE_CURRENT_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)
+		$ENV{CLIBD}/symop.lib ${CMAKE_CURRENT_SOURCE_DIR}/src/symop_table_data.hpp)
 
 	add_custom_target(
 		OUTPUT
-		${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp
+		${CMAKE_CURRENT_SOURCE_DIR}/src/symop_table_data.hpp
 		DEPENDS symop-map-generator "$ENV{CLIBD}/syminfo.lib"
 		"$ENV{CLIBD}/symop.lib")
 endif()
 
+# Create a revision file, containing the current git version info
+write_version_header("${CMAKE_CURRENT_SOURCE_DIR}/src/" LIB_NAME "LibCIFPP")
+
 # 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/pdb/reconstruct.cpp
-	${PROJECT_SOURCE_DIR}/src/pdb/validate-pdbx.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/category.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/condition.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/datablock.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/dictionary_parser.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/file.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/item.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/parser.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/row.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/validate.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/text.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/utilities.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/atom_type.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/compound.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/point.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/symmetry.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/model.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/pdb/cif2pdb.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/pdb/pdb2cif.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/pdb/pdb_record.hpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/pdb/pdb2cif_remark_3.hpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/pdb/pdb2cif_remark_3.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/pdb/reconstruct.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/pdb/validate-pdbx.cpp
 )
 
 set(project_headers
 	include/cif++.hpp
-	include/cif++/utilities.hpp
-	include/cif++/item.hpp
-	include/cif++/datablock.hpp
-	include/cif++/file.hpp
-	include/cif++/validate.hpp
-	include/cif++/iterator.hpp
-	include/cif++/parser.hpp
-	include/cif++/forward_decl.hpp
-	include/cif++/dictionary_parser.hpp
-	include/cif++/condition.hpp
-	include/cif++/category.hpp
-	include/cif++/row.hpp
 	include/cif++/atom_type.hpp
+	include/cif++/category.hpp
 	include/cif++/compound.hpp
-	include/cif++/point.hpp
-	include/cif++/symmetry.hpp
+	include/cif++/condition.hpp
+	include/cif++/datablock.hpp
+	include/cif++/dictionary_parser.hpp
+	include/cif++/exports.hpp
+	include/cif++/file.hpp
+	include/cif++/format.hpp
+	include/cif++/forward_decl.hpp
+	include/cif++/gzio.hpp
+	include/cif++/item.hpp
+	include/cif++/iterator.hpp
+	include/cif++/matrix.hpp
 	include/cif++/model.hpp
-	include/cif++/pdb.hpp
+	include/cif++/parser.hpp
 	include/cif++/pdb/cif2pdb.hpp
+	include/cif++/pdb.hpp
 	include/cif++/pdb/io.hpp
 	include/cif++/pdb/pdb2cif.hpp
-	include/cif++/pdb/tls.hpp)
+	include/cif++/pdb/tls.hpp
+	include/cif++/point.hpp
+	include/cif++/row.hpp
+	include/cif++/symmetry.hpp
+	include/cif++/text.hpp
+	include/cif++/utilities.hpp
+	include/cif++/validate.hpp
+)
 
-add_library(cifpp STATIC)
+add_library(cifpp)
 add_library(cifpp::cifpp ALIAS cifpp)
 
+if(TARGET my-eigen3)
+	add_dependencies(cifpp my-eigen3)
+endif()
+
 target_sources(cifpp
 	PRIVATE ${project_sources}
-	${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp
+	${CMAKE_CURRENT_SOURCE_DIR}/src/symop_table_data.hpp
 	PUBLIC
 	FILE_SET cifpp_headers TYPE HEADERS
 	BASE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/include
@@ -343,18 +320,8 @@ target_sources(cifpp
 # The code now really requires C++20
 target_compile_features(cifpp PUBLIC cxx_std_20)
 
-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)
-
-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)
-endif()
+	${CMAKE_CURRENT_SOURCE_DIR}/include/cif++/exports.hpp)
 
 if(MSVC)
 	target_compile_definitions(cifpp PUBLIC NOMINMAX=1)
@@ -364,12 +331,23 @@ set_target_properties(cifpp PROPERTIES POSITION_INDEPENDENT_CODE ON)
 
 target_include_directories(
 	cifpp
-	PUBLIC "$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>"
+	PUBLIC "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
 	"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
-	PRIVATE "${BOOST_REGEX_INCLUDE_DIR}" "${EIGEN_INCLUDE_DIR}")
+	PRIVATE "${EIGEN_INCLUDE_DIR}")
 
-target_link_libraries(cifpp PUBLIC Threads::Threads ZLIB::ZLIB
-	${CIFPP_REQUIRED_LIBRARIES})
+target_link_libraries(cifpp
+	PUBLIC Threads::Threads ZLIB::ZLIB $<$<TARGET_EXISTS:std::atomic>:std::atomic>)
+
+if(PCRE2_FOUND)
+	target_include_directories(cifpp PRIVATE ${PCRE2_INCLUDE_DIRS})
+	target_link_libraries(cifpp PRIVATE ${PCRE2_LINK_LIBRARIES})
+else()
+	target_link_libraries(cifpp PRIVATE $<BUILD_INTERFACE:pcre2s>)
+endif()
+
+if(NOT STD_CHARCONV_COMPILING)
+	target_link_libraries(cifpp PRIVATE FastFloat::fast_float)
+endif()
 
 if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
 	target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
@@ -377,13 +355,13 @@ 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)
+	set(COMPONENTS_CIF ${CMAKE_CURRENT_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")
+			message(STATUS "cifpp: Removing empty ${COMPONENTS_CIF} file")
 			file(REMOVE "${COMPONENTS_CIF}")
 		endif()
 	endif()
@@ -412,7 +390,7 @@ if(CIFPP_DOWNLOAD_CCD)
 			add_custom_command(
 				OUTPUT ${COMPONENTS_CIF}
 				COMMAND "${GUNZIP}" ${COMPONENTS_CIF}.gz
-				WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/rsrc/)
+				WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/rsrc/)
 
 			add_custom_target(COMPONENTS ALL DEPENDS ${COMPONENTS_CIF})
 		endif()
@@ -422,7 +400,7 @@ if(CIFPP_DOWNLOAD_CCD)
 
 		if(CCD_FETCH_STATUS_CODE)
 			message(
-				FATAL_ERROR "Error trying to download CCD file: ${CCD_FETCH_STATUS}")
+				FATAL_ERROR "cifpp: Error trying to download CCD file: ${CCD_FETCH_STATUS}")
 		endif()
 	endif()
 endif()
@@ -440,6 +418,11 @@ endif()
 
 if(CIFPP_DATA_DIR)
 	target_compile_definitions(cifpp PUBLIC DATA_DIR="${CIFPP_DATA_DIR}")
+	set_target_properties(cifpp PROPERTIES CIFPP_DATA_DIR ${CIFPP_DATA_DIR})
+endif()
+
+if(NOT PROJECT_IS_TOP_LEVEL)
+	set(CIFPP_SHARE_DIR ${CIFPP_DATA_DIR} PARENT_SCOPE)
 endif()
 
 if(UNIX AND NOT BUILD_FOR_CCP4)
@@ -481,7 +464,7 @@ file(GLOB OLD_CONFIG_FILES
 
 if(OLD_CONFIG_FILES)
 	message(
-		STATUS "Installation will remove old config files: ${OLD_CONFIG_FILES}")
+		STATUS "cifpp: Installation will remove old config files: ${OLD_CONFIG_FILES}")
 	install(CODE "file(REMOVE ${OLD_CONFIG_FILES})")
 endif()
 
@@ -490,23 +473,18 @@ install(EXPORT cifpp
 	FILE "cifpp-targets.cmake"
 	DESTINATION lib/cmake/cifpp)
 
+install(
+	FILES ${CMAKE_CURRENT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
+	${CMAKE_CURRENT_SOURCE_DIR}/rsrc/mmcif_pdbx.dic
+	${CMAKE_CURRENT_SOURCE_DIR}/rsrc/mmcif_ma.dic
+	DESTINATION ${CMAKE_INSTALL_DATADIR}/libcifpp)
+
 if(CIFPP_DATA_DIR AND CIFPP_DOWNLOAD_CCD)
-	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 ${COMPONENTS_CIF}
+		DESTINATION ${CMAKE_INSTALL_DATADIR}/libcifpp)
 endif()
 
-if(CIFPP_CACHE_DIR AND CIFPP_DOWNLOAD_CCD)
-	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)
+set(CONFIG_TEMPLATE_FILE ${CMAKE_CURRENT_SOURCE_DIR}/cmake/cifpp-config.cmake.in)
 
 configure_package_config_file(
 	${CONFIG_TEMPLATE_FILE} ${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config.cmake
@@ -534,60 +512,42 @@ write_basic_package_version_file(
 	VERSION ${PROJECT_VERSION}
 	COMPATIBILITY AnyNewerVersion)
 
-# In case we're included as sub_directory:
-if(NOT PROJECT_IS_TOP_LEVEL)
-	set(CIFPP_SHARE_DIR ${PROJECT_SOURCE_DIR}/rsrc PARENT_SCOPE)
-endif()
-
-if(BUILD_TESTING)
+if(BUILD_TESTING AND PROJECT_IS_TOP_LEVEL)
 	add_subdirectory(test)
 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
-			"${CIFPP_ETC_DIR}/periodic/weekly"
-			CACHE PATH "The cron directory, for the update script")
+	configure_file(${CMAKE_CURRENT_SOURCE_DIR}/tools/update-libcifpp-data.in
+		update-libcifpp-data @ONLY)
+
+	if(${CMAKE_SYSTEM_NAME} STREQUAL "Linux" OR
+		${CMAKE_SYSTEM_NAME} STREQUAL "GNU" OR
+		${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD")
+		install(
+			FILES ${CMAKE_CURRENT_BINARY_DIR}/update-libcifpp-data
+			DESTINATION ${CMAKE_INSTALL_SYSCONFDIR}/cron.weekly
+			PERMISSIONS OWNER_EXECUTE OWNER_READ GROUP_EXECUTE GROUP_READ WORLD_EXECUTE
+			WORLD_READ)
 	else()
-		message(FATAL_ERROR "Don't know where to install the update script")
+		message(FATAL_ERROR "cifpp: 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")
+	# install(DIRECTORY DESTINATION "${CMAKE_INSTALL_LOCALSTATEDIR}/libcifpp")
+	if(NOT EXISTS "${CMAKE_INSTALL_SYSCONFDIR}/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}")
+			DESTINATION ${CMAKE_INSTALL_SYSCONFDIR})
 		install(
-			CODE "message(\"A configuration file has been written to ${CIFPP_ETC_DIR}/libcifpp.conf, please edit this file to enable automatic updates\")"
+			CODE "message(\"cifpp: 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")
+		install(DIRECTORY DESTINATION ${CMAKE_INSTALL_SYSCONFDIR}/libcifpp/cache-update.d)
 	endif()
 
 	target_compile_definitions(cifpp PUBLIC CACHE_DIR="${CIFPP_CACHE_DIR}")
@@ -596,13 +556,3 @@ endif()
 if(BUILD_DOCUMENTATION)
 	add_subdirectory(docs)
 endif()
-
-set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")
-set(CPACK_SOURCE_TGZ ON)
-set(CPACK_SOURCE_TBZ2 OFF)
-set(CPACK_SOURCE_TXZ OFF)
-set(CPACK_SOURCE_TZ OFF)
-set(CPACK_SOURCE_IGNORE_FILES "/rsrc/components.cif;/build;/.vscode;/.git")
-set(CPACK_PACKAGE_FILE_NAME "${PROJECT_NAME}-${PROJECT_VERSION}")
-set(CPACK_SOURCE_PACKAGE_FILE_NAME ${CPACK_PACKAGE_FILE_NAME})
-include(CPack)

README.md

@@ -32,7 +32,7 @@ The documentation can be found at [github.io](https://pdb-redo.github.io/libcifp
 
 ## Synopsis
 
-```c++
+```cpp
 // A simple program counting residues with an OXT atom
 
 #include <filesystem>
@@ -52,7 +52,7 @@ int main(int argc, char *argv[])
 
     if (file.empty())
     {
-        std::cerr << "Empty file" << std::endl;
+        std::cerr << "Empty file\n";
         exit(1);
     }
 
@@ -66,8 +66,8 @@ int main(int argc, char *argv[])
     auto n = atom_site.count(cif::key("label_atom_id") == "OXT");
 
     std::cout << "File contains " << atom_site.size() << " atoms of which "
-              << n << (n == 1 ? " is" : " are") << " OXT" << std::endl
-              << "residues with an OXT are:" << std::endl;
+              << n << (n == 1 ? " is" : " are") << " OXT\n"
+              << "residues with an OXT are:\n";
 
     // Loop over all atoms with atom-id "OXT" and print out some info.
     // That info is extracted using structured binding in C++
@@ -76,7 +76,7 @@ int main(int argc, char *argv[])
                 cif::key("label_atom_id") == "OXT",
                 "label_asym_id", "label_comp_id", "label_seq_id"))
     {
-        std::cout << asym << ' ' << comp << ' ' << seqnr << std::endl;
+        std::cout << asym << ' ' << comp << ' ' << seqnr << '\n';
     }
 
     return 0;
@@ -117,12 +117,8 @@ Other libraries you might want to install beforehand are:
   `libeigen3-dev`
 - [zlib](https://github.com/madler/zlib), the development version of this
   library. On Debian/Ubuntu this is the package `zlib1g-dev`.
-- [boost](https://www.boost.org), in Debian/Ubuntu this is `libboost-dev`.
-  
-  The Boost libraries are only needed in case you are using GCC due to a long
-  standing bug in GNU's implementation of std::regex. It simply crashes
-  on the regular expressions used in the mmcif_pdbx dictionary and so
-  we use the boost regex implementation instead.
+- [pcre2](https://www.pcre.org/), the Perl Compatible Regular Expression
+  library. On Debian/Ubuntu this is the package `libpcre2-dev`.
 
 ### Building
 

changelog

@@ -1,3 +1,84 @@
+Version 9.0.6
+- Various small fixes
+
+Version 9.0.5
+- Added exists to compound_factory
+- Added sub_matrix, fix and extend determinant calculation
+- Added yet another structure::create_non_poly
+- Remove revision.hpp file in make clean (new VersionString.cmake)
+
+Version 9.0.4
+- Fix various stopping and reconstruction errors
+
+Version 9.0.3
+- Reconstruction fixed when some entity ids are missing
+
+Version 9.0.2
+- Fix code that reconstructs sequences, could throw a map::at
+- Many optimisations in validation and reconstruction code.
+
+Version 9.0.1
+- Use pcre2 from pkg-config if available, if not
+  build a version from the original code.
+
+Version 9.0.0
+- Rename fields of cif::mm::polymer to match the naming
+  in mmcif_pdbx.dic. Also, related, fix building mm::structure
+  using the correct mapping between atom_site and residues.
+- _atom_site.auth_alt_id does not exist, it should be
+  _atom_site.pdbx_auth_alt_id of course.
+- Added a more lightweight fixup for mmcif_pdbx files
+  that lack certain categories.
+
+Version 8.0.1
+- Fix cif::mm::structure::cleanup_empty_categories, removed too much
+- Add default value for B_iso_or_equiv in residue::create_new_atom
+- Reconstruct some branch records in bare pdbx files
+- Fix parsing PDB files (bug due to missing validator in dest. cat.)
+- Do not fail conversion of PDB files when compound info is missing
+
+Version 8.0.0
+- A dictionary is for a datablock and a file can have
+  datablocks with differing dictionaries.
+
+Version 7.0.10
+- Deal with missing _entity.type in reconstructing mmCIF files
+- Replace code creating quaternions from rotation matrices
+  that might sometimes give incorrect results. Or at least,
+  the test code failed on this particular kind of code. Sometimes.
+- Fix reconstruction to build pdbx_nonpoly_scheme
+
+Version 7.0.9
+- Using cif::file::load_dictionary it is now possible to
+  load a dictionary along with its extensions in one go.
+  E.g. file.load_dictionary("mmcif_pdbx;dssp-extension")
+- Fix in compound factory to avoid errors with lower case
+  compound id's
+- Fix sac_parser's index to be case insensitive
+
+Version 7.0.8
+- Fix PDB Remark 3 parser
+- Added three way comparison for point
+
+Version 7.0.7
+- Set CIFPP_DATA_DIR on target cifpp for use in projects that include
+  libcifpp directly
+
+Version 7.0.6
+- Fix linking to std::atomic
+
+Version 7.0.5
+- Fix case where category index was not updated for updated value
+
+Version 7.0.4
+- Do not install headers and library in case we're not the top project
+
+Version 7.0.3
+- Fix installation, write exports.hpp again
+
+Version 7.0.2
+- Fix in testing error_code results.
+
 Version 7.0.1
 - Various reconstruction fixes
 - category order in output fixed

cmake/FindFilesystem.cmake

@@ -1,75 +0,0 @@
-# Simplistic reimplementation of https://github.com/vector-of-bool/CMakeCM/blob/master/modules/FindFilesystem.cmake
-
-if(TARGET std::filesystem)
-	return()
-endif()
-
-cmake_minimum_required(VERSION 3.10)
-
-include(CMakePushCheckState)
-include(CheckIncludeFileCXX)
-include(CheckCXXSourceCompiles)
-
-cmake_push_check_state()
-
-check_include_file_cxx("filesystem" _CXX_FILESYSTEM_HAVE_HEADER)
-mark_as_advanced(_CXX_FILESYSTEM_HAVE_HEADER)
-
-set(code [[
-#include <cstdlib>
-#include <filesystem>
-
-int main() {
-	auto cwd = std::filesystem::current_path();
-	return EXIT_SUCCESS;
-}
-]])
-
-if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS_EQUAL 8.4.0)
-	# >> https://stackoverflow.com/questions/63902528/program-crashes-when-filesystempath-is-destroyed
-	set(CXX_FILESYSTEM_NO_LINK_NEEDED 0)
-else()
-	# Check a simple filesystem program without any linker flags
-	check_cxx_source_compiles("${code}" CXX_FILESYSTEM_NO_LINK_NEEDED)
-endif()
-
-if(CXX_FILESYSTEM_NO_LINK_NEEDED)
-	set(_found 1)
-else()
-	set(prev_libraries ${CMAKE_REQUIRED_LIBRARIES})
-	# Add the libstdc++ flag
-	set(CMAKE_REQUIRED_LIBRARIES ${prev_libraries} -lstdc++fs)
-	check_cxx_source_compiles("${code}" CXX_FILESYSTEM_STDCPPFS_NEEDED)
-	set(_found ${CXX_FILESYSTEM_STDCPPFS_NEEDED})
-	if(NOT CXX_FILESYSTEM_STDCPPFS_NEEDED)
-		# Try the libc++ flag
-		set(CMAKE_REQUIRED_LIBRARIES ${prev_libraries} -lc++fs)
-		check_cxx_source_compiles("${code}" CXX_FILESYSTEM_CPPFS_NEEDED)
-		set(_found ${CXX_FILESYSTEM_CPPFS_NEEDED})
-	endif()
-endif()
-
-if(_found)
-	add_library(std::filesystem INTERFACE IMPORTED)
-	set_property(TARGET std::filesystem APPEND PROPERTY INTERFACE_COMPILE_FEATURES cxx_std_17)
-
-	if(CXX_FILESYSTEM_NO_LINK_NEEDED)
-		# Nothing to add...
-	elseif(CXX_FILESYSTEM_STDCPPFS_NEEDED)
-		set_target_properties(std::filesystem PROPERTIES IMPORTED_LIBNAME stdc++fs)
-		set(STDCPPFS_LIBRARY stdc++fs)
-	elseif(CXX_FILESYSTEM_CPPFS_NEEDED)
-		set_target_properties(std::filesystem PROPERTIES IMPORTED_LIBNAME c++fs)
-		set(STDCPPFS_LIBRARY c++fs)
-	endif()
-endif()
-
-cmake_pop_check_state()
-
-set(Filesystem_FOUND ${_found} CACHE BOOL "TRUE if we can run a program using std::filesystem" FORCE)
-mark_as_advanced(Filesystem_FOUND)
-
-if(Filesystem_FIND_REQUIRED AND NOT Filesystem_FOUND)
-    message(FATAL_ERROR "Cannot run simple program using std::filesystem")
-endif()
-

cmake/FindPCRE2.cmake

@@ -0,0 +1,12 @@
+# The problem is, find_package(PCRE2) does not work
+# and using pkg-config results in linking to a shared library
+# causing all kinds of trouble later on
+
+find_path(PCRE2_INCLUDEDIR NAMES pcre2.h HINTS "C:/Program Files (x86)/PCRE2/include" REQUIRED)
+find_library(PCRE2_LIBRARY NAMES pcre2-8-static libpcre2-8.a HINTS "C:/Program Files (x86)/PCRE2/lib" REQUIRED)
+
+add_library(pcre2-8 IMPORTED STATIC)
+target_include_directories(pcre2-8 INTERFACE ${PCRE2_INCLUDEDIR})
+target_compile_definitions(pcre2-8 INTERFACE PCRE2_STATIC)
+set_target_properties(pcre2-8 PROPERTIES IMPORTED_LOCATION ${PCRE2_LIBRARY})
+set_target_properties(pcre2-8 PROPERTIES IMPORTED_IMPLIB ${PCRE2_LIBRARY})

cmake/VersionString.cmake

@@ -238,7 +238,7 @@ function(write_version_header dir)
 		if(res EQUAL 0)
 			set(REVISION_STRING "${out}")
 		else()
-			message(STATUS "Git hash not found, does this project has a 'build' tag?")
+			message(STATUS "Git hash not found, does this project have a 'build' tag?")
 		endif()
 	else()
 		message(STATUS "Git hash not found")

cmake/test-charconv.cpp

@@ -0,0 +1,17 @@
+#include <charconv>
+#include <cassert>
+#include <cstring>
+
+int main()
+{
+	float v;
+	char s[] = "1.0";
+
+	auto r = std::from_chars(s, s + strlen(s), v);
+
+	assert(r.ec == std::errc{});
+	assert(r.ptr = s + strlen(s));
+	assert(v == 1.0f);
+
+	return 0;
+}

cmake/test-rx.cpp

@@ -1,18 +0,0 @@
-// See: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=86164
-
-#include <iostream>
-#include <regex>
-
-int main()
-{
-	std::string s(100'000, '*');
-	std::smatch m;
-	std::regex r("^(.*?)$");
-
-	std::regex_search(s, m, r);
-
-	std::cout << s.substr(0, 10) << '\n';
-	std::cout << m.str(1).substr(0, 10) << '\n';
-
-	return 0;
-}

docs/basics.rst

@@ -217,7 +217,7 @@ A simple case:
     #include <cif++.hpp>
 
     cif::file f("1cbs.cif.gz");
-    f.load_dictionary("mmcif_pdbx");
+    f.load_dictionary("mmcif_pdbx.dic");
 
     if (not f.is_valid())
         std::cout << "This file is not valid\n";

docs/index.rst

@@ -27,7 +27,7 @@ Using *libcifpp* is easy, if you are familiar with modern C++:
 
 .. literalinclude:: ../README.md
 	:language: c++
-	:start-after: ```c++
+	:start-after: ```cpp
 	:end-before: ```
 
 .. toctree::

examples/example.cpp

@@ -13,7 +13,7 @@ int main(int argc, char *argv[])
 		exit(1);
 	}
 
-	cif::file file = cif::pdb::read(argv[1]);
+	cif::file file(argv[1]);
 
 	if (file.empty())
 	{

include/cif++/atom_type.hpp

@@ -200,7 +200,7 @@ enum class radius_type
 };
 
 /// @brief The number of radii per element which can be requested from atom_type_info
-constexpr size_t kRadiusTypeCount = static_cast<size_t>(radius_type::type_count);
+constexpr std::size_t kRadiusTypeCount = static_cast<std::size_t>(radius_type::type_count);
 
 /// An enum used to select either the effective or the crystal radius of an ion.
 /// See explanation on Wikipedia: https://en.wikipedia.org/wiki/Ionic_radius
@@ -276,7 +276,7 @@ class atom_type_traits
 	{
 		if (type >= radius_type::type_count)
 			throw std::invalid_argument("invalid radius requested");
-		return m_info->radii[static_cast<size_t>(type)] / 100.f;
+		return m_info->radii[static_cast<std::size_t>(type)] / 100.f;
 	}
 
 	/// \brief Return the radius for a charged version of this atom in a solid crystal

include/cif++/category.hpp

@@ -32,7 +32,6 @@
 #include "cif++/iterator.hpp"
 #include "cif++/row.hpp"
 #include "cif++/text.hpp"
-#include "cif++/validate.hpp"
 
 #include <array>
 
@@ -51,6 +50,11 @@
 namespace cif
 {
 
+class validator;
+struct category_validator;
+struct item_validator;
+struct link_validator;
+
 // --------------------------------------------------------------------
 // special exceptions
 
@@ -143,7 +147,17 @@ class category
 
 	category() = default;            ///< Default constructor
 	category(std::string_view name); ///< Constructor taking a \a name
-	category(const category &rhs);   ///< Copy constructor
+
+	/// @brief Constructor creating a category named @a name and filled with @a rows
+	/// @param name Name for the new category
+	/// @param rows The data stored in the category
+	category(std::string_view name, row_initializer &&rows)
+		: category(name)
+	{
+		emplace(std::forward<row_initializer>(rows));
+	}
+
+	category(const category &rhs); ///< Copy constructor
 
 	category(category &&rhs) noexcept ///< Move constructor
 	{
@@ -182,7 +196,7 @@ class category
 
 	/// @brief Update the links in this category
 	/// @param db The enclosing @ref datablock
-	void update_links(datablock &db);
+	void update_links(const datablock &db);
 
 	/// @brief Return the global @ref validator for the data
 	/// @return The @ref validator or nullptr if not assigned
@@ -209,6 +223,11 @@ class category
 	/// @return Returns true is all validations pass
 	bool validate_links() const;
 
+	/**
+	 * @brief Strip removes items from this category that are invalid according to the assigned validator
+	 */
+	void strip();
+
 	/// @brief Equality operator, returns true if @a rhs is equal to this
 	/// @param rhs The object to compare with
 	/// @return True if the data contained is equal
@@ -293,15 +312,15 @@ class category
 	}
 
 	/// Return a count of the rows in this container
-	size_t size() const
+	std::size_t size() const
 	{
 		return std::distance(cbegin(), cend());
 	}
 
 	/// Return the theoretical maximum number or rows that can be stored
-	size_t max_size() const
+	std::size_t max_size() const
 	{
-		return std::numeric_limits<size_t>::max(); // this is a bit optimistic, I guess
+		return std::numeric_limits<std::size_t>::max(); // this is a bit optimistic, I guess
 	}
 
 	/// Return true if the category is empty
@@ -313,8 +332,16 @@ class category
 	// --------------------------------------------------------------------
 	// A category can have a key, as defined by the validator/dictionary
 
+	/// @brief The type of an element of the key_type
+	struct key_element_type
+	{
+		std::string name;         ///< Name of the item
+		std::string value;        ///< Value to be found
+		bool may_be_null = false; ///< If true, value should be same or empty
+	};
+
 	/// @brief The key type
-	using key_type = row_initializer;
+	using key_type = std::vector<key_element_type>;
 
 	/// @brief Return a row_handle for the row specified by \a key
 	/// @param key The value for the key, items specified in the dictionary should have a value
@@ -831,9 +858,9 @@ class category
 	/// @brief Return the total number of rows that match condition @a cond
 	/// @param cond The condition to match
 	/// @return The count
-	size_t count(condition &&cond) const
+	std::size_t count(condition &&cond) const
 	{
-		size_t result = 0;
+		std::size_t result = 0;
 
 		if (cond)
 		{
@@ -903,14 +930,14 @@ class category
 	/// @brief Erase all rows that match condition @a cond
 	/// @param cond The condition
 	/// @return The number of rows that have been erased
-	size_t erase(condition &&cond);
+	std::size_t erase(condition &&cond);
 
 	/// @brief Erase all rows that match condition @a cond calling
 	/// the visitor function @a visit for each before actually erasing it.
 	/// @param cond The condition
 	/// @param visit The visitor function
 	/// @return The number of rows that have been erased
-	size_t erase(condition &&cond, std::function<void(row_handle)> &&visit);
+	std::size_t erase(condition &&cond, std::function<void(row_handle)> &&visit);
 
 	/// @brief Emplace the values in @a ri in a new row
 	/// @param ri An object containing the values to insert
@@ -947,6 +974,12 @@ class category
 		return insert_impl(cend(), r);
 	}
 
+	void emplace(const_iterator b, const_iterator e)
+	{
+		while (b != e)
+			emplace(*b++);
+	}
+
 	/// @brief Completely erase all rows contained in this category
 	void clear();
 
@@ -1079,25 +1112,7 @@ class category
 	// --------------------------------------------------------------------
 	/// \brief Return the index number for \a item_name
 
-	uint16_t get_item_ix(std::string_view item_name) const
-	{
-		uint16_t result;
-
-		for (result = 0; result < m_items.size(); ++result)
-		{
-			if (iequals(item_name, m_items[result].m_name))
-				break;
-		}
-
-		if (VERBOSE > 0 and result == m_items.size() and m_cat_validator != nullptr) // validate the name, if it is known at all (since it was not found)
-		{
-			auto iv = m_cat_validator->get_validator_for_item(item_name);
-			if (iv == nullptr)
-				std::cerr << "Invalid name used '" << item_name << "' is not a known item in " + m_name << '\n';
-		}
-
-		return result;
-	}
+	uint16_t get_item_ix(std::string_view item_name) const;
 
 	/// @brief Return the name for item with index @a ix
 	/// @param ix The index number
@@ -1113,28 +1128,7 @@ class category
 	/// @brief Make sure a item with name @a item_name is known and return its index number
 	/// @param item_name The name of the item
 	/// @return The index number of the item
-	uint16_t add_item(std::string_view item_name)
-	{
-		using namespace std::literals;
-
-		uint16_t result = get_item_ix(item_name);
-
-		if (result == m_items.size())
-		{
-			const item_validator *item_validator = nullptr;
-
-			if (m_cat_validator != nullptr)
-			{
-				item_validator = m_cat_validator->get_validator_for_item(item_name);
-				if (item_validator == nullptr)
-					m_validator->report_error(validation_error::item_not_allowed_in_category, m_name, item_name, false);
-			}
-
-			m_items.emplace_back(item_name, item_validator);
-		}
-
-		return result;
-	}
+	uint16_t add_item(std::string_view item_name);
 
 	/** @brief Remove item name @a colum_name
 	 * @param item_name The item to be removed
@@ -1263,6 +1257,7 @@ class category
 		{
 		}
 
+		// TODO: NEED TO FIX THIS!
 		category *linked;
 		const link_validator *v;
 	};

include/cif++/compound.hpp

@@ -138,7 +138,7 @@ struct compound_bond
 /// This information is derived from the CDD by default.
 ///
 /// To create compounds, you use the factory method. You can add your own
-/// compound definitions by calling the addExtraComponents function and
+/// compound definitions by calling the push_dictionary function and
 /// pass it a valid CCD formatted file.
 
 class compound
@@ -179,8 +179,7 @@ class compound
 	friend class compound_factory_impl;
 	friend class local_compound_factory_impl;
 
-	compound(cif::datablock &db);
-	compound(cif::datablock &db, int);
+	compound(datablock &db);
 
 	std::string m_id;
 	std::string m_name;
@@ -271,11 +270,15 @@ class compound_factory
 		return is_std_base(res_name) or is_std_peptide(res_name);
 	}
 
+	/// Return whether @a res_name is water
 	bool is_water(std::string_view res_name) const
 	{
 		return res_name == "HOH" or res_name == "H2O" or res_name == "WAT";
 	}
 
+	/// Return whether @a res_name already exists, without creating it.
+	bool exists(std::string_view res_name) const;
+
 	/// \brief Create the compound object for \a id
 	///
 	/// This will create the compound instance for \a id if it doesn't exist already.
@@ -291,6 +294,13 @@ class compound_factory
 
 	void report_missing_compound(std::string_view compound_id);
 
+	bool get_report_missing() const { return m_report_missing; }
+
+	void set_report_missing(bool report)
+	{
+		m_report_missing = report;
+	}
+
   private:
 	compound_factory();
 
@@ -302,6 +312,7 @@ class compound_factory
 	static bool s_use_thread_local_instance;
 
 	std::shared_ptr<compound_factory_impl> m_impl;
+	bool m_report_missing = true;
 };
 
 // --------------------------------------------------------------------
@@ -324,14 +335,14 @@ class compound_factory
 class compound_source
 {
   public:
-	compound_source(const cif::file &file)
+	compound_source(const file &file)
 	{
-		cif::compound_factory::instance().push_dictionary(file);
+		compound_factory::instance().push_dictionary(file);
 	}
 
 	~compound_source()
 	{
-		cif::compound_factory::instance().pop_dictionary();
+		compound_factory::instance().pop_dictionary();
 	}
 };
 

include/cif++/condition.hpp

@@ -27,8 +27,10 @@
 #pragma once
 
 #include "cif++/row.hpp"
+#include "cif++/format.hpp"
 
 #include <cassert>
+#include <concepts>
 #include <functional>
 #include <iostream>
 #include <regex>
@@ -48,49 +50,49 @@
  * @code {.cpp}
  * cif::condition c = cif::key("id") == 1;
  * @endcode
- * 
+ *
  * That will find rows where the ID item contains the number 1. If
  * using cif::key is a bit too much typing, you can also write:
- * 
+ *
  * @code{.cpp}
  * using namespace cif::literals;
- * 
+ *
  * cif::condition c2 = "id"_key == 1;
  * @endcode
- * 
+ *
  * Now if you want both ID = 1 and ID = 2 in the result:
- * 
+ *
  * @code{.cpp}
  * auto c3 = "id"_key == 1 or "id"_key == 2;
  * @endcode
- * 
+ *
  * There are some special values you can use. To find rows with item that
  * do not have a value:
- * 
+ *
  * @code{.cpp}
  * auto c4 = "type"_key == cif::null;
- * @endcode 
- * 
+ * @endcode
+ *
  * Of if it should not be NULL:
- * 
+ *
  * @code{.cpp}
  * auto c5 = "type"_key != cif::null;
- * @endcode 
- * 
+ * @endcode
+ *
  * There's even a way to find all records:
- * 
+ *
  * @code{.cpp}
  * auto c6 = cif::all;
  * @endcode
- * 
+ *
  * And when you want to search for any item containing the value 'foo':
- * 
+ *
  * @code{.cpp}
  * auto c7 = cif::any == "foo";
- * @endcode 
- * 
+ * @endcode
+ *
  * All these conditions can be chained together again:
- * 
+ *
  * @code{.cpp}
  * auto c8 = std::move(c3) and std::move(c5);
  * @endcode
@@ -105,7 +107,7 @@ namespace cif
 
 /**
  * @brief Get the items that can be used as key in conditions for a category
- * 
+ *
  * @param cat The category whose items to return
  * @return iset The set of key item names
  */
@@ -114,7 +116,7 @@ iset get_category_fields(const category &cat);
 
 /**
  * @brief Get the items that can be used as key in conditions for a category
- * 
+ *
  * @param cat The category whose items to return
  * @return iset The set of key field names
  */
@@ -122,7 +124,7 @@ iset get_category_items(const category &cat);
 
 /**
  * @brief Get the item index for item @a col in category @a cat
- * 
+ *
  * @param cat The category
  * @param col The name of the item
  * @return uint16_t The index
@@ -131,7 +133,7 @@ uint16_t get_item_ix(const category &cat, std::string_view col);
 
 /**
  * @brief Return whether the item @a col in category @a cat has a primitive type of *uchar*
- * 
+ *
  * @param cat The category
  * @param col The item name
  * @return true If the primitive type is of type *uchar*
@@ -174,14 +176,13 @@ namespace detail
 class condition
 {
   public:
-
 	/** @cond */
 	using condition_impl = detail::condition_impl;
 	/** @endcond */
 
 	/**
 	 * @brief Construct a new, empty condition object
-	 * 
+	 *
 	 */
 	condition()
 		: m_impl(nullptr)
@@ -190,7 +191,7 @@ class condition
 
 	/**
 	 * @brief Construct a new condition object with implementation @a impl
-	 * 
+	 *
 	 * @param impl The implementation to use
 	 */
 	explicit condition(condition_impl *impl)
@@ -229,15 +230,15 @@ class condition
 	/**
 	 * @brief Prepare the condition to be used on category @a c. This will
 	 * take care of setting the correct indices for items e.g.
-	 * 
+	 *
 	 * @param c The category this query should act upon
 	 */
 	void prepare(const category &c);
 
 	/**
-	 * @brief This operator returns true if the row referenced by @a r is 
+	 * @brief This operator returns true if the row referenced by @a r is
 	 * a match for this condition.
-	 * 
+	 *
 	 * @param r The reference to a row.
 	 * @return true If there is a match
 	 * @return false If there is no match
@@ -262,7 +263,7 @@ class condition
 	/**
 	 * @brief If the prepare step found out there is only one hit
 	 * this single hit can be returned by this method.
-	 * 
+	 *
 	 * @return std::optional<row_handle> The result will contain
 	 * a row reference if there is a single hit, it will be empty otherwise
 	 */
@@ -291,7 +292,7 @@ class condition
 
 	/**
 	 * @brief Operator to use to write out a condition to @a os, for debugging purposes
-	 * 
+	 *
 	 * @param os The std::ostream to write to
 	 * @param cond The condition to write
 	 * @return std::ostream& The same as @a os
@@ -470,6 +471,106 @@ namespace detail
 		std::optional<row_handle> m_single_hit;
 	};
 
+	struct key_equals_number_condition_impl : public condition_impl
+	{
+		key_equals_number_condition_impl(const std::string &name, double v)
+			: m_item_name(name)
+			, m_value(v)
+		{
+		}
+
+		condition_impl *prepare(const category &c) override;
+
+		bool test(row_handle r) const override
+		{
+			return m_single_hit.has_value() ? *m_single_hit == r : r[m_item_ix].compare(m_value) == 0;
+		}
+
+		void str(std::ostream &os) const override
+		{
+			os << m_item_name << " == " << m_value;
+		}
+
+		virtual std::optional<row_handle> single() const override
+		{
+			return m_single_hit;
+		}
+
+		virtual bool equals(const condition_impl *rhs) const override
+		{
+			if (typeid(*rhs) == typeid(key_equals_number_condition_impl))
+			{
+				auto ri = static_cast<const key_equals_number_condition_impl *>(rhs);
+				if (m_single_hit.has_value() or ri->m_single_hit.has_value())
+					return m_single_hit == ri->m_single_hit;
+				else
+					// watch out, both m_item_ix might be the same while item_names might be diffent (in case they both do not exist in the category)
+					return m_item_ix == ri->m_item_ix and m_value == ri->m_value and m_item_name == ri->m_item_name;
+			}
+			return this == rhs;
+		}
+
+		std::string m_item_name;
+		uint16_t m_item_ix = 0;
+		double m_value;
+		std::optional<row_handle> m_single_hit;
+	};
+
+	struct key_equals_number_or_empty_condition_impl : public condition_impl
+	{
+		key_equals_number_or_empty_condition_impl(key_equals_number_condition_impl *equals)
+			: m_item_name(equals->m_item_name)
+			, m_value(equals->m_value)
+			, m_single_hit(equals->m_single_hit)
+		{
+		}
+
+		condition_impl *prepare(const category &c) override
+		{
+			m_item_ix = get_item_ix(c, m_item_name);
+			return this;
+		}
+
+		bool test(row_handle r) const override
+		{
+			bool result = false;
+			if (m_single_hit.has_value())
+				result = *m_single_hit == r;
+			else
+				result = r[m_item_ix].empty() or r[m_item_ix].compare(m_value) == 0;
+			return result;
+		}
+
+		void str(std::ostream &os) const override
+		{
+			os << '(' << m_item_name << " == " << m_value << " OR " << m_item_name << " IS NULL)";
+		}
+
+		virtual std::optional<row_handle> single() const override
+		{
+			return m_single_hit;
+		}
+
+		virtual bool equals(const condition_impl *rhs) const override
+		{
+			if (typeid(*rhs) == typeid(key_equals_number_or_empty_condition_impl))
+			{
+				auto ri = static_cast<const key_equals_number_or_empty_condition_impl *>(rhs);
+				if (m_single_hit.has_value() or ri->m_single_hit.has_value())
+					return m_single_hit == ri->m_single_hit;
+				else
+					// watch out, both m_item_ix might be the same while item_names might be diffent (in case they both do not exist in the category)
+					return m_item_ix == ri->m_item_ix and m_value == ri->m_value and m_item_name == ri->m_item_name;
+			}
+			return this == rhs;
+		}
+
+		std::string m_item_name;
+		uint16_t m_item_ix = 0;
+		double m_value;
+		std::optional<row_handle> m_single_hit;
+	};
+
 	struct key_compare_condition_impl : public condition_impl
 	{
 		template <typename COMP>
@@ -651,28 +752,9 @@ namespace detail
 				delete sub;
 		}
 
-		condition_impl *prepare(const category &c) override
-		{
-			for (auto &sub : m_sub)
-				sub = sub->prepare(c);
-			return this;
-		}
+		condition_impl *prepare(const category &c) override;
 
-		bool test(row_handle r) const override
-		{
-			bool result = true;
-
-			for (auto sub : m_sub)
-			{
-				if (sub->test(r))
-					continue;
-
-				result = false;
-				break;
-			}
-
-			return result;
-		}
+		bool test(row_handle r) const override;
 
 		void str(std::ostream &os) const override
 		{
@@ -719,6 +801,7 @@ namespace detail
 		static condition_impl *combine_equal(std::vector<and_condition_impl *> &subs, or_condition_impl *oc);
 
 		std::vector<condition_impl *> m_sub;
+		std::optional<row_handle> m_single; // Potential result of index lookup
 	};
 
 	struct or_condition_impl : public condition_impl
@@ -876,8 +959,9 @@ inline condition operator or(condition &&a, condition &&b)
 			if (ci->m_item_name == ce->m_item_name)
 				return condition(new detail::key_equals_or_empty_condition_impl(ci));
 		}
-		else if (typeid(*b.m_impl) == typeid(detail::key_equals_condition_impl) and
-				 typeid(*a.m_impl) == typeid(detail::key_is_empty_condition_impl))
+
+		if (typeid(*b.m_impl) == typeid(detail::key_equals_condition_impl) and
+			typeid(*a.m_impl) == typeid(detail::key_is_empty_condition_impl))
 		{
 			auto ci = static_cast<detail::key_equals_condition_impl *>(b.m_impl);
 			auto ce = static_cast<detail::key_is_empty_condition_impl *>(a.m_impl);
@@ -886,6 +970,26 @@ inline condition operator or(condition &&a, condition &&b)
 				return condition(new detail::key_equals_or_empty_condition_impl(ci));
 		}
 
+		if (typeid(*a.m_impl) == typeid(detail::key_equals_number_condition_impl) and
+			typeid(*b.m_impl) == typeid(detail::key_is_empty_condition_impl))
+		{
+			auto ci = static_cast<detail::key_equals_number_condition_impl *>(a.m_impl);
+			auto ce = static_cast<detail::key_is_empty_condition_impl *>(b.m_impl);
+
+			if (ci->m_item_name == ce->m_item_name)
+				return condition(new detail::key_equals_number_or_empty_condition_impl(ci));
+		}
+
+		if (typeid(*b.m_impl) == typeid(detail::key_equals_number_condition_impl) and
+			typeid(*a.m_impl) == typeid(detail::key_is_empty_condition_impl))
+		{
+			auto ci = static_cast<detail::key_equals_number_condition_impl *>(b.m_impl);
+			auto ce = static_cast<detail::key_is_empty_condition_impl *>(a.m_impl);
+
+			if (ci->m_item_name == ce->m_item_name)
+				return condition(new detail::key_equals_number_or_empty_condition_impl(ci));
+		}
+
 		return condition(new detail::or_condition_impl(std::move(a), std::move(b)));
 	}
 
@@ -897,7 +1001,7 @@ inline condition operator or(condition &&a, condition &&b)
 
 /**
  * @brief A helper class to make it possible to search for empty items (NULL)
- * 
+ *
  * @code{.cpp}
  * "id"_key == cif::empty_type();
  * @endcode
@@ -909,7 +1013,7 @@ struct empty_type
 
 /**
  * @brief A helper to make it possible to have conditions like
- * 
+ *
  * @code{.cpp}
  * "id"_key == cif::null;
  * @endcode
@@ -919,14 +1023,14 @@ inline constexpr empty_type null = empty_type();
 
 /**
  * @brief Class to use in creating conditions, creates a reference to a item or item
- * 
+ *
  */
 struct key
 {
 	/**
 	 * @brief Construct a new key object using @a item_name as name
-	 * 
-	 * @param item_name 
+	 *
+	 * @param item_name
 	 */
 	explicit key(const std::string &item_name)
 		: m_item_name(item_name)
@@ -935,8 +1039,8 @@ struct key
 
 	/**
 	 * @brief Construct a new key object using @a item_name as name
-	 * 
-	 * @param item_name 
+	 *
+	 * @param item_name
 	 */
 	explicit key(const char *item_name)
 		: m_item_name(item_name)
@@ -945,8 +1049,8 @@ struct key
 
 	/**
 	 * @brief Construct a new key object using @a item_name as name
-	 * 
-	 * @param item_name 
+	 *
+	 * @param item_name
 	 */
 	explicit key(std::string_view item_name)
 		: m_item_name(item_name)
@@ -959,13 +1063,17 @@ struct key
 	std::string m_item_name; ///< The item name
 };
 
-/**
- * @brief Operator to create an equals condition based on a key @a key and a value @a v
- */
 template <typename T>
+concept Numeric = ((std::is_floating_point_v<T> or std::is_integral_v<T>) and not std::is_same_v<T, bool>);
+
+/**
+ * @brief Operator to create an equals condition based on a key @a key and a numeric value @a v
+ */
+template <Numeric T>
 condition operator==(const key &key, const T &v)
 {
-	return condition(new detail::key_equals_condition_impl({ key.m_item_name, v }));
+	// TODO: change key_equals_etc... to use std::variant<double,int64_t> or something
+	return condition(new detail::key_equals_number_condition_impl(key.m_item_name, static_cast<double>(v)));
 }
 
 /**
@@ -979,6 +1087,16 @@ inline condition operator==(const key &key, std::string_view value)
 		return condition(new detail::key_is_empty_condition_impl(key.m_item_name));
 }
 
+/**
+ * @brief Operator to create an equals condition based on a key @a key and a value @a value
+ */
+template <typename T>
+	requires std::is_same_v<T, bool>
+inline condition operator==(const key &key, T value)
+{
+	return condition(new detail::key_equals_condition_impl({ key.m_item_name, value ? "y" : "n" }));
+}
+
 /**
  * @brief Operator to create a not equals condition based on a key @a key and a value @a v
  */
@@ -999,61 +1117,93 @@ inline condition operator!=(const key &key, std::string_view value)
 /**
  * @brief Operator to create a greater than condition based on a key @a key and a value @a v
  */
-template <typename T>
+template <Numeric T>
 condition operator>(const key &key, const T &v)
 {
-	std::ostringstream s;
-	s << " > " << v;
-
 	return condition(new detail::key_compare_condition_impl(
 		key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
-		{ return r[item_name].template compare<T>(v, icase) > 0; },
-		s.str()));
+		{ return r[item_name].compare(v) > 0; },
+		cif::format(" > {}", v)));
 }
 
 /**
  * @brief Operator to create a greater than or equals condition based on a key @a key and a value @a v
  */
-template <typename T>
+template <Numeric T>
 condition operator>=(const key &key, const T &v)
 {
-	std::ostringstream s;
-	s << " >= " << v;
-
 	return condition(new detail::key_compare_condition_impl(
 		key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
-		{ return r[item_name].template compare<T>(v, icase) >= 0; },
-		s.str()));
+		{ return r[item_name].compare(v) >= 0; },
+		cif::format(" >= {}", v)));
 }
 
 /**
  * @brief Operator to create a less than condition based on a key @a key and a value @a v
  */
-template <typename T>
+template <Numeric T>
 condition operator<(const key &key, const T &v)
 {
-	std::ostringstream s;
-	s << " < " << v;
-
 	return condition(new detail::key_compare_condition_impl(
 		key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
-		{ return r[item_name].template compare<T>(v, icase) < 0; },
-		s.str()));
+		{ return r[item_name].compare(v) < 0; },
+		cif::format(" < {}", v)));
 }
 
 /**
  * @brief Operator to create a less than or equals condition based on a key @a key and a value @a v
  */
-template <typename T>
+template <Numeric T>
 condition operator<=(const key &key, const T &v)
 {
-	std::ostringstream s;
-	s << " <= " << v;
-
 	return condition(new detail::key_compare_condition_impl(
 		key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
-		{ return r[item_name].template compare<T>(v, icase) <= 0; },
-		s.str()));
+		{ return r[item_name].compare(v) <= 0; },
+		cif::format(" <= {}", v)));
+}
+
+/**
+ * @brief Operator to create a greater than condition based on a key @a key and a value @a v
+ */
+inline condition operator>(const key &key, std::string_view v)
+{
+	return condition(new detail::key_compare_condition_impl(
+		key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
+		{ return r[item_name].compare(v, icase) > 0; },
+		cif::format(" > {}", v)));
+}
+
+/**
+ * @brief Operator to create a greater than or equals condition based on a key @a key and a value @a v
+ */
+inline condition operator>=(const key &key, std::string_view v)
+{
+	return condition(new detail::key_compare_condition_impl(
+		key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
+		{ return r[item_name].compare(v, icase) >= 0; },
+		cif::format(" >= {}", v)));
+}
+
+/**
+ * @brief Operator to create a less than condition based on a key @a key and a value @a v
+ */
+inline condition operator<(const key &key, std::string_view v)
+{
+	return condition(new detail::key_compare_condition_impl(
+		key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
+		{ return r[item_name].compare(v, icase) < 0; },
+		cif::format(" < {}", v)));
+}
+
+/**
+ * @brief Operator to create a less than or equals condition based on a key @a key and a value @a v
+ */
+inline condition operator<=(const key &key, std::string_view v)
+{
+	return condition(new detail::key_compare_condition_impl(
+		key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
+		{ return r[item_name].compare(v, icase) <= 0; },
+		cif::format(" <= {}", v)));
 }
 
 /**
@@ -1093,6 +1243,19 @@ condition operator==(const key &key, const std::optional<T> &v)
 		return condition(new detail::key_is_empty_condition_impl(key.m_item_name));
 }
 
+/**
+ * @brief Create a condition to search any item for a value @a v if @a v contains a value
+ * compare to null if not.
+ */
+template <typename T>
+condition operator!=(const key &key, const std::optional<T> &v)
+{
+	if (v.has_value())
+		return condition(new detail::not_condition_impl(condition(new detail::key_equals_condition_impl({ key.m_item_name, *v }))));
+	else
+		return condition(new detail::not_condition_impl(condition(new detail::key_is_empty_condition_impl(key.m_item_name))));
+}
+
 /**
  * @brief Operator to create a boolean opposite of the condition in @a rhs
  */
@@ -1141,12 +1304,12 @@ namespace literals
 {
 	/**
 	 * @brief Return a cif::key for the item name @a text
-	 * 
+	 *
 	 * @param text The name of the item
 	 * @param length The length of @a text
 	 * @return key The cif::key created
 	 */
-	inline key operator""_key(const char *text, size_t length)
+	inline key operator""_key(const char *text, std::size_t length)
 	{
 		return key(std::string(text, length));
 	}

include/cif++/datablock.hpp

@@ -29,6 +29,8 @@
 #include "cif++/category.hpp"
 #include "cif++/forward_decl.hpp"
 
+#include <list>
+
 /** \file datablock.hpp
  * Each valid mmCIF file contains at least one @ref cif::datablock.
  * A datablock has a name and can contain one or more @ref cif::category "categories"
@@ -41,7 +43,7 @@ namespace cif
 
 /**
  * @brief A datablock is a list of category objects with some additional features
- * 
+ *
  */
 
 class datablock : public std::list<category>
@@ -51,7 +53,7 @@ class datablock : public std::list<category>
 
 	/**
 	 * @brief Construct a new datablock object with name @a name
-	 * 
+	 *
 	 * @param name The name for the new datablock
 	 */
 	datablock(std::string_view name)
@@ -78,7 +80,7 @@ class datablock : public std::list<category>
 	{
 		std::swap(a.m_name, b.m_name);
 		std::swap(a.m_validator, b.m_validator);
-		std::swap(static_cast<std::list<category>&>(a), static_cast<std::list<category>&>(b));
+		std::swap(static_cast<std::list<category> &>(a), static_cast<std::list<category> &>(b));
 	}
 
 	// --------------------------------------------------------------------
@@ -90,7 +92,7 @@ class datablock : public std::list<category>
 
 	/**
 	 * @brief Set the name of this datablock to @a name
-	 * 
+	 *
 	 * @param name The new name
 	 */
 	void set_name(std::string_view name)
@@ -98,52 +100,57 @@ class datablock : public std::list<category>
 		m_name = name;
 	}
 
+	/**
+	 * @brief Attempt to load the dictionary specified in audit_conform category
+	 *
+	 */
+	void load_dictionary();
+
 	/**
 	 * @brief Set the validator object to @a v
-	 * 
+	 *
 	 * @param v The new validator object, may be null
 	 */
 	void set_validator(const validator *v);
 
 	/**
 	 * @brief Get the validator object
-	 * 
+	 *
 	 * @return const validator* The validator or nullptr if there is none
 	 */
 	const validator *get_validator() const;
 
 	/**
 	 * @brief Validates the content of this datablock and all its content
-	 * 
+	 *
 	 * @return true If the content is valid
 	 * @return false If the content is not valid
 	 */
 	bool is_valid() const;
 
-	/**
-	 * @brief Validates the content of this datablock and all its content
-	 * and updates or removes the audit_conform category to match the result.
-	 * 
-	 * @return true If the content is valid
-	 * @return false If the content is not valid
-	 */
-	bool is_valid();
-
 	/**
 	 * @brief Validates all contained data for valid links between parents and children
 	 * as defined in the validator
-	 * 
+	 *
 	 * @return true If all links are valid
 	 * @return false If all links are not valid
 	 */
 	bool validate_links() const;
 
+	/**
+	 * @brief Strip removes all categories and items that are invalid according
+	 * to the assigned validator. Will also add a valid audit_conform block.
+	 *
+	 * @return true if the remaining datablock is valid
+	 */
+	bool strip();
+
 	// --------------------------------------------------------------------
 
 	/**
 	 * @brief Return the category named @a name, will create a new and empty
 	 * category named @a name if it does not exist.
-	 * 
+	 *
 	 * @param name The name of the category to return
 	 * @return category& Reference to the named category
 	 */
@@ -152,7 +159,7 @@ class datablock : public std::list<category>
 	/**
 	 * @brief Return the const category named @a name, will return a reference
 	 * to a static empty category if it was not found.
-	 * 
+	 *
 	 * @param name The name of the category to return
 	 * @return category& Reference to the named category
 	 */
@@ -161,7 +168,7 @@ class datablock : public std::list<category>
 	/**
 	 * @brief Return a pointer to the category named @a name or nullptr if
 	 * it does not exist.
-	 * 
+	 *
 	 * @param name The name of the category
 	 * @return category* Pointer to the category found or nullptr
 	 */
@@ -170,18 +177,26 @@ class datablock : public std::list<category>
 	/**
 	 * @brief Return a pointer to the category named @a name or nullptr if
 	 * it does not exist.
-	 * 
+	 *
 	 * @param name The name of the category
 	 * @return category* Pointer to the category found or nullptr
 	 */
 	const category *get(std::string_view name) const;
 
+	/**
+	 * @brief Return true if this datablock contains a non-empty category
+	 */
+	bool contains(std::string_view name) const
+	{
+		return get(name) != nullptr;
+	}
+
 	/**
 	 * @brief Tries to find a category with name @a name and will create a
 	 * new one if it is not found. The result is a tuple of an iterator
 	 * pointing to the category and a boolean indicating whether the category
 	 * was created or not.
-	 * 
+	 *
 	 * @param name The name for the category
 	 * @return std::tuple<iterator, bool> A tuple containing an iterator pointing
 	 * at the category and a boolean indicating whether the category was newly
@@ -234,4 +249,4 @@ class datablock : public std::list<category>
 	const validator *m_validator = nullptr;
 };
 
-} // namespace cif
+} // namespace cif

include/cif++/dictionary_parser.hpp

@@ -38,13 +38,8 @@ namespace cif
 {
 
 /**
- * @brief Parse the contents of @a is and create a new validator object with name @a name
+ * @brief Parse the contents of @a is and place content in validator @a v
  */
-validator parse_dictionary(std::string_view name, std::istream &is);
-
-/**
- * @brief Extend the definitions in validator @a v with the contents of stream @a is
- */
-void extend_dictionary(validator &v, std::istream &is);
+void parse_dictionary(validator &v, std::istream &is);
 
 } // namespace cif

include/cif++/file.hpp

@@ -85,11 +85,11 @@ class file : public std::list<datablock>
 	 * @param data The pointer to the character string with data to load
 	 * @param length The length of the data
 	 */
-	explicit file(const char *data, size_t length)
+	explicit file(const char *data, std::size_t length)
 	{
 		struct membuf : public std::streambuf
 		{
-			membuf(char *text, size_t length)
+			membuf(char *text, std::size_t length)
 			{
 				this->setg(text, text, text + length);
 			}
@@ -118,19 +118,6 @@ class file : public std::list<datablock>
 
 	/** @endcond */
 
-	/**
-	 * @brief Set the validator object to @a v
-	 */
-	void set_validator(const validator *v);
-
-	/**
-	 * @brief Get the validator object
-	 */
-	const validator *get_validator() const
-	{
-		return m_validator;
-	}
-
 	/**
 	 * @brief Validate the content and return true if everything was valid.
 	 * 
@@ -165,21 +152,6 @@ class file : public std::list<datablock>
 	 */
 	bool validate_links() const;
 
-	/**
-	 * @brief Attempt to load a dictionary (validator) based on
-	 * the contents of the *audit_conform* category, if available.
-	 */
-	void load_dictionary();
-
-
-	/**
-	 * @brief Attempt to load the named dictionary @a name and
-	 * create a validator based on it.
-	 * 
-	 * @param name The name of the dictionary to load
-	 */
-	void load_dictionary(std::string_view name);
-
 	/**
 	 * @brief Return true if a datablock with the name @a name is part of this file
 	 */
@@ -232,6 +204,12 @@ class file : public std::list<datablock>
 	/** Load the data from @a is */
 	void load(std::istream &is);
 
+	/** Load the data from the file specified by @a p using validator @a v */
+	void load(const std::filesystem::path &p, const validator &v);
+
+	/** Load the data from @a is using validator @a v */
+	void load(std::istream &is, const validator &v);
+
 	/** Save the data to the file specified by @a p */
 	void save(const std::filesystem::path &p) const;
 
@@ -246,9 +224,6 @@ class file : public std::list<datablock>
 		f.save(os);
 		return os;
 	}
-
-  private:
-	const validator *m_validator = nullptr;
 };
 
-} // namespace cif
+} // namespace cif

include/cif++/format.hpp

@@ -26,138 +26,28 @@
 
 #pragma once
 
+#if __has_include(<format>)
+#include <format>
+#define USE_STD_FORMAT 1
+#else
+#include <fmt/format.h>
+#endif
+
 #include <string>
 
 /**  \file format.hpp
  * 
- * File containing a basic reimplementation of boost::format
- * but then a bit more simplistic. Still this allowed me to move my code
- * from using boost::format to something without external dependency easily.
+ * Now using cif::format instead of a home grown rip off
  */
 
 namespace cif
 {
 
-namespace detail
-{
-	template <typename T>
-	struct to_varg
-	{
-		using type = T;
-
-		to_varg(const T &v)
-			: m_value(v)
-		{
-		}
-
-		type operator*() { return m_value; }
-
-		T m_value;
-	};
-
-	template <>
-	struct to_varg<const char *>
-	{
-		using type = const char *;
-
-		to_varg(const char *v)
-			: m_value(v)
-		{
-		}
-
-		type operator*() { return m_value.c_str(); }
-
-		std::string m_value;
-	};
-
-	template <>
-	struct to_varg<std::string>
-	{
-		using type = const char *;
-
-		to_varg(const std::string &v)
-			: m_value(v)
-		{
-		}
-
-		type operator*() { return m_value.c_str(); }
-
-		std::string m_value;
-	};
-
-} // namespace
-
-/** @cond */
-
-template <typename... Args>
-class format_plus_arg
-{
-  public:
-	using args_vector_type = std::tuple<detail::to_varg<Args>...>;
-	using vargs_vector_type = std::tuple<typename detail::to_varg<Args>::type...>;
-
-	format_plus_arg(const format_plus_arg &) = delete;
-	format_plus_arg &operator=(const format_plus_arg &) = delete;
-
-
-	format_plus_arg(std::string_view fmt, Args... args)
-		: m_fmt(fmt)
-		, m_args(std::forward<Args>(args)...)
-	{
-		auto ix = std::make_index_sequence<sizeof...(Args)>();
-		copy_vargs(ix);
-	}
-
-	std::string str()
-	{
-		char buffer[1024];
-		std::string::size_type r = std::apply(snprintf, std::tuple_cat(std::make_tuple(buffer, sizeof(buffer), m_fmt.c_str()), m_vargs));
-		return { buffer, r };
-	}
-
-	friend std::ostream &operator<<(std::ostream &os, const format_plus_arg &f)
-	{
-		char buffer[1024];
-		std::string::size_type r = std::apply(snprintf, std::tuple_cat(std::make_tuple(buffer, sizeof(buffer), f.m_fmt.c_str()), f.m_vargs));
-		os.write(buffer, r);
-		return os;
-	}
-
-  private:
-
-	template <size_t... I>
-	void copy_vargs(std::index_sequence<I...>)
-	{
-		((std::get<I>(m_vargs) = *std::get<I>(m_args)), ...);
-	}
-
-	std::string m_fmt;
-	args_vector_type m_args;
-	vargs_vector_type m_vargs;
-};
-
-/** @endcond */
-
-/**
- * @brief A simplistic reimplementation of boost::format, in fact it is
- * actually a way to call the C function snprintf to format the arguments
- * in @a args into the format string @a fmt
- * 
- * The string in @a fmt should thus be a C style format string.
- * 
- * TODO: Move to C++23 style of printing.
- * 
- * @tparam Args The types of the arguments
- * @param fmt The format string
- * @param args The arguments
- * @return An object that can be written out to a std::ostream using operator<<
- */
-
-template <typename... Args>
-constexpr auto format(std::string_view fmt, Args... args)
-{
-	return format_plus_arg(fmt, std::forward<Args>(args)...);
-}
+#if USE_STD_FORMAT
+using std::format;
+#else
+using fmt::format;
+#endif
 
 // --------------------------------------------------------------------
 /// A streambuf that fills out lines with spaces up until a specified width

include/cif++/gzio.hpp

@@ -1,7 +1,33 @@
-//          Copyright Maarten L. Hekkelman, 2022
-// Distributed under the Boost Software License, Version 1.0.
-//    (See accompanying file LICENSE_1_0.txt or copy at
-//          http://www.boost.org/LICENSE_1_0.txt)
+/*-
+ * SPDX-License-Identifier: BSD-2-Clause
+ * 
+ * Copyright (c) 2025 NKI/AVL, Netherlands Cancer Institute
+ * 
+ * Redistribution and use in source and binary forms, with or without
+ * 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
+ * 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 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.
+ */
+
+/*
+	Original code comes from libgxrio at https://github.com/mhekkel/gxrio
+	This is a stripped down version.
+*/
 
 #pragma once
 
@@ -36,7 +62,7 @@ namespace cif::gzio
 {
 
 /** The default buffer size to use */
-const size_t kDefaultBufferSize = 256;
+const std::size_t kDefaultBufferSize = 256;
 
 // --------------------------------------------------------------------
 
@@ -112,7 +138,7 @@ class basic_streambuf : public std::basic_streambuf<CharT, Traits>
 /// This implementation of streambuf can decompress (inflate) data compressed
 /// using zlib.
 
-template <typename CharT, typename Traits, size_t BufferSize = kDefaultBufferSize>
+template <typename CharT, typename Traits, std::size_t BufferSize = kDefaultBufferSize>
 class basic_igzip_streambuf : public basic_streambuf<CharT, Traits>
 {
   public:
@@ -317,7 +343,7 @@ class basic_igzip_streambuf : public basic_streambuf<CharT, Traits>
 ///
 /// This implementation of streambuf can compress (deflate) data using zlib.
 
-template <typename CharT, typename Traits, size_t BufferSize = kDefaultBufferSize>
+template <typename CharT, typename Traits, std::size_t BufferSize = kDefaultBufferSize>
 class basic_ogzip_streambuf : public basic_streambuf<CharT, Traits>
 {
   public:

include/cif++/item.hpp

@@ -53,12 +53,12 @@ namespace cif
 // --------------------------------------------------------------------
 /** @brief item is a transient class that is used to pass data into rows
  * but it also takes care of formatting data.
- * 
- * 
- * 
+ *
+ *
+ *
  * The class cif::item is often used implicitly when creating a row in a category
  * using the emplace function.
- * 
+ *
  * @code{.cpp}
  * cif::category cat("my-cat");
  * cat.emplace({
@@ -68,12 +68,12 @@ namespace cif
  *   { "item-4", std::make_optional<int>(42) },   // <- stores an item with value 42
  *   { "item-5" }                                 // <- stores an item with value .
  * });
- * 
+ *
  * std::cout << cat << '\n';
  * @endcode
- * 
+ *
  * Will result in:
- * 
+ *
  * @code{.txt}
  * _my-cat.item-1 1
  * _my-cat.item-2 1.00
@@ -117,7 +117,7 @@ class item
 		char buffer[32];
 
 		auto r = to_chars(buffer, buffer + sizeof(buffer) - 1, value, chars_format::fixed, precision);
-		if (r.ec != std::errc())
+		if ((bool)r.ec)
 			throw std::runtime_error("Could not format number");
 
 		m_value.assign(buffer, r.ptr - buffer);
@@ -136,7 +136,7 @@ class item
 		char buffer[32];
 
 		auto r = to_chars(buffer, buffer + sizeof(buffer) - 1, value, chars_format::general);
-		if (r.ec != std::errc())
+		if ((bool)r.ec)
 			throw std::runtime_error("Could not format number");
 
 		m_value.assign(buffer, r.ptr - buffer);
@@ -151,7 +151,7 @@ class item
 		char buffer[32];
 
 		auto r = std::to_chars(buffer, buffer + sizeof(buffer) - 1, value);
-		if (r.ec != std::errc())
+		if ((bool)r.ec)
 			throw std::runtime_error("Could not format number");
 
 		m_value.assign(buffer, r.ptr - buffer);
@@ -176,7 +176,7 @@ class item
 
 	/// \brief constructor for an item with name \a name and as
 	/// content value \a value
-	template<typename T, std::enable_if_t<std::is_same_v<T, std::string>, int> = 0>
+	template <typename T, std::enable_if_t<std::is_same_v<T, std::string>, int> = 0>
 	item(const std::string_view name, T &&value)
 		: m_name(name)
 		, m_value(std::move(value))
@@ -221,8 +221,8 @@ class item
 	item &operator=(item &&rhs) noexcept = default;
 	/** @endcond */
 
-	std::string_view name() const { return m_name; }   ///< Return the name of the item
-	std::string_view value() const & { return m_value; } ///< Return the value of the item
+	std::string_view name() const { return m_name; }            ///< Return the name of the item
+	std::string_view value() const & { return m_value; }        ///< Return the value of the item
 	std::string value() const && { return std::move(m_value); } ///< Return the value of the item
 
 	/// \brief replace the content of the stored value with \a v
@@ -238,10 +238,10 @@ class item
 	bool is_unknown() const { return m_value == "?"; }
 
 	/// \brief the length of the value string
-	size_t length() const { return m_value.length(); }
+	std::size_t length() const { return m_value.length(); }
 
 	/// \brief support for structured binding
-	template <size_t N>
+	template <std::size_t N>
 	decltype(auto) get() const
 	{
 		if constexpr (N == 0)
@@ -250,6 +250,8 @@ class item
 			return value();
 	}
 
+	auto operator<=>(const item &rhs) const = default;
+
   private:
 	std::string_view m_name;
 	std::string m_value;
@@ -319,7 +321,7 @@ struct item_value
 		return m_length != 0;
 	}
 
-	size_t m_length = 0; ///< Length of the data
+	std::size_t m_length = 0; ///< Length of the data
 	union
 	{
 		char m_local_data[8]; ///< Storage area for small strings (strings smaller than kBufferSize)
@@ -328,7 +330,7 @@ struct item_value
 	};
 
 	/** The maximum length of locally stored strings */
-	static constexpr size_t kBufferSize = sizeof(m_local_data);
+	static constexpr std::size_t kBufferSize = sizeof(m_local_data);
 
 	// By using std::string_view instead of c_str we obain a
 	// nice performance gain since we avoid many calls to strlen.
@@ -378,7 +380,7 @@ struct item_handle
 	template <typename T>
 	item_handle &operator=(T &&value)
 	{
-		assign_value(item{ "", std::move(value) }.value());
+		assign_value(item{ "", std::forward<T>(value) }.value());
 		return *this;
 	}
 
@@ -389,7 +391,7 @@ struct item_handle
 	 * @param value The value
 	 * @return reference to this item_handle
 	 */
-	template <size_t N>
+	template <std::size_t N>
 	item_handle &operator=(const char (&value)[N])
 	{
 		assign_value(item{ "", std::move(value) }.value());
@@ -558,9 +560,11 @@ struct item_handle::item_value_as<T, std::enable_if_t<std::is_arithmetic_v<T> an
 			auto b = txt.data();
 			auto e = txt.data() + txt.size();
 
-			std::from_chars_result r = (b + 1 < e and *b == '+' and std::isdigit(b[1])) ? selected_charconv<value_type>::from_chars(b + 1, e, result) : selected_charconv<value_type>::from_chars(b, e, result);
+			std::from_chars_result r = (b + 1 < e and *b == '+' and std::isdigit(b[1])) //
+			                               ? from_chars(b + 1, e, result)
+			                               : from_chars(b, e, result);
 
-			if (r.ec != std::errc() or r.ptr != e)
+			if ((bool)r.ec or r.ptr != e)
 			{
 				result = {};
 				if (cif::VERBOSE)
@@ -593,9 +597,11 @@ struct item_handle::item_value_as<T, std::enable_if_t<std::is_arithmetic_v<T> an
 			auto b = txt.data();
 			auto e = txt.data() + txt.size();
 
-			std::from_chars_result r = (b + 1 < e and *b == '+' and std::isdigit(b[1])) ? selected_charconv<value_type>::from_chars(b + 1, e, v) : selected_charconv<value_type>::from_chars(b, e, v);
+			std::from_chars_result r = (b + 1 < e and *b == '+' and std::isdigit(b[1]))
+			                               ? from_chars(b + 1, e, v)
+			                               : from_chars(b, e, v);
 
-			if (r.ec != std::errc() or r.ptr != e)
+			if ((bool)r.ec or r.ptr != e)
 			{
 				if (cif::VERBOSE)
 				{
@@ -608,6 +614,8 @@ struct item_handle::item_value_as<T, std::enable_if_t<std::is_arithmetic_v<T> an
 				}
 				result = 1;
 			}
+			else if (std::abs(v - value) <= std::numeric_limits<value_type>::epsilon())
+				result = 0;
 			else if (v < value)
 				result = -1;
 			else if (v > value)
@@ -662,7 +670,7 @@ struct item_handle::item_value_as<T, std::enable_if_t<std::is_same_v<T, bool>>>
 	}
 };
 
-template <size_t N>
+template <std::size_t N>
 struct item_handle::item_value_as<char[N]>
 {
 	static std::string convert(const item_handle &ref)

include/cif++/iterator.hpp

@@ -67,7 +67,7 @@ class iterator_impl
 	/** @endcond */
 
 	/** variable that contains the number of elements in the tuple */
-	static constexpr size_t N = sizeof...(Ts);
+	static constexpr std::size_t N = sizeof...(Ts);
 
 	/** @cond */
 	using category_type = std::remove_cv_t<Category>;
@@ -176,7 +176,7 @@ class iterator_impl
 	/** @endcond */
 
   private:
-	template <size_t... Is>
+	template <std::size_t... Is>
 	tuple_type get(std::index_sequence<Is...>) const
 	{
 		return m_current ? tuple_type{ m_current[m_item_ix[Is]].template as<Ts>()... } : tuple_type{};
@@ -450,7 +450,7 @@ class iterator_proxy
 {
   public:
 	/** @cond */
-	static constexpr const size_t N = sizeof...(Ts);
+	static constexpr const std::size_t N = sizeof...(Ts);
 
 	using category_type = Category;
 	using row_type = std::conditional_t<std::is_const_v<category_type>, const row, row>;
@@ -473,7 +473,7 @@ class iterator_proxy
 
 	bool empty() const { return m_begin == m_end; }               ///< Return true if the range is empty
 	explicit operator bool() const { return not empty(); }        ///< Easy way to detect if the range is empty
-	size_t size() const { return std::distance(begin(), end()); } ///< Return size of the range
+	std::size_t size() const { return std::distance(begin(), end()); } ///< Return size of the range
 
 	// row front() { return *begin(); }
 	// row back() { return *(std::prev(end())); }
@@ -512,7 +512,7 @@ class conditional_iterator_proxy
 {
   public:
 	/** @cond */
-	static constexpr const size_t N = sizeof...(Ts);
+	static constexpr const std::size_t N = sizeof...(Ts);
 
 	using category_type = std::remove_cv_t<CategoryType>;
 
@@ -606,7 +606,7 @@ class conditional_iterator_proxy
 
 	bool empty() const;                                           ///< Return true if the range is empty
 	explicit operator bool() const { return not empty(); }        ///< Easy way to detect if the range is empty
-	size_t size() const { return std::distance(begin(), end()); } ///< Return size of the range
+	std::size_t size() const { return std::distance(begin(), end()); } ///< Return size of the range
 
 	row_handle front() { return *begin(); } ///< Return reference to the first row
 	// row_handle back() { return *begin(); }

include/cif++/matrix.hpp

@@ -59,27 +59,27 @@ template <typename M>
 class matrix_expression
 {
   public:
-	constexpr size_t dim_m() const { return static_cast<const M &>(*this).dim_m(); } ///< Return the size (dimension) in direction m
-	constexpr size_t dim_n() const { return static_cast<const M &>(*this).dim_n(); } ///< Return the size (dimension) in direction n
+	constexpr std::size_t dim_m() const { return static_cast<const M &>(*this).dim_m(); } ///< Return the size (dimension) in direction m
+	constexpr std::size_t dim_n() const { return static_cast<const M &>(*this).dim_n(); } ///< Return the size (dimension) in direction n
 
 	constexpr bool empty() const { return dim_m() == 0 or dim_n() == 0; } ///< Convenient way to test for empty matrices
 
 	/** Return a reference to element [ @a i, @a j ] */
-	constexpr auto &operator()(size_t i, size_t j)
+	constexpr auto &operator()(std::size_t i, std::size_t j)
 	{
 		return static_cast<M &>(*this).operator()(i, j);
 	}
 
 	/** Return the value of element [ @a i, @a j ] */
-	constexpr auto operator()(size_t i, size_t j) const
+	constexpr auto operator()(std::size_t i, std::size_t j) const
 	{
 		return static_cast<const M &>(*this).operator()(i, j);
 	}
 
 	/** Swap the contents of rows @a r1 and @a r2 */
-	void swap_row(size_t r1, size_t r2)
+	void swap_row(std::size_t r1, std::size_t r2)
 	{
-		for (size_t c = 0; c < dim_m(); ++c)
+		for (std::size_t c = 0; c < dim_m(); ++c)
 		{
 			auto v = operator()(r1, c);
 			operator()(r1, c) = operator()(r2, c);
@@ -88,9 +88,9 @@ class matrix_expression
 	}
 
 	/** Swap the contents of columns @a c1 and @a c2 */
-	void swap_col(size_t c1, size_t c2)
+	void swap_col(std::size_t c1, std::size_t c2)
 	{
-		for (size_t r = 0; r < dim_n(); ++r)
+		for (std::size_t r = 0; r < dim_n(); ++r)
 		{
 			auto &a = operator()(r, c1);
 			auto &b = operator()(r, c2);
@@ -103,11 +103,11 @@ class matrix_expression
 	{
 		os << '[';
 
-		for (size_t i = 0; i < m.dim_m(); ++i)
+		for (std::size_t i = 0; i < m.dim_m(); ++i)
 		{
 			os << '[';
 
-			for (size_t j = 0; j < m.dim_n(); ++j)
+			for (std::size_t j = 0; j < m.dim_n(); ++j)
 			{
 				os << m(i, j);
 				if (j + 1 < m.dim_n())
@@ -124,6 +124,23 @@ class matrix_expression
 
 		return os;
 	}
+
+	template <typename M2>
+	constexpr bool operator==(const matrix_expression<M2> &m) const
+	{
+		bool same = false;
+		if (dim_m() == m.dim_m() and dim_n() == m.dim_n())
+		{
+			same = true;
+			for (std::size_t i = 0; same and i < m.dim_m(); ++i)
+			{
+				for (std::size_t j = 0; same and j < m.dim_n(); ++j)
+					same = operator()(i, j) == m(i, j);
+			}
+		}
+
+		return same;
+	}
 };
 
 // --------------------------------------------------------------------
@@ -156,9 +173,9 @@ class matrix : public matrix_expression<matrix<F>>
 		, m_n(m.dim_n())
 		, m_data(m_m * m_n)
 	{
-		for (size_t i = 0; i < m_m; ++i)
+		for (std::size_t i = 0; i < m_m; ++i)
 		{
-			for (size_t j = 0; j < m_n; ++j)
+			for (std::size_t j = 0; j < m_n; ++j)
 				operator()(i, j) = m(i, j);
 		}
 	}
@@ -171,7 +188,7 @@ class matrix : public matrix_expression<matrix<F>>
 	 * @param n Requested dimension N
 	 * @param v Value to store in each element
 	 */
-	matrix(size_t m, size_t n, value_type v = 0)
+	matrix(std::size_t m, std::size_t n, value_type v = 0)
 		: m_m(m)
 		, m_n(n)
 		, m_data(m_m * m_n)
@@ -187,11 +204,11 @@ class matrix : public matrix_expression<matrix<F>>
 	matrix &operator=(const matrix &m) = default;
 	/** @endcond */
 
-	constexpr size_t dim_m() const { return m_m; } ///< Return dimension m
-	constexpr size_t dim_n() const { return m_n; } ///< Return dimension n
+	constexpr std::size_t dim_m() const { return m_m; } ///< Return dimension m
+	constexpr std::size_t dim_n() const { return m_n; } ///< Return dimension n
 
 	/** Return the value of element [ @a i, @a j ] */
-	constexpr value_type operator()(size_t i, size_t j) const
+	constexpr value_type operator()(std::size_t i, std::size_t j) const
 	{
 		assert(i < m_m);
 		assert(j < m_n);
@@ -199,7 +216,7 @@ class matrix : public matrix_expression<matrix<F>>
 	}
 
 	/** Return a reference to element [ @a i, @a j ] */
-	constexpr value_type &operator()(size_t i, size_t j)
+	constexpr value_type &operator()(std::size_t i, std::size_t j)
 	{
 		assert(i < m_m);
 		assert(j < m_n);
@@ -207,7 +224,7 @@ class matrix : public matrix_expression<matrix<F>>
 	}
 
   private:
-	size_t m_m = 0, m_n = 0;
+	std::size_t m_m = 0, m_n = 0;
 	std::vector<value_type> m_data;
 };
 
@@ -224,7 +241,7 @@ class matrix : public matrix_expression<matrix<F>>
  * element m i,j is mapped to [i * n + j] and thus storage is row major
  */
 
-template <typename F, size_t M, size_t N>
+template <typename F, std::size_t M, std::size_t N>
 class matrix_fixed : public matrix_expression<matrix_fixed<F, M, N>>
 {
   public:
@@ -232,16 +249,16 @@ class matrix_fixed : public matrix_expression<matrix_fixed<F, M, N>>
 	using value_type = F;
 
 	/** The storage size */
-	static constexpr size_t kSize = M * N;
+	static constexpr std::size_t kSize = M * N;
 
 	/** Copy constructor */
 	template <typename M2>
 	matrix_fixed(const M2 &m)
 	{
 		assert(M == m.dim_m() and N == m.dim_n());
-		for (size_t i = 0; i < M; ++i)
+		for (std::size_t i = 0; i < M; ++i)
 		{
-			for (size_t j = 0; j < N; ++j)
+			for (std::size_t j = 0; j < N; ++j)
 				operator()(i, j) = m(i, j);
 		}
 	}
@@ -266,18 +283,18 @@ class matrix_fixed : public matrix_expression<matrix_fixed<F, M, N>>
 	/** @endcond */
 
 	/** Store the values in @a a in the matrix */
-	template<size_t... Ixs>
+	template<std::size_t... Ixs>
 	matrix_fixed& fill(const F (&a)[kSize], std::index_sequence<Ixs...>)
 	{
 		m_data = { a[Ixs]... };
 		return *this;
 	}
 
-	constexpr size_t dim_m() const { return M; } ///< Return dimension m
-	constexpr size_t dim_n() const { return N; } ///< Return dimension n
+	constexpr std::size_t dim_m() const { return M; } ///< Return dimension m
+	constexpr std::size_t dim_n() const { return N; } ///< Return dimension n
 
 	/** Return the value of element [ @a i, @a j ] */
-	constexpr value_type operator()(size_t i, size_t j) const
+	constexpr value_type operator()(std::size_t i, std::size_t j) const
 	{
 		assert(i < M);
 		assert(j < N);
@@ -285,7 +302,7 @@ class matrix_fixed : public matrix_expression<matrix_fixed<F, M, N>>
 	}
 
 	/** Return a reference to element [ @a i, @a j ] */
-	constexpr value_type &operator()(size_t i, size_t j)
+	constexpr value_type &operator()(std::size_t i, std::size_t j)
 	{
 		assert(i < M);
 		assert(j < N);
@@ -322,7 +339,7 @@ class symmetric_matrix : public matrix_expression<symmetric_matrix<F>>
 	using value_type = F;
 
 	/** constructor for a matrix of size @a n x @a n elements with value @a v */
-	symmetric_matrix(size_t n, value_type v = 0)
+	symmetric_matrix(std::size_t n, value_type v = 0)
 		: m_n(n)
 		, m_data((m_n * (m_n + 1)) / 2)
 	{
@@ -337,11 +354,11 @@ class symmetric_matrix : public matrix_expression<symmetric_matrix<F>>
 	symmetric_matrix &operator=(const symmetric_matrix &m) = default;
 	/** @endcond */
 
-	constexpr size_t dim_m() const { return m_n; } ///< Return dimension m
-	constexpr size_t dim_n() const { return m_n; } ///< Return dimension n
+	constexpr std::size_t dim_m() const { return m_n; } ///< Return dimension m
+	constexpr std::size_t dim_n() const { return m_n; } ///< Return dimension n
 
 	/** Return the value of element [ @a i, @a j ] */
-	constexpr value_type operator()(size_t i, size_t j) const
+	constexpr value_type operator()(std::size_t i, std::size_t j) const
 	{
 		return i < j
 		           ? m_data[(j * (j + 1)) / 2 + i]
@@ -349,7 +366,7 @@ class symmetric_matrix : public matrix_expression<symmetric_matrix<F>>
 	}
 
 	/** Return a reference to element [ @a i, @a j ] */
-	constexpr value_type &operator()(size_t i, size_t j)
+	constexpr value_type &operator()(std::size_t i, std::size_t j)
 	{
 		if (i > j)
 			std::swap(i, j);
@@ -358,7 +375,7 @@ class symmetric_matrix : public matrix_expression<symmetric_matrix<F>>
 	}
 
   private:
-	size_t m_n;
+	std::size_t m_n;
 	std::vector<value_type> m_data;
 };
 
@@ -373,7 +390,7 @@ class symmetric_matrix : public matrix_expression<symmetric_matrix<F>>
  * matrix is m x n, addressing i,j is 0 <= i < m and 0 <= j < n
  * element m i,j is mapped to [i * n + j] and thus storage is row major
  */
-template <typename F, size_t M>
+template <typename F, std::size_t M>
 class symmetric_matrix_fixed : public matrix_expression<symmetric_matrix_fixed<F, M>>
 {
   public:
@@ -393,11 +410,11 @@ class symmetric_matrix_fixed : public matrix_expression<symmetric_matrix_fixed<F
 	symmetric_matrix_fixed &operator=(const symmetric_matrix_fixed &m) = default;
 	/** @endcond */
 
-	constexpr size_t dim_m() const { return M; } ///< Return dimension m
-	constexpr size_t dim_n() const { return M; } ///< Return dimension n
+	constexpr std::size_t dim_m() const { return M; } ///< Return dimension m
+	constexpr std::size_t dim_n() const { return M; } ///< Return dimension n
 
 	/** Return the value of element [ @a i, @a j ] */
-	constexpr value_type operator()(size_t i, size_t j) const
+	constexpr value_type operator()(std::size_t i, std::size_t j) const
 	{
 		return i < j
 		           ? m_data[(j * (j + 1)) / 2 + i]
@@ -405,7 +422,7 @@ class symmetric_matrix_fixed : public matrix_expression<symmetric_matrix_fixed<F
 	}
 
 	/** Return a reference to element [ @a i, @a j ] */
-	constexpr value_type &operator()(size_t i, size_t j)
+	constexpr value_type &operator()(std::size_t i, std::size_t j)
 	{
 		if (i > j)
 			std::swap(i, j);
@@ -444,22 +461,22 @@ class identity_matrix : public matrix_expression<identity_matrix<F>>
 	using value_type = F;
 
 	/** constructor taking a dimension @a n */
-	identity_matrix(size_t n)
+	identity_matrix(std::size_t n)
 		: m_n(n)
 	{
 	}
 
-	constexpr size_t dim_m() const { return m_n; } ///< Return dimension m
-	constexpr size_t dim_n() const { return m_n; } ///< Return dimension n
+	constexpr std::size_t dim_m() const { return m_n; } ///< Return dimension m
+	constexpr std::size_t dim_n() const { return m_n; } ///< Return dimension n
 
 	/** Return the value of element [ @a i, @a j ] */
-	constexpr value_type operator()(size_t i, size_t j) const
+	constexpr value_type operator()(std::size_t i, std::size_t j) const
 	{
 		return static_cast<value_type>(i == j ? 1 : 0);
 	}
 
   private:
-	size_t m_n;
+	std::size_t m_n;
 };
 
 // --------------------------------------------------------------------
@@ -484,11 +501,11 @@ class matrix_subtraction : public matrix_expression<matrix_subtraction<M1, M2>>
 		assert(m_m1.dim_n() == m_m2.dim_n());
 	}
 
-	constexpr size_t dim_m() const { return m_m1.dim_m(); } ///< Return dimension m
-	constexpr size_t dim_n() const { return m_m1.dim_n(); } ///< Return dimension n
+	constexpr std::size_t dim_m() const { return m_m1.dim_m(); } ///< Return dimension m
+	constexpr std::size_t dim_n() const { return m_m1.dim_n(); } ///< Return dimension n
 
 	/** Access to the value of element [ @a i, @a j ] */
-	constexpr auto operator()(size_t i, size_t j) const
+	constexpr auto operator()(std::size_t i, std::size_t j) const
 	{
 		return m_m1(i, j) - m_m2(i, j);
 	}
@@ -523,17 +540,17 @@ class matrix_matrix_multiplication : public matrix_expression<matrix_matrix_mult
 		assert(m1.dim_m() == m2.dim_n());
 	}
 
-	constexpr size_t dim_m() const { return m_m1.dim_m(); } ///< Return dimension m
-	constexpr size_t dim_n() const { return m_m1.dim_n(); } ///< Return dimension n
+	constexpr std::size_t dim_m() const { return m_m1.dim_m(); } ///< Return dimension m
+	constexpr std::size_t dim_n() const { return m_m1.dim_n(); } ///< Return dimension n
 
 	/** Access to the value of element [ @a i, @a j ] */
-	constexpr auto operator()(size_t i, size_t j) const
+	constexpr auto operator()(std::size_t i, std::size_t j) const
 	{
 		using value_type = decltype(m_m1(0, 0));
 
 		value_type result = {};
 
-		for (size_t k = 0; k < m_m1.dim_m(); ++k)
+		for (std::size_t k = 0; k < m_m1.dim_m(); ++k)
 			result += m_m1(i, k) * m_m2(k, j);
 
 		return result;
@@ -564,11 +581,11 @@ class matrix_scalar_multiplication : public matrix_expression<matrix_scalar_mult
 	{
 	}
 
-	constexpr size_t dim_m() const { return m_m.dim_m(); } ///< Return dimension m
-	constexpr size_t dim_n() const { return m_m.dim_n(); } ///< Return dimension n
+	constexpr std::size_t dim_m() const { return m_m.dim_m(); } ///< Return dimension m
+	constexpr std::size_t dim_n() const { return m_m.dim_n(); } ///< Return dimension n
 
 	/** Access to the value of element [ @a i, @a j ] */
-	constexpr auto operator()(size_t i, size_t j) const
+	constexpr auto operator()(std::size_t i, std::size_t j) const
 	{
 		return m_m(i, j) * m_v;
 	}
@@ -594,6 +611,35 @@ auto operator*(const matrix_expression<M1> &m1, const matrix_expression<M2> &m2)
 
 // --------------------------------------------------------------------
 
+template <typename M2>
+class sub_matrix : public matrix_expression<sub_matrix<M2>>
+{
+  public:
+	sub_matrix(const M2 &m, int i, int j)
+		: m_m(m)
+		, m_i(i)
+		, m_j(j)
+	{
+	}
+
+	constexpr std::size_t dim_m() const { return m_m.dim_m() - 1; } ///< Return dimension m
+	constexpr std::size_t dim_n() const { return m_m.dim_n() - 1; } ///< Return dimension n
+
+	/** Access to the value of element [ @a i, @a j ] */
+	constexpr auto operator()(std::size_t i, std::size_t j) const
+	{
+		return m_m(
+			i >= m_i ? i + 1 : i,
+			j >= m_j ? j + 1 : j);
+	}
+
+  private:
+	const M2 &m_m;
+	std::size_t m_i, m_j;
+};
+
+// --------------------------------------------------------------------
+
 /** Generic routine to calculate the determinant of a matrix
  * 
  * @note This is currently only implemented for fixed matrices of size 3x3
@@ -605,11 +651,23 @@ auto determinant(const M &m);
 template <typename F = float>
 auto determinant(const matrix3x3<F> &m)
 {
-	return (m(0, 0) * (m(1, 1) * m(2, 2) - m(1, 2) * m(2, 1)) +
-			m(0, 1) * (m(1, 2) * m(2, 0) - m(1, 0) * m(2, 2)) +
-			m(0, 2) * (m(1, 0) * m(2, 1) - m(1, 1) * m(2, 0)));
+	return (m(0, 0) * ((m(1, 1) * m(2, 2) - m(1, 2) * m(2, 1))) +
+			m(0, 1) * ((m(1, 2) * m(2, 0) - m(1, 0) * m(2, 2))) +
+			m(0, 2) * ((m(1, 0) * m(2, 1) - m(1, 1) * m(2, 0))));
 }
 
+/** Implementation of the determinant function for fixed size matrices of size 4x4 */
+template <typename F = float>
+F determinant(const matrix4x4<F> &m)
+{
+	return m(0, 0) * determinant(matrix3x3<F>(sub_matrix<decltype(m)>(m, 0, 0))) -
+	       m(0, 1) * determinant(matrix3x3<F>(sub_matrix<decltype(m)>(m, 0, 1))) +
+	       m(0, 2) * determinant(matrix3x3<F>(sub_matrix<decltype(m)>(m, 0, 2))) -
+	       m(0, 3) * determinant(matrix3x3<F>(sub_matrix<decltype(m)>(m, 0, 3)));
+}
+
+// --------------------------------------------------------------------
+
 /** Generic routine to calculate the inverse of a matrix
  * 
  * @note This is currently only implemented for fixed matrices of size 3x3
@@ -655,21 +713,21 @@ class matrix_cofactors : public matrix_expression<matrix_cofactors<M>>
 	{
 	}
 
-	constexpr size_t dim_m() const { return m_m.dim_m(); } ///< Return dimension m
-	constexpr size_t dim_n() const { return m_m.dim_n(); } ///< Return dimension n
+	constexpr std::size_t dim_m() const { return m_m.dim_m(); } ///< Return dimension m
+	constexpr std::size_t dim_n() const { return m_m.dim_n(); } ///< Return dimension n
 
 	/** Access to the value of element [ @a i, @a j ] */
-	constexpr auto operator()(size_t i, size_t j) const
+	constexpr auto operator()(std::size_t i, std::size_t j) const
 	{
-		const size_t ixs[4][3] = {
+		const std::size_t ixs[4][3] = {
 			{ 1, 2, 3 },
 			{ 0, 2, 3 },
 			{ 0, 1, 3 },
 			{ 0, 1, 2 }
 		};
 
-		const size_t *ix = ixs[i];
-		const size_t *iy = ixs[j];
+		const std::size_t *ix = ixs[i];
+		const std::size_t *iy = ixs[j];
 
 		auto result =
 			m_m(ix[0], iy[0]) * m_m(ix[1], iy[1]) * m_m(ix[2], iy[2]) +

include/cif++/model.hpp

@@ -29,12 +29,13 @@
 #include "cif++/atom_type.hpp"
 #include "cif++/datablock.hpp"
 #include "cif++/point.hpp"
+#include "cif++/row.hpp"
 
 #include <memory>
 #include <numeric>
 
 #if __cpp_lib_format
-#include <format>
+# include <format>
 #endif
 
 /** @file model.hpp
@@ -106,8 +107,6 @@ class atom
 
 		atom_impl(const atom_impl &i) = default;
 
-		void prefetch();
-
 		int compare(const atom_impl &b) const;
 
 		// bool getAnisoU(float anisou[6]) const;
@@ -136,14 +135,20 @@ class atom
 
 		row_handle row_aniso()
 		{
+			row_handle result{};
 			auto cat = m_db.get("atom_site_anisotrop");
-			return cat ? cat->operator[]({ { "id", m_id } }) : row_handle{};
+			if (cat)
+				result = cat->operator[]({ { "id", m_id } });
+			return result;
 		}
 
 		const row_handle row_aniso() const
 		{
+			row_handle result{};
 			auto cat = m_db.get("atom_site_anisotrop");
-			return cat ? cat->operator[]({ { "id", m_id } }) : row_handle{};
+			if (cat)
+				result = cat->operator[]({ { "id", m_id } });
+			return result;
 		}
 
 		const datablock &m_db;
@@ -345,12 +350,17 @@ class atom
 	std::string get_auth_asym_id() const { return get_property("auth_asym_id"); }      ///< Return the auth_asym_id property
 	std::string get_auth_seq_id() const { return get_property("auth_seq_id"); }        ///< Return the auth_seq_id property
 	std::string get_auth_atom_id() const { return get_property("auth_atom_id"); }      ///< Return the auth_atom_id property
-	std::string get_auth_alt_id() const { return get_property("auth_alt_id"); }        ///< Return the auth_alt_id property
+	std::string get_auth_alt_id() const { return get_property("pdbx_auth_alt_id"); }   ///< Return the auth_alt_id property
 	std::string get_auth_comp_id() const { return get_property("auth_comp_id"); }      ///< Return the auth_comp_id property
 	std::string get_pdb_ins_code() const { return get_property("pdbx_PDB_ins_code"); } ///< Return the pdb_ins_code property
 
 	/// Return true if this atom is an alternate
-	bool is_alternate() const { return not get_label_alt_id().empty(); }
+	bool is_alternate() const
+	{
+		if (auto alt_id = get_label_alt_id(); alt_id.empty() or alt_id == ".")
+			return false;
+		return true;
+	}
 
 	/// Convenience method to return a string that might be ID in PDB space
 	std::string pdb_id() const
@@ -476,8 +486,8 @@ class residue
 		, m_compound_id(compoundID)
 		, m_asym_id(asymID)
 		, m_seq_id(seqID)
-		, m_auth_asym_id(authAsymID)
-		, m_auth_seq_id(authSeqID)
+		, m_pdb_strand_id(authAsymID)
+		, m_pdb_seq_num(authSeqID)
 		, m_pdb_ins_code(pdbInsCode)
 	{
 	}
@@ -504,9 +514,9 @@ class residue
 	const std::string &get_asym_id() const { return m_asym_id; } ///< Return the asym_id
 	int get_seq_id() const { return m_seq_id; }                  ///< Return the seq_id
 
-	const std::string get_auth_asym_id() const { return m_auth_asym_id; } ///< Return the auth_asym_id
-	const std::string get_auth_seq_id() const { return m_auth_seq_id; }   ///< Return the auth_seq_id
-	std::string get_pdb_ins_code() const { return m_pdb_ins_code; }       ///< Return the pdb_ins_code
+	const std::string get_pdb_strand_id() const { return m_pdb_strand_id; } ///< Return the pdb_strand_id
+	const std::string get_pdb_seq_num() const { return m_pdb_seq_num; }     ///< Return the pdb_seq_num
+	std::string get_pdb_ins_code() const { return m_pdb_ins_code; }         ///< Return the pdb_ins_code
 
 	const std::string &get_compound_id() const { return m_compound_id; } ///< Return the compound_id
 	void set_compound_id(const std::string &id) { m_compound_id = id; }  ///< Set the compound_id to @a id
@@ -535,6 +545,9 @@ class residue
 	/// \brief Return the atom with atom_id @a atomID
 	atom get_atom_by_atom_id(const std::string &atomID) const;
 
+	/// \brief Return the atom with atom_id @a atomID and alternate_id @a altID
+	atom get_atom_by_atom_id(const std::string &atomID, const std::string &altID) const;
+
 	/// \brief Return the list of atoms having ID \a atomID
 	///
 	/// This includes all alternate atoms with this ID
@@ -550,6 +563,9 @@ class residue
 	/// \brief Return true if this residue has alternate atoms
 	bool has_alternate_atoms() const;
 
+	/// \brief Return true if this residue has alternate atoms for the atom \a atomID
+	bool has_alternate_atoms_for(const std::string &atomID) const;
+
 	/// \brief Return the list of unique alt ID's present in this residue
 	std::set<std::string> get_alternate_ids() const;
 
@@ -569,9 +585,13 @@ class residue
 								   m_seq_id == rhs.m_seq_id and
 								   m_asym_id == rhs.m_asym_id and
 								   m_compound_id == rhs.m_compound_id and
-								   m_auth_seq_id == rhs.m_auth_seq_id);
+								   m_pdb_seq_num == rhs.m_pdb_seq_num);
 	}
 
+	/// @brief Create a new atom and add it to the list
+	/// @return newly created atom
+	virtual atom create_new_atom(atom_type inType, const std::string &inAtomID, point inLocation);
+
   protected:
 	/** @cond */
 	residue() {}
@@ -579,7 +599,7 @@ class residue
 	structure *m_structure = nullptr;
 	std::string m_compound_id, m_asym_id;
 	int m_seq_id = 0;
-	std::string m_auth_asym_id, m_auth_seq_id, m_pdb_ins_code;
+	std::string m_pdb_strand_id, m_pdb_seq_num, m_pdb_ins_code;
 	std::vector<atom> m_atoms;
 	/** @endcond */
 };
@@ -604,12 +624,15 @@ class monomer : public residue
 	monomer &operator=(monomer &&rhs);
 
 	/// \brief constructor with actual values
-	monomer(const polymer &polymer, size_t index, int seqID, const std::string &authSeqID,
+	monomer(const polymer &polymer, std::size_t index, int seqID, const std::string &authSeqID,
 		const std::string &pdbInsCode, const std::string &compoundID);
 
 	bool is_first_in_chain() const; ///< Return if this residue is the first residue in the chain
 	bool is_last_in_chain() const;  ///< Return if this residue is the last residue in the chain
 
+	const monomer &prev() const; // Return previous monomer in polymer
+	const monomer &next() const; // Return next monomer in polymer
+
 	// convenience
 	bool has_alpha() const; ///< Return if a alpha value can be calculated (depends on location in chain)
 	bool has_kappa() const; ///< Return if a kappa value can be calculated (depends on location in chain)
@@ -624,8 +647,8 @@ class monomer : public residue
 	float omega() const; ///< Return the omega value for this residue
 
 	// torsion angles
-	size_t nr_of_chis() const; ///< Return how many torsion angles can be calculated
-	float chi(size_t i) const; ///< Return torsion angle @a i
+	std::size_t nr_of_chis() const; ///< Return how many torsion angles can be calculated
+	float chi(std::size_t i) const; ///< Return torsion angle @a i
 
 	bool is_cis() const; ///< Return true if this residue is in a cis conformation
 
@@ -672,9 +695,11 @@ class monomer : public residue
 		return m_polymer == rhs.m_polymer and m_index == rhs.m_index;
 	}
 
+	atom create_new_atom(atom_type inType, const std::string &inAtomID, point inLocation) override;
+
   private:
 	const polymer *m_polymer;
-	size_t m_index;
+	std::size_t m_index;
 };
 
 // --------------------------------------------------------------------
@@ -694,15 +719,15 @@ class polymer : public std::vector<monomer>
 
 	structure *get_structure() const { return m_structure; } ///< Return the structure
 
-	std::string get_asym_id() const { return m_asym_id; }           ///< Return the asym_id
-	std::string get_auth_asym_id() const { return m_auth_asym_id; } ///< Return the PDB chain ID, actually
-	std::string get_entity_id() const { return m_entity_id; }       ///< Return the entity_id
+	std::string get_asym_id() const { return m_asym_id; }             ///< Return the asym_id
+	std::string get_pdb_strand_id() const { return m_pdb_strand_id; } ///< Return the PDB chain ID, actually
+	std::string get_entity_id() const { return m_entity_id; }         ///< Return the entity_id
 
   private:
 	structure *m_structure;
 	std::string m_entity_id;
 	std::string m_asym_id;
-	std::string m_auth_asym_id;
+	std::string m_pdb_strand_id;
 };
 
 // --------------------------------------------------------------------
@@ -740,8 +765,8 @@ class sugar : public residue
 	int num() const
 	{
 		int result;
-		auto r = std::from_chars(m_auth_seq_id.data(), m_auth_seq_id.data() + m_auth_seq_id.length(), result);
-		if (r.ec != std::errc())
+		auto r = std::from_chars(m_pdb_seq_num.data(), m_pdb_seq_num.data() + m_pdb_seq_num.length(), result);
+		if ((bool)r.ec)
 			throw std::runtime_error("The auth_seq_id should be a number for a sugar");
 		return result;
 	}
@@ -756,9 +781,9 @@ class sugar : public residue
 	void set_link(atom link) { m_link = link; }
 
 	/// \brief Return the sugar number of the sugar linked to C1
-	size_t get_link_nr() const
+	std::size_t get_link_nr() const
 	{
-		size_t result = 0;
+		std::size_t result = 0;
 		if (m_link)
 			result = m_link.get_property_int("auth_seq_id");
 		return result;
@@ -839,19 +864,38 @@ class branch : public std::vector<sugar>
 	std::string m_asym_id, m_entity_id;
 };
 
-// --------------------------------------------------------------------
-
-/// \brief A still very limited set of options for reading structures
-enum class StructureOpenOptions
+/** @brief Enumeration for controlling atom selection based on occupancy. */
+enum class occupancy_policy
 {
-	SkipHydrogen = 1 << 0 ///< Do not include hydrogen atoms in the structure object
+	/** @brief Include all atoms regardless of their occupancy factor. */
+	ALL = 0,
+
+	/** @brief Select only alternate atoms with the maximum occupancy factor.
+	 * If multiple atoms have the same maximum occupancy, choose the one with the minimum B-factor.
+	 * If multiple atoms share both the maximum occupancy and the minimum B-factor, select the first encountered atom.
+	 */
+	MAX = 1,
+
+	/** @brief Select only alternate atoms with the minimum occupancy factor.
+	 * Similar to MAX, if multiple atoms have the same minimum occupancy, choose the one with the minimum B-factor.
+	 * If multiple atoms share both the minimum occupancy and the minimum B-factor, select the first encountered atom.
+	 */
+	MIN = 2,
+
+	/** @brief Exclude all atoms with an occupancy factor greater than zero. */
+	UNOCCUPIED = 3
 };
 
-/// \brief A way to combine two options. Not very useful as there is only one...
-constexpr inline bool operator&(StructureOpenOptions a, StructureOpenOptions b)
+struct structure_open_options
 {
-	return static_cast<int>(a) bitand static_cast<int>(b);
-}
+	bool skip_hydrogen = false;                              ///< Do not include hydrogen atoms in the structure object
+	bool skip_hetatom = false;                               ///< Do not include HET atoms in the structure object
+	bool skip_water = false;                                 ///< Do not include water atoms in the structure object
+	occupancy_policy occupancy_mode = occupancy_policy::ALL; ///< By default, the occupancy policy is set to occupancy_policy::ALL
+	std::vector<std::string> asyms;                          ///< The asyms to load, if empty load all
+	std::optional<float> min_b_factor;                       ///< Only load atoms with at least this b_factor
+	std::optional<float> max_b_factor;                       ///< Only load atoms with at most this b_factor
+};
 
 // --------------------------------------------------------------------
 
@@ -865,10 +909,10 @@ class structure
 {
   public:
 	/// \brief Read the structure from cif::file @a p
-	structure(file &p, size_t modelNr = 1, StructureOpenOptions options = {});
+	structure(file &p, std::size_t modelNr = 1, structure_open_options options = {});
 
 	/// \brief Load the structure from already parsed mmCIF data in @a db
-	structure(datablock &db, size_t modelNr = 1, StructureOpenOptions options = {});
+	structure(datablock &db, std::size_t modelNr = 1, structure_open_options options = {});
 
 	/** @cond */
 	structure(structure &&s) = default;
@@ -881,7 +925,7 @@ class structure
 	~structure() = default;
 
 	/// \brief Return the model number
-	size_t get_model_nr() const { return m_model_nr; }
+	std::size_t get_model_nr() const { return m_model_nr; }
 
 	/// \brief Return a list of all the atoms in this structure
 	const std::vector<atom> &atoms() const { return m_atoms; }
@@ -978,18 +1022,18 @@ class structure
 	/**
 	 * @brief Change residue @a res to a new compound ID optionally
 	 * remapping atoms.
-	 * 
+	 *
 	 * A new chem_comp entry as well as an entity is created if needed and
 	 * if the list of @a remappedAtoms is not empty it is used to remap.
-	 * 
+	 *
 	 * The array in @a remappedAtoms contains tuples of strings, both
 	 * strings contain an atom_id. The first is the one in the current
 	 * residue and the second is the atom_id that should be used instead.
 	 * If the second string is empty, the atom is removed from the residue.
-	 * 
-	 * @param res 
-	 * @param newcompound 
-	 * @param remappedAtoms 
+	 *
+	 * @param res
+	 * @param newcompound
+	 * @param remappedAtoms
 	 */
 	void change_residue(residue &res, const std::string &newcompound,
 		const std::vector<std::tuple<std::string, std::string>> &remappedAtoms);
@@ -1022,12 +1066,30 @@ class structure
 	/// \return				The newly create asym ID
 	std::string create_non_poly(const std::string &entity_id, std::vector<row_initializer> atoms);
 
+	/// \brief Create a new NonPolymer struct_asym for a compound of type \a compound_id, returns asym_id.
+	/// This method creates new atom records filled with info from the CCD compound info.
+	///
+	/// \param compound_id	 The compound ID of the new nonpoly
+	/// \param skip_hydrogen Do not create hydrogen atoms when true
+	/// \return				 The newly create asym ID
+	std::string create_non_poly(const std::string &compound_id, bool skip_hydrogen);
+
 	/// \brief Create a new water with atom constructed from info in \a atom_info
 	/// This method creates a new atom record filled with info from the info.
 	///
 	/// \param atom			The set of item data containing the data for the atoms.
 	void create_water(row_initializer atom);
 
+	/// \brief Create a link, a struct_conn record for two atoms.
+	///
+	/// \param a1			Atom 1
+	/// \param a2			Atom 2
+	/// \param link_type	The struct_conn_type ID for the link
+	/// \param role			The pdbx_role field value
+	/// \return 			The ID of the struct_conn record created
+
+	std::string create_link(atom a1, atom a2, const std::string &link_type, const std::string &role);
+
 	/// \brief Create a new and empty (sugar) branch
 	branch &create_branch();
 
@@ -1091,11 +1153,14 @@ class structure
 	/// \brief emplace the moved atom @a atom
 	atom &emplace_atom(atom &&atom);
 
+	/// \brief Reorder atom_site atoms based on 'natural' ordering
+	void reorder_atoms();
+
   private:
 	friend polymer;
 	friend residue;
 
-	void load_atoms_for_model(StructureOpenOptions options);
+	void load_atoms_for_model(structure_open_options options);
 
 	std::string insert_compound(const std::string &compoundID, bool is_entity);
 
@@ -1107,9 +1172,9 @@ class structure
 	void remove_sugar(sugar &sugar);
 
 	datablock &m_db;
-	size_t m_model_nr;
+	std::size_t m_model_nr;
 	std::vector<atom> m_atoms;
-	std::vector<size_t> m_atom_index;
+	std::vector<std::size_t> m_atom_index;
 	std::list<polymer> m_polymers;
 	std::list<branch> m_branches;
 	std::vector<residue> m_non_polymers;

include/cif++/parser.hpp

@@ -39,6 +39,8 @@
 namespace cif
 {
 
+class validator;
+
 // --------------------------------------------------------------------
 
 /** Exception that is thrown when the mmCIF file contains a parsing error */
@@ -73,7 +75,15 @@ class sac_parser
 {
   public:
 	/** @cond */
-	using datablock_index = std::map<std::string, std::size_t>;
+	struct iless_op
+	{
+		bool operator()(std::string_view a, std::string_view b) const
+		{
+			return icompare(a, b) < 0;
+		}
+	};
+
+	using datablock_index = std::map<std::string, std::size_t, iless_op>;
 
 	virtual ~sac_parser() = default;
 	/** @endcond */
@@ -299,6 +309,14 @@ class sac_parser
 class parser : public sac_parser
 {
   public:
+	/// \brief constructor, generates data into @a file from @a is using validator @a v
+	parser(std::istream &is, file &file, const validator *v)
+		: sac_parser(is)
+		, m_file(file)
+		, m_validator(v)
+	{
+	}
+
 	/// \brief constructor, generates data into @a file from @a is
 	parser(std::istream &is, file &file)
 		: sac_parser(is)
@@ -319,6 +337,7 @@ class parser : public sac_parser
 	file &m_file;
 	datablock *m_datablock = nullptr;
 	category *m_category = nullptr;
+	const validator *m_validator = nullptr;
 	row_handle m_row;
 
 	/** @endcond */

include/cif++/pdb.hpp

@@ -27,6 +27,7 @@
 #pragma once
 
 #include "cif++/file.hpp"
+#include "cif++/validate.hpp"
 
 #include <system_error>
 
@@ -63,7 +64,7 @@ file read(std::istream &is);
  * @brief Read a file in legacy PDB format from std::istream @a is and
  * put the data into @a cifFile
  */
-file read_pdb_file(std::istream &pdbFile);
+void read_pdb_file(std::istream &pdbFile, cif::file &cifFile);
 
 // mmCIF to PDB
 
@@ -103,16 +104,50 @@ inline void write(const std::filesystem::path &p, const file &f)
 
 // --------------------------------------------------------------------
 
+/**
+ * @brief Quickly fix a PDB file that lacks some often needed categories
+ * 
+ * This differs from reconstruct_pdbx which does a much more thorough job
+ * 
+ * \param pdbx_file The cif::file that hopefully contains some valid data
+ */
+
+void fixup_pdbx(file &pdbx_file);
+
+/**
+ * @brief Quickly fix a PDB file that lacks some often needed categories
+ * 
+ * This differs from reconstruct_pdbx which does a much more thorough job
+ * 
+ * \param pdbx_file The cif::file that hopefully contains some valid data
+ * \param v The validator to use
+ */
+
+void fixup_pdbx(file &pdbx_file, const validator &v);
+
 /** \brief Reconstruct all missing categories for an assumed PDBx file.
  *
  * Some people believe that simply dumping some atom records is enough.
+ * 
+ * This version uses the audit_conform information and falls back to
+ * using mmcif_pdbx.dic if not specified.
  *
- * \param file The cif::file that hopefully contains some valid data
- * \param dictionary The mmcif dictionary to use
+ * \param pdbx_file The cif::file that hopefully contains some valid data
  * \result Returns true if the resulting file is valid
  */
 
-bool reconstruct_pdbx(file &pdbx_file, std::string_view dictionary = "mmcif_pdbx");
+ bool reconstruct_pdbx(file &pdbx_file);
+
+ /** \brief Reconstruct all missing categories for an assumed PDBx file.
+ *
+ * Some people believe that simply dumping some atom records is enough.
+ *
+ * \param pdbx_file The cif::file that hopefully contains some valid data
+ * \param v The validator to use
+ * \result Returns true if the resulting file is valid
+ */
+
+bool reconstruct_pdbx(file &pdbx_file, const validator &v);
 
 /** \brief This is an extension to cif::validator, use the logic in common
  * PDBx files to see if the file is internally consistent.
@@ -125,12 +160,13 @@ bool reconstruct_pdbx(file &pdbx_file, std::string_view dictionary = "mmcif_pdbx
  * 
  * This function throws a std::system_error in case of an error
  *
- * \param file The input file
- * \param dictionary The mmcif dictionary to use
+ * \param pdbx_file The input file
+ * \param v The validator to use
  * \result Returns true if the file was valid and consistent
  */
 
-bool is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary = "mmcif_pdbx");
+bool is_valid_pdbx_file(const file &pdbx_file,
+	const validator &v = validator_factory::instance().get("mmcif_pdbx.dic"));
 
 /** \brief This is an extension to cif::validator, use the logic in common
  * PDBx files to see if the file is internally consistent.
@@ -145,7 +181,6 @@ bool is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary = "mm
  * default mmcif_pdbx.dic dictionary.
  *
  * \param file The input file
- * \param ec The error_code in case something was wrong
  * \result Returns true if the file was valid and consistent
  */
 
@@ -161,12 +196,12 @@ bool is_valid_pdbx_file(const file &pdbx_file, std::error_code &ec);
  * Use the common \ref cif::VERBOSE flag to turn on diagnostic messages.
  * 
  * \param file The input file
- * \param dictionary The dictionary to use
+ * \param v The validator to use
  * \param ec The error_code in case something was wrong
  * \result Returns true if the file was valid and consistent
  */
 
-bool is_valid_pdbx_file(const file &pdbx_file, std::string_view dictionary,
+bool is_valid_pdbx_file(const file &pdbx_file, const validator &v,
 	std::error_code &ec);
 
 // --------------------------------------------------------------------

include/cif++/point.hpp

@@ -30,7 +30,9 @@
 #include <cmath>
 #include <complex>
 #include <cstdint>
+#include <format>
 #include <functional>
+#include <optional>
 #include <valarray>
 
 #if __has_include(<clipper/core/coords.h>)
@@ -365,11 +367,18 @@ class quaternion_type
 	}
 
 	/// \brief test for all zero values
-	constexpr operator bool() const
+	constexpr explicit operator bool() const
 	{
 		return a != 0 or b != 0 or c != 0 or d != 0;
 	}
 
+	/// \brief for debugging e.g.
+	friend std::ostream &operator<<(std::ostream &os, const quaternion_type &rhs)
+	{
+		os << std::format("{{ a: {}, b: {}, c: {}, d: {} }}", rhs.a, rhs.b, rhs.c, rhs.d);
+		return os;
+	}
+
   private:
 	value_type a, b, c, d;
 };
@@ -662,12 +671,23 @@ struct point_type
 		return std::make_tuple(std::ref(m_x), std::ref(m_y), std::ref(m_z));
 	}
 
-	/// \brief Compare with @a rhs
+#if defined(__cpp_impl_three_way_comparison)
+	/// \brief a default spaceship operator
+	constexpr auto operator<=>(const point_type &rhs) const = default;
+#else
+	/// \brief a default equals operator
 	constexpr bool operator==(const point_type &rhs) const
 	{
 		return m_x == rhs.m_x and m_y == rhs.m_y and m_z == rhs.m_z;
 	}
 
+	/// \brief a default not-equals operator
+	constexpr bool operator!=(const point_type &rhs) const
+	{
+		return not operator==(rhs);
+	}
+#endif
+
 	// consider point as a vector... perhaps I should rename point?
 
 	/// \brief looking at the point as if it is a vector, return the squared length
@@ -732,6 +752,55 @@ inline constexpr auto cross_product(const point_type<F1> &a, const point_type<F2
 		a.m_x * b.m_y - b.m_x * a.m_y);
 }
 
+/// \brief return the squared norm of point @a p
+template <typename F>
+constexpr F norm_squared(const point_type<F> &p)
+{
+	return p.m_x * p.m_x + p.m_y * p.m_y + p.m_z * p.m_z;
+}
+
+/// \brief return the norm of point @a p
+template <typename F>
+constexpr point_type<F> norm(const point_type<F> &p)
+{
+	return std::sqrt(norm_squared(p));
+}
+
+/// \brief return the point where two lines intersect, or an empty value if they don't intersect at all
+template <typename F>
+std::optional<cif::point> line_line_intersection(const point_type<F> &p1,
+	const point_type<F> &p2, const point_type<F> &p3, const point_type<F> &p4)
+{
+	auto p13 = p1 - p3;
+	auto p43 = p4 - p3;
+	if (std::abs(p43.m_x) < std::numeric_limits<F>::epsilon() and std::abs(p43.m_y) < std::numeric_limits<F>::epsilon() and std::abs(p43.m_z) < std::numeric_limits<F>::epsilon())
+		return {};
+
+	auto p21 = p2 - p1;
+	if (std::abs(p21.m_x) < std::numeric_limits<F>::epsilon() and std::abs(p21.m_y) < std::numeric_limits<F>::epsilon() and std::abs(p21.m_z) < std::numeric_limits<F>::epsilon())
+		return {};
+
+	auto d1343 = cif::dot_product(p43, p13);
+	auto d4321 = cif::dot_product(p43, p21);
+	auto d1321 = cif::dot_product(p13, p21);
+	auto d4343 = cif::dot_product(p43, p43);
+	auto d2121 = cif::dot_product(p21, p21);
+
+	auto denom = d2121 * d4343 - d4321 * d4321;
+	if (std::abs(denom) < std::numeric_limits<F>::epsilon())
+		return {};
+
+	auto numer = d1343 * d4321 - d1321 * d4343;
+
+	auto mua = numer / denom;
+	auto mub = (d1343 + d4321 * mua) / d4343;
+
+	auto pa = p1 + mua * p21;
+	auto pb = p3 + mub * p43;
+
+	return { (pa + pb) / 2 };
+}
+
 /// \brief return the angle in degrees between the vectors from point @a p2 to @a p1 and @a p2 to @a p3
 template <typename F>
 constexpr auto angle(const point_type<F> &p1, const point_type<F> &p2, const point_type<F> &p3)
@@ -795,6 +864,9 @@ constexpr auto distance_point_to_line(const point_type<F> &l1, const point_type<
 	return cross.length() / line.length();
 }
 
+/// \brief return the smallest sphere around the points in @a pts
+std::tuple<point, float> smallest_sphere_around_points(std::vector<point> pts);
+
 // --------------------------------------------------------------------
 /**
  * @brief For e.g. simulated annealing, returns a new point that is moved in
@@ -867,7 +939,7 @@ class spherical_dots
 	}
 
 	/// \brief The number of points
-	size_t size() const { return P; }
+	std::size_t size() const { return P; }
 
 	/// \brief Access a point by index
 	const point operator[](uint32_t inIx) const { return m_points[inIx]; }

include/cif++/row.hpp

@@ -85,7 +85,7 @@ namespace detail
 	template <typename... C>
 	struct get_row_result
 	{
-		static constexpr size_t N = sizeof...(C);
+		static constexpr std::size_t N = sizeof...(C);
 
 		get_row_result(const row_handle &r, std::array<uint16_t, N> &&items)
 			: m_row(r)
@@ -104,7 +104,7 @@ namespace detail
 			return get<Ts...>(std::index_sequence_for<Ts...>{});
 		}
 
-		template <typename... Ts, size_t... Is>
+		template <typename... Ts, std::size_t... Is>
 		std::tuple<Ts...> get(std::index_sequence<Is...>) const
 		{
 			return std::tuple<Ts...>{ m_row[m_items[Is]].template as<Ts>()... };

include/cif++/symmetry.hpp

@@ -300,7 +300,7 @@ namespace literals
 	 * @endcode
 	 *
 	 */
-	inline sym_op operator""_symop(const char *text, size_t length)
+	inline sym_op operator""_symop(const char *text, std::size_t length)
 	{
 		return sym_op({ text, length });
 	}
@@ -464,7 +464,7 @@ class spacegroup : public std::vector<transformation>
 
   private:
 	int m_nr;
-	size_t m_index;
+	std::size_t m_index;
 };
 
 // --------------------------------------------------------------------

include/cif++/text.hpp

@@ -352,272 +352,38 @@ std::string cif_id_for_number(int number);
  * a dynamic programming approach to get the most efficient filling of
  * the space.
  */
-std::vector<std::string> word_wrap(const std::string &text, size_t width);
+std::vector<std::string> word_wrap(const std::string &text, std::size_t width);
 
 // --------------------------------------------------------------------
-/// \brief std::from_chars for floating point types.
-///
-/// These are optional, there's a selected_charconv class below that selects
-/// the best option to use based on support by the stl library.
-///
-/// I.e. that in case of GNU < 12 (or something) the cif implementation will
-/// be used, all other cases will use the stl version.
 
-template <typename FloatType, std::enable_if_t<std::is_floating_point_v<FloatType>, int> = 0>
-std::from_chars_result from_chars(const char *first, const char *last, FloatType &value)
-{
-	std::from_chars_result result{ first, {} };
-
-	enum State
-	{
-		IntegerSign,
-		Integer,
-		Fraction,
-		ExponentSign,
-		Exponent
-	} state = IntegerSign;
-	int sign = 1;
-	unsigned long long vi = 0;
-	long double f = 1;
-	int exponent_sign = 1;
-	int exponent = 0;
-	bool done = false;
-
-	while (not done and result.ec == std::errc())
-	{
-		char ch = result.ptr != last ? *result.ptr : 0;
-		++result.ptr;
-
-		switch (state)
-		{
-			case IntegerSign:
-				if (ch == '-')
-				{
-					sign = -1;
-					state = Integer;
-				}
-				else if (ch == '+')
-					state = Integer;
-				else if (ch >= '0' and ch <= '9')
-				{
-					vi = ch - '0';
-					state = Integer;
-				}
-				else if (ch == '.')
-					state = Fraction;
-				else
-					result.ec = std::errc::invalid_argument;
-				break;
-
-			case Integer:
-				if (ch >= '0' and ch <= '9')
-					vi = 10 * vi + (ch - '0');
-				else if (ch == 'e' or ch == 'E')
-					state = ExponentSign;
-				else if (ch == '.')
-					state = Fraction;
-				else
-				{
-					done = true;
-					--result.ptr;
-				}
-				break;
-
-			case Fraction:
-				if (ch >= '0' and ch <= '9')
-				{
-					vi = 10 * vi + (ch - '0');
-					f /= 10;
-				}
-				else if (ch == 'e' or ch == 'E')
-					state = ExponentSign;
-				else
-				{
-					done = true;
-					--result.ptr;
-				}
-				break;
-
-			case ExponentSign:
-				if (ch == '-')
-				{
-					exponent_sign = -1;
-					state = Exponent;
-				}
-				else if (ch == '+')
-					state = Exponent;
-				else if (ch >= '0' and ch <= '9')
-				{
-					exponent = ch - '0';
-					state = Exponent;
-				}
-				else
-					result.ec = std::errc::invalid_argument;
-				break;
-
-			case Exponent:
-				if (ch >= '0' and ch <= '9')
-					exponent = 10 * exponent + (ch - '0');
-				else
-				{
-					done = true;
-					--result.ptr;
-				}
-				break;
-		}
-	}
-
-	if (result.ec == std::errc())
-	{
-		long double v = f * vi * sign;
-		if (exponent != 0)
-			v *= std::pow(10, exponent * exponent_sign);
-
-		if (std::isnan(v))
-			result.ec = std::errc::invalid_argument;
-		else if (std::abs(v) > std::numeric_limits<FloatType>::max())
-			result.ec = std::errc::result_out_of_range;
-
-		value = static_cast<FloatType>(v);
-	}
-
-	return result;
-}
-
-/// \brief duplication of std::chars_format for deficient STL implementations
-enum class chars_format
-{
-	scientific = 1,
-	fixed = 2,
-	// hex,
-	general = fixed | scientific
-};
-
-/// \brief a simplistic implementation of std::to_chars for old STL implementations
-template <typename FloatType, std::enable_if_t<std::is_floating_point_v<FloatType>, int> = 0>
-std::to_chars_result to_chars(char *first, char *last, FloatType &value, chars_format fmt)
-{
-	int size = static_cast<int>(last - first);
-	int r = 0;
-
-	switch (fmt)
-	{
-		case chars_format::scientific:
-			if constexpr (std::is_same_v<FloatType, long double>)
-				r = snprintf(first, last - first, "%le", value);
-			else
-				r = snprintf(first, last - first, "%e", value);
-			break;
-
-		case chars_format::fixed:
-			if constexpr (std::is_same_v<FloatType, long double>)
-				r = snprintf(first, last - first, "%lf", value);
-			else
-				r = snprintf(first, last - first, "%f", value);
-			break;
-
-		case chars_format::general:
-			if constexpr (std::is_same_v<FloatType, long double>)
-				r = snprintf(first, last - first, "%lg", value);
-			else
-				r = snprintf(first, last - first, "%g", value);
-			break;
-	}
-
-	std::to_chars_result result;
-	if (r < 0 or r >= size)
-		result = { first, std::errc::value_too_large };
-	else
-		result = { first + r, std::errc() };
-
-	return result;
-}
-
-/// \brief a simplistic implementation of std::to_chars for old STL implementations
-template <typename FloatType, std::enable_if_t<std::is_floating_point_v<FloatType>, int> = 0>
-std::to_chars_result to_chars(char *first, char *last, FloatType &value, chars_format fmt, int precision)
-{
-	int size = static_cast<int>(last - first);
-	int r = 0;
-
-	switch (fmt)
-	{
-		case chars_format::scientific:
-			if constexpr (std::is_same_v<FloatType, long double>)
-				r = snprintf(first, last - first, "%.*le", precision, value);
-			else
-				r = snprintf(first, last - first, "%.*e", precision, value);
-			break;
-
-		case chars_format::fixed:
-			if constexpr (std::is_same_v<FloatType, long double>)
-				r = snprintf(first, last - first, "%.*lf", precision, value);
-			else
-				r = snprintf(first, last - first, "%.*f", precision, value);
-			break;
-
-		case chars_format::general:
-			if constexpr (std::is_same_v<FloatType, long double>)
-				r = snprintf(first, last - first, "%.*lg", precision, value);
-			else
-				r = snprintf(first, last - first, "%.*g", precision, value);
-			break;
-	}
-
-	std::to_chars_result result;
-	if (r < 0 or r >= size)
-		result = { first, std::errc::value_too_large };
-	else
-		result = { first + r, std::errc() };
-
-	return result;
-}
-
-/// \brief class that uses our implementation of std::from_chars and std::to_chars
 template <typename T>
-struct my_charconv
-{
-	/// @brief Simply call our version of std::from_chars
-	static std::from_chars_result from_chars(const char *a, const char *b, T &d)
-	{
-		return cif::from_chars(a, b, d);
-	}
+using from_chars_function = decltype(std::from_chars(std::declval<const char *>(), std::declval<const char *>(), std::declval<T &>()));
 
-	/// @brief Simply call our version of std::to_chars
-	static std::to_chars_result to_chars(char *first, char *last, T &value, chars_format fmt)
-	{
-		return cif::to_chars(first, last, value, fmt);
-	}
-};
-
-/// \brief class that uses the STL implementation of std::from_chars and std::to_chars
 template <typename T>
 struct std_charconv
 {
-	/// @brief Simply call std::from_chars
 	static std::from_chars_result from_chars(const char *a, const char *b, T &d)
 	{
 		return std::from_chars(a, b, d);
 	}
-
-	/// @brief Simply call std::to_chars
-	static std::to_chars_result to_chars(char *first, char *last, T &value, chars_format fmt)
-	{
-		return std::to_chars(first, last, value, fmt);
-	}
 };
 
-/// \brief helper to find a from_chars function
-template <typename T>
-using from_chars_function = decltype(std::from_chars(std::declval<const char *>(), std::declval<const char *>(), std::declval<T &>()));
+template <typename T, typename = void>
+struct ff_charconv;
 
-/**
- * @brief Helper to select the best implementation of charconv based on availability of the
- * function in the std:: namespace
- *
- * @tparam T The type for which we want to find a from_chars/to_chars function
- */
 template <typename T>
-using selected_charconv = typename std::conditional_t<std_experimental::is_detected_v<from_chars_function, T>, std_charconv<T>, my_charconv<T>>;
+struct ff_charconv<T, typename std::enable_if_t<std::is_floating_point_v<T>>>
+{
+	static std::from_chars_result from_chars(const char *a, const char *b, T &v);
+};
+
+template <typename T>
+using charconv = typename std::conditional_t<std_experimental::is_detected_v<from_chars_function, T>, std_charconv<T>, ff_charconv<T>>;
+
+template <typename T>
+constexpr auto from_chars(const char *s, const char *e, T &v)
+{
+	return charconv<T>::from_chars(s, e, v);
+}
 
 } // namespace cif

include/cif++/utilities.hpp

@@ -53,6 +53,7 @@
 #pragma warning(disable : 4068) // unknown pragma
 #pragma warning(disable : 4100) // unreferenced formal parameter
 #pragma warning(disable : 4101) // unreferenced local variable
+#pragma warning(disable : 4702) // unreachable code (too bad, this one. Happens in for loops)
 #define _SILENCE_CXX17_CODECVT_HEADER_DEPRECATION_WARNING 1
 #endif
 
@@ -295,6 +296,11 @@ class progress_bar
 	 */
 	void message(const std::string &inMessage);
 
+	/**
+	 * @brief Flush the progress bar to the output stream
+	 */
+	void flush();
+
   private:
 	progress_bar(const progress_bar &) = delete;
 	progress_bar &operator=(const progress_bar &) = delete;

include/cif++/validate.hpp

@@ -26,12 +26,14 @@
 
 #pragma once
 
+#include "cif++/category.hpp"
 #include "cif++/text.hpp"
 
 #include <cassert>
 #include <filesystem>
 #include <list>
 #include <mutex>
+#include <optional>
 #include <system_error>
 #include <utility>
 
@@ -48,6 +50,7 @@
 namespace cif
 {
 
+class category;
 struct category_validator;
 
 // --------------------------------------------------------------------
@@ -227,38 +230,39 @@ struct type_validator
 {
 	std::string m_name;                 ///< The name of the type
 	DDL_PrimitiveType m_primitive_type; ///< The primitive_type of the type
-	regex_impl *m_rx;                   ///< The regular expression for the type
+	std::shared_ptr<regex_impl> m_rx;   ///< The regular expression for the type
 
 	type_validator() = delete;
 
 	/// @brief Constructor
 	type_validator(std::string_view name, DDL_PrimitiveType type, std::string_view rx);
 
-	type_validator(const type_validator &) = delete;
-
 	/// @brief Copy constructor
-	type_validator(type_validator &&rhs)
-		: m_name(std::move(rhs.m_name))
-		, m_primitive_type(rhs.m_primitive_type)
-	{
-		m_rx = std::exchange(rhs.m_rx, nullptr);
-	}
-
-	type_validator &operator=(const type_validator &) = delete;
+	type_validator(const type_validator &tv);
 
 	/// @brief Move constructor
-	type_validator &operator=(type_validator &&rhs)
+	type_validator(type_validator &&rhs)
 	{
-		m_name = std::move(rhs.m_name);
-		m_primitive_type = rhs.m_primitive_type;
-		m_rx = std::exchange(rhs.m_rx, nullptr);
+		swap(*this, rhs);
+	}
 
+	/// @brief Move constructor
+	type_validator &operator=(type_validator rhs)
+	{
+		swap(*this, rhs);
 		return *this;
 	}
 
 	/// @brief Destructor
 	~type_validator();
 
+	friend void swap(type_validator &a, type_validator &b)
+	{
+		std::swap(a.m_name, b.m_name);
+		std::swap(a.m_primitive_type, b.m_primitive_type);
+		std::swap(a.m_rx, b.m_rx);
+	}
+
 	/// @brief Return the sorting order
 	bool operator<(const type_validator &rhs) const
 	{
@@ -303,13 +307,13 @@ struct item_alias
  */
 struct item_validator
 {
-	std::string m_item_name;                  ///< The item name
-	bool m_mandatory;                         ///< Flag indicating this item is mandatory
-	const type_validator *m_type;             ///< The type for this item
-	cif::iset m_enums;                        ///< If filled, the set of allowed values
-	std::string m_default;                    ///< If filled, a default value for this item
-	category_validator *m_category = nullptr; ///< The category_validator this item_validator belongs to
-	std::vector<item_alias> m_aliases;        ///< The aliases for this item
+	std::string m_item_name;           ///< The item name
+	bool m_mandatory;                  ///< Flag indicating this item is mandatory
+	const type_validator *m_type;      ///< The type for this item
+	cif::iset m_enums;                 ///< If filled, the set of allowed values
+	std::string m_default;             ///< If filled, a default value for this item
+	std::string m_category;            ///< The category this item_validator belongs to
+	std::vector<item_alias> m_aliases; ///< The aliases for this item
 
 	/// @brief Compare based on the name
 	bool operator<(const item_validator &rhs) const
@@ -396,24 +400,48 @@ class validator
 	 *
 	 * @param name The name of the underlying dictionary
 	 */
-	validator(std::string_view name)
-		: m_name(name)
+	validator()
+		: m_audit_conform("audit_conform")
 	{
 	}
 
+	/**
+	 * @brief Construct a new validator object
+	 *
+	 * @param name The name of the underlying dictionary
+	 * @param is The data to parse
+	 */
+	validator(std::istream &is)
+		: m_audit_conform("audit_conform")
+	{
+		parse(is);
+	}
+
 	/// @brief destructor
 	~validator() = default;
 
-	validator(const validator &rhs) = delete;
-	validator &operator=(const validator &rhs) = delete;
+	validator(const validator &rhs);
 
 	/// @brief move constructor
-	validator(validator &&rhs) = default;
+	validator(validator &&rhs)
+	{
+		swap(*this, rhs);
+	}
 
-	/// @brief move assignment operator
-	validator &operator=(validator &&rhs) = default;
+	validator &operator=(validator rhs)
+	{
+		swap(*this, rhs);
+		return *this;
+	}
+
+	friend void swap(validator &a, validator &b) noexcept;
 
 	friend class dictionary_parser;
+	friend class validator_factory;
+
+	/// @brief Parse dictionary in @a is and put content in this validator, optionally extending it
+	/// @param is The stream containing a valid cif dictionary
+	void parse(std::istream &is);
 
 	/// @brief Add type_validator @a v to the list of type validators
 	void add_type_validator(type_validator &&v);
@@ -456,18 +484,22 @@ class validator
 	void report_error(std::error_code ec, std::string_view category,
 		std::string_view item, bool fatal = true) const;
 
-	const std::string &name() const { return m_name; }        ///< Get the name of this validator
-	void set_name(const std::string &name) { m_name = name; } ///< Set the name of this validator
+	/// @brief Write out the audit_conform data for this validator
+	/// @param audit_conform
+	void fill_audit_conform(category &audit_conform) const;
 
-	const std::string &version() const { return m_version; }              ///< Get the version of this validator
-	void set_version(const std::string &version) { m_version = version; } ///< Set the version of this validator
+	/// @brief Return true if this validator matches @a audit_conform
+	bool matches_audit_conform(const category &audit_conform) const;
+
+	/// @brief Add info
+	void append_audit_conform(const std::string &name, const std::optional<std::string> &version);
 
   private:
 	// name is fully qualified here:
 	item_validator *get_validator_for_item(std::string_view name) const;
 
-	std::string m_name;
-	std::string m_version;
+	category m_audit_conform;
+
 	bool m_strict = false;
 	std::set<type_validator> m_type_validators;
 	std::set<category_validator> m_category_validators;
@@ -487,17 +519,28 @@ class validator_factory
 	/// @brief Return the singleton instance
 	static validator_factory &instance();
 
-	/// @brief Return the validator with name @a dictionary_name
-	const validator &operator[](std::string_view dictionary_name);
+	/// @brief Return validator with info recorded in @a audit_conform
+	const validator &get(const category &audit_conform);
 
-	/// @brief Construct a new validator with name @a name from the data in @a is
-	const validator &construct_validator(std::string_view name, std::istream &is);
+	/// @brief Return the single-file validator with name @a dictionary_name
+	const validator &get(std::string_view dictionary_name);
+
+	/// @brief Return true if the version @a found is equal or higher than @a expected for dictionary @a name
+	static bool check_version(std::string_view name, std::string_view expected, std::string_view found);
+
+	/// @brief Add validator @a v to the list of known validators
+	const validator &add(validator &&v)
+	{
+		std::unique_lock lock(m_mutex);
+		return m_validators.emplace_back(std::move(v));
+	}
 
   private:
-	// --------------------------------------------------------------------
-
 	validator_factory() = default;
 
+	/// @brief Construct a new validator with name @a name from the data in @a is with at least version @a version if specified
+	validator construct_validator(std::string_view name, std::optional<std::string> version);
+
 	std::mutex m_mutex;
 	std::list<validator> m_validators;
 };

pcre2-simple/CMakeLists.txt

@@ -0,0 +1,316 @@
+# SPDX-License-Identifier: BSD-2-Clause
+# 
+# Copyright (c) 2025 Maarten L. Hekkelman
+# 
+# Redistribution and use in source and binary forms, with or without
+# 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
+# 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 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.
+
+# A simplified wrapper CMakeLists.txt file for PCRE2
+#
+# This will generate an OBJECT library so it can be linked into another library
+
+cmake_minimum_required(VERSION 3.25)
+
+include(FetchContent)
+
+project(pcre2s VERSION 1.0.0 LANGUAGES C CXX)
+
+# The original code:
+
+file(DOWNLOAD https://github.com/PCRE2Project/pcre2/releases/download/pcre2-10.46/pcre2-10.46.tar.gz
+    ${CMAKE_CURRENT_BINARY_DIR}/pcre2-code.tgz
+    EXPECTED_HASH SHA256=8d28d7f2c3b970c3a4bf3776bcbb5adfc923183ce74bc8df1ebaad8c1985bd07)
+file(ARCHIVE_EXTRACT INPUT ${CMAKE_CURRENT_BINARY_DIR}/pcre2-code.tgz
+    DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+set(PCRE2_SOURCE_DIR ${CMAKE_CURRENT_BINARY_DIR}/pcre2-10.46)
+set(PCRE2_MAJOR 10)
+set(PCRE2_MINOR 46)
+set(PCRE2_VERSION "${PCRE2_MAJOR}.${PCRE2_MINOR}")
+set(PCRE2_DATE "2024-06-09")
+
+# Some needed configuration options
+
+# option(PCRE2_BUILD_PCRE2_8 "Build 8 bit PCRE2 library" ON)
+# option(PCRE2_BUILD_PCRE2_16 "Build 16 bit PCRE2 library" OFF)
+# option(PCRE2_BUILD_PCRE2_32 "Build 32 bit PCRE2 library" OFF)
+
+option(PCRE2_STATIC_PIC "Build the static library with the option position independent code enabled." OFF)
+
+set(PCRE2_NEWLINE "LF" CACHE STRING "What to recognize as a newline (one of CR, LF, CRLF, ANY, ANYCRLF, NUL)." FORCE)
+set_property(CACHE PCRE2_NEWLINE PROPERTY STRINGS "CR" "LF" "CRLF" "ANY" "ANYCRLF" "NUL")
+
+set(PCRE2_LINK_SIZE "2" CACHE STRING "Internal link size (2, 3 or 4 allowed). See LINK_SIZE in config.h.in for details.")
+set_property(CACHE PCRE2_LINK_SIZE PROPERTY STRINGS "2" "3" "4")
+
+set(PCRE2_PARENS_NEST_LIMIT "250" CACHE STRING "Default nested parentheses limit. See PARENS_NEST_LIMIT in config.h.in for details.")
+set(PCRE2_HEAP_LIMIT "20000000" CACHE STRING "Default limit on heap memory (kibibytes). See HEAP_LIMIT in config.h.in for details.")
+set(PCRE2_MAX_VARLOOKBEHIND "255" CACHE STRING "Default limit on variable lookbehinds.")
+set(PCRE2_MATCH_LIMIT "10000000" CACHE STRING "Default limit on internal looping. See MATCH_LIMIT in config.h.in for details.")
+set(PCRE2_MATCH_LIMIT_DEPTH "MATCH_LIMIT" CACHE STRING "Default limit on internal depth of search. See MATCH_LIMIT_DEPTH in config.h.in for details.")
+set(PCRE2GREP_BUFSIZE "20480" CACHE STRING "Buffer starting size parameter for pcre2grep. See PCRE2GREP_BUFSIZE in config.h.in for details.")
+set(PCRE2GREP_MAX_BUFSIZE "1048576" CACHE STRING "Buffer maximum size parameter for pcre2grep. See PCRE2GREP_MAX_BUFSIZE in config.h.in for details.")
+set(PCRE2_SUPPORT_JIT OFF CACHE BOOL "Enable support for Just-in-time compiling.")
+
+if(${CMAKE_SYSTEM_NAME} MATCHES Linux|NetBSD)
+    set(PCRE2_SUPPORT_JIT_SEALLOC OFF CACHE BOOL "Enable SELinux compatible execmem allocator in JIT (experimental).")
+else()
+    set(PCRE2_SUPPORT_JIT_SEALLOC IGNORE)
+endif()
+
+set(PCRE2GREP_SUPPORT_JIT ON CACHE BOOL "Enable use of Just-in-time compiling in pcre2grep.")
+set(PCRE2GREP_SUPPORT_CALLOUT ON CACHE BOOL "Enable callout string support in pcre2grep.")
+set(PCRE2GREP_SUPPORT_CALLOUT_FORK ON CACHE BOOL "Enable callout string fork support in pcre2grep.")
+set(PCRE2_SUPPORT_UNICODE ON CACHE BOOL "Enable support for Unicode and UTF-8/UTF-16/UTF-32 encoding.")
+set(PCRE2_SUPPORT_BSR_ANYCRLF OFF CACHE BOOL "ON=Backslash-R matches only LF CR and CRLF, OFF=Backslash-R matches all Unicode Linebreaks")
+set(PCRE2_NEVER_BACKSLASH_C OFF CACHE BOOL "If ON, backslash-C (upper case C) is locked out.")
+set(PCRE2_SUPPORT_VALGRIND OFF CACHE BOOL "Enable Valgrind support.")
+
+if(MINGW)
+    option(NON_STANDARD_LIB_PREFIX "ON=Shared libraries built in mingw will be named pcre2.dll, etc., instead of libpcre2.dll, etc." OFF)
+    option(NON_STANDARD_LIB_SUFFIX "ON=Shared libraries built in mingw will be named libpcre2-0.dll, etc., instead of libpcre2.dll, etc." OFF)
+endif()
+
+# 
+
+set(NEWLINE_DEFAULT "")
+
+if(PCRE2_NEWLINE STREQUAL "CR")
+    set(NEWLINE_DEFAULT "1")
+elseif(PCRE2_NEWLINE STREQUAL "LF")
+    set(NEWLINE_DEFAULT "2")
+elseif(PCRE2_NEWLINE STREQUAL "CRLF")
+    set(NEWLINE_DEFAULT "3")
+elseif(PCRE2_NEWLINE STREQUAL "ANY")
+    set(NEWLINE_DEFAULT "4")
+elseif(PCRE2_NEWLINE STREQUAL "ANYCRLF")
+    set(NEWLINE_DEFAULT "5")
+elseif(PCRE2_NEWLINE STREQUAL "NUL")
+    set(NEWLINE_DEFAULT "6")
+else()
+    message(FATAL_ERROR "The PCRE2_NEWLINE variable must be set to one of the following values: \"LF\", \"CR\", \"CRLF\", \"ANY\", \"ANYCRLF\".")
+endif()
+
+# Some tests
+
+include(CheckCSourceCompiles)
+include(CheckFunctionExists)
+include(CheckSymbolExists)
+include(CheckIncludeFile)
+
+check_include_file(assert.h HAVE_ASSERT_H)
+check_include_file(dirent.h HAVE_DIRENT_H)
+check_include_file(sys/stat.h HAVE_SYS_STAT_H)
+check_include_file(sys/types.h HAVE_SYS_TYPES_H)
+check_include_file(unistd.h HAVE_UNISTD_H)
+check_include_file(windows.h HAVE_WINDOWS_H)
+
+check_symbol_exists(bcopy "strings.h" HAVE_BCOPY)
+check_symbol_exists(memfd_create "sys/mman.h" HAVE_MEMFD_CREATE)
+check_symbol_exists(memmove "string.h" HAVE_MEMMOVE)
+check_symbol_exists(secure_getenv "stdlib.h" HAVE_SECURE_GETENV)
+check_symbol_exists(strerror "string.h" HAVE_STRERROR)
+
+check_c_source_compiles(
+  "int main(void) { char buf[128] __attribute__((uninitialized)); (void)buf; return 0; }"
+  HAVE_ATTRIBUTE_UNINITIALIZED
+)
+
+check_c_source_compiles(
+  [=[
+  extern __attribute__ ((visibility ("default"))) int f(void);
+  int main(void) { return f(); }
+  int f(void) { return 42; }
+  ]=]
+  HAVE_VISIBILITY
+)
+
+if(HAVE_VISIBILITY)
+  set(PCRE2_EXPORT [=[__attribute__ ((visibility ("default")))]=])
+else()
+  set(PCRE2_EXPORT)
+endif()
+
+check_c_source_compiles("int main(void) { __assume(1); return 0; }" HAVE_BUILTIN_ASSUME)
+
+check_c_source_compiles(
+  [=[
+  #include <stddef.h>
+  int main(void) { int a,b; size_t m; __builtin_mul_overflow(a,b,&m); return 0; }
+  ]=]
+  HAVE_BUILTIN_MUL_OVERFLOW
+)
+
+check_c_source_compiles(
+  "int main(int c, char *v[]) { if (c) __builtin_unreachable(); return (int)(*v[0]); }"
+  HAVE_BUILTIN_UNREACHABLE
+)
+
+# # Check whether Intel CET is enabled, and if so, adjust compiler flags. This
+# # code was written by PH, trying to imitate the logic from the autotools
+# # configuration.
+
+# check_c_source_compiles(
+#   [=[
+#   #ifndef __CET__
+#   #error CET is not enabled
+#   #endif
+#   int main() { return 0; }
+#   ]=]
+#   INTEL_CET_ENABLED
+# )
+
+# if(INTEL_CET_ENABLED)
+#   set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -mshstk")
+# endif()
+
+# Set up some dependencies first
+
+configure_file(
+    ${PCRE2_SOURCE_DIR}/src/pcre2_chartables.c.dist
+    ${CMAKE_CURRENT_BINARY_DIR}/pcre2_chartables.c
+    COPYONLY
+)
+
+configure_file(
+    ${PCRE2_SOURCE_DIR}/config-cmake.h.in
+    ${CMAKE_CURRENT_BINARY_DIR}/interface/config.h
+    @ONLY
+)
+
+configure_file(
+    ${PCRE2_SOURCE_DIR}/src/pcre2.h.in
+    ${CMAKE_CURRENT_BINARY_DIR}/interface/pcre2.h
+    @ONLY
+)
+
+# Define our library
+
+list(APPEND PCRE2_HEADERS
+    ${CMAKE_CURRENT_BINARY_DIR}/interface/pcre2.h)
+
+list(APPEND PCRE2_SOURCES
+    ${PCRE2_SOURCE_DIR}/src/pcre2_auto_possess.c
+    ${CMAKE_CURRENT_BINARY_DIR}/pcre2_chartables.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_chkdint.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_compile.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_compile_class.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_config.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_context.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_convert.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_dfa_match.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_error.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_extuni.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_find_bracket.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_jit_compile.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_maketables.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_match.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_match_data.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_newline.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_ord2utf.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_pattern_info.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_script_run.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_serialize.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_string_utils.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_study.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_substitute.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_substring.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_tables.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_ucd.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_valid_utf.c
+    ${PCRE2_SOURCE_DIR}/src/pcre2_xclass.c
+)
+
+add_library(pcre2s OBJECT)
+
+target_sources(pcre2s
+    PRIVATE ${PCRE2_SOURCES}
+    PUBLIC
+    FILE_SET pcre2_headers TYPE HEADERS
+    BASE_DIRS ${PCRE2_SOURCE_DIR}/include ${CMAKE_CURRENT_BINARY_DIR}/interface
+    FILES ${PCRE2_HEADERS}
+)
+
+target_compile_definitions(pcre2s PUBLIC PCRE2_CODE_UNIT_WIDTH=8 HAVE_CONFIG_H)
+if(NOT BUILD_SHARED_LIBS)
+    target_compile_definitions(pcre2s PUBLIC PCRE2_STATIC)
+endif()
+
+target_include_directories(pcre2s PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/interface ${PCRE2_SOURCE_DIR}/src)
+
+if(PCRE2_STATIC_PIC)
+    set_target_properties(pcre2s PROPERTIES POSITION_INDEPENDENT_CODE 1)
+endif()
+
+# # Installation and config files
+
+# include(CMakePackageConfigHelpers)
+# include(GenerateExportHeader)
+
+# # Install rules
+# install(TARGETS pcre2s
+#     EXPORT pcre2s
+#     FILE_SET pcre2_headers DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+
+# if(MSVC AND BUILD_SHARED_LIBS)
+#     install(
+#         FILES $<TARGET_PDB_FILE:pcre2s>
+#         DESTINATION ${CMAKE_INSTALL_LIBDIR}
+#         OPTIONAL)
+# endif()
+
+# install(EXPORT pcre2s
+#     NAMESPACE pcre2s::
+#     FILE "pcre2s-targets.cmake"
+#     DESTINATION lib/cmake/pcre2s)
+
+# configure_package_config_file(
+#     ${CMAKE_CURRENT_SOURCE_DIR}/pcre2s-config.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/pcre2s/pcre2s-config.cmake
+#     INSTALL_DESTINATION lib/cmake/pcre2s)
+
+# install(
+#     FILES "${CMAKE_CURRENT_BINARY_DIR}/pcre2s/pcre2s-config.cmake"
+#     "${CMAKE_CURRENT_BINARY_DIR}/pcre2s/pcre2s-config-version.cmake"
+#     DESTINATION lib/cmake/pcre2s)
+
+# set_target_properties(
+#     pcre2s
+#     PROPERTIES VERSION ${PCRE2_VERSION}
+#     SOVERSION ${PCRE2_VERSION}
+#     INTERFACE_pcre2s_MAJOR_VERSION ${PCRE2_MAJOR})
+
+# set_property(
+#     TARGET pcre2s
+#     APPEND
+#     PROPERTY COMPATIBLE_INTERFACE_STRING pcre2s_MAJOR_VERSION)
+
+# write_basic_package_version_file(
+#     "${CMAKE_CURRENT_BINARY_DIR}/pcre2s/pcre2s-config-version.cmake"
+#     VERSION "${PCRE2_VERSION}"
+#     COMPATIBILITY AnyNewerVersion)
+
+# # Testing
+
+# if(PROJECT_IS_TOP_LEVEL)
+#     include(CTest)
+
+#     if(BUILD_TESTING)
+#         add_subdirectory(test)
+#     endif()
+# endif()

src/category.cpp

@@ -28,6 +28,7 @@
 #include "cif++/datablock.hpp"
 #include "cif++/parser.hpp"
 #include "cif++/utilities.hpp"
+#include "cif++/validate.hpp"
 
 #include <numeric>
 #include <stack>
@@ -91,7 +92,7 @@ class row_comparator
 		return d;
 	}
 
-	int operator()(const category &cat, const row_initializer &a, const row *b) const
+	int operator()(const category &cat, const category::key_type &a, const row *b) const
 	{
 		assert(b);
 
@@ -104,10 +105,11 @@ class row_comparator
 		{
 			assert(ai != a.end());
 
-			std::string_view ka = ai->value();
+			std::string_view ka = ai->value;
 			std::string_view kb = rhb[k].text();
 
-			d = f(ka, kb);
+			if (not (ai->may_be_null and rhb[k].empty()))
+				d = f(ka, kb);
 
 			if (d != 0)
 				break;
@@ -141,7 +143,7 @@ class category_index
 	}
 
 	row *find(const category &cat, row *k) const;
-	row *find_by_value(const category &cat, row_initializer k) const;
+	row *find_by_value(const category &cat, const category::key_type &k) const;
 
 	void insert(category &cat, row *r);
 	void erase(category &cat, row *r);
@@ -164,7 +166,7 @@ class category_index
 		return result;
 	}
 
-	size_t size() const;
+	std::size_t size() const;
 	//	bool isValid() const;
 
   private:
@@ -351,19 +353,19 @@ row *category_index::find(const category &cat, row *k) const
 	return r ? r->m_row : nullptr;
 }
 
-row *category_index::find_by_value(const category &cat, row_initializer k) const
+row *category_index::find_by_value(const category &cat, const category::key_type &k) const
 {
 	// sort the values in k first
 
-	row_initializer k2;
+	category::key_type k2;
 	for (auto &f : cat.key_item_indices())
 	{
 		auto fld = cat.get_item_name(f);
 
 		auto ki = find_if(k.begin(), k.end(), [&fld](auto &i)
-			{ return i.name() == fld; });
+			{ return i.name == fld; });
 		if (ki == k.end())
-			k2.emplace_back(fld, "");
+			k2.emplace_back(std::string{ fld }, "");
 		else
 			k2.emplace_back(*ki);
 	}
@@ -475,12 +477,12 @@ category_index::entry *category_index::erase(category &cat, entry *h, row *k)
 	return fix_up(h);
 }
 
-size_t category_index::size() const
+std::size_t category_index::size() const
 {
 	std::stack<entry *> s;
 	s.push(m_root);
 
-	size_t result = 0;
+	std::size_t result = 0;
 
 	while (not s.empty())
 	{
@@ -542,9 +544,52 @@ category::~category()
 
 // --------------------------------------------------------------------
 
+uint16_t category::get_item_ix(std::string_view item_name) const
+{
+	uint16_t result;
+
+	for (result = 0; result < m_items.size(); ++result)
+	{
+		if (iequals(item_name, m_items[result].m_name))
+			break;
+	}
+
+	if (VERBOSE > 0 and result == m_items.size() and m_cat_validator != nullptr) // validate the name, if it is known at all (since it was not found)
+	{
+		auto iv = m_cat_validator->get_validator_for_item(item_name);
+		if (iv == nullptr)
+			std::cerr << "Invalid name used '" << item_name << "' is not a known item in " + m_name << '\n';
+	}
+
+	return result;
+}
+
+uint16_t category::add_item(std::string_view item_name)
+{
+	using namespace std::literals;
+
+	uint16_t result = get_item_ix(item_name);
+
+	if (result == m_items.size())
+	{
+		const item_validator *item_validator = nullptr;
+
+		if (m_cat_validator != nullptr)
+		{
+			item_validator = m_cat_validator->get_validator_for_item(item_name);
+			if (item_validator == nullptr)
+				m_validator->report_error(validation_error::item_not_allowed_in_category, m_name, item_name, false);
+		}
+
+		m_items.emplace_back(item_name, item_validator);
+	}
+
+	return result;
+}
+
 void category::remove_item(std::string_view item_name)
 {
-	for (size_t ix = 0; ix < m_items.size(); ++ix)
+	for (std::size_t ix = 0; ix < m_items.size(); ++ix)
 	{
 		if (not iequals(item_name, m_items[ix].m_name))
 			continue;
@@ -563,7 +608,7 @@ void category::remove_item(std::string_view item_name)
 
 void category::rename_item(std::string_view from_name, std::string_view to_name)
 {
-	for (size_t ix = 0; ix < m_items.size(); ++ix)
+	for (std::size_t ix = 0; ix < m_items.size(); ++ix)
 	{
 		if (not iequals(from_name, m_items[ix].m_name))
 			continue;
@@ -666,7 +711,7 @@ void category::set_validator(const validator *v, datablock &db)
 	update_links(db);
 }
 
-void category::update_links(datablock &db)
+void category::update_links(const datablock &db)
 {
 	m_child_links.clear();
 	m_parent_links.clear();
@@ -675,7 +720,7 @@ void category::update_links(datablock &db)
 	{
 		for (auto link : m_validator->get_links_for_parent(m_name))
 		{
-			auto childCat = db.get(link->m_child_category);
+			auto childCat = const_cast<category *>(db.get(link->m_child_category));
 			if (childCat == nullptr)
 				continue;
 			m_child_links.emplace_back(childCat, link);
@@ -683,7 +728,7 @@ void category::update_links(datablock &db)
 
 		for (auto link : m_validator->get_links_for_child(m_name))
 		{
-			auto parentCat = db.get(link->m_parent_category);
+			auto parentCat = const_cast<category *>(db.get(link->m_parent_category));
 			if (parentCat == nullptr)
 				continue;
 			m_parent_links.emplace_back(parentCat, link);
@@ -718,7 +763,7 @@ bool category::is_valid() const
 		auto iv = m_cat_validator->get_validator_for_item(col.m_name);
 		if (iv == nullptr)
 		{
-			m_validator->report_error(validation_error::unknown_item, col.m_name, m_name, false);
+			m_validator->report_error(validation_error::unknown_item, m_name, col.m_name, false);
 			result = false;
 		}
 
@@ -791,7 +836,7 @@ bool category::is_valid() const
 
 				iv->validate_value(vi->text(), ec);
 
-				if (ec != std::errc())
+				if ((bool)ec)
 				{
 					m_validator->report_error(ec, m_name, m_items[cix].m_name, false);
 					continue;
@@ -832,7 +877,7 @@ bool category::validate_links() const
 		if (name() == "atom_site" and (parent->name() == "pdbx_poly_seq_scheme" or parent->name() == "entity_poly_seq"))
 			continue;
 
-		size_t missing = 0;
+		std::size_t missing = 0;
 		category first_missing_rows(name());
 
 		for (auto r : *this)
@@ -870,6 +915,24 @@ bool category::validate_links() const
 	return result;
 }
 
+void category::strip()
+{
+	std::vector<std::string> to_be_removed;
+
+	for (auto &item : m_items)
+	{
+		if (item.m_validator == nullptr)
+			to_be_removed.push_back(item.m_name);
+	}
+
+	for (auto item : to_be_removed)
+	{
+		if (cif::VERBOSE > 0)
+			std::clog << "Dropping item " << m_name << '.' << item << '\n';
+		remove_item(item);
+	}
+}
+
 // --------------------------------------------------------------------
 
 row_handle category::operator[](const key_type &key)
@@ -909,7 +972,7 @@ condition category::get_parents_condition(row_handle rh, const category &parentC
 		{
 			condition cond;
 
-			for (size_t ix = 0; ix < link->m_child_keys.size(); ++ix)
+			for (std::size_t ix = 0; ix < link->m_child_keys.size(); ++ix)
 			{
 				auto childValue = rh[link->m_child_keys[ix]];
 
@@ -951,7 +1014,7 @@ condition category::get_children_condition(row_handle rh, const category &childC
 		{
 			condition cond;
 
-			for (size_t ix = 0; ix < link->m_parent_keys.size(); ++ix)
+			for (std::size_t ix = 0; ix < link->m_parent_keys.size(); ++ix)
 			{
 				auto childKey = link->m_child_keys[ix];
 				auto parentKey = link->m_parent_keys[ix];
@@ -1127,14 +1190,14 @@ class save_value
 	const T m_sv;
 };
 
-size_t category::erase(condition &&cond)
+std::size_t category::erase(condition &&cond)
 {
 	return erase(std::move(cond), {});
 }
 
-size_t category::erase(condition &&cond, std::function<void(row_handle)> &&visit)
+std::size_t category::erase(condition &&cond, std::function<void(row_handle)> &&visit)
 {
-	size_t result = 0;
+	std::size_t result = 0;
 
 	cond.prepare(*this);
 
@@ -1274,10 +1337,9 @@ std::string category::get_unique_value(std::string_view item_name)
 	if (result.empty())
 	{
 		// brain-dead implementation
-		for (size_t ix = 0; ix < size(); ++ix)
+		for (std::size_t ix = 0; ix < size(); ++ix)
 		{
-			// result = m_name + "-" + std::to_string(ix);
-			result = cif_id_for_number(ix);
+			result = cif_id_for_number(static_cast<int>(ix));
 			if (not contains(key(item_name) == result))
 				break;
 		}
@@ -1321,7 +1383,7 @@ void category::update_value(const std::vector<row_handle> &rows, std::string_vie
 		std::string oldValue{ parent[item_name].text() };
 		std::string value{ value_provider(oldValue) };
 
-		parent.assign(colIx, value, false);
+		update_value(parent.get_row(), colIx, value, false, false);
 
 		for (auto &&[childCat, linked] : m_child_links)
 		{
@@ -1331,7 +1393,7 @@ void category::update_value(const std::vector<row_handle> &rows, std::string_vie
 			condition cond;
 			std::string childItemName;
 
-			for (size_t ix = 0; ix < linked->m_parent_keys.size(); ++ix)
+			for (std::size_t ix = 0; ix < linked->m_parent_keys.size(); ++ix)
 			{
 				std::string pk = linked->m_parent_keys[ix];
 				std::string ck = linked->m_child_keys[ix];
@@ -1362,7 +1424,7 @@ void category::update_value(const std::vector<row_handle> &rows, std::string_vie
 			{
 				condition cond_c;
 
-				for (size_t ix = 0; ix < linked->m_parent_keys.size(); ++ix)
+				for (std::size_t ix = 0; ix < linked->m_parent_keys.size(); ++ix)
 				{
 					std::string pk = linked->m_parent_keys[ix];
 					std::string ck = linked->m_child_keys[ix];
@@ -1380,7 +1442,7 @@ void category::update_value(const std::vector<row_handle> &rows, std::string_vie
 				// oops, we need to split this child, unless a row already exists for the new value
 				condition check;
 
-				for (size_t ix = 0; ix < linked->m_parent_keys.size(); ++ix)
+				for (std::size_t ix = 0; ix < linked->m_parent_keys.size(); ++ix)
 				{
 					std::string pk = linked->m_parent_keys[ix];
 					std::string ck = linked->m_child_keys[ix];
@@ -1444,8 +1506,7 @@ void category::update_value(row *row, uint16_t item, std::string_view value, boo
 	// before updating
 
 	bool reinsert = false;
-	if (updateLinked and // an update of an Item's value
-		m_index != nullptr and key_item_indices().count(item))
+	if (m_index != nullptr and key_item_indices().count(item))
 	{
 		reinsert = m_index->find(*this, row);
 		if (reinsert)
@@ -1476,7 +1537,7 @@ void category::update_value(row *row, uint16_t item, std::string_view value, boo
 			condition cond;
 			std::string childItemName;
 
-			for (size_t ix = 0; ix < linked->m_parent_keys.size(); ++ix)
+			for (std::size_t ix = 0; ix < linked->m_parent_keys.size(); ++ix)
 			{
 				std::string pk = linked->m_parent_keys[ix];
 				std::string ck = linked->m_child_keys[ix];
@@ -1513,7 +1574,7 @@ void category::update_value(row *row, uint16_t item, std::string_view value, boo
 
 			condition cond_n;
 
-			for (size_t ix = 0; ix < linked->m_parent_keys.size(); ++ix)
+			for (std::size_t ix = 0; ix < linked->m_parent_keys.size(); ++ix)
 			{
 				std::string pk = linked->m_parent_keys[ix];
 				std::string ck = linked->m_child_keys[ix];
@@ -1698,6 +1759,12 @@ void category::swap_item(uint16_t item_ix, row_handle &a, row_handle &b)
 	auto &ra = *a.m_row;
 	auto &rb = *b.m_row;
 
+	while (ra.size() <= item_ix)
+		ra.emplace_back("");
+
+	while (rb.size() <= item_ix)
+		rb.emplace_back("");
+
 	std::swap(ra.at(item_ix), rb.at(item_ix));
 }
 
@@ -1720,7 +1787,7 @@ void category::sort(std::function<int(row_handle, row_handle)> f)
 	m_tail = rows.back().get_row();
 
 	auto r = m_head;
-	for (size_t i = 1; i < rows.size(); ++i)
+	for (std::size_t i = 1; i < rows.size(); ++i)
 		r = r->m_next = rows[i].get_row();
 	r->m_next = nullptr;
 
@@ -1736,7 +1803,7 @@ void category::reorder_by_index()
 
 namespace detail
 {
-	size_t write_value(std::ostream &os, std::string_view value, size_t offset, size_t width, bool right_aligned)
+	std::size_t write_value(std::ostream &os, std::string_view value, std::size_t offset, std::size_t width, bool right_aligned)
 	{
 		if (value.find('\n') != std::string::npos or width == 0 or value.length() > 132) // write as text item
 		{
@@ -1897,7 +1964,7 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
 	{
 		os << "loop_\n";
 
-		std::vector<size_t> itemWidths(m_items.size());
+		std::vector<std::size_t> itemWidths(m_items.size());
 
 		for (auto cix : order)
 		{
@@ -1919,7 +1986,7 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
 
 				if (v->text().find('\n') == std::string_view::npos)
 				{
-					size_t l = v->text().length();
+					std::size_t l = v->text().length();
 
 					if (not sac_parser::is_unquoted_string(v->text()))
 						l += 2;
@@ -1935,11 +2002,11 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
 
 		for (auto r = m_head; r != nullptr; r = r->m_next) // loop over rows
 		{
-			size_t offset = 0;
+			std::size_t offset = 0;
 
 			for (uint16_t cix : order)
 			{
-				size_t w = itemWidths[cix];
+				std::size_t w = itemWidths[cix];
 
 				std::string_view s;
 				auto iv = r->get(cix);
@@ -1949,7 +2016,7 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
 				if (s.empty())
 					s = "?";
 
-				size_t l = s.length();
+				std::size_t l = s.length();
 				if (not sac_parser::is_unquoted_string(s))
 					l += 2;
 				if (l < w)
@@ -1977,7 +2044,7 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
 	else
 	{
 		// first find the indent level
-		size_t l = 0;
+		std::size_t l = 0;
 
 		for (auto &col : m_items)
 		{
@@ -1989,7 +2056,7 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
 
 		l += 3;
 
-		size_t width = 1;
+		std::size_t width = 1;
 
 		for (auto cix : order)
 		{
@@ -2004,7 +2071,7 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
 			if (s.empty())
 				s = "?";
 
-			size_t l2 = s.length();
+			std::size_t l2 = s.length();
 
 			if (not sac_parser::is_unquoted_string(s))
 				l2 += 2;
@@ -2030,7 +2097,7 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
 			if (s.empty())
 				s = "?";
 
-			size_t offset = l;
+			std::size_t offset = l;
 			if (s.length() + l >= kMaxLineLength)
 			{
 				os << '\n';
@@ -2070,7 +2137,7 @@ bool category::operator==(const category &rhs) const
 	typedef std::function<int(std::string_view, std::string_view)> compType;
 	std::vector<std::tuple<std::string, compType>> item_names;
 	std::vector<std::string> keys;
-	std::vector<size_t> keyIx;
+	std::vector<std::size_t> keyIx;
 
 	if (catValidator == nullptr)
 	{
@@ -2168,4 +2235,4 @@ bool category::operator==(const category &rhs) const
 	return true;
 }
 
-} // namespace cif
+} // namespace cif

src/compound.cpp

@@ -24,14 +24,38 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-#include "cif++.hpp"
+#include "cif++/compound.hpp" // for compound_atom, compound_bond, compoun...
 
-#include <filesystem>
-#include <fstream>
-#include <map>
-#include <mutex>
-#include <numeric>
-#include <shared_mutex>
+#include "cif++/atom_type.hpp" // for atom_type_traits
+#include "cif++/category.hpp"  // for category
+#include "cif++/datablock.hpp" // for datablock
+#include "cif++/file.hpp"      // for file
+#include "cif++/item.hpp"      // for item
+#include "cif++/iterator.hpp"  // for iterator_proxy
+#include "cif++/parser.hpp"    // for parser
+#include "cif++/point.hpp"     // for distance, point
+#include "cif++/row.hpp"       // for tie, row_initializer, tie_wrap
+#include "cif++/text.hpp"      // for iequals, replace_all, iset
+#include "cif++/utilities.hpp" // for load_resource, VERBOSE, colour_type
+
+#include <algorithm>    // for find_if
+#include <cstddef>      // for size_t
+#include <exception>    // for exception, throw_with_nested
+#include <filesystem>   // for path, exists
+#include <fstream>      // for char_traits, basic_ostream, operator<<
+#include <iomanip>      // for operator<<, quoted
+#include <iostream>     // for clog, cout, cerr
+#include <limits>       // for numeric_limits
+#include <list>         // for _List_iterator
+#include <map>          // for allocator, map, _Rb_tree_iterator
+#include <memory>       // for shared_ptr, unique_ptr, __shared_ptr_...
+#include <optional>     // for optional
+#include <shared_mutex> // for shared_lock, shared_timed_mutex
+#include <stdexcept>    // for runtime_error, invalid_argument, out_...
+#include <string>       // for basic_string, string, operator==, ope...
+#include <string_view>  // for string_view, basic_string_view
+#include <utility>      // for pair, exchange, move
+#include <vector>       // for vector
 
 namespace fs = std::filesystem;
 
@@ -140,7 +164,7 @@ compound::compound(cif::datablock &db)
 
 	cif::tie(m_id, m_name, m_type, m_formula, m_formula_weight, m_formal_charge, one_letter_code, m_parent_id) =
 		chemComp.front().get("id", "name", "type", "formula", "formula_weight", "pdbx_formal_charge", "one_letter_code", "mon_nstd_parent_comp_id");
-	
+
 	if (one_letter_code.length() == 1)
 		m_one_letter_code = one_letter_code.front();
 
@@ -159,7 +183,7 @@ compound::compound(cif::datablock &db)
 		if (stereo_config.empty())
 			atom.stereo_config = stereo_config_type::N;
 		else
-		atom.stereo_config = parse_stereo_config_from_string(stereo_config);
+			atom.stereo_config = parse_stereo_config_from_string(stereo_config);
 		m_atoms.push_back(std::move(atom));
 	}
 
@@ -172,94 +196,11 @@ compound::compound(cif::datablock &db)
 		if (valueOrder.empty())
 			bond.type = bond_type::sing;
 		else
-		bond.type = parse_bond_type_from_string(valueOrder);
+			bond.type = parse_bond_type_from_string(valueOrder);
 		m_bonds.push_back(std::move(bond));
 	}
 }
 
-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)
-	{
-		compound_atom atom;
-		std::string type_symbol;
-		cif::tie(atom.id, type_symbol, atom.charge, atom.x, atom.y, atom.z) =
-			row.get("atom_id", "type_symbol", "charge", "x", "y", "z");
-		atom.type_symbol = atom_type_traits(type_symbol).type();
-
-		m_formal_charge += atom.charge;
-
-		m_atoms.push_back(std::move(atom));
-	}
-
-	auto &chemCompBond = db["chem_comp_bond"];
-	for (auto row : chemCompBond)
-	{
-		compound_bond bond;
-		std::string btype;
-		cif::tie(bond.atom_id[0], bond.atom_id[1], btype, bond.aromatic) = row.get("atom_id_1", "atom_id_2", "type", "aromatic");
-
-		using cif::iequals;
-
-		if (iequals(btype, "single"))
-			bond.type = bond_type::sing;
-		else if (iequals(btype, "double"))
-			bond.type = bond_type::doub;
-		else if (iequals(btype, "triple"))
-			bond.type = bond_type::trip;
-		else if (iequals(btype, "deloc") or iequals(btype, "aromat") or iequals(btype, "aromatic"))
-			bond.type = bond_type::delo;
-		else
-		{
-			if (cif::VERBOSE > 0)
-				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
 {
 	compound_atom result = {};
@@ -314,12 +255,12 @@ float compound::bond_length(const std::string &atomId_1, const std::string &atom
 
 bool compound::is_peptide() const
 {
-	return iequals(m_type, "l-peptide linking")	or iequals(m_type, "peptide linking");
+	return iequals(m_type, "l-peptide linking") or iequals(m_type, "peptide linking");
 }
 
 bool compound::is_base() const
 {
-	return iequals(m_type, "dna linking")	or iequals(m_type, "rna linking");
+	return iequals(m_type, "dna linking") or iequals(m_type, "rna linking");
 }
 
 // --------------------------------------------------------------------
@@ -377,43 +318,38 @@ class compound_factory_impl : public std::enable_shared_from_this<compound_facto
 			delete c;
 	}
 
+	virtual bool exists_self(const std::string &id) const
+	{
+		if (m_missing.contains(id))
+			return false;
+
+		if (std::find_if(m_compounds.begin(), m_compounds.end(), [id](compound *c)
+				{ return c->id() == id; }) != m_compounds.end())
+			return true;
+
+		return m_next and m_next->exists_self(id);
+	}
+
+	bool exists(std::string_view id)
+	{
+		std::shared_lock lock(mMutex);
+
+		return exists_self(std::string{ id });
+	}
+
 	compound *get(std::string id)
 	{
-		cif::to_upper(id);
-
 		std::shared_lock lock(mMutex);
 
 		compound *result = nullptr;
 
-		// walk the list, see if any of the implementations has the compound already
 		for (auto impl = shared_from_this(); impl; impl = impl->m_next)
 		{
-			for (auto cmp : impl->m_compounds)
-			{
-				if (iequals(cmp->id(), id))
-				{
-					result = cmp;
-					break;
-				}
-			}
-
-			if (result)
+			result = impl->create(id);
+			if (result != nullptr)
 				break;
 		}
 
-		if (result == nullptr and m_missing.count(id) == 0)
-		{
-			for (auto impl = shared_from_this(); impl; impl = impl->m_next)
-			{
-				result = impl->create(id);
-				if (result != nullptr)
-					break;
-			}
-
-			if (result == nullptr)
-				m_missing.insert(id);
-		}
-
 		return result;
 	}
 
@@ -444,7 +380,7 @@ class compound_factory_impl : public std::enable_shared_from_this<compound_facto
 	cif::parser::datablock_index m_index;
 
 	std::vector<compound *> m_compounds;
-	std::set<std::string> m_missing;
+	cif::iset m_missing;
 	std::shared_ptr<compound_factory_impl> m_next;
 };
 
@@ -465,6 +401,16 @@ compound_factory_impl::compound_factory_impl(const fs::path &file, std::shared_p
 
 compound *compound_factory_impl::create(const std::string &id)
 {
+	// shortcut
+
+	if (m_missing.contains(id))
+		return nullptr;
+
+	if (auto i = find_if(m_compounds.begin(), m_compounds.end(), [id](compound *c)
+			{ return c->id() == id; });
+		i != m_compounds.end())
+		return *i;
+
 	compound *result = nullptr;
 
 	std::unique_ptr<std::istream> ccd;
@@ -496,7 +442,7 @@ compound *compound_factory_impl::create(const std::string &id)
 		m_index = parser.index_datablocks();
 
 		if (cif::VERBOSE > 1)
-			std::cout << " done" << std::endl;
+			std::cout << " done\n";
 
 		// reload the resource, perhaps this should be improved...
 		if (m_file.empty())
@@ -519,7 +465,7 @@ compound *compound_factory_impl::create(const std::string &id)
 	parser.parse_single_datablock(id, m_index);
 
 	if (cif::VERBOSE > 1)
-		std::cout << " done" << std::endl;
+		std::cout << " done\n";
 
 	if (not file.empty())
 	{
@@ -533,6 +479,9 @@ compound *compound_factory_impl::create(const std::string &id)
 		}
 	}
 
+	if (result == nullptr)
+		m_missing.insert(id);
+
 	return result;
 }
 
@@ -545,26 +494,11 @@ class local_compound_factory_impl : public compound_factory_impl
 		: compound_factory_impl(next)
 		, m_local_file(file)
 	{
-		const std::regex peptideRx("(?:[lmp]-)?peptide", std::regex::icase);
-
-		for (const auto &[id, name, threeLetterCode, group] :
-			file["comp_list"]["chem_comp"].rows<std::string, std::string, std::string, std::string>("id", "name", "three_letter_code", "group"))
-		{
-			auto &rdb = m_local_file["comp_" + id];
-			if (rdb.empty())
-			{
-				std::cerr << "Missing data in restraint file for id " + id + '\n';
-				continue;
-			}
-
-			construct_compound(rdb, id, name, threeLetterCode, group);
-		}
 	}
 
 	compound *create(const std::string &id) override;
 
   private:
-
 	compound *construct_compound(const datablock &db, const std::string &id, const std::string &name, const std::string &three_letter_code, const std::string &group);
 
 	cif::file m_local_file;
@@ -572,11 +506,19 @@ class local_compound_factory_impl : public compound_factory_impl
 
 compound *local_compound_factory_impl::create(const std::string &id)
 {
+	if (m_missing.contains(id))
+		return nullptr;
+
+	if (auto i = find_if(m_compounds.begin(), m_compounds.end(), [id](compound *c)
+			{ return c->id() == id; });
+		i != m_compounds.end())
+		return *i;
+
 	compound *result = nullptr;
 
 	for (auto &db : m_local_file)
 	{
-		if (db.name() == "comp_" + id)
+		if (db.name() == id)
 		{
 			auto chem_comp = db.get("chem_comp");
 			if (not chem_comp)
@@ -584,10 +526,13 @@ compound *local_compound_factory_impl::create(const std::string &id)
 
 			try
 			{
-				const auto &[id, name, threeLetterCode, group] =
+				const auto &[id2, name, threeLetterCode, group] =
 					chem_comp->front().get<std::string, std::string, std::string, std::string>("id", "name", "three_letter_code", "group");
 
-				result = construct_compound(db, id, name, threeLetterCode, group);
+				if (id == id2)
+					result = construct_compound(db, id, name, threeLetterCode, group);
+				else
+					throw std::runtime_error("Compound ID's don't match: id 1=" + id + ", id 2=" + id2);
 			}
 			catch (const std::exception &ex)
 			{
@@ -598,6 +543,9 @@ compound *local_compound_factory_impl::create(const std::string &id)
 		}
 	}
 
+	if (result == nullptr)
+		m_missing.insert(id);
+
 	return result;
 }
 
@@ -608,32 +556,32 @@ compound *local_compound_factory_impl::construct_compound(const datablock &rdb,
 
 	float formula_weight = 0;
 	int formal_charge = 0;
-	std::map<std::string,size_t> formula_data;
+	std::map<std::string, std::size_t> formula_data;
 
-	for (size_t ord = 1; const auto &[atom_id, type_symbol, type, charge, x, y, z] :
-		rdb["chem_comp_atom"].rows<std::string, std::string, std::string, int, float, float, float>(
-			"atom_id", "type_symbol", "type", "charge", "x", "y", "z"))
+	for (std::size_t ord = 1; const auto &[atom_id, type_symbol, type, charge, x, y, z, xi, yi, zi] :
+		rdb["chem_comp_atom"].rows<std::string, std::string, std::string, int, std::optional<float>, std::optional<float>, std::optional<float>, std::optional<float>, std::optional<float>, std::optional<float>>(
+			"atom_id", "type_symbol", "type", "charge",
+			"model_Cartn_x", "model_Cartn_y", "model_Cartn_z",
+			"pdbx_model_Cartn_x_ideal", "pdbx_model_Cartn_y_ideal", "pdbx_model_Cartn_z_ideal"))
 	{
 		auto atom = cif::atom_type_traits(type_symbol);
 		formula_weight += atom.weight();
 
 		formula_data[type_symbol] += 1;
 
-		db["chem_comp_atom"].emplace({
-			{ "comp_id", id },
+		db["chem_comp_atom"].emplace({ { "comp_id", id },
 			{ "atom_id", atom_id },
 			{ "type_symbol", type_symbol },
 			{ "charge", charge },
-			{ "model_Cartn_x",  x, 3 },
-			{ "model_Cartn_y",  y, 3 },
-			{ "model_Cartn_z",  z, 3 },
-			{ "pdbx_ordinal", ord++ }
-		});
+			{ "model_Cartn_x", x.has_value() ? x : xi, 3 },
+			{ "model_Cartn_y", y.has_value() ? y : yi, 3 },
+			{ "model_Cartn_z", z.has_value() ? z : zi, 3 },
+			{ "pdbx_ordinal", ord++ } });
 
 		formal_charge += charge;
 	}
 
-	for (size_t ord = 1; const auto &[atom_id_1, atom_id_2, type, aromatic] :
+	for (std::size_t ord = 1; const auto &[atom_id_1, atom_id_2, type, aromatic] :
 		rdb["chem_comp_bond"].rows<std::string, std::string, std::string, bool>("atom_id_1", "atom_id_2", "type", "aromatic"))
 	{
 		std::string value_order("SING");
@@ -645,21 +593,19 @@ compound *local_compound_factory_impl::construct_compound(const datablock &rdb,
 		else if (cif::iequals(type, "triple") or cif::iequals(type, "trip"))
 			value_order = "TRIP";
 
-		db["chem_comp_bond"].emplace({
-			{ "comp_id", id },
+		db["chem_comp_bond"].emplace({ { "comp_id", id },
 			{ "atom_id_1", atom_id_1 },
 			{ "atom_id_2", atom_id_2 },
 			{ "value_order", value_order },
 			{ "pdbx_aromatic_flag", aromatic },
 			// TODO: fetch stereo_config info from chem_comp_chir
-			{ "pdbx_ordinal", ord++ }
-		});
+			{ "pdbx_ordinal", ord++ } });
 	}
 
 	db.emplace_back(rdb["pdbx_chem_comp_descriptor"]);
 
 	std::string formula;
-	for (bool first = true; const auto &[symbol, count]: formula_data)
+	for (bool first = true; const auto &[symbol, count] : formula_data)
 	{
 		if (std::exchange(first, false))
 			formula += ' ';
@@ -678,15 +624,13 @@ compound *local_compound_factory_impl::construct_compound(const datablock &rdb,
 	else
 		type = "NON-POLYMER";
 
-	db["chem_comp"].emplace({
-		{ "id", id },
+	db["chem_comp"].emplace({ { "id", id },
 		{ "name", name },
 		{ "type", type },
 		{ "formula", formula },
 		{ "pdbx_formal_charge", formal_charge },
 		{ "formula_weight", formula_weight },
-		{ "three_letter_code", three_letter_code }
-	});
+		{ "three_letter_code", three_letter_code } });
 
 	std::shared_lock lock(mMutex);
 
@@ -792,6 +736,11 @@ void compound_factory::pop_dictionary()
 		m_impl = m_impl->next();
 }
 
+bool compound_factory::exists(std::string_view id) const
+{
+	return m_impl and m_impl->exists(id);
+}
+
 const compound *compound_factory::create(std::string_view id)
 {
 	auto result = m_impl ? m_impl->get(std::string{ id }) : nullptr;
@@ -816,7 +765,7 @@ bool compound_factory::is_peptide(std::string_view res_name) const
 	bool result = is_std_peptide(res_name);
 	if (not result and m_impl)
 	{
-		auto compound = const_cast<compound_factory&>(*this).create(res_name);
+		auto compound = const_cast<compound_factory &>(*this).create(res_name);
 		result = compound != nullptr and compound->is_peptide();
 	}
 	return result;
@@ -828,7 +777,7 @@ bool compound_factory::is_base(std::string_view res_name) const
 	bool result = is_std_base(res_name);
 	if (not result and m_impl)
 	{
-		auto compound = const_cast<compound_factory&>(*this).create(res_name);
+		auto compound = const_cast<compound_factory &>(*this).create(res_name);
 		result = compound != nullptr and compound->is_base();
 	}
 	return result;
@@ -854,8 +803,7 @@ bool compound_factory::is_monomer(std::string_view res_name) const
 
 void compound_factory::report_missing_compound(std::string_view compound_id)
 {
-	static bool s_reported = false;
-	if (std::exchange(s_reported, true) == false)
+	if (std::exchange(m_report_missing, false))
 	{
 		using namespace cif::colour;
 
@@ -879,7 +827,7 @@ void compound_factory::report_missing_compound(std::string_view compound_id)
 				  << "in /var/cache/libcifpp using the following commands:\n\n"
 				  << "curl -o " << CACHE_DIR << "/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif\n"
 				  << "curl -o " << CACHE_DIR << "/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic\n"
-				  << "curl -o " << CACHE_DIR << "/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic\n\n";
+				  << "curl -o " << CACHE_DIR << "/mmcif_ma.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_ma.dic\n\n";
 #endif
 
 		if (m_impl)

src/condition.cpp

@@ -24,8 +24,9 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-#include "cif++/category.hpp"
 #include "cif++/condition.hpp"
+#include "cif++/category.hpp"
+#include "cif++/validate.hpp"
 
 namespace cif
 {
@@ -60,6 +61,52 @@ bool is_item_type_uchar(const category &cat, std::string_view col)
 
 namespace detail
 {
+	// 	// index lookup
+	// 	struct index_lookup_condition_impl : public condition_impl
+	// 	{
+	// 		index_lookup_condition_impl(row_initializer &&key_values)
+	// 			: m_key_values(std::move(key_values))
+	// 		{
+	// 		}
+	//
+	// 		condition_impl *prepare(const category &c) override
+	// 		{
+	// 			m_single_hit = c[m_key_values];
+	// 			return this;
+	// 		}
+	//
+	// 		bool test(row_handle r) const override
+	// 		{
+	// 			return m_single_hit == r;
+	// 		}
+	//
+	// 		void str(std::ostream &os) const override
+	// 		{
+	// 			os << "index scan";
+	// 		}
+	//
+	// 		virtual std::optional<row_handle> single() const override
+	// 		{
+	// 			return m_single_hit;
+	// 		}
+	//
+	// 		virtual bool equals(const condition_impl *rhs) const override
+	// 		{
+	// 			if (typeid(*rhs) == typeid(index_lookup_condition_impl))
+	// 			{
+	// 				auto ri = static_cast<const index_lookup_condition_impl *>(rhs);
+	// 				if (m_single_hit or ri->m_single_hit)
+	// 					return m_single_hit == ri->m_single_hit;
+	// 				else
+	// 					// watch out, both m_item_ix might be the same while item_names might be diffent (in case they both do not exist in the category)
+	// 					return m_key_values == ri->m_key_values;
+	// 			}
+	// 			return this == rhs;
+	// 		}
+	//
+	// 		row_initializer m_key_values;
+	// 		row_handle m_single_hit;
+	// 	};
 
 	condition_impl *key_equals_condition_impl::prepare(const category &c)
 	{
@@ -76,6 +123,21 @@ namespace detail
 		return this;
 	}
 
+	condition_impl *key_equals_number_condition_impl::prepare(const category &c)
+	{
+		m_item_ix = c.get_item_ix(m_item_name);
+
+		if (c.get_cat_validator() != nullptr and
+			c.key_item_indices().contains(m_item_ix) and
+			c.key_item_indices().size() == 1)
+		{
+			item v(m_item_name, m_value);
+			m_single_hit = c[{ { m_item_name, std::string{ v.value() }, false } }];
+		}
+
+		return this;
+	}
+
 	bool found_in_range(condition_impl *c, std::vector<and_condition_impl *>::iterator b, std::vector<and_condition_impl *>::iterator e)
 	{
 		bool result = true;
@@ -84,7 +146,8 @@ namespace detail
 		{
 			auto &cs = (*s)->m_sub;
 
-			if (find_if(cs.begin(), cs.end(), [c](const condition_impl *i) { return i->equals(c); }) == cs.end())
+			if (find_if(cs.begin(), cs.end(), [c](const condition_impl *i)
+					{ return i->equals(c); }) == cs.end())
 			{
 				result = false;
 				break;
@@ -101,27 +164,35 @@ namespace detail
 		auto first = subs.front();
 		auto &fc = first->m_sub;
 
-		for (auto c : fc)
+		for (size_t fc_i = 0; fc_i < fc.size();)
 		{
+			auto c = fc[fc_i];
 			if (not found_in_range(c, subs.begin() + 1, subs.end()))
+			{
+				++fc_i;
 				continue;
+			}
 
 			if (and_result == nullptr)
 				and_result = new and_condition_impl();
 
 			and_result->m_sub.push_back(c);
-			fc.erase(remove(fc.begin(), fc.end(), c), fc.end());
+			fc.erase(fc.begin() + fc_i);
 
 			for (auto sub : subs)
 			{
 				auto &ssub = sub->m_sub;
 
-				for (auto sc : ssub)
+				for (size_t ssub_i = 0; ssub_i < ssub.size();)
 				{
+					auto sc = ssub[ssub_i];
 					if (not sc->equals(c))
+					{
+						++ssub_i;
 						continue;
-					
-					ssub.erase(remove(ssub.begin(), ssub.end(), sc), ssub.end());
+					}
+
+					ssub.erase(ssub.begin() + ssub_i);
 					delete sc;
 					break;
 				}
@@ -137,6 +208,99 @@ namespace detail
 		return oc;
 	}
 
+	condition_impl *and_condition_impl::prepare(const category &c)
+	{
+		for (auto &sub : m_sub)
+			sub = sub->prepare(c);
+
+		if (auto cv = c.get_cat_validator(); cv != nullptr)
+		{
+			// See if we can collapse a search part of this and_condition into a single index lookup
+
+			cif::iset keys{ cv->m_keys.begin(), cv->m_keys.end() };
+			category::key_type lookup;
+			std::vector<condition_impl *> subs;
+			std::vector<std::string> may_be_empty;
+
+			for (auto &sub : m_sub)
+			{
+				if (auto s = dynamic_cast<const key_equals_condition_impl *>(sub); s != nullptr)
+				{
+					if (keys.contains(s->m_item_name))
+					{
+						lookup.emplace_back(s->m_item_name, s->m_value);
+						subs.emplace_back(sub);
+					}
+					continue;
+				}
+
+				if (auto s = dynamic_cast<const key_equals_number_condition_impl *>(sub); s != nullptr)
+				{
+					if (keys.contains(s->m_item_name))
+					{
+						item v{ s->m_item_name, s->m_value };
+						lookup.emplace_back(s->m_item_name, std::string{ v.value() } );
+						subs.emplace_back(sub);
+					}
+					continue;
+				}
+
+				if (auto s = dynamic_cast<const key_equals_or_empty_condition_impl *>(sub); s != nullptr)
+				{
+					if (keys.contains(s->m_item_name))
+					{
+						lookup.emplace_back(s->m_item_name, s->m_value, true);
+						subs.emplace_back(sub);
+						may_be_empty.emplace_back(s->m_item_name);
+					}
+					continue;
+				}
+
+				if (auto s = dynamic_cast<const key_equals_number_or_empty_condition_impl *>(sub); s != nullptr)
+				{
+					if (keys.contains(s->m_item_name))
+					{
+						item v{ s->m_item_name, s->m_value };
+						lookup.emplace_back(s->m_item_name, std::string{ v.value() }, true );
+						subs.emplace_back(sub);
+					}
+					continue;
+				}
+			}
+
+			if (lookup.size() == keys.size())
+			{
+				m_single = c[lookup];
+
+				for (auto s : subs)
+					m_sub.erase(std::remove(m_sub.begin(), m_sub.end(), s), m_sub.end());
+			}
+		}
+
+		return this;
+	}
+
+	bool and_condition_impl::test(row_handle r) const
+	{
+		bool result = true;
+
+		if (m_single.has_value() and *m_single != r)
+			result = false;
+		else
+		{
+			for (auto sub : m_sub)
+			{
+				if (sub->test(r))
+					continue;
+
+				result = false;
+				break;
+			}
+		}
+
+		return result;
+	}
+
 	condition_impl *or_condition_impl::prepare(const category &c)
 	{
 		std::vector<and_condition_impl *> and_conditions;
@@ -160,7 +324,7 @@ void condition::prepare(const category &c)
 {
 	if (m_impl)
 		m_impl = m_impl->prepare(c);
-	
+
 	m_prepared = true;
 }
 

src/datablock.cpp

@@ -26,6 +26,10 @@
 
 #include "cif++/datablock.hpp"
 
+#include "cif++/validate.hpp"
+
+#include <exception>
+
 namespace cif
 {
 
@@ -38,6 +42,21 @@ datablock::datablock(const datablock &db)
 		cat.update_links(*this);
 }
 
+void datablock::load_dictionary()
+{
+	if (auto *audit_conform = get("audit_conform"); audit_conform and not audit_conform->empty())
+	{
+		try
+		{
+			set_validator(&validator_factory::instance().get(*audit_conform));
+		}
+		catch (const std::exception &ex)
+		{
+			std::clog << ex.what() << '\n';
+		}
+	}
+}
+
 void datablock::set_validator(const validator *v)
 {
 	m_validator = v;
@@ -49,6 +68,7 @@ void datablock::set_validator(const validator *v)
 	}
 	catch (const std::exception &)
 	{
+		m_validator = nullptr;
 		throw_with_nested(std::runtime_error("Error while setting validator in datablock " + m_name));
 	}
 }
@@ -61,7 +81,7 @@ const validator *datablock::get_validator() const
 bool datablock::is_valid() const
 {
 	if (m_validator == nullptr)
-		throw std::runtime_error("Validator not specified");
+		throw std::runtime_error("Validator not specified for datablock data_" + name());
 
 	bool result = true;
 	for (auto &cat : *this)
@@ -70,50 +90,59 @@ bool datablock::is_valid() const
 	return result;
 }
 
-bool datablock::is_valid()
-{
-	if (m_validator == nullptr)
-		throw std::runtime_error("Validator not specified");
-
-	bool result = true;
-	for (auto &cat : *this)
-		result = cat.is_valid() and result;
-	
-	// Add or remove the audit_conform block here.
-	if (result)
-	{
-		// If the dictionary declares an audit_conform category, put it in,
-		// but only if it does not exist already!
-
-		if (m_validator->get_validator_for_category("audit_conform") != nullptr)
-		{
-			auto &audit_conform = operator[]("audit_conform");
-
-			audit_conform.clear();
-			audit_conform.emplace({
-				// clang-format off
-				{ "dict_name", m_validator->name() },
-				{ "dict_version", m_validator->version() }
-				// clang-format on
-			});
-		}
-	}
-	else
-		erase(std::find_if(begin(), end(), [](category &cat) { return cat.name() == "audit_conform"; }), end());
-
-	return result;
-}
-
 bool datablock::validate_links() const
 {
 	bool result = true;
 
+	for (auto &cat : *this)
+		const_cast<category &>(cat).update_links(*this);
+
 	for (auto &cat : *this)
 		result = cat.validate_links() and result;
 
 	return result;
 }
 
+bool datablock::strip()
+{
+	bool result = true;
+
+	// remove all categories that have no validator
+	erase(std::remove_if(begin(), end(), [](category &c)
+			  {
+		bool result = false;
+		if (c.get_cat_validator() == nullptr)
+		{
+			if (cif::VERBOSE > 0)
+				std::clog << "Dropping category " << c.name() << '\n';
+			result = true;
+		}
+		return result; }),
+		end());
+
+	// then strip the remaining categories
+	for (auto &cat : *this)
+		cat.strip();
+
+	// Add or remove the audit_conform block here.
+	if (is_valid())
+	{
+		// If the dictionary declares an audit_conform category, put it in,
+		// but only if it does not exist already!
+
+		if (auto audit_conform = get("audit_conform");
+			audit_conform != nullptr and m_validator->get_validator_for_category("audit_conform") != nullptr)
+		{
+			audit_conform->clear();
+			m_validator->fill_audit_conform(*audit_conform);
+		}
+	}
+	else
+		result = false;
+
+	return result;
+}
+
 // --------------------------------------------------------------------
 
 category &datablock::operator[](std::string_view name)
@@ -170,11 +199,16 @@ std::tuple<datablock::iterator, bool> datablock::emplace(std::string_view name)
 
 	if (is_new)
 	{
-		i = insert(end(), {name});
+		i = insert(end(), { name });
 		i->set_validator(m_validator, *this);
 	}
 
 	assert(i != end());
+
+	// links may have changed...
+	for (auto &cat : *this)
+		cat.update_links(*this);
+
 	return std::make_tuple(i, is_new);
 }
 
@@ -434,4 +468,4 @@ bool datablock::operator==(const datablock &rhs) const
 	return true;
 }
 
-} // namespace cif
+} // namespace cif

src/dictionary_parser.cpp

@@ -28,6 +28,9 @@
 #include "cif++/dictionary_parser.hpp"
 #include "cif++/file.hpp"
 #include "cif++/parser.hpp"
+#include <exception>
+#include <iomanip>
+#include <stdexcept>
 
 namespace cif
 {
@@ -46,7 +49,7 @@ class dictionary_parser : public parser
 	void load_dictionary()
 	{
 		std::unique_ptr<datablock> dict;
-		auto savedDatablock = m_datablock;
+		auto savedDatablock = std::exchange(m_datablock, nullptr);
 
 		try
 		{
@@ -75,6 +78,9 @@ class dictionary_parser : public parser
 			error(ex.what());
 		}
 
+		if (m_datablock == nullptr)
+			throw std::runtime_error("Dictionary file is empty?");
+
 		// store all validators
 		for (auto &ic : mCategoryValidators)
 			m_validator.add_category_validator(std::move(ic));
@@ -96,14 +102,10 @@ class dictionary_parser : public parser
 			link_items();
 
 		// store meta information
-		datablock::iterator info;
-		bool is_new;
-		std::tie(info, is_new) = m_datablock->emplace("dictionary");
-		if (not is_new and not info->empty())
+		if (auto dictionary = m_datablock->get("dictionary"); dictionary != nullptr and not dictionary->empty())
 		{
-			auto r = info->front();
-			m_validator.set_name(r["title"].as<std::string>());
-			m_validator.set_version(r["version"].as<std::string>());
+			const auto &[name, version] = dictionary->front().get<std::string,std::optional<std::string>>("title", "version");
+			m_validator.append_audit_conform(name, version);
 		}
 
 		m_datablock = savedDatablock;
@@ -252,7 +254,7 @@ class dictionary_parser : public parser
 
 				auto vi = find(ivs.begin(), ivs.end(), item_validator{ item_name });
 				if (vi == ivs.end())
-					ivs.push_back(item_validator{ item_name, iequals(mandatory, "yes"), tv, ess, defaultValue, nullptr, std::move(aliases) });
+					ivs.push_back(item_validator{ item_name, iequals(mandatory, "yes"), tv, ess, defaultValue, cat_name, std::move(aliases) });
 				else
 				{
 					// need to update the itemValidator?
@@ -308,17 +310,17 @@ class dictionary_parser : public parser
 
 		using key_type = std::tuple<std::string, std::string, int>;
 
-		std::map<key_type, size_t> linkIndex;
+		std::map<key_type, std::size_t> linkIndex;
 
 		// Each link group consists of a set of keys
 		std::vector<std::tuple<std::vector<std::string>, std::vector<std::string>>> linkKeys;
 
-		auto addLink = [&](size_t ix, const std::string &pk, const std::string &ck)
+		auto addLink = [&](std::size_t ix, const std::string &pk, const std::string &ck)
 		{
 			auto &&[pkeys, ckeys] = linkKeys.at(ix);
 
 			bool found = false;
-			for (size_t i = 0; i < pkeys.size(); ++i)
+			for (std::size_t i = 0; i < pkeys.size(); ++i)
 			{
 				if (pkeys[i] == pk and ckeys[i] == ck)
 				{
@@ -350,14 +352,14 @@ class dictionary_parser : public parser
 			if (piv == nullptr)
 				error("in pdbx_item_linked_group_list, item '" + parent + "' is not specified");
 
-			key_type key{ piv->m_category->m_name, civ->m_category->m_name, link_group_id };
+			key_type key{ piv->m_category, civ->m_category, link_group_id };
 			if (not linkIndex.count(key))
 			{
 				linkIndex[key] = linkKeys.size();
 				linkKeys.push_back({});
 			}
 
-			size_t ix = linkIndex.at(key);
+			std::size_t ix = linkIndex.at(key);
 			addLink(ix, piv->m_item_name, civ->m_item_name);
 		}
 
@@ -378,14 +380,14 @@ class dictionary_parser : public parser
 				if (piv == nullptr)
 					error("in pdbx_item_linked_group_list, item '" + parent + "' is not specified");
 
-				key_type key{ piv->m_category->m_name, civ->m_category->m_name, 0 };
+				key_type key{ piv->m_category, civ->m_category, 0 };
 				if (not linkIndex.count(key))
 				{
 					linkIndex[key] = linkKeys.size();
 					linkKeys.push_back({});
 				}
 
-				size_t ix = linkIndex.at(key);
+				std::size_t ix = linkIndex.at(key);
 				addLink(ix, piv->m_item_name, civ->m_item_name);
 			}
 		}
@@ -477,18 +479,7 @@ class dictionary_parser : public parser
 
 // --------------------------------------------------------------------
 
-validator parse_dictionary(std::string_view name, std::istream &is)
-{
-	validator result(name);
-
-	file f;
-	dictionary_parser p(result, is, f);
-	p.load_dictionary();
-
-	return result;
-}
-
-void extend_dictionary(validator &v, std::istream &is)
+void parse_dictionary(validator &v, std::istream &is)
 {
 	file f;
 	dictionary_parser p(v, is, f);

src/file.cpp

@@ -25,24 +25,14 @@
  */
 
 #include "cif++/file.hpp"
+#include "cif++/condition.hpp"
 #include "cif++/gzio.hpp"
 
 namespace cif
 {
 
-// --------------------------------------------------------------------
-void file::set_validator(const validator *v)
-{
-	m_validator = v;
-	for (auto &db : *this)
-		db.set_validator(v);
-}
-
 bool file::is_valid() const
 {
-	if (m_validator == nullptr)
-		std::runtime_error("No validator loaded explicitly, cannot continue");
-
 	bool result = true;
 	for (auto &d : *this)
 		result = d.is_valid() and result;
@@ -55,18 +45,18 @@ bool file::is_valid() const
 
 bool file::is_valid()
 {
-	if (m_validator == nullptr)
-	{
-		if (VERBOSE > 0)
-			std::cerr << "No dictionary loaded explicitly, loading default\n";
-
-		load_dictionary();
-	}
-
 	bool result = not empty();
 
-	for (auto &d : *this)
-		result = d.is_valid() and result;
+	for (bool first = true; auto &d : *this)
+	{
+		if (first)
+		{
+			result = d.is_valid() and result;
+			first = false;
+		}
+		else if (d.get_validator() != nullptr)
+			result = d.is_valid() and result;
+	}
 
 	if (result)
 		result = validate_links();
@@ -76,56 +66,18 @@ bool file::is_valid()
 
 bool file::validate_links() const
 {
-	if (m_validator == nullptr)
-		std::runtime_error("No validator loaded explicitly, cannot continue");
-	
 	bool result = true;
 
 	for (auto &db : *this)
 		result = db.validate_links() and result;
-	
+
 	return result;
 }
 
-void file::load_dictionary()
-{
-	if (not empty())
-	{
-		auto *audit_conform = front().get("audit_conform");
-		if (audit_conform and not audit_conform->empty())
-		{
-			std::string name = audit_conform->front().get<std::string>("dict_name");
-
-			if (name == "mmcif_pdbx_v50")
-				name = "mmcif_pdbx.dic";	// we had a bug here in libcifpp... 
-
-			if (not name.empty())
-			{
-				try
-				{
-					load_dictionary(name);
-				}
-				catch (const std::exception &ex)
-				{
-					if (VERBOSE)
-						std::cerr << "Failed to load dictionary " << std::quoted(name) << ": " << ex.what() << '\n';
-				}
-			}
-		}
-	}
-
-	// if (not m_validator)
-	// 	load_dictionary("mmcif_pdbx.dic");	// TODO: maybe incorrect? Perhaps improve?
-}
-
-void file::load_dictionary(std::string_view name)
-{
-	set_validator(&validator_factory::instance()[name]);
-}
-
 bool file::contains(std::string_view name) const
 {
-	return std::find_if(begin(), end(), [name](const datablock &db) { return iequals(db.name(), name); }) != end();
+	return std::find_if(begin(), end(), [name](const datablock &db)
+			   { return iequals(db.name(), name); }) != end();
 }
 
 datablock &file::operator[](std::string_view name)
@@ -165,10 +117,7 @@ std::tuple<file::iterator, bool> file::emplace(std::string_view name)
 	}
 
 	if (is_new)
-	{
 		i = insert(end(), { name });
-		i->set_validator(m_validator);
-	}
 
 	assert(i != end());
 	return std::make_tuple(i, is_new);
@@ -190,18 +139,34 @@ void file::load(const std::filesystem::path &p)
 	}
 }
 
-void file::load(std::istream &is)
+void file::load(const std::filesystem::path &p, const validator &v)
 {
-	auto saved = m_validator;
-	set_validator(nullptr);
+	gzio::ifstream in(p);
+	if (not in.is_open())
+		throw std::runtime_error("Could not open file '" + p.string() + '\'');
 
+	try
+	{
+		load(in, v);
+	}
+	catch (const std::exception &)
+	{
+		throw_with_nested(std::runtime_error("Error reading file '" + p.string() + '\''));
+	}
+}
+
+void file::load(std::istream &is, const validator &v)
+{
 	parser p(is, *this);
 	p.parse_file();
+	for (auto &db : *this)
+		db.set_validator(&v);
+}
 
-	if (saved != nullptr)
-		set_validator(saved);
-	else
-		load_dictionary();
+void file::load(std::istream &is)
+{
+	parser p(is, *this);
+	p.parse_file();
 }
 
 void file::save(const std::filesystem::path &p) const
@@ -219,4 +184,4 @@ void file::save(std::ostream &os) const
 		db.write(os);
 }
 
-} // namespace cif
+} // namespace cif

src/parser.cpp

@@ -837,6 +837,9 @@ void parser::produce_datablock(std::string_view name)
 
 	const auto &[iter, ignore] = m_file.emplace(name);
 	m_datablock = &(*iter);
+
+	if (m_validator)
+		m_datablock->set_validator(m_validator);
 }
 
 void parser::produce_category(std::string_view name)

src/pdb/cif2pdb.cpp

@@ -33,7 +33,6 @@
 #include <regex>
 #include <set>
 
-
 namespace cif::pdb
 {
 
@@ -58,9 +57,9 @@ std::string cif2pdbDate(const std::string &d)
 		int month = std::stoi(m[2].str());
 
 		if (m[3].matched)
-			result = cif::format("%02.2d-%3.3s-%02.2d", stoi(m[3].str()), kMonths[month - 1], (year % 100)).str();
+			result = cif::format("{:02}-{:3.3}-{:02}", stoi(m[3].str()), kMonths[month - 1], (year % 100));
 		else
-			result = cif::format("%3.3s-%02.2d", kMonths[month - 1], (year % 100)).str();
+			result = cif::format("{:3.3}-{:02}", kMonths[month - 1], (year % 100));
 	}
 
 	return result;
@@ -182,7 +181,7 @@ std::vector<std::string> MapAsymIDs2ChainIDs(const std::vector<std::string> &asy
 }
 
 // support for wrapping text using a 'continuation marker'
-size_t WriteContinuedLine(std::ostream &pdbFile, std::string header, int &count, int cLen, std::string text, std::string::size_type lStart = 0)
+std::size_t WriteContinuedLine(std::ostream &pdbFile, std::string header, int &count, int cLen, std::string text, std::string::size_type lStart = 0)
 {
 	if (lStart == 0)
 	{
@@ -217,15 +216,15 @@ size_t WriteContinuedLine(std::ostream &pdbFile, std::string header, int &count,
 	return lines.size();
 }
 
-size_t WriteOneContinuedLine(std::ostream &pdbFile, std::string header, int cLen, std::string line, int lStart = 0)
+std::size_t WriteOneContinuedLine(std::ostream &pdbFile, std::string header, int cLen, std::string line, int lStart = 0)
 {
 	int count = 0;
 	return WriteContinuedLine(pdbFile, header, count, cLen, line, lStart);
 }
 
-size_t WriteCitation(std::ostream &pdbFile, const datablock &db, row_handle r, int reference)
+std::size_t WriteCitation(std::ostream &pdbFile, const datablock &db, row_handle r, int reference)
 {
-	size_t result = 0;
+	std::size_t result = 0;
 
 	std::string s1;
 
@@ -258,16 +257,14 @@ size_t WriteCitation(std::ostream &pdbFile, const datablock &db, row_handle r, i
 	{
 		to_upper(pubname);
 
-		const std::string kRefHeader = s1 + "REF %2.2s %-28.28s  %2.2s%4.4s %5.5s %4.4s";
-		pdbFile << cif::format(kRefHeader, "" /* continuation */, pubname, (volume.empty() ? "" : "V."), volume, pageFirst, year)
+		pdbFile << s1 << cif::format("REF {:2.2s} {:<28.28s}  {:2.2s}{:>4.4s} {:>5.5s} {:4.4s}", "" /* continuation */, pubname, (volume.empty() ? "" : "V."), volume, pageFirst, year)
 				<< '\n';
 		++result;
 	}
 
 	if (not issn.empty())
 	{
-		const std::string kRefHeader = s1 + "REFN                   ISSN %-25.25s";
-		pdbFile << cif::format(kRefHeader, issn) << '\n';
+		pdbFile << s1 << cif::format("REFN                   ISSN {:<25.25s}", issn) << '\n';
 		++result;
 	}
 
@@ -276,27 +273,25 @@ size_t WriteCitation(std::ostream &pdbFile, const datablock &db, row_handle r, i
 	////    0         1         2         3         4         5         6         7         8
 	////    HEADER    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxDDDDDDDDD   IIII
 	// const char kRefHeader[] =
-	//          "REMARK   1  REFN    %4.4s %-6.6s  %2.2s %-25.25s";
+	//          "REMARK   1  REFN    {:4.4s} {:<6.6s}  {:2.2s} {:<25.25s}";
 	//
 	//			pdbFile << (boost::cif::format(kRefHeader)
 	//						% (astm.empty() ? "" : "ASTN")
 	//						% astm
 	//						% country
-	//						% issn).str()
+	//						% issn)
 	//					<< '\n';
 	//		}
 
 	if (not pmid.empty())
 	{
-		const std::string kPMID = s1 + "PMID   %-60.60s ";
-		pdbFile << cif::format(kPMID, pmid) << '\n';
+		pdbFile << s1 << cif::format("PMID   {:<60.60s} ", pmid) << '\n';
 		++result;
 	}
 
 	if (not doi.empty())
 	{
-		const std::string kDOI = s1 + "DOI    %-60.60s ";
-		pdbFile << cif::format(kDOI, doi) << '\n';
+		pdbFile << s1 << cif::format("DOI    {:<60.60s} ", doi) << '\n';
 		++result;
 	}
 
@@ -307,10 +302,10 @@ void write_header_lines(std::ostream &pdbFile, const datablock &db)
 {
 	//    0         1         2         3         4         5         6         7         8
 	//    HEADER    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxDDDDDDDDD   IIII
-	const char kHeader[] =
-		"HEADER    %-40.40s"
-		"%-9.9s"
-		"   %-4.4s";
+	// const char kHeader[] =
+	// 	"HEADER    {:<40.40s}"
+	// 	"{:<9.9s}"
+	// 	"   {:<4.4s}";
 
 	// HEADER
 
@@ -345,7 +340,12 @@ void write_header_lines(std::ostream &pdbFile, const datablock &db)
 		}
 	}
 
-	pdbFile << cif::format(kHeader, keywords, date, db.name()) << '\n';
+	pdbFile << cif::format(/* kHeader */
+		"HEADER    {:<40.40s}"
+		"{:<9.9s}"
+		"   {:<4.4s}"
+	
+	, keywords, date, db.name()) << '\n';
 
 	// TODO: implement
 	// OBSLTE (skip for now)
@@ -535,7 +535,6 @@ void WriteTitle(std::ostream &pdbFile, const datablock &db)
 	write_header_lines(pdbFile, db);
 
 	// REVDAT
-	const char kRevDatFmt[] = "REVDAT %3d%2.2s %9.9s %4.4s    %1d      ";
 	auto &cat2 = db["database_PDB_rev"];
 	std::vector<row_handle> rev(cat2.begin(), cat2.end());
 	sort(rev.begin(), rev.end(), [](row_handle a, row_handle b) -> bool
@@ -559,9 +558,9 @@ void WriteTitle(std::ostream &pdbFile, const datablock &db)
 		{
 			std::string cs = ++continuation > 1 ? std::to_string(continuation) : std::string();
 
-			pdbFile << cif::format(kRevDatFmt, revNum, cs, date, db.name(), modType);
-			for (size_t i = 0; i < 4; ++i)
-				pdbFile << cif::format(" %-6.6s", (i < types.size() ? types[i] : std::string()));
+			pdbFile << cif::format("REVDAT {:3}{:2.2s} {:9.9s} {:4.4s}    {:1}      ", revNum, cs, date, db.name(), modType);
+			for (std::size_t i = 0; i < 4; ++i)
+				pdbFile << cif::format(" {:<6.6s}", (i < types.size() ? types[i] : std::string()));
 			pdbFile << '\n';
 
 			if (types.size() > 4)
@@ -614,7 +613,7 @@ void WriteRemark2(std::ostream &pdbFile, const datablock &db)
 		{
 			float resHigh = refine.front()["ls_d_res_high"].as<float>();
 			pdbFile << "REMARK   2\n"
-					<< cif::format("REMARK   2 RESOLUTION. %7.2f ANGSTROMS.", resHigh) << '\n';
+					<< cif::format("REMARK   2 RESOLUTION. {:7.2f} ANGSTROMS.", resHigh) << '\n';
 		}
 		catch (...)
 		{ /* skip it */
@@ -681,7 +680,7 @@ class Fi : public FBase
 		{
 			long l = 0;
 			auto r = std::from_chars(s.data(), s.data() + s.length(), l);
-			if (r.ec != std::errc())
+			if ((bool)r.ec)
 			{
 				if (VERBOSE > 0)
 					std::cerr << "Failed to write '" << s << "' as a long from field " << mField << ", this indicates an error in the code for writing PDB files\n";
@@ -719,7 +718,7 @@ class Ff : public FBase
 
 			double d = 0;
 			auto r = cif::from_chars(s.data(), s.data() + s.length(), d);
-			if (r.ec != std::errc())
+			if ((bool)r.ec)
 			{
 				if (VERBOSE > 0)
 					std::cerr << "Failed to write '" << s << "' as a double from field " << mField << ", this indicates an error in the code for writing PDB files\n";
@@ -748,7 +747,7 @@ class Fs : public FBase
 	virtual void out(std::ostream &os)
 	{
 		std::string s{ text() };
-		size_t width = os.width();
+		std::size_t width = os.width();
 
 		if (s.empty())
 		{
@@ -761,10 +760,7 @@ class Fs : public FBase
 		else
 		{
 			os << '\n';
-
-			std::stringstream ss;
-			ss << "REMARK " << std::setw(3) << std::right << mNr << ' ';
-			WriteOneContinuedLine(os, ss.str(), 0, s);
+			WriteOneContinuedLine(os, cif::format("REMARK {:3} ", mNr), 0, s);
 		}
 	}
 
@@ -1617,7 +1613,7 @@ void WriteRemark3Phenix(std::ostream &pdbFile, const datablock &db)
 
 		percent_reflns_obs /= 100;
 
-		pdbFile << RM3("  ") << cif::format("%3d %7.4f - %7.4f    %4.2f %8d %5d  %6.4f %6.4f", bin++, d_res_low, d_res_high, percent_reflns_obs, number_reflns_R_work, number_reflns_R_free, R_factor_R_work, R_factor_R_free) << '\n';
+		pdbFile << RM3("  ") << cif::format("{:3} {:7.4f} - {:7.4f}    {:4.2f} {:8} {:5}  {:6.4f} {:6.4f}", bin++, d_res_low, d_res_high, percent_reflns_obs, number_reflns_R_work, number_reflns_R_free, R_factor_R_work, R_factor_R_free) << '\n';
 	}
 
 	pdbFile << RM3("") << '\n'
@@ -2368,7 +2364,7 @@ void WriteRemark280(std::ostream &pdbFile, const datablock &db)
 
 			const char *keys[] = { "pdbx_details", "ph", "method", "temp" };
 
-			for (size_t i = 0; i < (sizeof(keys) / sizeof(const char *)); ++i)
+			for (std::size_t i = 0; i < (sizeof(keys) / sizeof(const char *)); ++i)
 			{
 				const char *c = keys[i];
 
@@ -2585,7 +2581,7 @@ void WriteRemark465(std::ostream &pdbFile, const datablock &db)
 		cif::tie(modelNr, resName, chainID, iCode, seqNr) =
 			r.get("PDB_model_num", "auth_comp_id", "auth_asym_id", "PDB_ins_code", "auth_seq_id");
 
-		pdbFile << cif::format("REMARK 465 %3.3s %3.3s %1.1s %5d%1.1s", modelNr, resName, chainID, seqNr, iCode) << '\n';
+		pdbFile << cif::format("REMARK 465 {:3.3s} {:3.3s} {:1.1s} {:5}{:1.1s}", modelNr, resName, chainID, seqNr, iCode) << '\n';
 	}
 }
 
@@ -2632,9 +2628,9 @@ void WriteRemark470(std::ostream &pdbFile, const datablock &db)
 
 			while (not a.second.empty())
 			{
-				pdbFile << cif::format("REMARK 470 %3.3s %3.3s %1.1s%4d%1.1s  ", modelNr, resName, chainID, seqNr, iCode) << "  ";
+				pdbFile << cif::format("REMARK 470 {:>3.3s} {:3.3s} {:1.1s}{:4}{:1.1s}  ", modelNr, resName, chainID, seqNr, iCode) << "  ";
 
-				for (size_t i = 0; i < 6 and not a.second.empty(); ++i)
+				for (std::size_t i = 0; i < 6 and not a.second.empty(); ++i)
 				{
 					pdbFile << cif2pdbAtomName(a.second.front(), resName, db) << ' ';
 					a.second.pop_front();
@@ -2730,16 +2726,16 @@ int WritePrimaryStructure(std::ostream &pdbFile, const datablock &db)
 
 			if (dbAccession.length() > 8 or db_code.length() > 12 or atoi(dbseqEnd.c_str()) >= 100000)
 				pdbFile << cif::format(
-							   "DBREF1 %4.4s %1.1s %4.4s%1.1s %4.4s%1.1s %-6.6s               %-20.20s",
+							   "DBREF1 {:>4.4s} {:1.1s} {:>4.4s}{:1.1s} {:>4.4s}{:1.1s} {:<6.6s}               {:<20.20s}",
 							   idCode, chainID, seqBegin, insertBegin, seqEnd, insertEnd, db_name, db_code)
 						<< '\n'
 						<< cif::format(
-							   "DBREF2 %4.4s %1.1s     %-22.22s     %10.10s  %10.10s",
+							   "DBREF2 {:>4.4s} {:1.1s}     {:<22.22s}     {:10.10s}  {:10.10s}",
 							   idCode, chainID, dbAccession, dbseqBegin, dbseqEnd)
 						<< '\n';
 			else
 				pdbFile << cif::format(
-							   "DBREF  %4.4s %1.1s %4.4s%1.1s %4.4s%1.1s %-6.6s %-8.8s %-12.12s %5.5s%1.1s %5.5s%1.1s",
+							   "DBREF  {:>4.4s} {:1.1s} {:>4.4s}{:1.1s} {:>4.4s}{:1.1s} {:<6.6s} {:<8.8s} {:<12.12s} {:>5.5s}{:1.1s} {:>5.5s}{:1.1s}",
 							   idCode, chainID, seqBegin, insertBegin, seqEnd, insertEnd, db_name, dbAccession, db_code, dbseqBegin, dbinsBeg, dbseqEnd, dbinsEnd)
 						<< '\n';
 		}
@@ -2758,9 +2754,8 @@ int WritePrimaryStructure(std::ostream &pdbFile, const datablock &db)
 		to_upper(conflict);
 
 		pdbFile << cif::format(
-					   "SEQADV %4.4s %3.3s %1.1s %4.4s%1.1s %-4.4s %-9.9s %3.3s %5.5s %-21.21s",
+					   "SEQADV {:4.4s} {:3.3s} {:1.1s} {:>4.4s}{:1.1s} {:<4.4s} {:<9.9s} {:3.3s} {:>5.5s} {:<21.21s}",
 					   idCode, resName, chainID, seqNum, iCode, database, dbAccession, dbRes, dbSeq, conflict)
-					   .str()
 				<< '\n';
 	}
 
@@ -2788,7 +2783,7 @@ int WritePrimaryStructure(std::ostream &pdbFile, const datablock &db)
 				t = 13;
 
 			pdbFile << cif::format(
-						   "SEQRES %3d %1.1s %4d  %-51.51s          ",
+						   "SEQRES {:3} {:1.1s} {:4}  {:<51.51s}          ",
 						   n++, std::string{ chainID }, seqresl[chainID], join(seq.begin(), seq.begin() + t, " "))
 					<< '\n';
 
@@ -2808,9 +2803,8 @@ int WritePrimaryStructure(std::ostream &pdbFile, const datablock &db)
 			r.get("auth_asym_id", "auth_seq_id", "auth_comp_id", "PDB_ins_code", "parent_comp_id", "details");
 
 		pdbFile << cif::format(
-					   "MODRES %4.4s %3.3s %1.1s %4.4s%1.1s %3.3s  %-41.41s",
+					   "MODRES {:4.4s} {:3.3s} {:1.1s} {:4.4s}{:1.1s} {:3.3s}  {:<41.41s}",
 					   db.name(), resName, chainID, seqNum, iCode, stdRes, comment)
-					   .str()
 				<< '\n';
 	}
 
@@ -2925,7 +2919,7 @@ int WriteHeterogen(std::ostream &pdbFile, const datablock &db)
 	{
 		if (h.water)
 			continue;
-		pdbFile << cif::format("HET    %3.3s  %c%4d%c  %5d", h.hetID, h.chainID, h.seqNum, h.iCode, h.numHetAtoms) << '\n';
+		pdbFile << cif::format("HET    {:3.3s}  {:1c}{:4}{:1c}  {:5}", h.hetID, h.chainID, h.seqNum, h.iCode, h.numHetAtoms) << '\n';
 		++numHet;
 	}
 
@@ -2940,7 +2934,7 @@ int WriteHeterogen(std::ostream &pdbFile, const datablock &db)
 
 		for (;;)
 		{
-			pdbFile << cif::format("HETNAM  %2.2s %3.3s ", (c > 1 ? std::to_string(c) : std::string()), id);
+			pdbFile << cif::format("HETNAM  {:2.2s} {:3.3s} ", (c > 1 ? std::to_string(c) : std::string()), id);
 			++c;
 
 			if (name.length() > 55)
@@ -3032,7 +3026,7 @@ int WriteHeterogen(std::ostream &pdbFile, const datablock &db)
 			{
 				std::stringstream fs;
 
-				fs << cif::format("FORMUL  %2d  %3.3s %2.2s%c", componentNr, hetID, (c > 1 ? std::to_string(c) : std::string()), (hetID == water_comp_id ? '*' : ' '));
+				fs << cif::format("FORMUL  {:2}  {:3.3s} {:2.2s}{:1c}", componentNr, hetID, (c > 1 ? std::to_string(c) : std::string()), (hetID == water_comp_id ? '*' : ' '));
 				++c;
 
 				if (formula.length() > 51)
@@ -3099,7 +3093,7 @@ std::tuple<int, int> WriteSecondaryStructure(std::ostream &pdbFile, const databl
 				"pdbx_PDB_helix_class", "pdbx_PDB_helix_length", "beg_auth_seq_id", "end_auth_seq_id");
 
 		++numHelix;
-		pdbFile << cif::format("HELIX  %3d %3.3s %3.3s %1.1s %4d%1.1s %3.3s %1.1s %4d%1.1s%2d%-30.30s %5d",
+		pdbFile << cif::format("HELIX  {:3} {:>3.3s} {:3.3s} {:1.1s} {:4}{:1.1s} {:3.3s} {:1.1s} {:4}{:1.1s}{:2}{:<30.30s} {:5}",
 					   numHelix, pdbx_PDB_helix_id, beg_label_comp_id, beg_auth_asym_id, beg_auth_seq_id, pdbx_beg_PDB_ins_code, end_label_comp_id, end_auth_asym_id, end_auth_seq_id, pdbx_end_PDB_ins_code, pdbx_PDB_helix_class, details, pdbx_PDB_helix_length)
 				<< '\n';
 	}
@@ -3136,7 +3130,7 @@ std::tuple<int, int> WriteSecondaryStructure(std::ostream &pdbFile, const databl
 					"pdbx_end_PDB_ins_code", "beg_auth_comp_id", "beg_auth_asym_id", "beg_auth_seq_id",
 					"end_auth_comp_id", "end_auth_asym_id", "end_auth_seq_id");
 
-				pdbFile << cif::format("SHEET  %3.3s %3.3s%2d %3.3s %1.1s%4d%1.1s %3.3s %1.1s%4d%1.1s%2d", rangeID1, sheetID, numStrands, initResName, initChainID, initSeqNum, initICode, endResName, endChainID, endSeqNum, endICode, 0) << '\n';
+				pdbFile << cif::format("SHEET  {:>3.3s} {:>3.3s}{:2} {:3.3s} {:1.1s}{:4}{:1.1s} {:3.3s} {:1.1s}{:4}{:1.1s}{:2}", rangeID1, sheetID, numStrands, initResName, initChainID, initSeqNum, initICode, endResName, endChainID, endSeqNum, endICode, 0) << '\n';
 
 				first = false;
 			}
@@ -3155,7 +3149,7 @@ std::tuple<int, int> WriteSecondaryStructure(std::ostream &pdbFile, const databl
 
 			if (h.empty())
 			{
-				pdbFile << cif::format("SHEET  %3.3s %3.3s%2d %3.3s %1.1s%4d%1.1s %3.3s %1.1s%4d%1.1s%2d", rangeID2, sheetID, numStrands, initResName, initChainID, initSeqNum, initICode, endResName, endChainID, endSeqNum, endICode, sense) << '\n';
+				pdbFile << cif::format("SHEET  {:>3.3s} {:>3.3s}{:2} {:3.3s} {:1.1s}{:4}{:1.1s} {:3.3s} {:1.1s}{:4}{:1.1s}{:2}", rangeID2, sheetID, numStrands, initResName, initChainID, initSeqNum, initICode, endResName, endChainID, endSeqNum, endICode, sense) << '\n';
 			}
 			else
 			{
@@ -3168,8 +3162,8 @@ std::tuple<int, int> WriteSecondaryStructure(std::ostream &pdbFile, const databl
 				curAtom = cif2pdbAtomName(curAtom, compID[0], db);
 				prevAtom = cif2pdbAtomName(prevAtom, compID[1], db);
 
-				pdbFile << cif::format("SHEET  %3.3s %3.3s%2d %3.3s %1.1s%4d%1.1s %3.3s %1.1s%4d%1.1s%2d "
-										"%-4.4s%3.3s %1.1s%4d%1.1s %-4.4s%3.3s %1.1s%4d%1.1s",
+				pdbFile << cif::format("SHEET  {:>3.3s} {:>3.3s}{:2} {:3.3s} {:1.1s}{:4}{:1.1s} {:3.3s} {:1.1s}{:4}{:1.1s}{:2} "
+										"{:<4.4s}{:3.3s} {:1.1s}{:4}{:1.1s} {:<4.4s}{:3.3s} {:1.1s}{:4}{:1.1s}",
 							   rangeID2, sheetID, numStrands, initResName, initChainID, initSeqNum, initICode, endResName, endChainID, endSeqNum, endICode, sense, curAtom, curResName, curChainID, curResSeq, curICode, prevAtom, prevResName, prevChainID, prevResSeq, prevICode)
 						<< '\n';
 			}
@@ -3207,7 +3201,7 @@ void WriteConnectivity(std::ostream &pdbFile, const datablock &db)
 		sym1 = cif2pdbSymmetry(sym1);
 		sym2 = cif2pdbSymmetry(sym2);
 
-		pdbFile << cif::format("SSBOND %3d CYS %1.1s %4d%1.1s   CYS %1.1s %4d%1.1s                       %6.6s %6.6s %5.2f", nr, chainID1, seqNum1, icode1, chainID2, seqNum2, icode2, sym1, sym2, Length) << '\n';
+		pdbFile << cif::format("SSBOND {:3} CYS {:1.1s} {:4}{:1.1s}   CYS {:1.1s} {:4}{:1.1s}                       {:6.6s} {:6.6s} {:5.2f}", nr, chainID1, seqNum1, icode1, chainID2, seqNum2, icode2, sym1, sym2, Length) << '\n';
 
 		++nr;
 	}
@@ -3234,10 +3228,10 @@ void WriteConnectivity(std::ostream &pdbFile, const datablock &db)
 		sym1 = cif2pdbSymmetry(sym1);
 		sym2 = cif2pdbSymmetry(sym2);
 
-		pdbFile << cif::format("LINK        %-4.4s%1.1s%3.3s %1.1s%4d%1.1s               %-4.4s%1.1s%3.3s %1.1s%4d%1.1s  %6.6s %6.6s", name1, altLoc1, resName1, chainID1, resSeq1, iCode1, name2, altLoc2, resName2, chainID2, resSeq2, iCode2, sym1, sym2);
+		pdbFile << cif::format("LINK        {:<4.4s}{:1.1s}{:3.3s} {:1.1s}{:4}{:1.1s}               {:<4.4s}{:1.1s}{:3.3s} {:1.1s}{:4}{:1.1s}  {:>6.6s} {:>6.6s}", name1, altLoc1, resName1, chainID1, resSeq1, iCode1, name2, altLoc2, resName2, chainID2, resSeq2, iCode2, sym1, sym2);
 
 		if (not Length.empty())
-			pdbFile << cif::format(" %5.2f", stod(Length));
+			pdbFile << cif::format(" {:5.2f}", stod(Length));
 
 		pdbFile << '\n';
 	}
@@ -3255,7 +3249,7 @@ void WriteConnectivity(std::ostream &pdbFile, const datablock &db)
 				"pdbx_label_comp_id_2", "pdbx_auth_asym_id_2", "pdbx_auth_seq_id_2", "pdbx_PDB_ins_code_2",
 				"pdbx_PDB_model_num", "pdbx_omega_angle");
 
-		pdbFile << cif::format("CISPEP %3.3s %3.3s %1.1s %4d%1.1s   %3.3s %1.1s %4d%1.1s       %3.3s       %6.2f",
+		pdbFile << cif::format("CISPEP {:3.3s} {:3.3s} {:1.1s} {:4}{:1.1s}   {:3.3s} {:1.1s} {:4}{:1.1s}       {:3.3s}       {:6.2f}",
 			serNum, pep1, chainID1, seqNum1, icode1, pep2, chainID2, seqNum2, icode2, modNum, measure) << '\n';
 	}
 }
@@ -3276,7 +3270,7 @@ int WriteMiscellaneousFeatures(std::ostream &pdbFile, const datablock &db)
 		cif::tie(siteID, resName, chainID, seq, iCode) =
 			r.get("site_id", "auth_comp_id", "auth_asym_id", "auth_seq_id", "pdbx_auth_ins_code");
 
-		sites[siteID].push_back(cif::format("%3.3s %1.1s%4d%1.1s ", resName, chainID, seq, iCode).str());
+		sites[siteID].push_back(cif::format("{:3.3s} {:1.1s}{:4}{:1.1s} ", resName, chainID, seq, iCode));
 	}
 
 	for (auto s : sites)
@@ -3284,12 +3278,12 @@ int WriteMiscellaneousFeatures(std::ostream &pdbFile, const datablock &db)
 		std::string siteID = std::get<0>(s);
 		std::deque<std::string> &res = std::get<1>(s);
 
-		size_t numRes = res.size();
+		std::size_t numRes = res.size();
 
 		int nr = 1;
 		while (res.empty() == false)
 		{
-			pdbFile << cif::format("SITE   %3d %3.3s %2d ", nr, siteID, numRes);
+			pdbFile << cif::format("SITE   {:3} {:3.3s} {:2} ", nr, siteID, numRes);
 
 			for (int i = 0; i < 4; ++i)
 			{
@@ -3318,7 +3312,7 @@ void WriteCrystallographic(std::ostream &pdbFile, const datablock &db)
 
 	r = db["cell"].find_first(key("entry_id") == db.name());
 
-	pdbFile << cif::format("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11.11s%4d", r["length_a"].as<double>(), r["length_b"].as<double>(), r["length_c"].as<double>(), r["angle_alpha"].as<double>(), r["angle_beta"].as<double>(), r["angle_gamma"].as<double>(), symmetry, r["Z_PDB"].as<int>()) << '\n';
+	pdbFile << cif::format("CRYST1{:9.3f}{:9.3f}{:9.3f}{:7.2f}{:7.2f}{:7.2f} {:<11.11s}{:4}", r["length_a"].as<double>(), r["length_b"].as<double>(), r["length_c"].as<double>(), r["angle_alpha"].as<double>(), r["angle_beta"].as<double>(), r["angle_gamma"].as<double>(), symmetry, r["Z_PDB"].as<int>()) << '\n';
 }
 
 int WriteCoordinateTransformation(std::ostream &pdbFile, const datablock &db)
@@ -3327,18 +3321,18 @@ int WriteCoordinateTransformation(std::ostream &pdbFile, const datablock &db)
 
 	for (auto r : db["database_PDB_matrix"])
 	{
-		pdbFile << cif::format("ORIGX%1d    %10.6f%10.6f%10.6f     %10.5f", 1, r["origx[1][1]"].as<float>(), r["origx[1][2]"].as<float>(), r["origx[1][3]"].as<float>(), r["origx_vector[1]"].as<float>()) << '\n';
-		pdbFile << cif::format("ORIGX%1d    %10.6f%10.6f%10.6f     %10.5f", 2, r["origx[2][1]"].as<float>(), r["origx[2][2]"].as<float>(), r["origx[2][3]"].as<float>(), r["origx_vector[2]"].as<float>()) << '\n';
-		pdbFile << cif::format("ORIGX%1d    %10.6f%10.6f%10.6f     %10.5f", 3, r["origx[3][1]"].as<float>(), r["origx[3][2]"].as<float>(), r["origx[3][3]"].as<float>(), r["origx_vector[3]"].as<float>()) << '\n';
+		pdbFile << cif::format("ORIGX{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 1, r["origx[1][1]"].as<float>(), r["origx[1][2]"].as<float>(), r["origx[1][3]"].as<float>(), r["origx_vector[1]"].as<float>()) << '\n';
+		pdbFile << cif::format("ORIGX{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 2, r["origx[2][1]"].as<float>(), r["origx[2][2]"].as<float>(), r["origx[2][3]"].as<float>(), r["origx_vector[2]"].as<float>()) << '\n';
+		pdbFile << cif::format("ORIGX{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 3, r["origx[3][1]"].as<float>(), r["origx[3][2]"].as<float>(), r["origx[3][3]"].as<float>(), r["origx_vector[3]"].as<float>()) << '\n';
 		result += 3;
 		break;
 	}
 
 	for (auto r : db["atom_sites"])
 	{
-		pdbFile << cif::format("SCALE%1d    %10.6f%10.6f%10.6f     %10.5f", 1, r["fract_transf_matrix[1][1]"].as<float>(), r["fract_transf_matrix[1][2]"].as<float>(), r["fract_transf_matrix[1][3]"].as<float>(), r["fract_transf_vector[1]"].as<float>()) << '\n';
-		pdbFile << cif::format("SCALE%1d    %10.6f%10.6f%10.6f     %10.5f", 2, r["fract_transf_matrix[2][1]"].as<float>(), r["fract_transf_matrix[2][2]"].as<float>(), r["fract_transf_matrix[2][3]"].as<float>(), r["fract_transf_vector[2]"].as<float>()) << '\n';
-		pdbFile << cif::format("SCALE%1d    %10.6f%10.6f%10.6f     %10.5f", 3, r["fract_transf_matrix[3][1]"].as<float>(), r["fract_transf_matrix[3][2]"].as<float>(), r["fract_transf_matrix[3][3]"].as<float>(), r["fract_transf_vector[3]"].as<float>()) << '\n';
+		pdbFile << cif::format("SCALE{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 1, r["fract_transf_matrix[1][1]"].as<float>(), r["fract_transf_matrix[1][2]"].as<float>(), r["fract_transf_matrix[1][3]"].as<float>(), r["fract_transf_vector[1]"].as<float>()) << '\n';
+		pdbFile << cif::format("SCALE{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 2, r["fract_transf_matrix[2][1]"].as<float>(), r["fract_transf_matrix[2][2]"].as<float>(), r["fract_transf_matrix[2][3]"].as<float>(), r["fract_transf_vector[2]"].as<float>()) << '\n';
+		pdbFile << cif::format("SCALE{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 3, r["fract_transf_matrix[3][1]"].as<float>(), r["fract_transf_matrix[3][2]"].as<float>(), r["fract_transf_matrix[3][3]"].as<float>(), r["fract_transf_vector[3]"].as<float>()) << '\n';
 		result += 3;
 		break;
 	}
@@ -3348,9 +3342,9 @@ int WriteCoordinateTransformation(std::ostream &pdbFile, const datablock &db)
 	{
 		std::string given = r["code"] == "given" ? "1" : "";
 
-		pdbFile << cif::format("MTRIX%1d %3d%10.6f%10.6f%10.6f     %10.5f    %1.1s", 1, nr, r["matrix[1][1]"].as<float>(), r["matrix[1][2]"].as<float>(), r["matrix[1][3]"].as<float>(), r["vector[1]"].as<float>(), given) << '\n';
-		pdbFile << cif::format("MTRIX%1d %3d%10.6f%10.6f%10.6f     %10.5f    %1.1s", 2, nr, r["matrix[2][1]"].as<float>(), r["matrix[2][2]"].as<float>(), r["matrix[2][3]"].as<float>(), r["vector[2]"].as<float>(), given) << '\n';
-		pdbFile << cif::format("MTRIX%1d %3d%10.6f%10.6f%10.6f     %10.5f    %1.1s", 3, nr, r["matrix[3][1]"].as<float>(), r["matrix[3][2]"].as<float>(), r["matrix[3][3]"].as<float>(), r["vector[3]"].as<float>(), given) << '\n';
+		pdbFile << cif::format("MTRIX{:1} {:3}{:10.6f}{:10.6f}{:10.6f}     {:10.5f}    {:1.1s}", 1, nr, r["matrix[1][1]"].as<float>(), r["matrix[1][2]"].as<float>(), r["matrix[1][3]"].as<float>(), r["vector[1]"].as<float>(), given) << '\n';
+		pdbFile << cif::format("MTRIX{:1} {:3}{:10.6f}{:10.6f}{:10.6f}     {:10.5f}    {:1.1s}", 2, nr, r["matrix[2][1]"].as<float>(), r["matrix[2][2]"].as<float>(), r["matrix[2][3]"].as<float>(), r["vector[2]"].as<float>(), given) << '\n';
+		pdbFile << cif::format("MTRIX{:1} {:3}{:10.6f}{:10.6f}{:10.6f}     {:10.5f}    {:1.1s}", 3, nr, r["matrix[3][1]"].as<float>(), r["matrix[3][2]"].as<float>(), r["matrix[3][3]"].as<float>(), r["vector[3]"].as<float>(), given) << '\n';
 
 		++nr;
 		result += 3;
@@ -3369,10 +3363,6 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 
 	auto &atom_site = db["atom_site"];
 	auto &atom_site_anisotrop = db["atom_site_anisotrop"];
-	auto &entity = db["entity"];
-	// auto &pdbx_poly_seq_scheme = db["pdbx_poly_seq_scheme"];
-	// auto &pdbx_nonpoly_scheme = db["pdbx_nonpoly_scheme"];
-	auto &pdbx_branch_scheme = db["pdbx_branch_scheme"];
 
 	int serial = 1;
 	auto ri = atom_site.begin();
@@ -3393,7 +3383,7 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 		{
 			int nr = 0;
 			auto r = std::from_chars(modelNum.data(), modelNum.data() + modelNum.length(), nr);
-			if (r.ec != std::errc())
+			if ((bool)r.ec)
 			{
 				if (VERBOSE > 0)
 					std::cerr << "Model number '" << modelNum << "' is not a valid integer\n";
@@ -3417,7 +3407,7 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 
 			if (terminate)
 			{
-				pdbFile << cif::format("TER   %5d      %3.3s %1.1s%4d%1.1s",  serial,  resName,  chainID,  resSeq,  iCode) << '\n';
+				pdbFile << cif::format("TER   {:5}      {:3.3s} {:1.1s}{:4}{:1.1s}",  serial,  resName,  chainID,  resSeq,  iCode) << '\n';
 
 				++serial;
 				terminatedChains.insert(chainID);
@@ -3446,26 +3436,6 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 			r.get("id", "group_PDB", "label_atom_id", "label_alt_id", "auth_comp_id", "auth_asym_id", "auth_seq_id",
 				"pdbx_PDB_ins_code", "Cartn_x", "Cartn_y", "Cartn_z", "occupancy", "B_iso_or_equiv", "type_symbol", "pdbx_formal_charge");
 
-		if (resName != "HOH")
-		{
-			int entity_id = r.get<int>("label_entity_id");
-			try
-			{
-				auto type = entity.find1<std::string>("id"_key == entity_id, "type");
-
-				if (type == "branched")	// find the real auth_seq_num, since sugars have their auth_seq_num reused as sugar number... sigh.
-					resSeq = pdbx_branch_scheme.find1<int>("asym_id"_key == r.get<std::string>("label_asym_id") and "pdb_seq_num"_key == resSeq, "auth_seq_num");
-				// else if (type == "non-polymer")	// same for non-polymers
-				// 	resSeq = pdbx_nonpoly_scheme.find1<int>("asym_id"_key == r.get<std::string>("label_asym_id") and "pdb_seq_num"_key == resSeq, "auth_seq_num");
-				// else if (type == "polymer")
-				// 	resSeq = pdbx_poly_seq_scheme.find1<int>("asym_id"_key == r.get<std::string>("label_asym_id") and "pdb_seq_num"_key == resSeq, "auth_seq_num");
-			}
-			catch (const std::exception &ex)
-			{
-				std::cerr << "Oops, there was not exactly one entity with id " << entity_id << '\n';
-			}
-		}
-		
 		if (chainID.length() > 1)
 			throw std::runtime_error("Chain ID " + chainID + " won't fit into a PDB file");
 
@@ -3476,7 +3446,8 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 		if (charge != 0)
 			sCharge = std::to_string(charge) + (charge > 0 ? '+' : '-');
 
-		pdbFile << cif::format("%-6.6s%5d %-4.4s%1.1s%3.3s %1.1s%4d%1.1s   %8.3f%8.3f%8.3f%6.2f%6.2f          %2.2s%2.2s", group, serial, name, altLoc, resName, chainID, resSeq, iCode, x, y, z, occupancy, tempFactor, element, sCharge) << '\n';
+		pdbFile << cif::format("{:<6.6s}{:5} {:<4.4s}{:1.1s}{:3.3s} {:1.1s}{:4}{:1.1s}   {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f}          {:>2.2s}{:2.2s}",
+			group, serial, name, altLoc, resName, chainID, resSeq, iCode, x, y, z, occupancy, tempFactor, element, sCharge) << '\n';
 
 		++numCoord;
 
@@ -3491,7 +3462,7 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 			tie(u11, u22, u33, u12, u13, u23) =
 				ai.get("U[1][1]", "U[2][2]", "U[3][3]", "U[1][2]", "U[1][3]", "U[2][3]");
 
-			pdbFile << cif::format("ANISOU%5d %-4.4s%1.1s%3.3s %1.1s%4d%1.1s %7d%7d%7d%7d%7d%7d      %2.2s%2.2s", serial, name, altLoc, resName, chainID, resSeq, iCode, std::lrintf(u11 * 10000), std::lrintf(u22 * 10000), std::lrintf(u33 * 10000), std::lrintf(u12 * 10000), std::lrintf(u13 * 10000), std::lrintf(u23 * 10000), element, sCharge) << '\n';
+			pdbFile << cif::format("ANISOU{:5} {:<4.4s}{:1.1s}{:3.3s} {:1.1s}{:4}{:1.1s} {:7}{:7}{:7}{:7}{:7}{:7}      {:2.2s}{:2.2s}", serial, name, altLoc, resName, chainID, resSeq, iCode, std::lrintf(u11 * 10000), std::lrintf(u22 * 10000), std::lrintf(u33 * 10000), std::lrintf(u12 * 10000), std::lrintf(u13 * 10000), std::lrintf(u23 * 10000), element, sCharge) << '\n';
 		}
 
 		++serial;
@@ -3543,7 +3514,7 @@ std::tuple<int, int> WriteCoordinate(std::ostream &pdbFile, const datablock &db)
 		for (int model_nr : models)
 		{
 			if (models.size() > 1)
-				pdbFile << cif::format("MODEL     %4d",  model_nr) << '\n';
+				pdbFile << cif::format("MODEL     {:4}",  model_nr) << '\n';
 
 			std::set<std::string> TERminatedChains;
 			auto n = WriteCoordinatesForModel(pdbFile, db, last_resseq_for_chain_map, TERminatedChains, model_nr);
@@ -3615,7 +3586,7 @@ std::string get_HEADER_line(const datablock &db, std::string::size_type truncate
 		}
 	}
 
-	return FixStringLength(cif::format("HEADER    %-40.40s%-9.9s   %-4.4s", keywords, date, db.name()).str(), truncate_at);
+	return FixStringLength(cif::format("HEADER    {:<40.40s}{:<9.9s}   {:<4.4s}", keywords, date, db.name()), truncate_at);
 }
 
 std::string get_COMPND_line(const datablock &db, std::string::size_type truncate_at)
@@ -3788,7 +3759,7 @@ void write(std::ostream &os, const datablock &db)
 	numXform = WriteCoordinateTransformation(os, db);
 	std::tie(numCoord, numTer) = WriteCoordinate(os, db);
 
-	os << cif::format("MASTER    %5d    0%5d%5d%5d%5d%5d%5d%5d%5d%5d%5d",  numRemark,  numHet,  numHelix,  numSheet,  numTurn,  numSite,  numXform,  numCoord,  numTer,  numConect,  numSeq) << '\n'
+	os << cif::format("MASTER    {:5}    0{:5}{:5}{:5}{:5}{:5}{:5}{:5}{:5}{:5}{:5}",  numRemark,  numHet,  numHelix,  numSheet,  numTurn,  numSite,  numXform,  numCoord,  numTer,  numConect,  numSeq) << '\n'
 			<< "END\n";
 }
 

src/pdb/pdb2cif.cpp

@@ -32,6 +32,7 @@
 #include <map>
 #include <set>
 #include <stack>
+#include <stdexcept>
 
 using cif::category;
 using cif::datablock;
@@ -160,7 +161,7 @@ PDBRecord::~PDBRecord()
 {
 }
 
-void *PDBRecord::operator new(size_t size, size_t vLen)
+void *PDBRecord::operator new(std::size_t size, std::size_t vLen)
 {
 	return malloc(size + vLen + 1);
 }
@@ -170,7 +171,7 @@ void PDBRecord::operator delete(void *p)
 	free(p);
 }
 
-void PDBRecord::operator delete(void *p, size_t vLen)
+void PDBRecord::operator delete(void *p, std::size_t vLen)
 {
 	free(p);
 }
@@ -180,7 +181,7 @@ bool PDBRecord::is(const char *name) const
 	return iequals(mName, name);
 }
 
-char PDBRecord::vC(size_t column)
+char PDBRecord::vC(std::size_t column)
 {
 	char result = ' ';
 	if (column - 7 < mVlen)
@@ -188,7 +189,7 @@ char PDBRecord::vC(size_t column)
 	return result;
 }
 
-std::string PDBRecord::vS(size_t columnFirst, size_t columnLast)
+std::string PDBRecord::vS(std::size_t columnFirst, std::size_t columnLast)
 {
 	std::string result;
 
@@ -272,7 +273,7 @@ int PDBRecord::vI(int columnFirst, int columnLast)
 	return result;
 }
 
-std::string PDBRecord::vF(size_t columnFirst, size_t columnLast)
+std::string PDBRecord::vF(std::size_t columnFirst, std::size_t columnLast)
 {
 	// for now... TODO: check format?
 	return vS(columnFirst, columnLast);
@@ -780,17 +781,17 @@ class PDBFileParser
 
 	// ----------------------------------------------------------------
 
-	char vC(size_t column) const
+	char vC(std::size_t column) const
 	{
 		return mRec->vC(column);
 	}
 
-	std::string vS(size_t columnFirst, size_t columnLast = std::numeric_limits<size_t>::max()) const
+	std::string vS(std::size_t columnFirst, std::size_t columnLast = std::numeric_limits<std::size_t>::max()) const
 	{
 		return mRec->vS(columnFirst, columnLast);
 	}
 
-	std::string vF(size_t columnFirst, size_t columnLast) const
+	std::string vF(std::size_t columnFirst, std::size_t columnLast) const
 	{
 		return mRec->vF(columnFirst, columnLast);
 	}
@@ -847,7 +848,7 @@ class PDBFileParser
 	void ParseRemarks();
 
 	//	void ParseRemark3();
-	//	size_t ParseRemark3(const std::string& program, const Remark3Template templ[], size_t N);
+	//	std::size_t ParseRemark3(const std::string& program, const Remark3Template templ[], std::size_t N);
 	//	std::string NextRemark3Line();
 
 	void ParseRemark200();
@@ -895,12 +896,7 @@ class PDBFileParser
 				if (year < 1950)
 					year += 100;
 
-				std::stringstream ss;
-				ss << std::setw(4) << std::setfill('0') << year << '-'
-				   << std::setw(2) << std::setfill('0') << month << '-'
-				   << std::setw(2) << std::setfill('0') << day;
-
-				s = ss.str();
+				s = cif::format("{:04}-{:02}-{:02}", year, month, day);
 			}
 			else if (regex_match(s, m, rx2))
 			{
@@ -912,7 +908,7 @@ class PDBFileParser
 				if (year < 1950)
 					year += 100;
 
-				s = cif::format("%04d-%02d", year, month).str();
+				s = cif::format("{:04}-{:02}", year, month);
 			}
 			else
 				ec = error::make_error_code(error::pdbErrors::invalidDate);
@@ -1132,7 +1128,7 @@ void PDBFileParser::PreParseInput(std::istream &is)
 		if (not cs.empty())
 		{
 			auto r = std::from_chars(cs.data(), cs.data() + cs.length(), result);
-			if (r.ec != std::errc())
+			if ((bool)r.ec)
 				throw std::runtime_error("Continuation std::string '" + cs + "' is not valid");
 		}
 
@@ -1320,7 +1316,7 @@ void PDBFileParser::PreParseInput(std::istream &is)
 		{
 			std::string siteName = value.substr(5, 3);
 			cif::trim_right(value);
-			size_t n = value.length() - 12;
+			std::size_t n = value.length() - 12;
 			value += std::string(11 - (n % 11), ' ');
 
 			while (lookahead.substr(0, 6) == type and lookahead.substr(11, 3) == siteName)
@@ -1397,7 +1393,7 @@ void PDBFileParser::PreParseInput(std::istream &is)
 			{
 				auto f = cur->vF(74, 78);
 				auto r = cif::from_chars(f.data(), f.data() + f.length(), link.distance);
-				if (r.ec != std::errc() and cif::VERBOSE > 0)
+				if ((bool)r.ec and cif::VERBOSE > 0)
 					std::cerr << "Error parsing link distance at line " << cur->mLineNr << '\n';
 			}
 			//	74 – 78         Real(5.2)      Length          Link distance
@@ -1962,7 +1958,7 @@ void PDBFileParser::ParseRemarks()
 			switch (remarkNr)
 			{
 				case 1:
-					while (mRec->is("REMARK   1"))
+					while (mRec->is("REMARK   1") or mRec->is("REMARK 001"))
 					{
 						if (mRec->mVlen > 15 and vS(12, 20) == "REFERENCE")
 						{
@@ -3146,7 +3142,6 @@ void PDBFileParser::ParseRemark350()
 	std::map<std::string, std::string> values;
 	std::vector<std::string> asymIdList;
 	std::smatch m;
-	cif::row_handle genR;
 
 	std::vector<double> mat, vec;
 
@@ -3334,38 +3329,27 @@ void PDBFileParser::ParseRemark350()
 
 						std::string type = mat == std::vector<double>{ 1, 0, 0, 0, 1, 0, 0, 0, 1 } and vec == std::vector<double>{ 0, 0, 0 } ? "identity operation" : "crystal symmetry operation";
 
-						// if (type == "identity operation")
-						// {
-
-						// }
-						// else
-						try
-						{
-							// clang-format off
-							getCategory("pdbx_struct_oper_list")->emplace({
+						auto pdbx_struct_oper_list = getCategory("pdbx_struct_oper_list");
+						if (not pdbx_struct_oper_list->contains(cif::key("id") == operID))
+							getCategory("pdbx_struct_oper_list")->emplace({ // clang-format off
 								{ "id", operID },
 								{ "type", type },
 								// { "name", "" },
 							    // { "symmetryOperation", "" },
-								{ "matrix[1][1]", cif::format("%12.10f", mat[0]).str() },
-								{ "matrix[1][2]", cif::format("%12.10f", mat[1]).str() },
-								{ "matrix[1][3]", cif::format("%12.10f", mat[2]).str() },
-								{ "vector[1]", cif::format("%12.10f", vec[0]).str() },
-								{ "matrix[2][1]", cif::format("%12.10f", mat[3]).str() },
-								{ "matrix[2][2]", cif::format("%12.10f", mat[4]).str() },
-								{ "matrix[2][3]", cif::format("%12.10f", mat[5]).str() },
-								{ "vector[2]", cif::format("%12.10f", vec[1]).str() },
-								{ "matrix[3][1]", cif::format("%12.10f", mat[6]).str() },
-								{ "matrix[3][2]", cif::format("%12.10f", mat[7]).str() },
-								{ "matrix[3][3]", cif::format("%12.10f", mat[8]).str() },
-								{ "vector[3]", cif::format("%12.10f", vec[2]).str() }
+								{ "matrix[1][1]", cif::format("{:12.10f}", mat[0]) },
+								{ "matrix[1][2]", cif::format("{:12.10f}", mat[1]) },
+								{ "matrix[1][3]", cif::format("{:12.10f}", mat[2]) },
+								{ "vector[1]", cif::format("{:12.10f}", vec[0]) },
+								{ "matrix[2][1]", cif::format("{:12.10f}", mat[3]) },
+								{ "matrix[2][2]", cif::format("{:12.10f}", mat[4]) },
+								{ "matrix[2][3]", cif::format("{:12.10f}", mat[5]) },
+								{ "vector[2]", cif::format("{:12.10f}", vec[1]) },
+								{ "matrix[3][1]", cif::format("{:12.10f}", mat[6]) },
+								{ "matrix[3][2]", cif::format("{:12.10f}", mat[7]) },
+								{ "matrix[3][3]", cif::format("{:12.10f}", mat[8]) },
+								{ "vector[3]", cif::format("{:12.10f}", vec[2]) }
 							});
-							// clang-format on
-						}
-						catch (duplicate_key_error &ex)
-						{
-							// so what?
-						}
+																			// clang-format on
 
 						mat.clear();
 						vec.clear();
@@ -4202,7 +4186,7 @@ void PDBFileParser::ConstructEntities()
 
 			chains.push_back(std::string{ chain.mDbref.chainID });
 
-			size_t seqLen = 0, seqCanLen = 0;
+			std::size_t seqLen = 0, seqCanLen = 0;
 
 			for (auto &res : chain.mSeqres)
 			{
@@ -4265,7 +4249,7 @@ void PDBFileParser::ConstructEntities()
 			}
 
 			auto cat_ps = getCategory("entity_poly_seq");
-			for (size_t i = 0; i < chain.mSeqres.size(); ++i)
+			for (std::size_t i = 0; i < chain.mSeqres.size(); ++i)
 			{
 				auto &rs = chain.mSeqres[i];
 
@@ -4300,6 +4284,8 @@ void PDBFileParser::ConstructEntities()
 			type = "polypeptide(L)";
 		else if (mightBeDNA and not mightBePolyPeptide)
 			type = "polyribonucleotide";
+		else
+			type = "other";
 
 		// clang-format off
 		getCategory("entity_poly")->emplace({
@@ -4327,7 +4313,7 @@ void PDBFileParser::ConstructEntities()
 	}
 
 	// build sugar trees first
-	ConstructSugarTrees(asymNr);
+	// ConstructSugarTrees(asymNr);
 
 	// done with the sugar, resume operation as before
 
@@ -4335,7 +4321,7 @@ void PDBFileParser::ConstructEntities()
 	std::map<std::tuple<std::string, std::string>, int> ndbSeqNum; // for nonpoly scheme
 	std::map<std::string, int> entityAuthSeqNum;                   // for nonpoly scheme too
 
-	for (size_t i = 0; i < mHets.size(); ++i)
+	for (std::size_t i = 0; i < mHets.size(); ++i)
 	{
 		auto &heti = mHets[i];
 
@@ -4505,7 +4491,7 @@ void PDBFileParser::ConstructEntities()
 	int modResID = 1;
 	std::set<std::string> modResSet;
 	for (auto rec = FindRecord("MODRES"); rec != nullptr and rec->is("MODRES");
-		 rec = rec->mNext)                     //	 1 -  6        Record name   "MODRES"
+		rec = rec->mNext)                      //	 1 -  6        Record name   "MODRES"
 	{                                          //	 8 - 11        IDcode        idCode      ID code of this datablock.
 		std::string resName = rec->vS(13, 15); //	13 - 15        Residue name  resName     Residue name used in this datablock.
 		char chainID = rec->vC(17);            //	17             Character     chainID     Chain identifier.
@@ -5306,7 +5292,7 @@ void PDBFileParser::ParseConnectivtyAnnotation()
 
 				double d;
 				auto r = cif::from_chars(distance.data(), distance.data() + distance.length(), d);
-				if (r.ec != std::errc())
+				if ((bool)r.ec)
 				{
 					if (cif::VERBOSE > 0)
 						std::cerr << "Distance value '" << distance << "' is not a valid float in LINK record\n";
@@ -5627,7 +5613,7 @@ void PDBFileParser::ParseCoordinateTransformation()
 			igiven = vC(60) == '1';   //	60             Integer       iGiven        1 if coordinates for the  representations
 			                          //	                                           which  are approximately related by the
 			GetNextRecord();          //	                                           transformations  of the molecule are
-		}                             //	                                           contained in the datablock. Otherwise, blank.
+		} //	                                           contained in the datablock. Otherwise, blank.
 
 		// clang-format off
 		getCategory("struct_ncs_oper")->emplace({
@@ -5712,7 +5698,7 @@ void PDBFileParser::ParseCoordinate(int modelNr)
 	stable_sort(atoms.begin(), atoms.end(), rLess);
 
 	// now reiterate the atoms to reorder alternates
-	for (size_t i = 0; i + 1 < atoms.size(); ++i)
+	for (std::size_t i = 0; i + 1 < atoms.size(); ++i)
 	{
 		char altLoc = std::get<3>(atoms[i])->vC(17);
 
@@ -5781,6 +5767,9 @@ void PDBFileParser::ParseCoordinate(int modelNr)
 		std::string element = vS(77, 78);    //	77 - 78        LString(2)    element      Element symbol, right-justified.
 		std::string charge = vS(79, 80);     //	79 - 80        LString(2)    charge       Charge  on the atom.
 
+		if (element.empty())
+			throw std::runtime_error("Empty element column in PDB file at line " + std::to_string(mRec->mLineNr));
+
 		std::string entityID = mAsymID2EntityID[asymID];
 
 		charge = pdb2cifCharge(charge);
@@ -5859,7 +5848,7 @@ void PDBFileParser::ParseCoordinate(int modelNr)
 
 			auto f = [](float f) -> std::string
 			{
-				return cif::format("%6.4f", f).str();
+				return cif::format("{:6.4f}", f);
 			};
 
 			// clang-format off
@@ -5909,7 +5898,8 @@ void PDBFileParser::Parse(std::istream &is, cif::file &result)
 {
 	try
 	{
-		mDatablock.set_validator(result.get_validator());
+		if (mDatablock.get_validator() == nullptr)
+			mDatablock.load_dictionary();
 
 		PreParseInput(is);
 
@@ -6361,7 +6351,7 @@ bool PDBFileParser::PDBChain::SameSequence(const PDBChain &rhs) const
 {
 	bool result = mSeqres.size() == rhs.mSeqres.size();
 
-	for (size_t i = 0; result and i < mSeqres.size(); ++i)
+	for (std::size_t i = 0; result and i < mSeqres.size(); ++i)
 		result = mSeqres[i].mMonID == rhs.mSeqres[i].mMonID;
 
 	return result;
@@ -6373,12 +6363,22 @@ void read_pdb_file(std::istream &pdbFile, cif::file &cifFile)
 {
 	PDBFileParser p;
 
-	cifFile.load_dictionary("mmcif_pdbx.dic");
-
 	p.Parse(pdbFile, cifFile);
 
-	if (not cifFile.is_valid() and cif::VERBOSE >= 0)
-		std::cerr << "Resulting mmCIF file is not valid!\n";
+	if (cifFile.empty())
+	{
+		if (VERBOSE >= 0)
+			std::cerr << "PDB is empty!\n";
+	}
+	else
+	{
+		cifFile.front().load_dictionary();
+		if (cifFile.front().get_validator() == nullptr)
+			cifFile.front().set_validator(&validator_factory::instance().get("mmcif_pdbx.dic"));
+
+		if (not cifFile.is_valid() and cif::VERBOSE >= 0)
+			std::cerr << "Resulting mmCIF file is not valid!\n";
+	}
 }
 
 // --------------------------------------------------------------------
@@ -6402,7 +6402,10 @@ file read(std::istream &is)
 		// apart from the letter 'd', the test has changed into the following:
 
 		if (std::isalpha(ch) and std::toupper(ch) != 'D')
+		{
 			read_pdb_file(is, result);
+			fixup_pdbx(result);
+		}
 		else
 		{
 			try
@@ -6413,16 +6416,38 @@ file read(std::istream &is)
 			{
 				std::throw_with_nested(std::runtime_error("Since the file did not start with a valid PDB HEADER line mmCIF was assumed, but that failed."));
 			}
-		}
 
-		// Since we're using the cif::pdb way of reading the file, the data may need
-		// reconstruction
-		reconstruct_pdbx(result);
+			if (not(result.empty() or result.front().empty()))
+			{
+				if (auto &db = result.front(); db.get("audit_conform") == nullptr)
+					reconstruct_pdbx(result);
+				else
+				{
+					try
+					{
+						// Try to see if we can create an mm::structure out of this data.
+						// If that fails, we need to reconstruct a PDBx file out of it.
+
+						cif::mm::structure s(result);
+					}
+					catch (const std::exception &e)
+					{
+						reconstruct_pdbx(result);
+					}
+				}
+			}
+		}
 	}
 
 	// Must be a PDB like file, right?
-	if (result.get_validator() == nullptr)
-		result.load_dictionary("mmcif_pdbx.dic");
+	if (not result.empty())
+	{
+		auto &db = result.front();
+		if (db.get_validator() == nullptr)
+			db.set_validator(&validator_factory::instance().get("mmcif_pdbx.dic"));
+		if (db.is_valid())
+			db.get_validator()->fill_audit_conform(db["audit_conform"]);
+	}
 
 	return result;
 }

src/pdb/pdb2cif_remark_3.cpp

@@ -980,8 +980,8 @@ std::string Remark3Parser::nextLine()
 
 	while (mRec != nullptr and mRec->is("REMARK   3"))
 	{
-		size_t valueIndent = 0;
-		for (size_t i = 4; i < mRec->mVlen; ++i)
+		std::size_t valueIndent = 0;
+		for (std::size_t i = 4; i < mRec->mVlen; ++i)
 		{
 			if (mRec->mValue[i] == ' ')
 				continue;
@@ -1232,7 +1232,7 @@ void Remark3Parser::storeCapture(const char *category, std::initializer_list<con
 			}
 			//			else if (iequals(category, "struct_ncs_dom"))
 			//			{
-			//				size_t id = cat.size() + 1;
+			//				std::size_t id = cat.size() + 1;
 			//
 			//				cat.emplace({
 			//					{ "id", id }
@@ -1478,8 +1478,13 @@ bool Remark3Parser::parse(const std::string &expMethod, PDBRecord *r, cif::datab
 
 		best.parser->fixup();
 
+		auto &validator = cif::validator_factory::instance().get("mmcif_pdbx.dic");
+
 		for (auto &cat1 : best.parser->mDb)
 		{
+			if (cat1.empty())
+				continue;
+
 			auto &cat2 = db[cat1.name()];
 
 			// copy only the values in the first row for the following categories
@@ -1493,8 +1498,15 @@ bool Remark3Parser::parse(const std::string &expMethod, PDBRecord *r, cif::datab
 					auto r1 = cat1.front();
 					auto r2 = cat2.front();
 
-					for (auto item : cat1.key_items())
-						r2[item] = r1[item].text();
+					auto cv = cat1.get_cat_validator();
+					if (cv == nullptr)
+						cv = validator.get_validator_for_category(cat1.name());
+					
+					if (cv == nullptr)
+						continue;
+
+					for (auto &iv : cv->m_item_validators)
+						r2[iv.m_item_name] = r1[iv.m_item_name].text();
 				}
 			}
 			else

src/pdb/pdb_record.hpp

@@ -40,24 +40,24 @@ struct PDBRecord
 	PDBRecord *mNext;
 	uint32_t mLineNr;
 	char mName[11];
-	size_t mVlen;
+	std::size_t mVlen;
 	char mValue[1];
 
 	PDBRecord(uint32_t lineNr, const std::string &name, const std::string &value);
 	~PDBRecord();
 
-	void *operator new(size_t);
-	void *operator new(size_t size, size_t vLen);
+	void *operator new(std::size_t);
+	void *operator new(std::size_t size, std::size_t vLen);
 
 	void operator delete(void *p);
-	void operator delete(void *p, size_t vLen);
+	void operator delete(void *p, std::size_t vLen);
 
 	bool is(const char *name) const;
 
-	char vC(size_t column);
-	std::string vS(size_t columnFirst, size_t columnLast = std::numeric_limits<size_t>::max());
+	char vC(std::size_t column);
+	std::string vS(std::size_t columnFirst, std::size_t columnLast = std::numeric_limits<std::size_t>::max());
 	int vI(int columnFirst, int columnLast);
-	std::string vF(size_t columnFirst, size_t columnLast);
+	std::string vF(std::size_t columnFirst, std::size_t columnLast);
 };
 
 } // namespace pdbx

src/pdb/validate-pdbx.cpp

@@ -48,7 +48,7 @@ condition get_parents_condition(const validator &validator, row_handle rh, const
 		{
 			condition cond;
 
-			for (size_t ix = 0; ix < link->m_child_keys.size(); ++ix)
+			for (std::size_t ix = 0; ix < link->m_child_keys.size(); ++ix)
 			{
 				auto childValue = rh[link->m_child_keys[ix]];
 
@@ -61,17 +61,15 @@ condition get_parents_condition(const validator &validator, row_handle rh, const
 			result = std::move(result) or std::move(cond);
 		}
 	}
-	else if (cif::VERBOSE > 0)
-		std::cerr << "warning: no child to parent links were found for child " << childName << " and parent " << parentName << '\n';
 
 	return result;
 }
 
-bool is_valid_pdbx_file(const file &file, std::string_view dictionary)
+bool is_valid_pdbx_file(const file &file, const validator &v)
 {
 	std::error_code ec;
-	bool result = is_valid_pdbx_file(file, dictionary, ec);
-	return result and ec == std::errc();
+	bool result = is_valid_pdbx_file(file, v, ec);
+	return result and not(bool) ec;
 }
 
 bool is_valid_pdbx_file(const file &file, std::error_code &ec)
@@ -80,42 +78,23 @@ bool is_valid_pdbx_file(const file &file, std::error_code &ec)
 
 	if (file.empty())
 		ec = make_error_code(validation_error::empty_file);
+	else if (auto ac = file.front().get("audit_conform"); ac != nullptr)
+		result = is_valid_pdbx_file(file, validator_factory::instance().get(*ac), ec);
 	else
-	{
-		std::string dictionary = "mmcif_pdbx";
+		result = is_valid_pdbx_file(file, validator_factory::instance().get("mmcif_pdbx.dic"), ec);
 
-		for (auto &db : file)
-		{
-			auto audit_conform = db.get("audit_conform");
-			if (audit_conform == nullptr)
-				continue;
-			
-			if (not audit_conform->empty())
-			{
-				auto specified_dict = audit_conform->front()["dict_name"];
-				if (not specified_dict.empty())
-					dictionary = specified_dict.as<std::string>();
-			}
-
-			break;
-		}
-
-		result = is_valid_pdbx_file(file, dictionary, ec);
-	}
-	
 	return result;
 }
 
-bool is_valid_pdbx_file(const file &file, std::string_view dictionary, std::error_code &ec)
+bool is_valid_pdbx_file(const file &file, const validator &validator, std::error_code &ec)
 {
 	using namespace cif::literals;
 
-	bool result = true;
+	bool result = true, warned_missing_parents = false;
 
 	try
 	{
 		auto &cf = cif::compound_factory::instance();
-		auto &validator = cif::validator_factory::instance().operator[](dictionary);
 
 		if (file.empty())
 			throw std::runtime_error("Empty file");
@@ -148,10 +127,18 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary, std::erro
 			if (not cf.is_monomer(comp_id))
 				continue;
 
-			auto p = pdbx_poly_seq_scheme.find(get_parents_condition(validator, r, pdbx_poly_seq_scheme));
+			auto cond = get_parents_condition(validator, r, pdbx_poly_seq_scheme);
+			if (not cond)
+			{
+				if (VERBOSE > 0 and std::exchange(warned_missing_parents, true) == false)
+					std::cerr << "warning: missing links for atom_site/pdbx_poly_seq_scheme\n";
+				continue;
+			}
+
+			auto p = pdbx_poly_seq_scheme.find(std::move(cond));
 			if (p.size() != 1)
 			{
-				if (cif::VERBOSE > 0)
+				if (VERBOSE > 0)
 					std::clog << "In atom_site record: " << r["id"].text() << '\n';
 				throw std::runtime_error("For each monomer in atom_site there should be exactly one pdbx_poly_seq_scheme record");
 			}
@@ -180,7 +167,7 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary, std::erro
 
 			const auto entity_poly_type = entity_poly.find1<std::string>("entity_id"_key == entity_id, "type");
 
-			std::map<int,std::set<std::string>> mon_per_seq_id;
+			std::map<int, std::set<std::string>> mon_per_seq_id;
 
 			for (const auto &[num, mon_id, hetero] : entity_poly_seq.find<int, std::string, bool>("entity_id"_key == entity_id, "num", "mon_id", "hetero"))
 			{
@@ -189,6 +176,7 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary, std::erro
 				for (auto asym_id : struct_asym.find<std::string>("entity_id"_key == entity_id, "id"))
 				{
 					if (pdbx_poly_seq_scheme.count(
+							"entity_id"_key == entity_id and
 							"asym_id"_key == asym_id and
 							"mon_id"_key == mon_id and
 							"seq_id"_key == num and
@@ -202,6 +190,7 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary, std::erro
 			for (const auto &[seq_id, mon_id, hetero] : pdbx_poly_seq_scheme.find<int, std::string, bool>("entity_id"_key == entity_id, "seq_id", "mon_id", "hetero"))
 			{
 				if (entity_poly_seq.count(
+						"entity_id"_key == entity_id and
 						"mon_id"_key == mon_id and
 						"num"_key == seq_id and
 						"hetero"_key == hetero) != 1)
@@ -213,28 +202,37 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary, std::erro
 					throw std::runtime_error("Mismatch between the hetero flag in the poly seq schemes and the number residues per seq_id");
 			}
 
-			for (const auto &[seq_id, mon_ids] : mon_per_seq_id)
-			{
-				for (auto asym_id : struct_asym.find<std::string>("entity_id"_key == entity_id, "id"))
-				{
-					condition cond;
-					
-					for (auto mon_id : mon_ids)
-						cond = std::move(cond) or "label_comp_id"_key == mon_id;
+			// This code proved to take too much time ...
 
-					cond = "label_entity_id"_key == entity_id and
-						"label_asym_id"_key == asym_id and
-						"label_seq_id"_key == seq_id and not std::move(cond);
-					
-					if (atom_site.contains(std::move(cond)))
-						throw std::runtime_error("An atom_site record exists that has no parent in the poly seq scheme categories");
-				}
+			// for (const auto &[seq_id, mon_ids] : mon_per_seq_id)
+			// {
+			// 	for (auto asym_id : struct_asym.find<std::string>("entity_id"_key == entity_id, "id"))
+			// 	{
+			// 		condition cond;
+
+			// 		for (auto mon_id : mon_ids)
+			// 			cond = std::move(cond) or "label_comp_id"_key == mon_id;
+
+			// 		cond = "label_entity_id"_key == entity_id and
+			// 			"label_asym_id"_key == asym_id and
+			// 			"label_seq_id"_key == seq_id and not std::move(cond);
+
+			// 		if (atom_site.contains(std::move(cond)))
+			// 			throw std::runtime_error("An atom_site record exists that has no parent in the poly seq scheme categories");
+			// 	}
+			// }
+
+			// ... so we're using this instead, should be almost the same...
+
+			for (const auto &[comp_id, seq_id] :
+				atom_site.find<std::string, int>("label_entity_id"_key == entity_id, "label_comp_id", "label_seq_id"))
+			{
+				if (not mon_per_seq_id[seq_id].contains(comp_id))
+					throw std::runtime_error("An atom_site record exists that has no parent in the poly seq scheme categories");
 			}
 
 			auto &&[seq, seq_can] = entity_poly.find1<std::optional<std::string>, std::optional<std::string>>("entity_id"_key == entity_id,
 				"pdbx_seq_one_letter_code", "pdbx_seq_one_letter_code_can");
-			
-			std::string::const_iterator si, sci, se, sce;
 
 			auto seq_match = [&](bool can, std::string::const_iterator si, std::string::const_iterator se)
 			{
@@ -271,8 +269,8 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary, std::erro
 							else
 								letter = '(' + comp_id + ')';
 						}
-						
-						if (iequals(std::string{si, si + letter.length()}, letter))
+
+						if (iequals(std::string{ si, si + letter.length() }, letter))
 						{
 							match = true;
 							si += letter.length();
@@ -291,12 +289,14 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary, std::erro
 
 			if (not seq.has_value())
 			{
-				if (cif::VERBOSE > 0)
+				if (VERBOSE > 0)
 					std::clog << "Warning: entity_poly has no sequence for entity_id " << entity_id << '\n';
 			}
 			else
 			{
-				seq->erase(std::remove_if(seq->begin(), seq->end(), [](char ch) { return std::isspace(ch); }), seq->end());
+				seq->erase(std::remove_if(seq->begin(), seq->end(), [](char ch)
+							   { return std::isspace(ch); }),
+					seq->end());
 
 				if (not seq_match(false, seq->begin(), seq->end()))
 					throw std::runtime_error("Sequences do not match for entity " + entity_id);
@@ -304,12 +304,14 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary, std::erro
 
 			if (not seq_can.has_value())
 			{
-				if (cif::VERBOSE > 0)
-					std::clog << "Warning: entity_poly has no sequence for entity_id " << entity_id << '\n';
+				if (VERBOSE > 1)
+					std::clog << "Warning: entity_poly has no canonical sequence for entity_id " << entity_id << '\n';
 			}
 			else
 			{
-				seq_can->erase(std::remove_if(seq_can->begin(), seq_can->end(), [](char ch) { return std::isspace(ch); }), seq_can->end());
+				seq_can->erase(std::remove_if(seq_can->begin(), seq_can->end(), [](char ch)
+								   { return std::isspace(ch); }),
+					seq_can->end());
 
 				if (not seq_match(true, seq_can->begin(), seq_can->end()))
 					throw std::runtime_error("Canonical sequences do not match for entity " + entity_id);
@@ -321,16 +323,15 @@ bool is_valid_pdbx_file(const file &file, std::string_view dictionary, std::erro
 	catch (const std::exception &ex)
 	{
 		result = false;
-		if (cif::VERBOSE > 0)
+		if (VERBOSE > 0)
 			std::clog << ex.what() << '\n';
 		ec = make_error_code(validation_error::not_valid_pdbx);
 	}
 
-	if (not result and ec == std::errc())
+	if (not result and (bool) ec)
 		ec = make_error_code(validation_error::not_valid_pdbx);
 
 	return result;
 }
 
 } // namespace cif::pdb
-  

src/point.cpp

@@ -25,17 +25,19 @@
  */
 
 #include "cif++/point.hpp"
-#include "cif++/matrix.hpp"
 
-#include <cassert>
-#include <random>
+#include "cif++/matrix.hpp" // for matrix_subtraction, matrix_cofactors
+
+#include <initializer_list>
+#include <random> // for uniform_real_distribution, normal_distri...
+#include <stdexcept>
 
 namespace cif
 {
 
 // --------------------------------------------------------------------
 
-template<typename T>
+template <typename T>
 quaternion_type<T> normalize(quaternion_type<T> q)
 {
 	std::valarray<double> t(4);
@@ -126,10 +128,9 @@ quaternion construct_for_dihedral_angle(point p1, point p2, point p3, point p4,
 	p4 -= p3;
 	p3 -= p3;
 
-	quaternion q;
 	auto axis = -p2;
-
 	float dh = dihedral_angle(p1, p2, p3, p4);
+
 	return construct_from_angle_axis(angle - dh, axis);
 }
 
@@ -293,9 +294,9 @@ quaternion align_points(const std::vector<point> &pa, const std::vector<point> &
 	}
 
 	quaternion q(
-		static_cast<float>(cf(maxR, 0)), 
-		static_cast<float>(cf(maxR, 1)), 
-		static_cast<float>(cf(maxR, 2)), 
+		static_cast<float>(cf(maxR, 0)),
+		static_cast<float>(cf(maxR, 1)),
+		static_cast<float>(cf(maxR, 2)),
 		static_cast<float>(cf(maxR, 3)));
 	q = normalize(q);
 
@@ -327,4 +328,251 @@ point nudge(point p, float offset)
 	return p + r;
 }
 
+// --------------------------------------------------------------------
+
+std::tuple<point, float> smallest_sphere_around_2_points(std::array<cif::point, 2> pts)
+{
+	return { (pts[0] + pts[1]) / 2, distance(pts[0], pts[1]) / 2 };
+}
+
+std::tuple<point, float> smallest_sphere_around_3_points(std::array<cif::point, 3> pts)
+{
+	// Find two bisectors
+	auto vz = cross_product(pts[1] - pts[0], pts[2] - pts[0]);
+
+	auto bs1 = cross_product(vz, pts[1] - pts[0]);
+	bs1.normalize();
+
+	auto v1 = (pts[1] - pts[0]);
+	v1.normalize();
+
+	auto s1 = pts[0] + (distance(pts[1], pts[0]) / 2) * v1;
+
+	auto bs2 = cross_product(vz, pts[2] - pts[0]);
+	bs2.normalize();
+
+	auto v2 = (pts[2] - pts[0]);
+	v2.normalize();
+
+	auto s2 = pts[0] + (distance(pts[2], pts[0]) / 2) * v2;
+
+	auto c = line_line_intersection(s1, s1 + bs1, s2, s2 + bs2);
+	if (c)
+		return { *c, distance(*c, pts[0]) };
+
+	// Colinear points I guess, try something else
+	auto l1 = distance_squared(pts[0], pts[1]);
+	auto l2 = distance_squared(pts[0], pts[2]);
+	auto l3 = distance_squared(pts[1], pts[2]);
+
+	if (l1 > l2 and l1 > l3)
+		return smallest_sphere_around_2_points({ pts[0], pts[1] });
+	else if (l2 > l1 and l2 > l3)
+		return smallest_sphere_around_2_points({ pts[0], pts[2] });
+	else
+		return smallest_sphere_around_2_points({ pts[1], pts[2] });
+}
+
+std::tuple<point, float> smallest_sphere_around_4_points(std::array<cif::point, 4> pts)
+{
+	auto t0 = -norm_squared(pts[0]);
+	auto t1 = -norm_squared(pts[1]);
+	auto t2 = -norm_squared(pts[2]);
+	auto t3 = -norm_squared(pts[3]);
+
+	// clang-format off
+	matrix4x4<float> Tm({
+		pts[0].m_x, pts[0].m_y, pts[0].m_z, 1,
+		pts[1].m_x, pts[1].m_y, pts[1].m_z, 1,
+		pts[2].m_x, pts[2].m_y, pts[2].m_z, 1,
+		pts[3].m_x, pts[3].m_y, pts[3].m_z, 1
+	});
+	auto T = determinant(Tm);
+
+	if (T != 0)
+	{
+		matrix4x4<float> Dm({
+			t0, pts[0].m_y, pts[0].m_z, 1,
+			t1, pts[1].m_y, pts[1].m_z, 1,
+			t2, pts[2].m_y, pts[2].m_z, 1,
+			t3, pts[3].m_y, pts[3].m_z, 1
+		});
+		auto D = determinant(Dm) / T;
+		
+		matrix4x4<float> Em({
+			pts[0].m_x, t0, pts[0].m_z, 1,
+			pts[1].m_x, t1, pts[1].m_z, 1,
+			pts[2].m_x, t2, pts[2].m_z, 1,
+			pts[3].m_x, t3, pts[3].m_z, 1
+		});
+		auto E = determinant(Em) / T;
+		
+		matrix4x4<float> Fm({
+			pts[0].m_x, pts[0].m_y, t0, 1,
+			pts[1].m_x, pts[1].m_y, t1, 1,
+			pts[2].m_x, pts[2].m_y, t2, 1,
+			pts[3].m_x, pts[3].m_y, t3, 1
+		});
+		
+		auto F = determinant(Fm) / T;
+		
+		matrix4x4<float> Gm({
+			pts[0].m_x, pts[0].m_y, pts[0].m_z, t0,
+			pts[1].m_x, pts[1].m_y, pts[1].m_z, t1,
+			pts[2].m_x, pts[2].m_y, pts[2].m_z, t2,
+			pts[3].m_x, pts[3].m_y, pts[3].m_z, t3
+		});
+		auto G = determinant(Gm) / T;
+		
+		point center{ -D / 2, -E / 2, -F / 2 };
+		float radius = std::sqrt(D * D + E * E + F * F - 4 * G) / 2;
+
+		// clang-format on
+
+		return { center, radius };
+	}
+
+	// Perhaps some colinear points, try something else:
+
+	for (auto ix : std::initializer_list<std::array<size_t, 4>>{
+			 { 1, 2, 3, 0 },
+			 { 0, 2, 3, 1 },
+			 { 0, 1, 3, 2 },
+			 { 0, 1, 2, 3 },
+		 })
+	{
+		auto [center, radius] =
+			smallest_sphere_around_3_points({ pts[ix[0]], pts[ix[1]], pts[ix[2]] });
+
+		if (distance(pts[ix[3]], center) <= radius)
+			return { center, radius };
+	}
+
+	assert(false);
+	exit(1);
+}
+
+std::tuple<point, float> smallest_sphere_around_all_points(std::vector<point> P, std::vector<point> R)
+{
+	if (P.empty() or R.size() == 4)
+	{
+		switch (R.size())
+		{
+			case 1:
+				return { R[0], 0 };
+
+			case 2:
+				return smallest_sphere_around_2_points({ R[0], R[1] });
+
+			case 3:
+				return smallest_sphere_around_3_points({ R[0], R[1], R[2] });
+
+			case 4:
+				return smallest_sphere_around_4_points({ R[0], R[1], R[2], R[3] });
+
+			default:
+				assert(false);
+		}
+	}
+
+	auto p = P.back();
+	P.pop_back();
+
+	auto [c, r] = smallest_sphere_around_all_points(P, R);
+	assert(not std::isnan(r));
+	if (distance(c, p) <= r)
+		return { c, r };
+
+	R.emplace_back(p);
+	return smallest_sphere_around_all_points(P, R);
+}
+
+bool point_in_circle(point p, std::vector<point> c)
+{
+	switch (c.size())
+	{
+		case 0:
+			return false;
+
+		case 1:
+			return p == c.front();
+
+		case 2:
+		{
+			auto [center, radius] = smallest_sphere_around_2_points({ c[0], c[1] });
+			return cif::distance_squared(p, center) <= radius * radius;
+		}
+
+		case 3:
+		{
+			auto [center, radius] = smallest_sphere_around_3_points({ c[0], c[1], c[2] });
+			return cif::distance_squared(p, center) <= radius * radius;
+		}
+
+		case 4:
+		{
+			auto [center, radius] = smallest_sphere_around_4_points({ c[0], c[1], c[2], c[3] });
+			return cif::distance_squared(p, center) <= radius * radius;
+		}
+
+		default:
+			assert(false);
+			throw std::runtime_error("Error finding smallest sphere");
+	}
+}
+
+std::tuple<point, float> smallest_sphere_around_points(std::vector<point> pts)
+{
+	std::random_device rd;
+	std::mt19937 g(rd());
+
+	std::shuffle(pts.begin(), pts.end(), g);
+
+	std::vector<size_t> cix;
+
+	auto cirle_points = [&]()
+	{
+		std::vector<point> result;
+		for (auto ix : cix)
+			result.emplace_back(pts[ix]);
+		return result;
+	};
+
+	size_t i = 0;
+	while (i < pts.size())
+	{
+		if (std::find(cix.begin(), cix.end(), i) != cix.end() or
+			point_in_circle(pts[i], cirle_points()))
+		{
+			++i;
+		}
+		else
+		{
+			cix.erase(std::remove_if(cix.begin(), cix.end(), [i](size_t j)
+						  { return j < i; }),
+				cix.end());
+			cix.push_back(i);
+			if (cix.size() < 4)
+				i = 0;
+			else
+				++i;
+		}
+	}
+
+	switch (cix.size())
+	{
+		case 1:
+			return { pts[cix[0]], 0 };
+		case 2:
+			return smallest_sphere_around_2_points({ pts[cix[0]], pts[cix[1]] });
+		case 3:
+			return smallest_sphere_around_3_points({ pts[cix[0]], pts[cix[1]], pts[cix[2]] });
+		case 4:
+			return smallest_sphere_around_4_points({ pts[cix[0]], pts[cix[1]], pts[cix[2]], pts[cix[3]] });
+		default:
+			assert(false);
+			throw std::runtime_error("Error finding smallest sphere");
+	}
+}
+
 } // namespace cif

src/symmetry.cpp

@@ -32,7 +32,12 @@
 
 #include "symop_table_data.hpp"
 
-#include <Eigen/Eigenvalues>
+#if defined(_MSC_VER)
+#pragma warning (disable : 5054)	// warning C5054: operator '&': deprecated between enumerations of different types
+#pragma warning (disable : 4127)	// conditional expression is constant
+#endif
+
+#include <Eigen/Eigen>
 
 namespace cif
 {
@@ -90,10 +95,10 @@ float cell::get_volume() const
 	auto cos_beta = std::cos(beta);
 	auto cos_gamma = std::cos(gamma);
 
-	auto vol = m_a * m_b * m_c;
+	double vol = m_a * m_b * m_c;
 	vol *= std::sqrt(1.0f - cos_alpha * cos_alpha - cos_beta * cos_beta - cos_gamma * cos_gamma + 2.0f * cos_alpha * cos_beta * cos_gamma);
 
-	return vol;
+	return static_cast<float>(vol);
 }
 
 // --------------------------------------------------------------------
@@ -103,15 +108,15 @@ sym_op::sym_op(std::string_view s)
 	auto b = s.data();
 	auto e = b + s.length();
 
-	int rnri = 256;	// default to unexisting number
+	int rnri = 256; // default to unexisting number
 	auto r = std::from_chars(b, e, rnri);
-	
+
 	m_nr = static_cast<uint8_t>(rnri);
 	m_ta = r.ptr[1] - '0';
 	m_tb = r.ptr[2] - '0';
 	m_tc = r.ptr[3] - '0';
 
-	if (r.ec != std::errc() or rnri > 192 or r.ptr[0] != '_' or m_ta > 9 or m_tb > 9 or m_tc > 9)
+	if ((bool)r.ec or rnri > 192 or r.ptr[0] != '_' or m_ta > 9 or m_tb > 9 or m_tc > 9)
 		throw std::invalid_argument("Could not convert string into sym_op");
 }
 
@@ -119,16 +124,16 @@ std::string sym_op::string() const
 {
 	char b[9];
 	auto r = std::to_chars(b, b + sizeof(b), m_nr);
-	if (r.ec != std::errc() or r.ptr > b + 4)
+	if ((bool)r.ec or r.ptr > b + 4)
 		throw std::runtime_error("Could not write out symmetry operation to string");
-	
+
 	*r.ptr++ = '_';
 	*r.ptr++ = '0' + m_ta;
 	*r.ptr++ = '0' + m_tb;
 	*r.ptr++ = '0' + m_tc;
 	*r.ptr = 0;
 
-	return { b, static_cast<size_t>(r.ptr - b) };
+	return { b, static_cast<std::size_t>(r.ptr - b) };
 }
 
 // --------------------------------------------------------------------
@@ -163,41 +168,16 @@ transformation::transformation(const matrix3x3<float> &r, const cif::point &t)
 
 void transformation::try_create_quaternion()
 {
-	float Qxx = m_rotation(0, 0);
-	float Qxy = m_rotation(0, 1);
-	float Qxz = m_rotation(0, 2);
-	float Qyx = m_rotation(1, 0);
-	float Qyy = m_rotation(1, 1);
-	float Qyz = m_rotation(1, 2);
-	float Qzx = m_rotation(2, 0);
-	float Qzy = m_rotation(2, 1);
-	float Qzz = m_rotation(2, 2);
+	Eigen::Matrix3f rot;
 
-	Eigen::Matrix4f em;
+	rot << m_rotation(0, 0), m_rotation(0, 1), m_rotation(0, 2),
+		m_rotation(1, 0), m_rotation(1, 1), m_rotation(1, 2),
+		m_rotation(2, 0), m_rotation(2, 1), m_rotation(2, 2);
 
-	em << Qxx - Qyy - Qzz, Qyx + Qxy, Qzx + Qxz, Qzy - Qyz,
-			Qyx + Qxy, Qyy - Qxx - Qzz, Qzy + Qyz, Qxz - Qzx,
-			Qzx + Qxz, Qzy + Qyz, Qzz - Qxx - Qyy, Qyx - Qxy,
-			Qzy - Qyz, Qxz - Qzx, Qyx - Qxy, Qxx + Qyy + Qzz;
-
-	Eigen::EigenSolver<Eigen::Matrix4f> es(em / 3);
-
-	auto ev = es.eigenvalues();
-
-	for (size_t j = 0; j < 4; ++j)
+	if (rot * rot.transpose() == Eigen::Matrix3f::Identity() and rot.determinant() == 1)
 	{
-		if (std::abs(ev[j].real() - 1) > 0.01)
-			continue;
-		
-		auto col = es.eigenvectors().col(j);
-
-		m_q = normalize(cif::quaternion{
-			static_cast<float>(col(3).real()),
-			static_cast<float>(col(0).real()),
-			static_cast<float>(col(1).real()),
-			static_cast<float>(col(2).real()) });
-
-		break;
+		Eigen::Quaternionf qe(rot);
+		m_q = normalize(cif::quaternion{ qe.w(), qe.x(), qe.y(), qe.z() });
 	}
 }
 
@@ -221,7 +201,7 @@ transformation inverse(const transformation &t)
 spacegroup::spacegroup(int nr)
 	: m_nr(nr)
 {
-	const size_t N = kSymopNrTableSize;
+	const std::size_t N = kSymopNrTableSize;
 	int32_t L = 0, R = static_cast<int32_t>(N - 1);
 	while (L <= R)
 	{
@@ -234,7 +214,7 @@ spacegroup::spacegroup(int nr)
 
 	m_index = L;
 
-	for (size_t i = L; i < N and kSymopNrTable[i].spacegroup() == m_nr; ++i)
+	for (std::size_t i = L; i < N and kSymopNrTable[i].spacegroup() == m_nr; ++i)
 		emplace_back(kSymopNrTable[i].symop().data());
 }
 
@@ -297,7 +277,7 @@ point spacegroup::operator()(const point &pt, const cell &c, sym_op symop) const
 {
 	if (symop.m_nr < 1 or symop.m_nr > size())
 		throw std::out_of_range("symmetry operator number out of range");
-	
+
 	transformation t = at(symop.m_nr - 1);
 
 	t.m_translation.m_x += symop.m_ta - 5;
@@ -316,7 +296,7 @@ point spacegroup::inverse(const point &pt, const cell &c, sym_op symop) const
 {
 	if (symop.m_nr < 1 or symop.m_nr > size())
 		throw std::out_of_range("symmetry operator number out of range");
-	
+
 	transformation t = at(symop.m_nr - 1);
 
 	t.m_translation.m_x += symop.m_ta - 5;
@@ -343,7 +323,7 @@ int get_space_group_number(std::string_view spacegroup)
 
 	int result = 0;
 
-	const size_t N = kNrOfSpaceGroups;
+	const std::size_t N = kNrOfSpaceGroups;
 	int32_t L = 0, R = static_cast<int32_t>(N - 1);
 	while (L <= R)
 	{
@@ -365,7 +345,7 @@ int get_space_group_number(std::string_view spacegroup)
 	// not found, see if we can find a match based on xHM name
 	if (result == 0)
 	{
-		for (size_t i = 0; i < kNrOfSpaceGroups; ++i)
+		for (std::size_t i = 0; i < kNrOfSpaceGroups; ++i)
 		{
 			auto &sp = kSpaceGroups[i];
 			if (sp.xHM == spacegroup)
@@ -395,7 +375,7 @@ int get_space_group_number(std::string_view spacegroup, space_group_name type)
 
 	if (type == space_group_name::full)
 	{
-		const size_t N = kNrOfSpaceGroups;
+		const std::size_t N = kNrOfSpaceGroups;
 		int32_t L = 0, R = static_cast<int32_t>(N - 1);
 		while (L <= R)
 		{
@@ -450,13 +430,13 @@ int get_space_group_number(const datablock &db)
 
 	if (_symmetry.size() != 1)
 		throw std::runtime_error("Could not find a unique symmetry in this mmCIF file");
-	
+
 	return _symmetry.front().get<int>("Int_Tables_number");
 }
 
 // --------------------------------------------------------------------
 
-std::tuple<float,point,sym_op> crystal::closest_symmetry_copy(point a, point b) const
+std::tuple<float, point, sym_op> crystal::closest_symmetry_copy(point a, point b) const
 {
 	if (m_cell.get_a() == 0 or m_cell.get_b() == 0 or m_cell.get_c() == 0)
 		throw std::runtime_error("Invalid cell, contains a dimension that is zero");
@@ -475,7 +455,7 @@ std::tuple<float,point,sym_op> crystal::closest_symmetry_copy(point a, point b)
 
 	a = orthogonal(fa, m_cell);
 
-	for (size_t i = 0; i < m_spacegroup.size(); ++i)
+	for (std::size_t i = 0; i < m_spacegroup.size(); ++i)
 	{
 		sym_op s(static_cast<uint8_t>(i + 1));
 		auto &t = m_spacegroup[i];
@@ -491,7 +471,7 @@ std::tuple<float,point,sym_op> crystal::closest_symmetry_copy(point a, point b)
 		while (fsb.m_x + 0.5f < fa.m_x)
 		{
 			fsb.m_x += 1;
-			s.m_ta += 1;			
+			s.m_ta += 1;
 		}
 
 		while (fsb.m_y - 0.5f > fa.m_y)
@@ -503,7 +483,7 @@ std::tuple<float,point,sym_op> crystal::closest_symmetry_copy(point a, point b)
 		while (fsb.m_y + 0.5f < fa.m_y)
 		{
 			fsb.m_y += 1;
-			s.m_tb += 1;			
+			s.m_tb += 1;
 		}
 
 		while (fsb.m_z - 0.5f > fa.m_z)
@@ -515,7 +495,7 @@ std::tuple<float,point,sym_op> crystal::closest_symmetry_copy(point a, point b)
 		while (fsb.m_z + 0.5f < fa.m_z)
 		{
 			fsb.m_z += 1;
-			s.m_tc += 1;			
+			s.m_tc += 1;
 		}
 
 		auto p = orthogonal(fsb, m_cell);

src/symop-map-generator.cpp

@@ -280,7 +280,7 @@ int main(int argc, char* const argv[])
 			if (std::isdigit(line[0]))	// start of new spacegroup
 			{
 				auto r = std::from_chars(line.data(), line.data() + line.length(), sgnr);
-				if (r.ec != std::errc())
+				if ((bool)r.ec)
 					throw std::runtime_error("Error parsing symop.lib file");
 				rnr = 1;
 				continue;
@@ -426,7 +426,7 @@ const space_group kSpaceGroups[] =
 out << R"(
 };
 
-const size_t kNrOfSpaceGroups = sizeof(kSpaceGroups) / sizeof(space_group);
+const std::size_t kNrOfSpaceGroups = sizeof(kSpaceGroups) / sizeof(space_group);
 
 const symop_datablock kSymopNrTable[] = {
 )";
@@ -450,7 +450,7 @@ const symop_datablock kSymopNrTable[] = {
 
 		out << R"(};
 
-const size_t kSymopNrTableSize = sizeof(kSymopNrTable) / sizeof(symop_datablock);
+const std::size_t kSymopNrTableSize = sizeof(kSymopNrTable) / sizeof(symop_datablock);
 
 } // namespace mmcif
 )";

src/symop_table_data.hpp

@@ -361,7 +361,7 @@ const space_group kSpaceGroups[] =
 
 };
 
-const size_t kNrOfSpaceGroups = sizeof(kSpaceGroups) / sizeof(space_group);
+const std::size_t kNrOfSpaceGroups = sizeof(kSpaceGroups) / sizeof(space_group);
 
 const symop_datablock kSymopNrTable[] = {
     // P 1
@@ -5286,6 +5286,6 @@ const symop_datablock kSymopNrTable[] = {
     { 5005,   4, { -1, 0, 0, 0, 1, 0, 0, 0,-1, 1, 2, 0, 0, 1, 2, } },
 };
 
-const size_t kSymopNrTableSize = sizeof(kSymopNrTable) / sizeof(symop_datablock);
+const std::size_t kSymopNrTableSize = sizeof(kSymopNrTable) / sizeof(symop_datablock);
 
 } // namespace mmcif

src/text.cpp

@@ -28,6 +28,11 @@
 
 #include <algorithm>
 #include <cassert>
+#include <charconv>
+
+#if __has_include("fast_float/fast_float.h")
+#include "fast_float/fast_float.h"
+#endif
 
 namespace cif
 {
@@ -69,7 +74,7 @@ bool iequals(const char *a, const char *b)
 {
 	bool result = true;
 	for (; result and *a and *b; ++a, ++b)
-		result = tolower(*a) == tolower(*b);
+		result = kCharToLowerMap[uint8_t(*a)] == kCharToLowerMap[uint8_t(*b)];
 
 	return result and *a == *b;
 }
@@ -80,7 +85,7 @@ int icompare(std::string_view a, std::string_view b)
 	auto ai = a.begin(), bi = b.begin();
 
 	for (; d == 0 and ai != a.end() and bi != b.end(); ++ai, ++bi)
-		d = tolower(*ai) - tolower(*bi);
+		d = (int)kCharToLowerMap[uint8_t(*ai)] - (int)kCharToLowerMap[uint8_t(*bi)];
 
 	if (d == 0)
 	{
@@ -98,7 +103,7 @@ int icompare(const char *a, const char *b)
 	int d = 0;
 
 	for (; d == 0 and *a != 0 and *b != 0; ++a, ++b)
-		d = tolower(*a) - tolower(*b);
+		d = (int)kCharToLowerMap[uint8_t(*a)] - (int)kCharToLowerMap[uint8_t(*b)];
 
 	if (d == 0)
 	{
@@ -433,10 +438,10 @@ std::string::const_iterator nextLineBreak(std::string::const_iterator text, std:
 	return text;
 }
 
-std::vector<std::string> wrapLine(const std::string &text, size_t width)
+std::vector<std::string> wrapLine(const std::string &text, std::size_t width)
 {
 	std::vector<std::string> result;
-	std::vector<size_t> offsets = { 0 };
+	std::vector<std::size_t> offsets = { 0 };
 
 	auto b = text.begin();
 	while (b != text.end())
@@ -448,18 +453,18 @@ std::vector<std::string> wrapLine(const std::string &text, size_t width)
 		b = e;
 	}
 
-	size_t count = offsets.size() - 1;
+	std::size_t count = offsets.size() - 1;
 
-	std::vector<size_t> minima(count + 1, 1000000);
+	std::vector<std::size_t> minima(count + 1, 1000000);
 	minima[0] = 0;
-	std::vector<size_t> breaks(count + 1, 0);
+	std::vector<std::size_t> breaks(count + 1, 0);
 
-	for (size_t i = 0; i < count; ++i)
+	for (std::size_t i = 0; i < count; ++i)
 	{
-		size_t j = i + 1;
+		std::size_t j = i + 1;
 		while (j <= count)
 		{
-			size_t w = offsets[j] - offsets[i];
+			std::size_t w = offsets[j] - offsets[i];
 
 			if (w > width)
 				break;
@@ -467,7 +472,7 @@ std::vector<std::string> wrapLine(const std::string &text, size_t width)
 			while (w > 0 and isspace(text[offsets[i] + w - 1]))
 				--w;
 
-			size_t cost = minima[i];
+			std::size_t cost = minima[i];
 			if (j < count) // last line may be shorter
 				cost += (width - w) * (width - w);
 
@@ -481,10 +486,10 @@ std::vector<std::string> wrapLine(const std::string &text, size_t width)
 		}
 	}
 
-	size_t j = count;
+	std::size_t j = count;
 	while (j > 0)
 	{
-		size_t i = breaks[j];
+		std::size_t i = breaks[j];
 		result.push_back(text.substr(offsets[i], offsets[j] - offsets[i]));
 		j = i;
 	}
@@ -494,7 +499,7 @@ std::vector<std::string> wrapLine(const std::string &text, size_t width)
 	return result;
 }
 
-std::vector<std::string> word_wrap(const std::string &text, size_t width)
+std::vector<std::string> word_wrap(const std::string &text, std::size_t width)
 {
 	std::vector<std::string> result;
 	for (auto p : cif::split<std::string>(text, "\n"))
@@ -512,4 +517,32 @@ std::vector<std::string> word_wrap(const std::string &text, size_t width)
 	return result;
 }
 
+#if __has_include("fast_float/fast_float.h")
+
+template <typename T>
+std::from_chars_result ff_charconv<T, typename std::enable_if_t<std::is_floating_point_v<T>>>::from_chars(const char *a, const char *b, T &v)
+{
+	auto r = fast_float::from_chars(a, b, v);
+	return { r.ptr, r.ec };
+}
+
+template struct ff_charconv<float>;
+template struct ff_charconv<double>;
+// template struct ff_charconv<long double>;
+
+#ifdef __STDCPP_FLOAT64_T__
+template struct ff_charconv<std::float64_t>;
+#endif
+#ifdef __STDCPP_FLOAT32_T__
+template struct ff_charconv<std::float32_t>;
+#endif
+#ifdef __STDCPP_FLOAT16_T__
+template struct ff_charconv<std::float16_t>;
+#endif
+#ifdef __STDCPP_BFLOAT16_T__
+template struct ff_charconv<std::bfloat16_t>;
+#endif
+
+#endif
+
 } // namespace cif

src/utilities.cpp

@@ -34,14 +34,20 @@
 #include <condition_variable>
 #include <cstring>
 #include <deque>
+#include <format>
 #include <fstream>
-#include <functional>
 #include <iomanip>
 #include <iostream>
 #include <map>
 #include <mutex>
 #include <sstream>
+#include <string>
 #include <thread>
+#include <utility>
+
+#if __cpp_lib_jthread >= 201911L
+#include <stop_token>
+#endif
 
 namespace fs = std::filesystem;
 
@@ -63,29 +69,52 @@ std::string get_version_nr()
 
 // --------------------------------------------------------------------
 
-#ifdef _WIN32
+#if defined(_WIN32) or defined(__MINGW32__)
 }
-#include <Windows.h>
-#include <libloaderapi.h>
-#include <wincon.h>
-
-#include <codecvt>
+// clang-format off
+# include <windows.h>
+# include <libloaderapi.h>
+# include <wincon.h>
+// clang-format on
 
 namespace cif
 {
 
 uint32_t get_terminal_width()
 {
-    CONSOLE_SCREEN_BUFFER_INFO csbi;
-    ::GetConsoleScreenBufferInfo(::GetStdHandle(STD_OUTPUT_HANDLE), &csbi);
-    return csbi.srWindow.Right - csbi.srWindow.Left + 1;
+	CONSOLE_SCREEN_BUFFER_INFO csbi;
+	return ::GetConsoleScreenBufferInfo(::GetStdHandle(STD_OUTPUT_HANDLE), &csbi)
+	           ? csbi.srWindow.Right - csbi.srWindow.Left + 1
+	           : 80;
+}
+
+void write_to_console(const std::string &s)
+{
+	auto h = ::GetStdHandle(STD_OUTPUT_HANDLE);
+	CONSOLE_SCREEN_BUFFER_INFO csbi;
+
+	if (auto l = ::MultiByteToWideChar(CP_UTF8, 0, s.data(), s.length(), nullptr, 0);
+		l > 0 and ::GetConsoleScreenBufferInfo(::GetStdHandle(STD_OUTPUT_HANDLE), &csbi))
+	{
+		std::u16string ws(l, 0);
+
+		::MultiByteToWideChar(CP_UTF8, 0, s.data(), s.length(), (LPWSTR)ws.data(), l);
+
+		DWORD w;
+		::WriteConsoleW(h, ws.data(), ws.length(), &w, nullptr);
+	}
+	else
+	{
+		std::cout.write(s.data(), s.length());
+		std::cout.flush();
+	}
 }
 
 #else
 
-#include <sys/ioctl.h>
-#include <termios.h>
-#include <limits.h>
+# include <limits.h>
+# include <sys/ioctl.h>
+# include <termios.h>
 
 uint32_t get_terminal_width()
 {
@@ -100,59 +129,220 @@ uint32_t get_terminal_width()
 	return result;
 }
 
+inline void write_to_console(const std::string &s)
+{
+	std::cout << s << std::flush;
+}
+
 #endif
 
 // --------------------------------------------------------------------
 
 struct progress_bar_impl
 {
-	progress_bar_impl(int64_t inMax, const std::string &inAction)
-		: m_max_value(inMax)
+	progress_bar_impl(uint64_t max_value, const std::string &message)
+		: m_max_value(max_value)
 		, m_consumed(0)
-		, m_action(inAction)
-		, m_message(inAction)
-		, m_thread(std::bind(&progress_bar_impl::run, this))
+		, m_action(message)
+		, m_message(message)
 	{
 	}
 
-	progress_bar_impl(const progress_bar_impl&) = delete;
-	progress_bar_impl &operator=(const progress_bar_impl &) = delete;
+	virtual ~progress_bar_impl() {}
 
-	~progress_bar_impl();
-
-	void run();
-
-	void consumed(int64_t n);
-	void progress(int64_t p);
-	void message(const std::string &msg);
-
-	void print_progress();
-	void print_done();
+	virtual void consumed(uint64_t n);
+	virtual void progress(uint64_t p);
+	virtual void message(const std::string &msg);
+	virtual void print_done();
 
 	using time_point = std::chrono::time_point<std::chrono::system_clock>;
 
-	int64_t m_max_value;
-	std::atomic<int64_t> m_consumed;
-	int64_t m_last_consumed = 0;
-	int m_spinner_index = 0;
+	uint64_t m_max_value;
+	std::atomic<uint64_t> m_consumed;
 	std::string m_action, m_message;
-	std::mutex m_mutex;
-	std::thread m_thread;
 	time_point m_start = std::chrono::system_clock::now();
-	time_point m_last = std::chrono::system_clock::now();
-	bool m_stop = false;
 };
 
-progress_bar_impl::~progress_bar_impl()
+void progress_bar_impl::consumed(uint64_t n)
+{
+	m_consumed += n;
+}
+
+void progress_bar_impl::progress(uint64_t p)
+{
+	m_consumed = p;
+}
+
+void progress_bar_impl::message(const std::string &msg)
+{
+	m_message = msg;
+}
+
+void progress_bar_impl::print_done()
+{
+	std::chrono::duration<double> elapsed = std::chrono::system_clock::now() - m_start;
+	std::string days, hours, minutes, seconds;
+
+	uint64_t s = static_cast<uint64_t>(std::trunc(elapsed.count()));
+	if (s > 24 * 60 * 60)
+	{
+		days = std::format("{:d}d ", s / (24 * 60 * 60));
+		s %= 24 * 60 * 60;
+	}
+
+	if (s > 60 * 60)
+	{
+		hours = std::format("{:2d}h ", s / (60 * 60));
+		s %= 60 * 60;
+	}
+
+	if (s > 60)
+	{
+		minutes = std::format("{:2d}m ", s / 60);
+		s %= 60;
+	}
+
+	std::string msg = std::format("{} done in {}{}{}{:.1f}s", m_action, days, hours, minutes, s + 1e-6 * (elapsed.count() - s));
+
+	uint32_t width = get_terminal_width();
+
+	if (msg.length() < width)
+		msg += std::string(width - msg.length(), ' ');
+
+	write_to_console(msg += '\n');
+}
+
+// --------------------------------------------------------------------
+
+struct simple_progress_bar_impl : public progress_bar_impl
+{
+	simple_progress_bar_impl(uint64_t max_value, const std::string &message)
+		: progress_bar_impl(max_value, message)
+	{
+	}
+
+	~simple_progress_bar_impl()
+	{
+		if (m_printed_any)
+			print_done();
+	}
+
+	void consumed(uint64_t n) override
+	{
+		using namespace std::literals;
+
+		progress_bar_impl::consumed(n);
+
+		// print at most 10 steps, but only if it took long enough
+
+		int percentile = static_cast<int>(std::floor(10.f * m_consumed / m_max_value));
+		if (percentile > m_last_percentile and (m_printed_any or std::chrono::system_clock::now() - m_start >= 1s))
+		{
+			if (not std::exchange(m_printed_any, true))
+				write_to_console(m_action + ": ");
+
+			write_to_console(std::format("...{:d}0%", percentile));
+			m_last_percentile = percentile;
+		}
+	}
+
+	void progress(uint64_t p) override
+	{
+		consumed(p - m_consumed);
+	}
+
+	void print_done() override
+	{
+		if (m_printed_any)
+		{
+			write_to_console("\n");
+			progress_bar_impl::print_done();
+		}
+	}
+
+	bool m_printed_any = false;
+	int m_last_percentile = 0;
+};
+
+// --------------------------------------------------------------------
+
+struct fancy_progress_bar_impl : public progress_bar_impl
+{
+	fancy_progress_bar_impl(uint64_t max_value, const std::string &message)
+		: progress_bar_impl(max_value, message)
+		, m_thread(
+#if __cpp_lib_jthread >= 201911L
+			  [this](std::stop_token stoken)
+			  { this->run(stoken); }
+#else
+			  [this]()
+			  { this->run(); }
+#endif
+		  )
+	{
+	}
+
+	~fancy_progress_bar_impl();
+
+#if __cpp_lib_jthread >= 201911L
+	void run(std::stop_token stoken);
+#else
+	void run();
+#endif
+
+	void consumed(uint64_t n) override;
+	void progress(uint64_t p) override;
+	void message(const std::string &msg) override;
+
+	void print_progress();
+
+	std::mutex m_mutex;
+	std::condition_variable m_cv;
+
+	float m_progress;
+	uint32_t m_width, m_bar_width;
+	uint32_t m_steps, m_last_steps = 0;
+	uint64_t m_last_consumed = 0;
+#if __cpp_lib_jthread >= 201911L
+	std::jthread m_thread;
+#else
+	std::thread m_thread;
+	bool m_stop = false;
+#endif
+};
+
+const char *kBlocks[] = {
+	" ",
+	"▏",
+	"▎",
+	"▍",
+	"▌",
+	"▋",
+	"▊",
+	"▉",
+	"█",
+};
+
+const size_t kBlockCount = sizeof(kBlocks) / sizeof(void *) - 1;
+
+fancy_progress_bar_impl::~fancy_progress_bar_impl()
 {
 	using namespace std::literals;
 	assert(m_thread.joinable());
 
+#if __cpp_lib_jthread >= 201911L
+	m_thread.request_stop();
+#else
 	m_stop = true;
+#endif
 	m_thread.join();
 }
 
-void progress_bar_impl::run()
+#if __cpp_lib_jthread >= 201911L
+void fancy_progress_bar_impl::run(std::stop_token stoken)
+#else
+void fancy_progress_bar_impl::run()
+#endif
 {
 	using namespace std::literals;
 
@@ -160,25 +350,44 @@ void progress_bar_impl::run()
 
 	try
 	{
-		while (not m_stop)
+		for (;;)
 		{
+			std::unique_lock lock(m_mutex);
+
+			m_cv.wait_for(lock, 25ms);
+
+#if __cpp_lib_jthread >= 201911L
+			if (stoken.stop_requested())
+				break;
+#else
+			if (m_stop)
+				break;
+#endif
+
 			auto now = std::chrono::system_clock::now();
 
-			if (now - m_start < 2s or now - m_last < 100ms)
-			{
-				std::this_thread::sleep_for(10ms);
+			if (m_consumed == m_last_consumed or now - m_start < 1s)
 				continue;
-			}
 
-			std::lock_guard lock(m_mutex);
+			m_last_consumed = m_consumed;
 
-			if (not printedAny and isatty(STDOUT_FILENO))
-				std::cout << "\x1b[?25l";
+			// See if we need to do work
+			m_width = get_terminal_width();
+			m_progress = static_cast<float>(m_consumed) / m_max_value;
+			m_bar_width = 7 * m_width / 10; // 70% of the width of the terminal
+			m_steps = static_cast<uint32_t>(std::ceil(m_progress * m_bar_width * kBlockCount));
+
+			if (m_steps == m_last_steps)
+				continue;
+
+			m_last_steps = m_steps;
+
+			if (not printedAny)
+				write_to_console("\x1b[?25l");
 
 			print_progress();
 
 			printedAny = true;
-			m_last = std::chrono::system_clock::now();
 		}
 	}
 	catch (...)
@@ -187,161 +396,94 @@ void progress_bar_impl::run()
 
 	if (printedAny)
 	{
+		write_to_console("\r\x1b[?25h");
 		print_done();
-		if (isatty(STDOUT_FILENO))
-			std::cout << "\x1b[?25h";
 	}
 }
 
-void progress_bar_impl::consumed(int64_t n)
+void fancy_progress_bar_impl::consumed(uint64_t n)
 {
-	m_consumed += n;
+	progress_bar_impl::consumed(n);
+	// m_cv.notify_one();
 }
 
-void progress_bar_impl::progress(int64_t p)
+void fancy_progress_bar_impl::progress(uint64_t p)
 {
-	m_consumed = p;
+	progress_bar_impl::progress(p);
+	// m_cv.notify_one();
 }
 
-void progress_bar_impl::message(const std::string &msg)
+void fancy_progress_bar_impl::message(const std::string &msg)
 {
 	std::unique_lock lock(m_mutex);
-	m_message = msg;
+	progress_bar_impl::message(msg);
+	// m_cv.notify_one();
 }
 
-const char* kSpinner[] = {
-	// ".", "o", "O", "0", "O", "o", ".", " "
-	// "⢄", "⢂", "⢁", "⡁", "⡈", "⡐", "⡠"
-	 ".", "o", "O", "0", "@", "*", " "
-};
-
-const size_t kSpinnerCount = sizeof(kSpinner) / sizeof(char*);
-
-const int kSpinnerTimeInterval = 100;
-
 const uint32_t kMinBarWidth = 40, kMinMsgWidth = 12;
 
-void progress_bar_impl::print_progress()
+void fancy_progress_bar_impl::print_progress()
 {
-	const char *kBlocks[] = {
-		// "▯", // 0
-		// "▮", // 1
-		"=",
-		"-"
-	};
+	const uint32_t pct_width = 5;
+	uint32_t msg_width = m_width - m_bar_width - pct_width - 1;
 
-	uint32_t width = get_terminal_width();
-
-	float progress = static_cast<float>(m_consumed) / m_max_value;
-	
-	if (width < kMinBarWidth)
-		std::cout << (100 * progress) << '%' << std::endl;
-	else
+	if (msg_width < kMinMsgWidth)
 	{
-		uint32_t bar_width = 7 * width / 10;
-		uint32_t pct_width = 7;
-		uint32_t msg_width = width - bar_width - pct_width - 1;
+		m_bar_width += kMinMsgWidth - msg_width;
+		msg_width = kMinMsgWidth;
+	}
 
-		if (msg_width < kMinMsgWidth)
-		{
-			bar_width += kMinMsgWidth - msg_width;
-			msg_width = kMinMsgWidth;
-		}
+	std::string bar;
+	bar.reserve(m_bar_width * 4);
 
-		std::ostringstream msg;
-
-		if (m_message.length() <= msg_width)
-		{
-			msg << m_message;
-			if (m_message.length() < msg_width)
-				msg << std::string(msg_width - m_message.length(), ' ');
-		}
+	for (uint32_t i = 0; i < m_bar_width; ++i)
+	{
+		if (i * kBlockCount <= m_steps)
+			bar += kBlocks[kBlockCount];
+		else if (i * kBlockCount > m_steps + kBlockCount)
+			bar += kBlocks[0];
 		else
-			msg << m_message.substr(0, msg_width - 3) << "...";
-
-		msg << ' ';
-
-		uint32_t pi = static_cast<uint32_t>(std::ceil(progress * bar_width));
-
-		for (uint32_t i = 0; i < bar_width; ++i)
-			msg << kBlocks[i > pi ? 1 : 0];
-
-		msg << ' ';
-
-		msg << std::setw(3) << static_cast<int>(std::ceil(progress * 100)) << "% ";
-
-		auto now = std::chrono::system_clock::now();
-		m_spinner_index = (std::chrono::duration_cast<std::chrono::milliseconds>(now - m_start).count() / kSpinnerTimeInterval) % kSpinnerCount;
-
-		msg << kSpinner[m_spinner_index];
-
-		std::cout << '\r' << msg.str();
-		std::cout.flush();
+			bar += kBlocks[1 + m_steps % kBlockCount];
 	}
-}
 
-namespace
-{
-
-	std::ostream &operator<<(std::ostream &os, const std::chrono::duration<double> &t)
+	// make the bar more colorfull
+	struct color_type
 	{
-		uint64_t s = static_cast<uint64_t>(std::trunc(t.count()));
-		if (s > 24 * 60 * 60)
-		{
-			auto days = s / (24 * 60 * 60);
-			os << days << "d ";
-			s %= 24 * 60 * 60;
-		}
+		uint8_t r, g, b;
+	} fg{ 0, 3, 5 }, bg{ 0, 1, 2 };
 
-		if (s > 60 * 60)
-		{
-			auto hours = s / (60 * 60);
-			os << hours << "h ";
-			s %= 60 * 60;
-		}
+	auto esc_1 = std::format("\x1b[38;5;{}m\x1b[48;5;{}m",
+		16 + (fg.r * 36) + (fg.g * 6) + fg.b,
+		16 + (bg.r * 36) + (bg.g * 6) + bg.b);
+	std::string esc_2("\x1b[0m");
 
-		if (s > 60)
-		{
-			auto minutes = s / 60;
-			os << minutes << "m ";
-			s %= 60;
-		}
+	bar = esc_1 + bar + esc_2;
 
-		double ss = s + 1e-6 * (t.count() - s);
+	std::string msg = m_message.length() <= msg_width
+	                      ? m_message
+	                      : m_message.substr(0, msg_width - 3) + "...";
 
-		os << std::fixed << std::setprecision(1) << ss << 's';
-
-		return os;
-	}
-
-} // namespace
-
-void progress_bar_impl::print_done()
-{
-	std::chrono::duration<double> elapsed = std::chrono::system_clock::now() - m_start;
-
-	std::ostringstream msgstr;
-	msgstr << m_action << " done in " << elapsed << " seconds";
-	auto msg = msgstr.str();
-
-	uint32_t width = get_terminal_width();
-
-	if (msg.length() < width)
-		msg += std::string(width - msg.length(), ' ');
-
-	std::cout << '\r' << msg << std::endl;
+	write_to_console(std::format("{:{}} {} {:3d}%\r", msg, msg_width, bar,
+		static_cast<int>(std::ceil(m_progress * 100))));
 }
 
-progress_bar::progress_bar(int64_t inMax, const std::string &inAction)
+// --------------------------------------------------------------------
+
+progress_bar::progress_bar(int64_t max_value, const std::string &message)
 	: m_impl(nullptr)
 {
-	if (isatty(STDOUT_FILENO) and VERBOSE >= 0)
-		m_impl = new progress_bar_impl(inMax, inAction);
+	if (VERBOSE >= 0)
+	{
+		if (isatty(STDOUT_FILENO) and get_terminal_width() > kMinBarWidth)
+			m_impl = new fancy_progress_bar_impl(max_value, message);
+		else
+			m_impl = new simple_progress_bar_impl(max_value, message);
+	}
 }
 
 progress_bar::~progress_bar()
 {
-	delete m_impl;
+	flush();
 }
 
 void progress_bar::consumed(int64_t inConsumed)
@@ -350,16 +492,25 @@ void progress_bar::consumed(int64_t inConsumed)
 		m_impl->consumed(inConsumed);
 }
 
-void progress_bar::progress(int64_t inProgress)
+void progress_bar::progress(int64_t value)
 {
 	if (m_impl != nullptr)
-		m_impl->progress(inProgress);
+		m_impl->progress(value);
 }
 
-void progress_bar::message(const std::string &inMessage)
+void progress_bar::message(const std::string &message)
 {
 	if (m_impl != nullptr)
-		m_impl->message(inMessage);
+		m_impl->message(message);
+}
+
+void progress_bar::flush()
+{
+	if (m_impl)
+	{
+		delete m_impl;
+		m_impl = nullptr;
+	}
 }
 
 } // namespace cif
@@ -387,13 +538,13 @@ struct rsrc_imp
 
 #if _WIN32
 
-#if __MINGW32__
+# if __MINGW32__
 
 extern "C" __attribute__((weak, alias("gResourceIndexDefault"))) const mrsrc::rsrc_imp gResourceIndex[];
 extern "C" __attribute__((weak, alias("gResourceDataDefault"))) const char gResourceData[];
 extern "C" __attribute__((weak, alias("gResourceNameDefault"))) const char gResourceName[];
 
-#else
+# else
 
 extern "C" const mrsrc::rsrc_imp *gResourceIndexDefault[1] = {};
 extern "C" const char *gResourceDataDefault[1] = {};
@@ -403,11 +554,11 @@ extern "C" const mrsrc::rsrc_imp gResourceIndex[];
 extern "C" const char gResourceData[];
 extern "C" const char gResourceName[];
 
-#pragma comment(linker, "/alternatename:gResourceIndex=gResourceIndexDefault")
-#pragma comment(linker, "/alternatename:gResourceData=gResourceDataDefault")
-#pragma comment(linker, "/alternatename:gResourceName=gResourceNameDefault")
+#  pragma comment(linker, "/alternatename:gResourceIndex=gResourceIndexDefault")
+#  pragma comment(linker, "/alternatename:gResourceData=gResourceDataDefault")
+#  pragma comment(linker, "/alternatename:gResourceName=gResourceNameDefault")
 
-#endif
+# endif
 
 #else
 extern const __attribute__((weak)) mrsrc::rsrc_imp gResourceIndex[];
@@ -877,6 +1028,21 @@ class resource_pool
 
 resource_pool::resource_pool()
 {
+	// directories are searched in reverse order
+
+	// As a last resort, try the location that might have been
+	// used during installation, works only when running on an
+	// OS with a proc file system.
+
+	std::error_code ec;
+	if (auto exefile = fs::read_symlink("/proc/self/exe", ec); not ec and exefile.parent_path().filename() == "bin")
+	{
+		auto install_prefix = exefile.parent_path().parent_path();
+		auto data_dir = install_prefix / "share" / "libcifpp";
+		if (fs::exists(data_dir, ec))
+			pushDir(data_dir);
+	}
+
 #if defined(DATA_DIR)
 	pushDir(DATA_DIR);
 #endif

src/validate.cpp

@@ -25,26 +25,21 @@
  */
 
 #include "cif++/validate.hpp"
+#include "cif++/category.hpp"
 #include "cif++/dictionary_parser.hpp"
-#include "cif++/gzio.hpp"
 #include "cif++/utilities.hpp"
 
 #include <cassert>
-#include <fstream>
 #include <iostream>
+#include <mutex>
 
 // The validator depends on regular expressions. Unfortunately,
 // the implementation of std::regex in g++ is buggy and crashes
-// on reading the pdbx dictionary. Therefore, in case g++ is used
-// the code will use boost::regex instead.
+// on reading the pdbx dictionary. We used to use boost regex
+// instead but using pcre2 is even easier and faster.
 
-#if USE_BOOST_REGEX
-# include <boost/regex.hpp>
-using boost::regex;
-#else
-# include <regex>
-using std::regex;
-#endif
+#define PCRE2_CODE_UNIT_WIDTH 8
+#include <pcre2.h>
 
 namespace cif
 {
@@ -66,14 +61,63 @@ validation_exception::validation_exception(std::error_code ec, std::string_view
 
 // --------------------------------------------------------------------
 
-struct regex_impl : public regex
+struct regex_impl
 {
-	regex_impl(std::string_view rx)
-		: regex(rx.begin(), rx.end(), regex::extended | regex::optimize)
-	{
-	}
+	regex_impl(std::string_view rx);
+	~regex_impl();
+
+	regex_impl(const regex_impl &) = delete;
+	regex_impl &operator=(const regex_impl &) = delete;
+
+	bool match(std::string_view v) const;
+
+  private:
+	pcre2_code *m_rx = nullptr;
+	pcre2_match_data *m_data = nullptr;
+	mutable std::mutex m_mutex;
 };
 
+regex_impl::regex_impl(std::string_view rx)
+{
+	int err_code;
+	size_t err_offset;
+	m_rx = pcre2_compile((PCRE2_SPTR)rx.data(), rx.length(), 0, &err_code, &err_offset, nullptr);
+	if (m_rx == nullptr)
+	{
+		PCRE2_UCHAR buffer[256];
+		int n = pcre2_get_error_message(err_code, buffer, sizeof(buffer));
+
+		throw std::runtime_error(std::string("PCRE2 compilation failed: ") + std::string{ (char *)buffer, (char *)buffer + n });
+	}
+
+	m_data = pcre2_match_data_create_from_pattern(m_rx, nullptr);
+}
+
+regex_impl::~regex_impl()
+{
+	std::unique_lock lock(m_mutex);
+
+	if (m_data)
+		pcre2_match_data_free(m_data);
+
+	if (m_rx)
+		pcre2_code_free(m_rx);
+}
+
+bool regex_impl::match(std::string_view v) const
+{
+	std::unique_lock lock(m_mutex);
+
+	bool result = false;
+
+	if (int rc = pcre2_match(m_rx, (PCRE2_SPTR)v.data(), v.length(), 0, 0, m_data, nullptr); rc >= 0)
+		result = true;
+	else if (rc != PCRE2_ERROR_NOMATCH)
+		std::cerr << "Error matching with pcre\n";
+
+	return result;
+}
+
 // --------------------------------------------------------------------
 
 DDL_PrimitiveType map_to_primitive_type(std::string_view s, std::error_code &ec) noexcept
@@ -109,9 +153,15 @@ type_validator::type_validator(std::string_view name, DDL_PrimitiveType type, st
 {
 }
 
+type_validator::type_validator(const type_validator &tv)
+	: m_name(tv.m_name)
+	, m_primitive_type(tv.m_primitive_type)
+	, m_rx(tv.m_rx)
+{
+}
+
 type_validator::~type_validator()
 {
-	delete m_rx;
 }
 
 int type_validator::compare(std::string_view a, std::string_view b) const
@@ -135,10 +185,10 @@ int type_validator::compare(std::string_view a, std::string_view b) const
 
 				std::from_chars_result ra, rb;
 
-				ra = selected_charconv<double>::from_chars(a.data(), a.data() + a.length(), da);
-				rb = selected_charconv<double>::from_chars(b.data(), b.data() + b.length(), db);
+				ra = from_chars(a.data(), a.data() + a.length(), da);
+				rb = from_chars(b.data(), b.data() + b.length(), db);
 
-				if (ra.ec == std::errc() and rb.ec == std::errc())
+				if (not(bool) ra.ec and not(bool) rb.ec)
 				{
 					auto d = da - db;
 					if (std::abs(d) > std::numeric_limits<double>::epsilon())
@@ -149,7 +199,7 @@ int type_validator::compare(std::string_view a, std::string_view b) const
 							result = -1;
 					}
 				}
-				else if (ra.ec == std::errc())
+				else if ((bool)ra.ec)
 					result = 1;
 				else
 					result = -1;
@@ -222,17 +272,17 @@ void item_validator::operator()(std::string_view value) const
 
 bool item_validator::validate_value(std::string_view value, std::error_code &ec) const noexcept
 {
-	ec = {};
+	ec.clear();
 
 	if (not value.empty() and value != "?" and value != ".")
 	{
-		if (m_type != nullptr and not regex_match(value.begin(), value.end(), *m_type->m_rx))
+		if (m_type != nullptr and not m_type->m_rx->match(value))
 			ec = make_error_code(validation_error::value_does_not_match_rx);
 		else if (not m_enums.empty() and m_enums.count(std::string{ value }) == 0)
 			ec = make_error_code(validation_error::value_is_not_in_enumeration_list);
 	}
 
-	return ec == std::errc();
+	return not(bool) ec;
 }
 
 // --------------------------------------------------------------------
@@ -242,7 +292,7 @@ void category_validator::add_item_validator(item_validator &&v)
 	if (v.m_mandatory)
 		m_mandatory_items.insert(v.m_item_name);
 
-	v.m_category = this;
+	v.m_category = m_name;
 
 	auto r = m_item_validators.insert(std::move(v));
 	if (not r.second and VERBOSE >= 4)
@@ -284,6 +334,29 @@ const item_validator *category_validator::get_validator_for_aliased_item(std::st
 
 // --------------------------------------------------------------------
 
+validator::validator(const validator &rhs)
+	: m_audit_conform(rhs.m_audit_conform)
+	, m_strict(rhs.m_strict)
+	, m_type_validators(rhs.m_type_validators)
+	, m_category_validators(rhs.m_category_validators)
+	, m_link_validators(rhs.m_link_validators)
+{
+}
+
+void swap(validator &a, validator &b) noexcept
+{
+	std::swap(a.m_audit_conform, b.m_audit_conform);
+	std::swap(a.m_strict, b.m_strict);
+	std::swap(a.m_type_validators, b.m_type_validators);
+	std::swap(a.m_category_validators, b.m_category_validators);
+	std::swap(a.m_link_validators, b.m_link_validators);
+}
+
+void validator::parse(std::istream &is)
+{
+	parse_dictionary(*this, is);
+}
+
 void validator::add_type_validator(type_validator &&v)
 {
 	auto r = m_type_validators.insert(std::move(v));
@@ -353,7 +426,7 @@ void validator::add_link_validator(link_validator &&v)
 	if (ccv == nullptr)
 		throw std::runtime_error("unknown child category " + v.m_child_category);
 
-	for (size_t i = 0; i < v.m_parent_keys.size(); ++i)
+	for (std::size_t i = 0; i < v.m_parent_keys.size(); ++i)
 	{
 		auto piv = pcv->get_validator_for_item(v.m_parent_keys[i]);
 
@@ -401,23 +474,63 @@ void validator::report_error(std::error_code ec, bool fatal) const
 {
 	if (m_strict or fatal)
 		throw validation_exception(ec);
-	else
+	else if (VERBOSE > 0)
 		std::cerr << ec.message() << '\n';
 }
 
 void validator::report_error(std::error_code ec, std::string_view category,
 	std::string_view item, bool fatal) const
 {
-	auto ex = item.empty() ?
-		validation_exception(ec, category) :
-		validation_exception(ec, category, item);
+	auto ex = item.empty() ? validation_exception(ec, category) : validation_exception(ec, category, item);
 
 	if (m_strict or fatal)
 		throw ex;
-	else
+	else if (VERBOSE > 0)
 		std::cerr << ex.what() << '\n';
 }
 
+void validator::fill_audit_conform(category &audit_conform) const
+{
+	audit_conform.clear();
+	audit_conform.emplace(m_audit_conform.begin(), m_audit_conform.end());
+}
+
+bool validator::matches_audit_conform(const category &audit_conform) const
+{
+	if (audit_conform.empty())
+		return false;
+
+	auto ai = m_audit_conform.begin();
+	auto bi = audit_conform.begin();
+
+	while (ai != m_audit_conform.end() and bi != audit_conform.end())
+	{
+		const auto &[name_a, version_a] = ai->get<std::string, std::optional<std::string>>("dict_name", "dict_version");
+		const auto &[name_b, version_b] = bi->get<std::string, std::optional<std::string>>("dict_name", "dict_version");
+
+		++ai;
+		++bi;
+
+		if (name_a != name_b)
+			return false;
+
+		if (not version_b.has_value() or not version_a.has_value())
+			continue;
+
+		if (validator_factory::check_version(name_a, *version_b, *version_a) == false)
+			return false;
+	}
+
+	return ai == m_audit_conform.end() and bi == audit_conform.end();
+}
+
+void validator::append_audit_conform(const std::string &name, const std::optional<std::string> &version)
+{
+	m_audit_conform.emplace({ //
+		{ "dict_name", name },
+		{ "dict_version", version } });
+}
+
 // --------------------------------------------------------------------
 
 validator_factory &validator_factory::instance()
@@ -426,101 +539,127 @@ validator_factory &validator_factory::instance()
 	return s_instance;
 }
 
-const validator &validator_factory::operator[](std::string_view dictionary_name)
+const validator &validator_factory::get(std::string_view dictionary_name)
 {
-	try
-	{
-		std::lock_guard lock(m_mutex);
+	category audit_conform("audit_conform");
+	for (auto part : cif::split(dictionary_name, ";", true))
+		audit_conform.emplace({ { "dict_name", part } });
 
-		for (auto &validator : m_validators)
-		{
-			if (iequals(validator.name(), dictionary_name))
-				return validator;
-		}
-
-		// not found, try to see if it helps if we tweak the name a little
-
-		// too bad clang version 10 did not have a constructor for std::filesystem::path that accepts a std::string_view
-		std::filesystem::path dictionary(dictionary_name.data(), dictionary_name.data() + dictionary_name.length());
-
-		if (dictionary.extension() != ".dic")
-		{
-			auto dict_name = dictionary.filename().string() + ".dic";
-
-			for (auto &validator : m_validators)
-			{
-				if (iequals(validator.name(), dict_name))
-					return validator;
-			}
-		}
-
-		// not found, add it
-		auto data = load_resource(dictionary_name);
-
-		if (not data and dictionary.extension().string() != ".dic")
-			data = load_resource(dictionary.parent_path() / (dictionary.filename().string() + ".dic"));
-
-		if (data)
-			construct_validator(dictionary_name, *data);
-		else
-		{
-			std::error_code ec;
-
-			// might be a compressed dictionary on disk
-			std::filesystem::path p = dictionary;
-			if (p.extension() == ".dic")
-				p = p.parent_path() / (p.filename().string() + ".gz");
-			else
-				p = p.parent_path() / (p.filename().string() + ".dic.gz");
-
-#if defined(CACHE_DIR) or defined(DATA_DIR)
-			if (not std::filesystem::exists(p, ec) or ec)
-			{
-				for (const char *dir : {
-# if defined(CACHE_DIR)
-						 CACHE_DIR,
-# endif
-# if defined(DATA_DIR)
-							 DATA_DIR
-# endif
-					 })
-				{
-					auto p2 = std::filesystem::path(dir) / p;
-					if (std::filesystem::exists(p2, ec) and not ec)
-					{
-						swap(p, p2);
-						break;
-					}
-				}
-			}
-#endif
-
-			if (std::filesystem::exists(p, ec) and not ec)
-			{
-				gzio::ifstream in(p);
-
-				if (not in.is_open())
-					throw std::runtime_error("Could not open dictionary (" + p.string() + ")");
-
-				construct_validator(dictionary_name, in);
-			}
-			else
-				throw std::runtime_error("Dictionary not found or defined (" + dictionary.string() + ")");
-		}
-
-		return m_validators.back();
-	}
-	catch (const std::exception &ex)
-	{
-		std::string msg = "Error while loading dictionary ";
-		msg += dictionary_name;
-		std::throw_with_nested(std::runtime_error(msg));
-	}
+	return get(audit_conform);
 }
 
-const validator &validator_factory::construct_validator(std::string_view name, std::istream &is)
+const validator &validator_factory::get(const category &audit_conform)
 {
-	return m_validators.emplace_back(parse_dictionary(name, is));
+	if (audit_conform.empty())
+		throw std::runtime_error("Empty audit_conform category, cannot create a validator");
+
+	std::lock_guard lock(m_mutex);
+
+	// Check existing first
+	for (auto &v : m_validators)
+	{
+		if (v.matches_audit_conform(audit_conform))
+			return v;
+	}
+
+	// If the audit conform contains only one record, this is easy
+	if (audit_conform.size() == 1)
+	{
+		const auto &[name, version] =
+			audit_conform.front().get<std::string, std::optional<std::string>>("dict_name", "dict_version");
+		if (not name.empty())
+			return m_validators.emplace_back(construct_validator(name, version));
+	}
+
+	// A new, merged dictionary
+
+	std::optional<validator> v;
+	for (const auto &[name, version] : audit_conform.rows<std::string, std::optional<std::string>>("dict_name", "dict_version"))
+	{
+		if (name.empty())
+			continue;
+
+		if (not v)
+			v = construct_validator(name, version);
+		else
+		{
+			auto data = load_resource(name);
+			if (not data)
+				throw std::runtime_error("Could not load dictionary " + std::string{ name });
+
+			v->parse(*data);
+		}
+	}
+
+	if (not v)
+		throw std::runtime_error("Missing dictionary information?");
+
+	return m_validators.emplace_back(std::move(*v));
+}
+
+validator validator_factory::construct_validator(std::string_view name, std::optional<std::string> version)
+{
+	auto data = load_resource(name);
+	if (not data and name == "mmcif_pdbx_v50")
+		data = load_resource("mmcif_pdbx.dic");
+
+	if (not data)
+		throw std::runtime_error("Could not load dictionary " + std::string{ name });
+
+	validator v;
+	v.parse(*data);
+
+	if (version.has_value() and VERBOSE >= 0 and
+		not v.matches_audit_conform(category{ "audit_conform", //
+			{ { "dict_name", name }, { "dict_version", version } } }))
+	{
+		std::clog << "Loaded dictionary does not match name=" << name << " and version=" << version.value_or("''") << "\n";
+	}
+
+	return v;
+}
+
+bool validator_factory::check_version(std::string_view name, std::string_view expected, std::string_view found)
+{
+	bool result = true;
+	auto el = cif::split(expected, ".");
+	auto fl = cif::split(found, ".");
+
+	auto eli = el.begin();
+	auto fli = fl.begin();
+
+	while (eli != el.end() and fli != fl.end())
+	{
+		int e_int, f_int;
+		if (auto [ptr, ec] = std::from_chars(eli->data(), eli->data() + eli->length(), e_int); ec != std::errc{})
+		{
+			std::clog << "Could not parse requested version string for dictionary " << std::quoted(expected) << "\n";
+			result = false;
+			break;
+		}
+
+		if (auto [ptr, ec] = std::from_chars(fli->data(), fli->data() + fli->length(), f_int); ec != std::errc{})
+		{
+			std::clog << "Could not parse version string in dictionary " << name << " " << std::quoted(found) << "\n";
+			result = false;
+			break;
+		}
+
+		if (f_int > e_int) // newer version, assume this is ok
+			break;
+
+		if (f_int < e_int)
+		{
+			std::clog << "The version in dictionary " << name << " is lower than requested, this may cause validation errors\n";
+			result = false;
+			break;
+		}
+
+		++eli;
+		++fli;
+	}
+
+	return result;
 }
 
 } // namespace cif

test/CMakeLists.txt

@@ -1,16 +1,40 @@
-# We're using the older version 2 of Catch2
+# SPDX-License-Identifier: BSD-2-Clause
+# 
+# Copyright (c) 2025  NKI/AVL, Netherlands Cancer Institute
+# 
+# Redistribution and use in source and binary forms, with or without
+# 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
+# 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 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.
 
-find_package(Catch2 QUIET)
+if(NOT (Catch2_FOUND OR TARGET Catch2))
+	find_package(Catch2 3 QUIET)
 
-if(NOT Catch2_FOUND)
-	FetchContent_Declare(
-		Catch2
-		GIT_REPOSITORY https://github.com/catchorg/Catch2.git
-		GIT_TAG v2.13.9)
+	if(NOT Catch2_FOUND)
+		FetchContent_Declare(
+			Catch2
+			GIT_REPOSITORY https://github.com/catchorg/Catch2.git
+			GIT_TAG v3.4.0)
 
-	FetchContent_MakeAvailable(Catch2)
+		FetchContent_MakeAvailable(Catch2)
 
-	set(Catch2_VERSION "2.13.9")
+		target_compile_features(Catch2 PRIVATE cxx_std_20)
+	endif()
 endif()
 
 list(
@@ -18,24 +42,20 @@ list(
 	CIFPP_tests
 	unit-v2
 	unit-3d
-	format
 	model
+	query
 	rename-compound
 	sugar
 	spinner
 	reconstruction
-	validate-pdbx)
+	validate-pdbx
+	matrix
+)
 
 add_library(test-main OBJECT "${CMAKE_CURRENT_SOURCE_DIR}/test-main.cpp")
 
 target_link_libraries(test-main cifpp::cifpp Catch2::Catch2)
 
-if(${Catch2_VERSION} VERSION_GREATER_EQUAL 3.0.0)
-	target_compile_definitions(test-main PUBLIC CATCH22=0)
-else()
-	target_compile_definitions(test-main PUBLIC CATCH22=1)
-endif()
-
 foreach(CIFPP_TEST IN LISTS CIFPP_tests)
 	set(CIFPP_TEST "${CIFPP_TEST}-test")
 	set(CIFPP_TEST_SOURCE "${CMAKE_CURRENT_SOURCE_DIR}/${CIFPP_TEST}.cpp")
@@ -43,14 +63,7 @@ foreach(CIFPP_TEST IN LISTS CIFPP_tests)
 	add_executable(
 		${CIFPP_TEST} ${CIFPP_TEST_SOURCE} $<TARGET_OBJECTS:test-main>)
 
-	if(${Catch2_VERSION} VERSION_GREATER_EQUAL 3.0.0)
-		target_compile_definitions(${CIFPP_TEST} PUBLIC CATCH22=0)
-	else()
-		target_compile_definitions(${CIFPP_TEST} PUBLIC CATCH22=1)
-	endif()
-
-	target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp::cifpp
-		Catch2::Catch2)
+	target_link_libraries(${CIFPP_TEST} PRIVATE cifpp::cifpp Catch2::Catch2)
 	target_include_directories(${CIFPP_TEST} PRIVATE "${EIGEN_INCLUDE_DIR}")
 
 	if(MSVC)
@@ -58,15 +71,8 @@ foreach(CIFPP_TEST IN LISTS CIFPP_tests)
 		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})
-
-	add_test(NAME ${CIFPP_TEST} COMMAND $<TARGET_FILE:${CIFPP_TEST}> --data-dir
-		${CMAKE_CURRENT_SOURCE_DIR})
-endforeach()
+	if(NOT (CIFPP_TEST STREQUAL "spinner-test"))
+		add_test(NAME ${CIFPP_TEST}
+			COMMAND $<TARGET_FILE:${CIFPP_TEST}> --data-dir ${CMAKE_CURRENT_SOURCE_DIR})
+	endif()
+endforeach()

test/brak.pdb

@@ -0,0 +1,822 @@
+REMARK 001 design 0 N 3 RMSD 1.605
+MODEL       1
+ATOM      1  N   MET A   1     -24.216  -7.571  -1.155  1.00 31.87           N
+ATOM      2  CA  MET A   1     -22.971  -7.756  -0.416  1.00 31.87           C
+ATOM      3  C   MET A   1     -21.814  -7.051  -1.114  1.00 31.87           C
+ATOM      4  CB  MET A   1     -22.656  -9.245  -0.256  1.00 31.87           C
+ATOM      5  O   MET A   1     -21.516  -7.338  -2.275  1.00 31.87           O
+ATOM      6  CG  MET A   1     -22.779  -9.747   1.174  1.00 31.87           C
+ATOM      7  SD  MET A   1     -22.473 -11.551   1.314  1.00 31.87           S
+ATOM      8  CE  MET A   1     -22.597 -11.758   3.112  1.00 31.87           C
+ATOM      9  N   LYS A   2     -21.652  -5.596  -0.909  1.00 33.06           N
+ATOM     10  CA  LYS A   2     -21.035  -4.320  -0.554  1.00 33.06           C
+ATOM     11  C   LYS A   2     -19.531  -4.475  -0.351  1.00 33.06           C
+ATOM     12  CB  LYS A   2     -21.678  -3.747   0.710  1.00 33.06           C
+ATOM     13  O   LYS A   2     -19.087  -5.326   0.423  1.00 33.06           O
+ATOM     14  CG  LYS A   2     -22.957  -2.963   0.453  1.00 33.06           C
+ATOM     15  CD  LYS A   2     -23.454  -2.275   1.717  1.00 33.06           C
+ATOM     16  CE  LYS A   2     -24.810  -1.615   1.500  1.00 33.06           C
+ATOM     17  NZ  LYS A   2     -25.284  -0.906   2.725  1.00 33.06           N
+ATOM     18  N   ILE A   3     -18.889  -4.065  -1.586  1.00 34.22           N
+ATOM     19  CA  ILE A   3     -17.539  -3.550  -1.381  1.00 34.22           C
+ATOM     20  C   ILE A   3     -17.331  -2.297  -2.229  1.00 34.22           C
+ATOM     21  CB  ILE A   3     -16.471  -4.612  -1.721  1.00 34.22           C
+ATOM     22  O   ILE A   3     -17.508  -2.330  -3.449  1.00 34.22           O
+ATOM     23  CG1 ILE A   3     -16.524  -5.766  -0.713  1.00 34.22           C
+ATOM     24  CG2 ILE A   3     -15.075  -3.982  -1.759  1.00 34.22           C
+ATOM     25  CD1 ILE A   3     -15.743  -7.000  -1.142  1.00 34.22           C
+ATOM     26  N   ILE A   4     -17.776  -0.985  -1.831  1.00 40.18           N
+ATOM     27  CA  ILE A   4     -17.255   0.212  -1.181  1.00 40.18           C
+ATOM     28  C   ILE A   4     -16.631   1.136  -2.224  1.00 40.18           C
+ATOM     29  CB  ILE A   4     -16.218  -0.142  -0.091  1.00 40.18           C
+ATOM     30  O   ILE A   4     -15.717   0.736  -2.949  1.00 40.18           O
+ATOM     31  CG1 ILE A   4     -16.844  -1.063   0.963  1.00 40.18           C
+ATOM     32  CG2 ILE A   4     -15.658   1.128   0.555  1.00 40.18           C
+ATOM     33  CD1 ILE A   4     -15.839  -1.662   1.937  1.00 40.18           C
+ATOM     34  N   GLU A   5     -17.325   2.198  -2.769  1.00 38.95           N
+ATOM     35  CA  GLU A   5     -17.243   3.640  -2.553  1.00 38.95           C
+ATOM     36  C   GLU A   5     -15.944   4.019  -1.848  1.00 38.95           C
+ATOM     37  CB  GLU A   5     -18.445   4.131  -1.741  1.00 38.95           C
+ATOM     38  O   GLU A   5     -15.602   3.445  -0.812  1.00 38.95           O
+ATOM     39  CG  GLU A   5     -19.296   5.162  -2.466  1.00 38.95           C
+ATOM     40  CD  GLU A   5     -20.407   5.738  -1.602  1.00 38.95           C
+ATOM     41  OE1 GLU A   5     -20.194   6.791  -0.960  1.00 38.95           O
+ATOM     42  OE2 GLU A   5     -21.500   5.129  -1.566  1.00 38.95           O
+ATOM     43  N   LYS A   6     -14.697   4.048  -2.514  1.00 40.24           N
+ATOM     44  CA  LYS A   6     -13.793   5.173  -2.294  1.00 40.24           C
+ATOM     45  C   LYS A   6     -12.348   4.784  -2.593  1.00 40.24           C
+ATOM     46  CB  LYS A   6     -13.911   5.684  -0.857  1.00 40.24           C
+ATOM     47  O   LYS A   6     -11.769   3.946  -1.899  1.00 40.24           O
+ATOM     48  CG  LYS A   6     -14.799   6.911  -0.707  1.00 40.24           C
+ATOM     49  CD  LYS A   6     -14.696   7.508   0.690  1.00 40.24           C
+ATOM     50  CE  LYS A   6     -15.689   8.645   0.887  1.00 40.24           C
+ATOM     51  NZ  LYS A   6     -15.523   9.301   2.219  1.00 40.24           N
+ATOM     52  N   TYR A   7     -12.096   4.360  -3.877  1.00 55.19           N
+ATOM     53  CA  TYR A   7     -10.695   4.330  -4.282  1.00 55.19           C
+ATOM     54  C   TYR A   7      -9.919   5.478  -3.647  1.00 55.19           C
+ATOM     55  CB  TYR A   7     -10.574   4.398  -5.807  1.00 55.19           C
+ATOM     56  O   TYR A   7     -10.324   6.639  -3.746  1.00 55.19           O
+ATOM     57  CG  TYR A   7     -11.069   3.159  -6.511  1.00 55.19           C
+ATOM     58  CD1 TYR A   7     -10.245   2.047  -6.669  1.00 55.19           C
+ATOM     59  CD2 TYR A   7     -12.361   3.097  -7.021  1.00 55.19           C
+ATOM     60  CE1 TYR A   7     -10.696   0.903  -7.319  1.00 55.19           C
+ATOM     61  CE2 TYR A   7     -12.823   1.958  -7.673  1.00 55.19           C
+ATOM     62  OH  TYR A   7     -12.437  -0.262  -8.461  1.00 55.19           O
+ATOM     63  CZ  TYR A   7     -11.985   0.868  -7.817  1.00 55.19           C
+ATOM     64  N   VAL A   8      -9.308   5.253  -2.484  1.00 55.50           N
+ATOM     65  CA  VAL A   8      -8.469   6.226  -1.792  1.00 55.50           C
+ATOM     66  C   VAL A   8      -7.196   6.476  -2.597  1.00 55.50           C
+ATOM     67  CB  VAL A   8      -8.112   5.754  -0.364  1.00 55.50           C
+ATOM     68  O   VAL A   8      -6.488   5.534  -2.960  1.00 55.50           O
+ATOM     69  CG1 VAL A   8      -7.215   6.774   0.333  1.00 55.50           C
+ATOM     70  CG2 VAL A   8      -9.381   5.509   0.450  1.00 55.50           C
+ATOM     71  N   PHE A   9      -7.225   7.625  -3.250  1.00 66.91           N
+ATOM     72  CA  PHE A   9      -6.004   8.094  -3.895  1.00 66.91           C
+ATOM     73  C   PHE A   9      -4.934   8.414  -2.858  1.00 66.91           C
+ATOM     74  CB  PHE A   9      -6.289   9.330  -4.754  1.00 66.91           C
+ATOM     75  O   PHE A   9      -5.089   9.345  -2.065  1.00 66.91           O
+ATOM     76  CG  PHE A   9      -6.868   9.009  -6.105  1.00 66.91           C
+ATOM     77  CD1 PHE A   9      -6.039   8.797  -7.200  1.00 66.91           C
+ATOM     78  CD2 PHE A   9      -8.243   8.920  -6.281  1.00 66.91           C
+ATOM     79  CE1 PHE A   9      -6.572   8.499  -8.452  1.00 66.91           C
+ATOM     80  CE2 PHE A   9      -8.783   8.623  -7.530  1.00 66.91           C
+ATOM     81  CZ  PHE A   9      -7.946   8.414  -8.614  1.00 66.91           C
+ATOM     82  N   LEU A  10      -4.065   7.388  -2.607  1.00 72.14           N
+ATOM     83  CA  LEU A  10      -2.967   7.542  -1.658  1.00 72.14           C
+ATOM     84  C   LEU A  10      -2.342   8.929  -1.771  1.00 72.14           C
+ATOM     85  CB  LEU A  10      -1.902   6.469  -1.893  1.00 72.14           C
+ATOM     86  O   LEU A  10      -1.903   9.499  -0.770  1.00 72.14           O
+ATOM     87  CG  LEU A  10      -2.222   5.069  -1.365  1.00 72.14           C
+ATOM     88  CD1 LEU A  10      -1.258   4.046  -1.957  1.00 72.14           C
+ATOM     89  CD2 LEU A  10      -2.165   5.045   0.158  1.00 72.14           C
+ATOM     90  N   ALA A  11      -2.498   9.659  -2.947  1.00 69.94           N
+ATOM     91  CA  ALA A  11      -1.847  10.939  -3.211  1.00 69.94           C
+ATOM     92  C   ALA A  11      -2.571  12.080  -2.501  1.00 69.94           C
+ATOM     93  CB  ALA A  11      -1.786  11.206  -4.713  1.00 69.94           C
+ATOM     94  O   ALA A  11      -1.971  13.117  -2.207  1.00 69.94           O
+ATOM     95  N   GLU A  12      -3.713  11.866  -1.974  1.00 76.23           N
+ATOM     96  CA  GLU A  12      -4.520  12.921  -1.368  1.00 76.23           C
+ATOM     97  C   GLU A  12      -4.620  12.741   0.144  1.00 76.23           C
+ATOM     98  CB  GLU A  12      -5.920  12.951  -1.987  1.00 76.23           C
+ATOM     99  O   GLU A  12      -5.178  13.590   0.841  1.00 76.23           O
+ATOM    100  CG  GLU A  12      -5.939  13.391  -3.444  1.00 76.23           C
+ATOM    101  CD  GLU A  12      -7.343  13.548  -4.005  1.00 76.23           C
+ATOM    102  OE1 GLU A  12      -7.904  14.665  -3.935  1.00 76.23           O
+ATOM    103  OE2 GLU A  12      -7.888  12.544  -4.518  1.00 76.23           O
+ATOM    104  N   LEU A  13      -3.986  11.682   0.620  1.00 82.70           N
+ATOM    105  CA  LEU A  13      -4.106  11.386   2.043  1.00 82.70           C
+ATOM    106  C   LEU A  13      -2.951  12.001   2.826  1.00 82.70           C
+ATOM    107  CB  LEU A  13      -4.146   9.873   2.274  1.00 82.70           C
+ATOM    108  O   LEU A  13      -1.826  12.073   2.327  1.00 82.70           O
+ATOM    109  CG  LEU A  13      -5.347   9.129   1.688  1.00 82.70           C
+ATOM    110  CD1 LEU A  13      -5.171   7.623   1.857  1.00 82.70           C
+ATOM    111  CD2 LEU A  13      -6.640   9.598   2.346  1.00 82.70           C
+ATOM    112  N   SER A  14      -3.339  12.631   3.947  1.00 86.03           N
+ATOM    113  CA  SER A  14      -2.328  13.121   4.878  1.00 86.03           C
+ATOM    114  C   SER A  14      -1.680  11.974   5.645  1.00 86.03           C
+ATOM    115  CB  SER A  14      -2.942  14.120   5.859  1.00 86.03           C
+ATOM    116  O   SER A  14      -2.161  10.839   5.599  1.00 86.03           O
+ATOM    117  OG  SER A  14      -3.526  15.211   5.168  1.00 86.03           O
+ATOM    118  N   ASP A  15      -0.488  12.215   6.359  1.00 86.85           N
+ATOM    119  CA  ASP A  15       0.221  11.246   7.189  1.00 86.85           C
+ATOM    120  C   ASP A  15      -0.734  10.542   8.149  1.00 86.85           C
+ATOM    121  CB  ASP A  15       1.345  11.930   7.971  1.00 86.85           C
+ATOM    122  O   ASP A  15      -0.647   9.327   8.340  1.00 86.85           O
+ATOM    123  CG  ASP A  15       2.418  12.521   7.074  1.00 86.85           C
+ATOM    124  OD1 ASP A  15       3.279  11.766   6.575  1.00 86.85           O
+ATOM    125  OD2 ASP A  15       2.403  13.754   6.867  1.00 86.85           O
+ATOM    126  N   GLU A  16      -1.606  11.353   8.835  1.00 86.30           N
+ATOM    127  CA  GLU A  16      -2.590  10.797   9.760  1.00 86.30           C
+ATOM    128  C   GLU A  16      -3.555   9.859   9.041  1.00 86.30           C
+ATOM    129  CB  GLU A  16      -3.366  11.918  10.456  1.00 86.30           C
+ATOM    130  O   GLU A  16      -3.871   8.780   9.545  1.00 86.30           O
+ATOM    131  CG  GLU A  16      -2.547  12.688  11.481  1.00 86.30           C
+ATOM    132  CD  GLU A  16      -3.342  13.770  12.194  1.00 86.30           C
+ATOM    133  OE1 GLU A  16      -3.925  13.489  13.266  1.00 86.30           O
+ATOM    134  OE2 GLU A  16      -3.384  14.908  11.676  1.00 86.30           O
+ATOM    135  N   GLU A  17      -4.022  10.266   7.880  1.00 87.05           N
+ATOM    136  CA  GLU A  17      -4.956   9.466   7.093  1.00 87.05           C
+ATOM    137  C   GLU A  17      -4.305   8.172   6.613  1.00 87.05           C
+ATOM    138  CB  GLU A  17      -5.477  10.268   5.898  1.00 87.05           C
+ATOM    139  O   GLU A  17      -4.937   7.114   6.618  1.00 87.05           O
+ATOM    140  CG  GLU A  17      -6.410  11.407   6.281  1.00 87.05           C
+ATOM    141  CD  GLU A  17      -7.322  11.844   5.146  1.00 87.05           C
+ATOM    142  OE1 GLU A  17      -8.505  11.433   5.125  1.00 87.05           O
+ATOM    143  OE2 GLU A  17      -6.850  12.602   4.270  1.00 87.05           O
+ATOM    144  N   LEU A  18      -3.057   8.282   6.290  1.00 88.16           N
+ATOM    145  CA  LEU A  18      -2.291   7.120   5.855  1.00 88.16           C
+ATOM    146  C   LEU A  18      -2.194   6.084   6.970  1.00 88.16           C
+ATOM    147  CB  LEU A  18      -0.889   7.539   5.407  1.00 88.16           C
+ATOM    148  O   LEU A  18      -2.374   4.888   6.730  1.00 88.16           O
+ATOM    149  CG  LEU A  18      -0.785   8.201   4.032  1.00 88.16           C
+ATOM    150  CD1 LEU A  18       0.627   8.730   3.803  1.00 88.16           C
+ATOM    151  CD2 LEU A  18      -1.179   7.219   2.934  1.00 88.16           C
+ATOM    152  N   LYS A  19      -1.979   6.558   8.141  1.00 87.30           N
+ATOM    153  CA  LYS A  19      -1.908   5.682   9.308  1.00 87.30           C
+ATOM    154  C   LYS A  19      -3.243   4.984   9.553  1.00 87.30           C
+ATOM    155  CB  LYS A  19      -1.495   6.474  10.549  1.00 87.30           C
+ATOM    156  O   LYS A  19      -3.280   3.787   9.843  1.00 87.30           O
+ATOM    157  CG  LYS A  19      -0.007   6.781  10.620  1.00 87.30           C
+ATOM    158  CD  LYS A  19       0.352   7.515  11.906  1.00 87.30           C
+ATOM    159  CE  LYS A  19       1.818   7.927  11.926  1.00 87.30           C
+ATOM    160  NZ  LYS A  19       2.176   8.639  13.189  1.00 87.30           N
+ATOM    161  N   LYS A  20      -4.246   5.781   9.525  1.00 88.15           N
+ATOM    162  CA  LYS A  20      -5.586   5.234   9.715  1.00 88.15           C
+ATOM    163  C   LYS A  20      -5.907   4.185   8.654  1.00 88.15           C
+ATOM    164  CB  LYS A  20      -6.631   6.350   9.682  1.00 88.15           C
+ATOM    165  O   LYS A  20      -6.511   3.153   8.956  1.00 88.15           O
+ATOM    166  CG  LYS A  20      -6.661   7.208  10.937  1.00 88.15           C
+ATOM    167  CD  LYS A  20      -7.772   8.249  10.877  1.00 88.15           C
+ATOM    168  CE  LYS A  20      -7.774   9.138  12.113  1.00 88.15           C
+ATOM    169  NZ  LYS A  20      -8.875  10.146  12.069  1.00 88.15           N
+ATOM    170  N   LEU A  21      -5.444   4.518   7.462  1.00 86.41           N
+ATOM    171  CA  LEU A  21      -5.662   3.611   6.341  1.00 86.41           C
+ATOM    172  C   LEU A  21      -4.974   2.271   6.583  1.00 86.41           C
+ATOM    173  CB  LEU A  21      -5.148   4.234   5.040  1.00 86.41           C
+ATOM    174  O   LEU A  21      -5.577   1.214   6.385  1.00 86.41           O
+ATOM    175  CG  LEU A  21      -5.364   3.417   3.765  1.00 86.41           C
+ATOM    176  CD1 LEU A  21      -6.842   3.400   3.391  1.00 86.41           C
+ATOM    177  CD2 LEU A  21      -4.524   3.976   2.622  1.00 86.41           C
+ATOM    178  N   VAL A  22      -3.737   2.304   6.914  1.00 87.19           N
+ATOM    179  CA  VAL A  22      -2.953   1.109   7.205  1.00 87.19           C
+ATOM    180  C   VAL A  22      -3.627   0.307   8.316  1.00 87.19           C
+ATOM    181  CB  VAL A  22      -1.504   1.464   7.609  1.00 87.19           C
+ATOM    182  O   VAL A  22      -3.719  -0.921   8.236  1.00 87.19           O
+ATOM    183  CG1 VAL A  22      -0.752   0.218   8.073  1.00 87.19           C
+ATOM    184  CG2 VAL A  22      -0.774   2.130   6.444  1.00 87.19           C
+ATOM    185  N   GLU A  23      -4.070   0.928   9.305  1.00 88.34           N
+ATOM    186  CA  GLU A  23      -4.790   0.285  10.400  1.00 88.34           C
+ATOM    187  C   GLU A  23      -6.050  -0.414   9.897  1.00 88.34           C
+ATOM    188  CB  GLU A  23      -5.151   1.308  11.480  1.00 88.34           C
+ATOM    189  O   GLU A  23      -6.364  -1.525  10.328  1.00 88.34           O
+ATOM    190  CG  GLU A  23      -3.959   1.792  12.292  1.00 88.34           C
+ATOM    191  CD  GLU A  23      -4.356   2.595  13.521  1.00 88.34           C
+ATOM    192  OE1 GLU A  23      -4.486   2.004  14.616  1.00 88.34           O
+ATOM    193  OE2 GLU A  23      -4.539   3.826  13.386  1.00 88.34           O
+ATOM    194  N   GLU A  24      -6.671   0.256   9.129  1.00 87.82           N
+ATOM    195  CA  GLU A  24      -7.883  -0.315   8.549  1.00 87.82           C
+ATOM    196  C   GLU A  24      -7.569  -1.568   7.737  1.00 87.82           C
+ATOM    197  CB  GLU A  24      -8.595   0.717   7.670  1.00 87.82           C
+ATOM    198  O   GLU A  24      -8.334  -2.535   7.758  1.00 87.82           O
+ATOM    199  CG  GLU A  24      -9.372   1.763   8.456  1.00 87.82           C
+ATOM    200  CD  GLU A  24     -10.598   1.200   9.157  1.00 87.82           C
+ATOM    201  OE1 GLU A  24     -10.544   0.974  10.387  1.00 87.82           O
+ATOM    202  OE2 GLU A  24     -11.621   0.982   8.469  1.00 87.82           O
+ATOM    203  N   TRP A  25      -6.452  -1.421   6.925  1.00 87.98           N
+ATOM    204  CA  TRP A  25      -6.008  -2.576   6.152  1.00 87.98           C
+ATOM    205  C   TRP A  25      -5.804  -3.789   7.054  1.00 87.98           C
+ATOM    206  CB  TRP A  25      -4.712  -2.256   5.403  1.00 87.98           C
+ATOM    207  O   TRP A  25      -6.237  -4.895   6.724  1.00 87.98           O
+ATOM    208  CG  TRP A  25      -4.867  -1.219   4.332  1.00 87.98           C
+ATOM    209  CD1 TRP A  25      -6.030  -0.819   3.734  1.00 87.98           C
+ATOM    210  CD2 TRP A  25      -3.820  -0.453   3.727  1.00 87.98           C
+ATOM    211  CE2 TRP A  25      -4.422   0.394   2.770  1.00 87.98           C
+ATOM    212  CE3 TRP A  25      -2.431  -0.399   3.902  1.00 87.98           C
+ATOM    213  NE1 TRP A  25      -5.769   0.151   2.794  1.00 87.98           N
+ATOM    214  CH2 TRP A  25      -2.324   1.317   2.182  1.00 87.98           C
+ATOM    215  CZ2 TRP A  25      -3.681   1.285   1.990  1.00 87.98           C
+ATOM    216  CZ3 TRP A  25      -1.695   0.488   3.125  1.00 87.98           C
+ATOM    217  N   ILE A  26      -5.164  -3.521   8.121  1.00 86.80           N
+ATOM    218  CA  ILE A  26      -4.842  -4.578   9.074  1.00 86.80           C
+ATOM    219  C   ILE A  26      -6.123  -5.095   9.724  1.00 86.80           C
+ATOM    220  CB  ILE A  26      -3.855  -4.082  10.155  1.00 86.80           C
+ATOM    221  O   ILE A  26      -6.287  -6.302   9.913  1.00 86.80           O
+ATOM    222  CG1 ILE A  26      -2.511  -3.706   9.519  1.00 86.80           C
+ATOM    223  CG2 ILE A  26      -3.667  -5.144  11.243  1.00 86.80           C
+ATOM    224  CD1 ILE A  26      -1.549  -3.010  10.471  1.00 86.80           C
+ATOM    225  N   LYS A  27      -7.085  -4.130  10.074  1.00 88.23           N
+ATOM    226  CA  LYS A  27      -8.358  -4.482  10.697  1.00 88.23           C
+ATOM    227  C   LYS A  27      -9.231  -5.292   9.743  1.00 88.23           C
+ATOM    228  CB  LYS A  27      -9.101  -3.224  11.147  1.00 88.23           C
+ATOM    229  O   LYS A  27      -9.857  -6.273  10.148  1.00 88.23           O
+ATOM    230  CG  LYS A  27     -10.280  -3.498  12.070  1.00 88.23           C
+ATOM    231  CD  LYS A  27     -10.890  -2.206  12.597  1.00 88.23           C
+ATOM    232  CE  LYS A  27     -12.096  -2.477  13.486  1.00 88.23           C
+ATOM    233  NZ  LYS A  27     -12.726  -1.212  13.967  1.00 88.23           N
+ATOM    234  N   SER A  28      -9.257  -4.866   8.486  1.00 88.60           N
+ATOM    235  CA  SER A  28     -10.097  -5.462   7.453  1.00 88.60           C
+ATOM    236  C   SER A  28      -9.499  -6.767   6.939  1.00 88.60           C
+ATOM    237  CB  SER A  28     -10.292  -4.488   6.290  1.00 88.60           C
+ATOM    238  O   SER A  28     -10.208  -7.598   6.366  1.00 88.60           O
+ATOM    239  OG  SER A  28     -11.021  -3.347   6.707  1.00 88.60           O
+ATOM    240  N   LYS A  29      -8.274  -7.060   7.266  1.00 87.22           N
+ATOM    241  CA  LYS A  29      -7.552  -8.279   6.911  1.00 87.22           C
+ATOM    242  C   LYS A  29      -7.546  -8.493   5.400  1.00 87.22           C
+ATOM    243  CB  LYS A  29      -8.169  -9.491   7.609  1.00 87.22           C
+ATOM    244  O   LYS A  29      -7.336  -9.612   4.927  1.00 87.22           O
+ATOM    245  CG  LYS A  29      -7.958  -9.511   9.116  1.00 87.22           C
+ATOM    246  CD  LYS A  29      -8.508 -10.787   9.741  1.00 87.22           C
+ATOM    247  CE  LYS A  29      -8.322 -10.795  11.252  1.00 87.22           C
+ATOM    248  NZ  LYS A  29      -8.836 -12.056  11.866  1.00 87.22           N
+ATOM    249  N   GLU A  30      -7.995  -7.561   4.711  1.00 90.12           N
+ATOM    250  CA  GLU A  30      -7.955  -7.620   3.253  1.00 90.12           C
+ATOM    251  C   GLU A  30      -7.715  -6.239   2.650  1.00 90.12           C
+ATOM    252  CB  GLU A  30      -9.254  -8.215   2.703  1.00 90.12           C
+ATOM    253  O   GLU A  30      -8.286  -5.248   3.110  1.00 90.12           O
+ATOM    254  CG  GLU A  30      -9.273  -8.357   1.188  1.00 90.12           C
+ATOM    255  CD  GLU A  30     -10.542  -9.008   0.662  1.00 90.12           C
+ATOM    256  OE1 GLU A  30     -11.585  -8.321   0.575  1.00 90.12           O
+ATOM    257  OE2 GLU A  30     -10.494 -10.215   0.335  1.00 90.12           O
+ATOM    258  N   VAL A  31      -6.835  -6.090   1.610  1.00 86.60           N
+ATOM    259  CA  VAL A  31      -6.583  -4.828   0.922  1.00 86.60           C
+ATOM    260  C   VAL A  31      -6.313  -5.090  -0.558  1.00 86.60           C
+ATOM    261  CB  VAL A  31      -5.397  -4.064   1.553  1.00 86.60           C
+ATOM    262  O   VAL A  31      -5.684  -6.090  -0.912  1.00 86.60           O
+ATOM    263  CG1 VAL A  31      -4.102  -4.859   1.404  1.00 86.60           C
+ATOM    264  CG2 VAL A  31      -5.255  -2.682   0.919  1.00 86.60           C
+ATOM    265  N   THR A  32      -6.886  -4.281  -1.455  1.00 86.60           N
+ATOM    266  CA  THR A  32      -6.648  -4.386  -2.890  1.00 86.60           C
+ATOM    267  C   THR A  32      -5.875  -3.173  -3.400  1.00 86.60           C
+ATOM    268  CB  THR A  32      -7.971  -4.518  -3.667  1.00 86.60           C
+ATOM    269  O   THR A  32      -6.311  -2.033  -3.224  1.00 86.60           O
+ATOM    270  CG2 THR A  32      -7.715  -4.710  -5.159  1.00 86.60           C
+ATOM    271  OG1 THR A  32      -8.700  -5.647  -3.170  1.00 86.60           O
+ATOM    272  N   PHE A  33      -4.627  -3.379  -3.960  1.00 85.17           N
+ATOM    273  CA  PHE A  33      -3.825  -2.315  -4.552  1.00 85.17           C
+ATOM    274  C   PHE A  33      -4.096  -2.201  -6.048  1.00 85.17           C
+ATOM    275  CB  PHE A  33      -2.333  -2.565  -4.307  1.00 85.17           C
+ATOM    276  O   PHE A  33      -4.048  -3.198  -6.771  1.00 85.17           O
+ATOM    277  CG  PHE A  33      -1.918  -2.397  -2.870  1.00 85.17           C
+ATOM    278  CD1 PHE A  33      -1.696  -1.132  -2.340  1.00 85.17           C
+ATOM    279  CD2 PHE A  33      -1.750  -3.504  -2.050  1.00 85.17           C
+ATOM    280  CE1 PHE A  33      -1.312  -0.973  -1.011  1.00 85.17           C
+ATOM    281  CE2 PHE A  33      -1.366  -3.354  -0.720  1.00 85.17           C
+ATOM    282  CZ  PHE A  33      -1.146  -2.087  -0.203  1.00 85.17           C
+ATOM    283  N   VAL A  34      -4.488  -1.033  -6.377  1.00 79.71           N
+ATOM    284  CA  VAL A  34      -4.738  -0.771  -7.791  1.00 79.71           C
+ATOM    285  C   VAL A  34      -3.582   0.033  -8.380  1.00 79.71           C
+ATOM    286  CB  VAL A  34      -6.072  -0.020  -8.002  1.00 79.71           C
+ATOM    287  O   VAL A  34      -3.285   1.137  -7.917  1.00 79.71           O
+ATOM    288  CG1 VAL A  34      -6.363   0.156  -9.491  1.00 79.71           C
+ATOM    289  CG2 VAL A  34      -7.216  -0.762  -7.314  1.00 79.71           C
+ATOM    290  N   ILE A  35      -2.823  -0.596  -9.337  1.00 77.12           N
+ATOM    291  CA  ILE A  35      -1.721   0.099  -9.993  1.00 77.12           C
+ATOM    292  C   ILE A  35      -2.004   0.218 -11.489  1.00 77.12           C
+ATOM    293  CB  ILE A  35      -0.376  -0.624  -9.757  1.00 77.12           C
+ATOM    294  O   ILE A  35      -2.768  -0.572 -12.047  1.00 77.12           O
+ATOM    295  CG1 ILE A  35      -0.441  -2.059 -10.291  1.00 77.12           C
+ATOM    296  CG2 ILE A  35      -0.007  -0.608  -8.271  1.00 77.12           C
+ATOM    297  CD1 ILE A  35       0.916  -2.740 -10.402  1.00 77.12           C
+ATOM    298  N   SER A  36      -1.599   1.325 -11.947  1.00 72.93           N
+ATOM    299  CA  SER A  36      -1.731   1.517 -13.387  1.00 72.93           C
+ATOM    300  C   SER A  36      -0.484   1.040 -14.125  1.00 72.93           C
+ATOM    301  CB  SER A  36      -1.994   2.988 -13.711  1.00 72.93           C
+ATOM    302  O   SER A  36       0.613   1.040 -13.564  1.00 72.93           O
+ATOM    303  OG  SER A  36      -1.967   3.208 -15.110  1.00 72.93           O
+ATOM    304  N   SER A  37      -0.670   0.403 -15.236  1.00 69.39           N
+ATOM    305  CA  SER A  37       0.426  -0.073 -16.073  1.00 69.39           C
+ATOM    306  C   SER A  37       1.372   1.064 -16.443  1.00 69.39           C
+ATOM    307  CB  SER A  37      -0.115  -0.731 -17.343  1.00 69.39           C
+ATOM    308  O   SER A  37       2.505   0.823 -16.867  1.00 69.39           O
+ATOM    309  OG  SER A  37      -1.045   0.119 -17.992  1.00 69.39           O
+ATOM    310  N   ALA A  38       0.862   2.297 -16.248  1.00 67.39           N
+ATOM    311  CA  ALA A  38       1.656   3.492 -16.525  1.00 67.39           C
+ATOM    312  C   ALA A  38       2.561   3.834 -15.344  1.00 67.39           C
+ATOM    313  CB  ALA A  38       0.745   4.672 -16.853  1.00 67.39           C
+ATOM    314  O   ALA A  38       3.386   4.746 -15.431  1.00 67.39           O
+ATOM    315  N   ASP A  39       2.279   3.071 -14.251  1.00 72.75           N
+ATOM    316  CA  ASP A  39       3.057   3.298 -13.037  1.00 72.75           C
+ATOM    317  C   ASP A  39       4.501   2.833 -13.215  1.00 72.75           C
+ATOM    318  CB  ASP A  39       2.417   2.580 -11.847  1.00 72.75           C
+ATOM    319  O   ASP A  39       4.780   1.959 -14.039  1.00 72.75           O
+ATOM    320  CG  ASP A  39       1.183   3.292 -11.320  1.00 72.75           C
+ATOM    321  OD1 ASP A  39       1.293   4.454 -10.874  1.00 72.75           O
+ATOM    322  OD2 ASP A  39       0.091   2.684 -11.348  1.00 72.75           O
+ATOM    323  N   SER A  40       5.475   3.562 -12.768  1.00 72.73           N
+ATOM    324  CA  SER A  40       6.908   3.286 -12.803  1.00 72.73           C
+ATOM    325  C   SER A  40       7.256   2.065 -11.958  1.00 72.73           C
+ATOM    326  CB  SER A  40       7.700   4.499 -12.314  1.00 72.73           C
+ATOM    327  O   SER A  40       6.491   1.677 -11.073  1.00 72.73           O
+ATOM    328  OG  SER A  40       7.410   5.640 -13.101  1.00 72.73           O
+ATOM    329  N   GLU A  41       8.265   1.200 -12.472  1.00 83.34           N
+ATOM    330  CA  GLU A  41       8.802   0.051 -11.749  1.00 83.34           C
+ATOM    331  C   GLU A  41       8.950   0.356 -10.261  1.00 83.34           C
+ATOM    332  CB  GLU A  41      10.152  -0.371 -12.336  1.00 83.34           C
+ATOM    333  O   GLU A  41       8.722  -0.515  -9.418  1.00 83.34           O
+ATOM    334  CG  GLU A  41      10.046  -1.058 -13.689  1.00 83.34           C
+ATOM    335  CD  GLU A  41      11.377  -1.586 -14.200  1.00 83.34           C
+ATOM    336  OE1 GLU A  41      11.690  -2.775 -13.962  1.00 83.34           O
+ATOM    337  OE2 GLU A  41      12.113  -0.805 -14.842  1.00 83.34           O
+ATOM    338  N   GLU A  42       9.164   1.541  -9.996  1.00 85.29           N
+ATOM    339  CA  GLU A  42       9.324   1.965  -8.608  1.00 85.29           C
+ATOM    340  C   GLU A  42       8.026   1.793  -7.825  1.00 85.29           C
+ATOM    341  CB  GLU A  42       9.789   3.422  -8.541  1.00 85.29           C
+ATOM    342  O   GLU A  42       8.031   1.257  -6.715  1.00 85.29           O
+ATOM    343  CG  GLU A  42      10.241   3.861  -7.156  1.00 85.29           C
+ATOM    344  CD  GLU A  42      11.177   5.059  -7.182  1.00 85.29           C
+ATOM    345  OE1 GLU A  42      10.689   6.208  -7.276  1.00 85.29           O
+ATOM    346  OE2 GLU A  42      12.408   4.847  -7.108  1.00 85.29           O
+ATOM    347  N   ILE A  43       6.916   2.343  -8.302  1.00 82.81           N
+ATOM    348  CA  ILE A  43       5.610   2.254  -7.658  1.00 82.81           C
+ATOM    349  C   ILE A  43       5.202   0.789  -7.519  1.00 82.81           C
+ATOM    350  CB  ILE A  43       4.537   3.036  -8.447  1.00 82.81           C
+ATOM    351  O   ILE A  43       4.717   0.370  -6.465  1.00 82.81           O
+ATOM    352  CG1 ILE A  43       4.822   4.541  -8.387  1.00 82.81           C
+ATOM    353  CG2 ILE A  43       3.137   2.722  -7.911  1.00 82.81           C
+ATOM    354  CD1 ILE A  43       3.876   5.384  -9.232  1.00 82.81           C
+ATOM    355  N   LYS A  44       5.549  -0.013  -8.535  1.00 83.23           N
+ATOM    356  CA  LYS A  44       5.294  -1.450  -8.502  1.00 83.23           C
+ATOM    357  C   LYS A  44       6.064  -2.118  -7.366  1.00 83.23           C
+ATOM    358  CB  LYS A  44       5.667  -2.093  -9.838  1.00 83.23           C
+ATOM    359  O   LYS A  44       5.511  -2.944  -6.636  1.00 83.23           O
+ATOM    360  CG  LYS A  44       4.624  -1.902 -10.929  1.00 83.23           C
+ATOM    361  CD  LYS A  44       4.985  -2.679 -12.189  1.00 83.23           C
+ATOM    362  CE  LYS A  44       4.004  -2.398 -13.320  1.00 83.23           C
+ATOM    363  NZ  LYS A  44       4.334  -3.183 -14.547  1.00 83.23           N
+ATOM    364  N   LYS A  45       7.296  -1.791  -7.304  1.00 88.48           N
+ATOM    365  CA  LYS A  45       8.146  -2.345  -6.255  1.00 88.48           C
+ATOM    366  C   LYS A  45       7.628  -1.967  -4.870  1.00 88.48           C
+ATOM    367  CB  LYS A  45       9.589  -1.867  -6.424  1.00 88.48           C
+ATOM    368  O   LYS A  45       7.601  -2.800  -3.962  1.00 88.48           O
+ATOM    369  CG  LYS A  45      10.363  -2.605  -7.506  1.00 88.48           C
+ATOM    370  CD  LYS A  45      11.819  -2.159  -7.554  1.00 88.48           C
+ATOM    371  CE  LYS A  45      12.582  -2.860  -8.670  1.00 88.48           C
+ATOM    372  NZ  LYS A  45      14.014  -2.437  -8.712  1.00 88.48           N
+ATOM    373  N   LEU A  46       7.267  -0.760  -4.707  1.00 90.20           N
+ATOM    374  CA  LEU A  46       6.764  -0.277  -3.426  1.00 90.20           C
+ATOM    375  C   LEU A  46       5.478  -1.001  -3.040  1.00 90.20           C
+ATOM    376  CB  LEU A  46       6.516   1.233  -3.481  1.00 90.20           C
+ATOM    377  O   LEU A  46       5.308  -1.401  -1.886  1.00 90.20           O
+ATOM    378  CG  LEU A  46       7.756   2.126  -3.413  1.00 90.20           C
+ATOM    379  CD1 LEU A  46       7.391   3.567  -3.755  1.00 90.20           C
+ATOM    380  CD2 LEU A  46       8.398   2.045  -2.033  1.00 90.20           C
+ATOM    381  N   VAL A  47       4.634  -1.055  -3.956  1.00 87.72           N
+ATOM    382  CA  VAL A  47       3.355  -1.724  -3.743  1.00 87.72           C
+ATOM    383  C   VAL A  47       3.592  -3.184  -3.363  1.00 87.72           C
+ATOM    384  CB  VAL A  47       2.454  -1.638  -4.995  1.00 87.72           C
+ATOM    385  O   VAL A  47       2.953  -3.705  -2.446  1.00 87.72           O
+ATOM    386  CG1 VAL A  47       1.201  -2.494  -4.819  1.00 87.72           C
+ATOM    387  CG2 VAL A  47       2.077  -0.186  -5.282  1.00 87.72           C
+ATOM    388  N   GLU A  48       4.453  -3.832  -4.059  1.00 89.12           N
+ATOM    389  CA  GLU A  48       4.817  -5.214  -3.761  1.00 89.12           C
+ATOM    390  C   GLU A  48       5.366  -5.347  -2.344  1.00 89.12           C
+ATOM    391  CB  GLU A  48       5.843  -5.729  -4.774  1.00 89.12           C
+ATOM    392  O   GLU A  48       5.015  -6.283  -1.622  1.00 89.12           O
+ATOM    393  CG  GLU A  48       5.260  -6.014  -6.150  1.00 89.12           C
+ATOM    394  CD  GLU A  48       6.211  -6.777  -7.058  1.00 89.12           C
+ATOM    395  OE1 GLU A  48       6.128  -8.025  -7.112  1.00 89.12           O
+ATOM    396  OE2 GLU A  48       7.046  -6.122  -7.721  1.00 89.12           O
+ATOM    397  N   GLU A  49       6.263  -4.525  -2.078  1.00 92.03           N
+ATOM    398  CA  GLU A  49       6.825  -4.532  -0.731  1.00 92.03           C
+ATOM    399  C   GLU A  49       5.738  -4.339   0.322  1.00 92.03           C
+ATOM    400  CB  GLU A  49       7.894  -3.445  -0.589  1.00 92.03           C
+ATOM    401  O   GLU A  49       5.730  -5.026   1.346  1.00 92.03           O
+ATOM    402  CG  GLU A  49       9.203  -3.773  -1.292  1.00 92.03           C
+ATOM    403  CD  GLU A  49      10.340  -2.840  -0.909  1.00 92.03           C
+ATOM    404  OE1 GLU A  49      10.970  -3.054   0.152  1.00 92.03           O
+ATOM    405  OE2 GLU A  49      10.603  -1.886  -1.675  1.00 92.03           O
+ATOM    406  N   ASN A  50       4.950  -3.304   0.106  1.00 90.05           N
+ATOM    407  CA  ASN A  50       3.830  -3.068   1.010  1.00 90.05           C
+ATOM    408  C   ASN A  50       2.960  -4.313   1.161  1.00 90.05           C
+ATOM    409  CB  ASN A  50       2.987  -1.887   0.524  1.00 90.05           C
+ATOM    410  O   ASN A  50       2.539  -4.651   2.269  1.00 90.05           O
+ATOM    411  CG  ASN A  50       3.539  -0.550   0.978  1.00 90.05           C
+ATOM    412  ND2 ASN A  50       4.277   0.116   0.098  1.00 90.05           N
+ATOM    413  OD1 ASN A  50       3.305  -0.120   2.110  1.00 90.05           O
+ATOM    414  N   ALA A  51       2.704  -4.904   0.020  1.00 89.43           N
+ATOM    415  CA  ALA A  51       1.897  -6.121  -0.004  1.00 89.43           C
+ATOM    416  C   ALA A  51       2.538  -7.220   0.839  1.00 89.43           C
+ATOM    417  CB  ALA A  51       1.701  -6.602  -1.439  1.00 89.43           C
+ATOM    418  O   ALA A  51       1.849  -7.920   1.585  1.00 89.43           O
+ATOM    419  N   GLU A  52       3.815  -7.414   0.696  1.00 91.12           N
+ATOM    420  CA  GLU A  52       4.547  -8.437   1.437  1.00 91.12           C
+ATOM    421  C   GLU A  52       4.436  -8.213   2.942  1.00 91.12           C
+ATOM    422  CB  GLU A  52       6.018  -8.457   1.015  1.00 91.12           C
+ATOM    423  O   GLU A  52       4.209  -9.158   3.700  1.00 91.12           O
+ATOM    424  CG  GLU A  52       6.248  -9.005  -0.387  1.00 91.12           C
+ATOM    425  CD  GLU A  52       7.720  -9.166  -0.733  1.00 91.12           C
+ATOM    426  OE1 GLU A  52       8.313 -10.215  -0.392  1.00 91.12           O
+ATOM    427  OE2 GLU A  52       8.285  -8.235  -1.350  1.00 91.12           O
+ATOM    428  N   ILE A  53       4.609  -7.008   3.402  1.00 91.89           N
+ATOM    429  CA  ILE A  53       4.531  -6.669   4.819  1.00 91.89           C
+ATOM    430  C   ILE A  53       3.112  -6.910   5.330  1.00 91.89           C
+ATOM    431  CB  ILE A  53       4.950  -5.204   5.074  1.00 91.89           C
+ATOM    432  O   ILE A  53       2.921  -7.486   6.403  1.00 91.89           O
+ATOM    433  CG1 ILE A  53       6.419  -4.994   4.686  1.00 91.89           C
+ATOM    434  CG2 ILE A  53       4.710  -4.819   6.536  1.00 91.89           C
+ATOM    435  CD1 ILE A  53       6.878  -3.544   4.762  1.00 91.89           C
+ATOM    436  N   LEU A  54       2.220  -6.422   4.598  1.00 90.60           N
+ATOM    437  CA  LEU A  54       0.817  -6.592   4.960  1.00 90.60           C
+ATOM    438  C   LEU A  54       0.454  -8.071   5.048  1.00 90.60           C
+ATOM    439  CB  LEU A  54      -0.087  -5.892   3.942  1.00 90.60           C
+ATOM    440  O   LEU A  54      -0.274  -8.482   5.955  1.00 90.60           O
+ATOM    441  CG  LEU A  54      -0.161  -4.367   4.036  1.00 90.60           C
+ATOM    442  CD1 LEU A  54      -0.837  -3.792   2.797  1.00 90.60           C
+ATOM    443  CD2 LEU A  54      -0.900  -3.944   5.301  1.00 90.60           C
+ATOM    444  N   GLU A  55       0.909  -8.858   4.086  1.00 90.94           N
+ATOM    445  CA  GLU A  55       0.715 -10.305   4.103  1.00 90.94           C
+ATOM    446  C   GLU A  55       1.303 -10.926   5.367  1.00 90.94           C
+ATOM    447  CB  GLU A  55       1.342 -10.946   2.862  1.00 90.94           C
+ATOM    448  O   GLU A  55       0.712 -11.837   5.950  1.00 90.94           O
+ATOM    449  CG  GLU A  55       0.549 -10.716   1.584  1.00 90.94           C
+ATOM    450  CD  GLU A  55       0.996 -11.603   0.432  1.00 90.94           C
+ATOM    451  OE1 GLU A  55       0.436 -12.710   0.266  1.00 90.94           O
+ATOM    452  OE2 GLU A  55       1.915 -11.187  -0.308  1.00 90.94           O
+ATOM    453  N   LYS A  56       2.477 -10.439   5.689  1.00 90.58           N
+ATOM    454  CA  LYS A  56       3.128 -10.914   6.907  1.00 90.58           C
+ATOM    455  C   LYS A  56       2.303 -10.564   8.143  1.00 90.58           C
+ATOM    456  CB  LYS A  56       4.533 -10.324   7.031  1.00 90.58           C
+ATOM    457  O   LYS A  56       2.287 -11.317   9.119  1.00 90.58           O
+ATOM    458  CG  LYS A  56       5.551 -10.945   6.085  1.00 90.58           C
+ATOM    459  CD  LYS A  56       6.949 -10.393   6.327  1.00 90.58           C
+ATOM    460  CE  LYS A  56       7.967 -11.008   5.376  1.00 90.58           C
+ATOM    461  NZ  LYS A  56       9.350 -10.516   5.651  1.00 90.58           N
+ATOM    462  N   LEU A  57       1.666  -9.472   8.081  1.00 89.28           N
+ATOM    463  CA  LEU A  57       0.843  -8.979   9.180  1.00 89.28           C
+ATOM    464  C   LEU A  57      -0.522  -9.661   9.185  1.00 89.28           C
+ATOM    465  CB  LEU A  57       0.668  -7.462   9.080  1.00 89.28           C
+ATOM    466  O   LEU A  57      -1.332  -9.430  10.085  1.00 89.28           O
+ATOM    467  CG  LEU A  57       1.906  -6.615   9.381  1.00 89.28           C
+ATOM    468  CD1 LEU A  57       1.651  -5.157   9.016  1.00 89.28           C
+ATOM    469  CD2 LEU A  57       2.298  -6.744  10.849  1.00 89.28           C
+ATOM    470  N   GLY A  58      -0.801 -10.562   8.254  1.00 89.24           N
+ATOM    471  CA  GLY A  58      -2.043 -11.316   8.202  1.00 89.24           C
+ATOM    472  C   GLY A  58      -3.109 -10.651   7.352  1.00 89.24           C
+ATOM    473  O   GLY A  58      -4.304 -10.868   7.563  1.00 89.24           O
+ATOM    474  N   VAL A  59      -2.742  -9.745   6.559  1.00 90.59           N
+ATOM    475  CA  VAL A  59      -3.658  -9.015   5.689  1.00 90.59           C
+ATOM    476  C   VAL A  59      -3.626  -9.615   4.285  1.00 90.59           C
+ATOM    477  CB  VAL A  59      -3.312  -7.511   5.634  1.00 90.59           C
+ATOM    478  O   VAL A  59      -2.551  -9.854   3.730  1.00 90.59           O
+ATOM    479  CG1 VAL A  59      -4.305  -6.760   4.750  1.00 90.59           C
+ATOM    480  CG2 VAL A  59      -3.290  -6.917   7.042  1.00 90.59           C
+ATOM    481  N   LYS A  60      -4.796 -10.038   3.669  1.00 91.31           N
+ATOM    482  CA  LYS A  60      -4.890 -10.525   2.295  1.00 91.31           C
+ATOM    483  C   LYS A  60      -4.751  -9.380   1.296  1.00 91.31           C
+ATOM    484  CB  LYS A  60      -6.215 -11.256   2.074  1.00 91.31           C
+ATOM    485  O   LYS A  60      -5.554  -8.444   1.300  1.00 91.31           O
+ATOM    486  CG  LYS A  60      -6.280 -12.039   0.771  1.00 91.31           C
+ATOM    487  CD  LYS A  60      -7.562 -12.856   0.673  1.00 91.31           C
+ATOM    488  CE  LYS A  60      -7.618 -13.657  -0.621  1.00 91.31           C
+ATOM    489  NZ  LYS A  60      -8.859 -14.483  -0.707  1.00 91.31           N
+ATOM    490  N   VAL A  61      -3.640  -9.388   0.542  1.00 90.50           N
+ATOM    491  CA  VAL A  61      -3.325  -8.295  -0.373  1.00 90.50           C
+ATOM    492  C   VAL A  61      -3.627  -8.719  -1.808  1.00 90.50           C
+ATOM    493  CB  VAL A  61      -1.849  -7.856  -0.246  1.00 90.50           C
+ATOM    494  O   VAL A  61      -3.177  -9.776  -2.258  1.00 90.50           O
+ATOM    495  CG1 VAL A  61      -1.548  -6.696  -1.192  1.00 90.50           C
+ATOM    496  CG2 VAL A  61      -1.531  -7.470   1.197  1.00 90.50           C
+ATOM    497  N   LYS A  62      -4.464  -7.942  -2.568  1.00 89.89           N
+ATOM    498  CA  LYS A  62      -4.755  -8.135  -3.986  1.00 89.89           C
+ATOM    499  C   LYS A  62      -4.271  -6.948  -4.813  1.00 89.89           C
+ATOM    500  CB  LYS A  62      -6.254  -8.348  -4.202  1.00 89.89           C
+ATOM    501  O   LYS A  62      -4.598  -5.799  -4.510  1.00 89.89           O
+ATOM    502  CG  LYS A  62      -6.615  -8.835  -5.598  1.00 89.89           C
+ATOM    503  CD  LYS A  62      -8.100  -9.156  -5.711  1.00 89.89           C
+ATOM    504  CE  LYS A  62      -8.454  -9.686  -7.094  1.00 89.89           C
+ATOM    505  NZ  LYS A  62      -9.906 -10.018  -7.205  1.00 89.89           N
+ATOM    506  N   VAL A  63      -3.369  -7.174  -5.795  1.00 85.66           N
+ATOM    507  CA  VAL A  63      -2.847  -6.112  -6.649  1.00 85.66           C
+ATOM    508  C   VAL A  63      -3.490  -6.198  -8.032  1.00 85.66           C
+ATOM    509  CB  VAL A  63      -1.309  -6.185  -6.772  1.00 85.66           C
+ATOM    510  O   VAL A  63      -3.359  -7.211  -8.723  1.00 85.66           O
+ATOM    511  CG1 VAL A  63      -0.779  -5.034  -7.625  1.00 85.66           C
+ATOM    512  CG2 VAL A  63      -0.663  -6.171  -5.388  1.00 85.66           C
+ATOM    513  N   VAL A  64      -4.304  -5.230  -8.309  1.00 83.17           N
+ATOM    514  CA  VAL A  64      -5.001  -5.174  -9.589  1.00 83.17           C
+ATOM    515  C   VAL A  64      -4.339  -4.137 -10.494  1.00 83.17           C
+ATOM    516  CB  VAL A  64      -6.499  -4.843  -9.406  1.00 83.17           C
+ATOM    517  O   VAL A  64      -4.094  -3.004 -10.073  1.00 83.17           O
+ATOM    518  CG1 VAL A  64      -7.221  -4.843 -10.753  1.00 83.17           C
+ATOM    519  CG2 VAL A  64      -7.152  -5.836  -8.447  1.00 83.17           C
+ATOM    520  N   GLU A  65      -3.914  -4.576 -11.655  1.00 82.38           N
+ATOM    521  CA  GLU A  65      -3.300  -3.697 -12.646  1.00 82.38           C
+ATOM    522  C   GLU A  65      -4.341  -3.154 -13.621  1.00 82.38           C
+ATOM    523  CB  GLU A  65      -2.198  -4.434 -13.410  1.00 82.38           C
+ATOM    524  O   GLU A  65      -5.007  -3.922 -14.318  1.00 82.38           O
+ATOM    525  CG  GLU A  65      -1.357  -3.531 -14.300  1.00 82.38           C
+ATOM    526  CD  GLU A  65      -0.228  -4.266 -15.005  1.00 82.38           C
+ATOM    527  OE1 GLU A  65      -0.445  -4.784 -16.124  1.00 82.38           O
+ATOM    528  OE2 GLU A  65       0.884  -4.325 -14.433  1.00 82.38           O
+ATOM    529  N   LEU A  66      -4.731  -1.848 -13.511  1.00 73.61           N
+ATOM    530  CA  LEU A  66      -5.704  -1.232 -14.407  1.00 73.61           C
+ATOM    531  C   LEU A  66      -5.031  -0.737 -15.682  1.00 73.61           C
+ATOM    532  CB  LEU A  66      -6.417  -0.072 -13.708  1.00 73.61           C
+ATOM    533  O   LEU A  66      -3.927  -0.189 -15.634  1.00 73.61           O
+ATOM    534  CG  LEU A  66      -7.425  -0.450 -12.622  1.00 73.61           C
+ATOM    535  CD1 LEU A  66      -7.847   0.787 -11.836  1.00 73.61           C
+ATOM    536  CD2 LEU A  66      -8.638  -1.141 -13.234  1.00 73.61           C
+ATOM    537  N   GLY A  67      -5.215  -1.540 -16.831  1.00 61.81           N
+ATOM    538  CA  GLY A  67      -4.761  -1.145 -18.155  1.00 61.81           C
+ATOM    539  C   GLY A  67      -5.505   0.056 -18.708  1.00 61.81           C
+ATOM    540  O   GLY A  67      -6.738   0.065 -18.746  1.00 61.81           O
+ATOM    541  N   GLY A  68      -5.090   1.390 -18.491  1.00 60.96           N
+ATOM    542  CA  GLY A  68      -5.697   2.625 -18.962  1.00 60.96           C
+ATOM    543  C   GLY A  68      -4.768   3.820 -18.865  1.00 60.96           C
+ATOM    544  O   GLY A  68      -3.738   3.760 -18.191  1.00 60.96           O
+ATOM    545  N   GLU A  69      -4.531   4.607 -19.986  1.00 63.19           N
+ATOM    546  CA  GLU A  69      -3.769   5.840 -20.158  1.00 63.19           C
+ATOM    547  C   GLU A  69      -3.863   6.725 -18.918  1.00 63.19           C
+ATOM    548  CB  GLU A  69      -4.257   6.607 -21.389  1.00 63.19           C
+ATOM    549  O   GLU A  69      -4.938   6.870 -18.332  1.00 63.19           O
+ATOM    550  CG  GLU A  69      -3.142   7.015 -22.341  1.00 63.19           C
+ATOM    551  CD  GLU A  69      -3.653   7.632 -23.634  1.00 63.19           C
+ATOM    552  OE1 GLU A  69      -3.936   8.852 -23.654  1.00 63.19           O
+ATOM    553  OE2 GLU A  69      -3.771   6.890 -24.634  1.00 63.19           O
+ATOM    554  N   LEU A  70      -2.763   6.805 -18.127  1.00 62.85           N
+ATOM    555  CA  LEU A  70      -2.656   7.713 -16.990  1.00 62.85           C
+ATOM    556  C   LEU A  70      -3.013   9.139 -17.398  1.00 62.85           C
+ATOM    557  CB  LEU A  70      -1.242   7.676 -16.406  1.00 62.85           C
+ATOM    558  O   LEU A  70      -2.495   9.653 -18.391  1.00 62.85           O
+ATOM    559  CG  LEU A  70      -0.896   6.460 -15.544  1.00 62.85           C
+ATOM    560  CD1 LEU A  70       0.611   6.230 -15.534  1.00 62.85           C
+ATOM    561  CD2 LEU A  70      -1.425   6.642 -14.126  1.00 62.85           C
+ATOM    562  N   ASP A  71      -4.382   9.504 -17.115  1.00 67.78           N
+ATOM    563  CA  ASP A  71      -4.779  10.889 -17.347  1.00 67.78           C
+ATOM    564  C   ASP A  71      -3.796  11.859 -16.695  1.00 67.78           C
+ATOM    565  CB  ASP A  71      -6.193  11.139 -16.819  1.00 67.78           C
+ATOM    566  O   ASP A  71      -3.070  11.487 -15.770  1.00 67.78           O
+ATOM    567  CG  ASP A  71      -6.996  12.083 -17.696  1.00 67.78           C
+ATOM    568  OD1 ASP A  71      -7.054  13.295 -17.394  1.00 67.78           O
+ATOM    569  OD2 ASP A  71      -7.578  11.611 -18.697  1.00 67.78           O
+ATOM    570  N   GLU A  72      -3.069  12.841 -17.280  1.00 66.31           N
+ATOM    571  CA  GLU A  72      -2.192  13.936 -16.876  1.00 66.31           C
+ATOM    572  C   GLU A  72      -2.299  14.205 -15.378  1.00 66.31           C
+ATOM    573  CB  GLU A  72      -2.521  15.207 -17.663  1.00 66.31           C
+ATOM    574  O   GLU A  72      -1.296  14.487 -14.719  1.00 66.31           O
+ATOM    575  CG  GLU A  72      -1.767  15.327 -18.980  1.00 66.31           C
+ATOM    576  CD  GLU A  72      -2.109  16.590 -19.754  1.00 66.31           C
+ATOM    577  OE1 GLU A  72      -1.474  17.642 -19.511  1.00 66.31           O
+ATOM    578  OE2 GLU A  72      -3.020  16.529 -20.609  1.00 66.31           O
+ATOM    579  N   LEU A  73      -3.365  13.942 -14.773  1.00 66.33           N
+ATOM    580  CA  LEU A  73      -3.564  14.142 -13.342  1.00 66.33           C
+ATOM    581  C   LEU A  73      -2.893  13.032 -12.539  1.00 66.33           C
+ATOM    582  CB  LEU A  73      -5.058  14.196 -13.010  1.00 66.33           C
+ATOM    583  O   LEU A  73      -2.291  13.292 -11.495  1.00 66.33           O
+ATOM    584  CG  LEU A  73      -5.727  15.567 -13.115  1.00 66.33           C
+ATOM    585  CD1 LEU A  73      -7.205  15.411 -13.456  1.00 66.33           C
+ATOM    586  CD2 LEU A  73      -5.551  16.349 -11.818  1.00 66.33           C
+ATOM    587  N   THR A  74      -2.894  11.771 -13.049  1.00 65.78           N
+ATOM    588  CA  THR A  74      -2.225  10.632 -12.430  1.00 65.78           C
+ATOM    589  C   THR A  74      -0.710  10.750 -12.575  1.00 65.78           C
+ATOM    590  CB  THR A  74      -2.699   9.303 -13.046  1.00 65.78           C
+ATOM    591  O   THR A  74       0.035  10.429 -11.646  1.00 65.78           O
+ATOM    592  CG2 THR A  74      -2.057   8.111 -12.344  1.00 65.78           C
+ATOM    593  OG1 THR A  74      -4.124   9.206 -12.920  1.00 65.78           O
+ATOM    594  N   LEU A  75      -0.311  11.344 -13.746  1.00 68.90           N
+ATOM    595  CA  LEU A  75       1.107  11.593 -13.982  1.00 68.90           C
+ATOM    596  C   LEU A  75       1.625  12.698 -13.068  1.00 68.90           C
+ATOM    597  CB  LEU A  75       1.348  11.970 -15.446  1.00 68.90           C
+ATOM    598  O   LEU A  75       2.740  12.610 -12.550  1.00 68.90           O
+ATOM    599  CG  LEU A  75       1.401  10.812 -16.445  1.00 68.90           C
+ATOM    600  CD1 LEU A  75       1.017  11.297 -17.839  1.00 68.90           C
+ATOM    601  CD2 LEU A  75       2.788  10.179 -16.456  1.00 68.90           C
+ATOM    602  N   LYS A  76       0.708  13.698 -12.805  1.00 71.32           N
+ATOM    603  CA  LYS A  76       1.071  14.813 -11.936  1.00 71.32           C
+ATOM    604  C   LYS A  76       1.146  14.372 -10.477  1.00 71.32           C
+ATOM    605  CB  LYS A  76       0.068  15.959 -12.086  1.00 71.32           C
+ATOM    606  O   LYS A  76       1.991  14.854  -9.720  1.00 71.32           O
+ATOM    607  CG  LYS A  76       0.514  17.260 -11.436  1.00 71.32           C
+ATOM    608  CD  LYS A  76      -0.488  18.381 -11.684  1.00 71.32           C
+ATOM    609  CE  LYS A  76      -0.066  19.672 -10.996  1.00 71.32           C
+ATOM    610  NZ  LYS A  76      -1.069  20.760 -11.197  1.00 71.32           N
+ATOM    611  N   HIS A  77       0.420  13.365 -10.189  1.00 75.38           N
+ATOM    612  CA  HIS A  77       0.315  12.913  -8.807  1.00 75.38           C
+ATOM    613  C   HIS A  77       1.167  11.672  -8.567  1.00 75.38           C
+ATOM    614  CB  HIS A  77      -1.144  12.626  -8.446  1.00 75.38           C
+ATOM    615  O   HIS A  77       1.146  11.101  -7.474  1.00 75.38           O
+ATOM    616  CG  HIS A  77      -1.983  13.857  -8.316  1.00 75.38           C
+ATOM    617  CD2 HIS A  77      -1.961  14.855  -7.401  1.00 75.38           C
+ATOM    618  ND1 HIS A  77      -2.994  14.166  -9.199  1.00 75.38           N
+ATOM    619  CE1 HIS A  77      -3.559  15.304  -8.833  1.00 75.38           C
+ATOM    620  NE2 HIS A  77      -2.951  15.743  -7.744  1.00 75.38           N
+ATOM    621  N   LYS A  78       1.936  11.316  -9.653  1.00 73.17           N
+ATOM    622  CA  LYS A  78       2.824  10.158  -9.610  1.00 73.17           C
+ATOM    623  C   LYS A  78       3.862  10.302  -8.500  1.00 73.17           C
+ATOM    624  CB  LYS A  78       3.521   9.965 -10.957  1.00 73.17           C
+ATOM    625  O   LYS A  78       4.117   9.353  -7.755  1.00 73.17           O
+ATOM    626  CG  LYS A  78       4.245   8.633 -11.095  1.00 73.17           C
+ATOM    627  CD  LYS A  78       4.838   8.461 -12.487  1.00 73.17           C
+ATOM    628  CE  LYS A  78       5.641   7.172 -12.598  1.00 73.17           C
+ATOM    629  NZ  LYS A  78       6.222   6.996 -13.963  1.00 73.17           N
+ATOM    630  N   GLU A  79       4.467  11.425  -8.459  1.00 82.01           N
+ATOM    631  CA  GLU A  79       5.451  11.676  -7.410  1.00 82.01           C
+ATOM    632  C   GLU A  79       4.810  11.619  -6.027  1.00 82.01           C
+ATOM    633  CB  GLU A  79       6.127  13.034  -7.621  1.00 82.01           C
+ATOM    634  O   GLU A  79       5.388  11.062  -5.091  1.00 82.01           O
+ATOM    635  CG  GLU A  79       7.125  13.052  -8.769  1.00 82.01           C
+ATOM    636  CD  GLU A  79       7.967  14.317  -8.812  1.00 82.01           C
+ATOM    637  OE1 GLU A  79       9.088  14.320  -8.254  1.00 82.01           O
+ATOM    638  OE2 GLU A  79       7.502  15.314  -9.408  1.00 82.01           O
+ATOM    639  N   LYS A  80       3.748  12.178  -5.930  1.00 81.73           N
+ATOM    640  CA  LYS A  80       3.031  12.190  -4.659  1.00 81.73           C
+ATOM    641  C   LYS A  80       2.604  10.781  -4.255  1.00 81.73           C
+ATOM    642  CB  LYS A  80       1.808  13.105  -4.740  1.00 81.73           C
+ATOM    643  O   LYS A  80       2.693  10.412  -3.082  1.00 81.73           O
+ATOM    644  CG  LYS A  80       2.129  14.583  -4.570  1.00 81.73           C
+ATOM    645  CD  LYS A  80       0.863  15.427  -4.516  1.00 81.73           C
+ATOM    646  CE  LYS A  80       1.184  16.914  -4.444  1.00 81.73           C
+ATOM    647  NZ  LYS A  80      -0.055  17.744  -4.351  1.00 81.73           N
+ATOM    648  N   ILE A  81       2.180  10.044  -5.166  1.00 80.10           N
+ATOM    649  CA  ILE A  81       1.790   8.655  -4.957  1.00 80.10           C
+ATOM    650  C   ILE A  81       2.993   7.848  -4.473  1.00 80.10           C
+ATOM    651  CB  ILE A  81       1.208   8.030  -6.245  1.00 80.10           C
+ATOM    652  O   ILE A  81       2.875   7.039  -3.550  1.00 80.10           O
+ATOM    653  CG1 ILE A  81      -0.130   8.688  -6.600  1.00 80.10           C
+ATOM    654  CG2 ILE A  81       1.050   6.515  -6.087  1.00 80.10           C
+ATOM    655  CD1 ILE A  81      -0.679   8.279  -7.960  1.00 80.10           C
+ATOM    656  N   LEU A  82       4.081   8.122  -5.134  1.00 83.52           N
+ATOM    657  CA  LEU A  82       5.328   7.478  -4.739  1.00 83.52           C
+ATOM    658  C   LEU A  82       5.679   7.813  -3.294  1.00 83.52           C
+ATOM    659  CB  LEU A  82       6.470   7.905  -5.666  1.00 83.52           C
+ATOM    660  O   LEU A  82       5.984   6.919  -2.501  1.00 83.52           O
+ATOM    661  CG  LEU A  82       7.813   7.204  -5.456  1.00 83.52           C
+ATOM    662  CD1 LEU A  82       7.738   5.760  -5.939  1.00 83.52           C
+ATOM    663  CD2 LEU A  82       8.927   7.957  -6.174  1.00 83.52           C
+ATOM    664  N   GLU A  83       5.694   9.021  -2.968  1.00 87.96           N
+ATOM    665  CA  GLU A  83       6.011   9.477  -1.618  1.00 87.96           C
+ATOM    666  C   GLU A  83       5.056   8.873  -0.593  1.00 87.96           C
+ATOM    667  CB  GLU A  83       5.967  11.005  -1.542  1.00 87.96           C
+ATOM    668  O   GLU A  83       5.488   8.386   0.454  1.00 87.96           O
+ATOM    669  CG  GLU A  83       6.496  11.571  -0.233  1.00 87.96           C
+ATOM    670  CD  GLU A  83       6.453  13.090  -0.175  1.00 87.96           C
+ATOM    671  OE1 GLU A  83       5.424  13.652   0.264  1.00 87.96           O
+ATOM    672  OE2 GLU A  83       7.456  13.723  -0.573  1.00 87.96           O
+ATOM    673  N   LYS A  84       3.752   8.925  -0.931  1.00 87.17           N
+ATOM    674  CA  LYS A  84       2.749   8.416   0.000  1.00 87.17           C
+ATOM    675  C   LYS A  84       2.865   6.903   0.160  1.00 87.17           C
+ATOM    676  CB  LYS A  84       1.342   8.787  -0.470  1.00 87.17           C
+ATOM    677  O   LYS A  84       2.708   6.376   1.264  1.00 87.17           O
+ATOM    678  CG  LYS A  84       1.031  10.274  -0.383  1.00 87.17           C
+ATOM    679  CD  LYS A  84       0.932  10.739   1.064  1.00 87.17           C
+ATOM    680  CE  LYS A  84       0.563  12.214   1.154  1.00 87.17           C
+ATOM    681  NZ  LYS A  84       0.580  12.705   2.564  1.00 87.17           N
+ATOM    682  N   THR A  85       3.075   6.194  -0.878  1.00 86.48           N
+ATOM    683  CA  THR A  85       3.277   4.749  -0.859  1.00 86.48           C
+ATOM    684  C   THR A  85       4.478   4.381   0.007  1.00 86.48           C
+ATOM    685  CB  THR A  85       3.478   4.195  -2.282  1.00 86.48           C
+ATOM    686  O   THR A  85       4.438   3.396   0.747  1.00 86.48           O
+ATOM    687  CG2 THR A  85       3.571   2.673  -2.271  1.00 86.48           C
+ATOM    688  OG1 THR A  85       2.371   4.589  -3.103  1.00 86.48           O
+ATOM    689  N   LYS A  86       5.560   5.179  -0.120  1.00 89.61           N
+ATOM    690  CA  LYS A  86       6.738   4.988   0.722  1.00 89.61           C
+ATOM    691  C   LYS A  86       6.390   5.146   2.199  1.00 89.61           C
+ATOM    692  CB  LYS A  86       7.840   5.975   0.335  1.00 89.61           C
+ATOM    693  O   LYS A  86       6.864   4.379   3.040  1.00 89.61           O
+ATOM    694  CG  LYS A  86       8.596   5.594  -0.930  1.00 89.61           C
+ATOM    695  CD  LYS A  86       9.745   6.555  -1.205  1.00 89.61           C
+ATOM    696  CE  LYS A  86      10.475   6.201  -2.494  1.00 89.61           C
+ATOM    697  NZ  LYS A  86      11.592   7.151  -2.777  1.00 89.61           N
+ATOM    698  N   LEU A  87       5.725   6.133   2.442  1.00 90.63           N
+ATOM    699  CA  LEU A  87       5.303   6.398   3.814  1.00 90.63           C
+ATOM    700  C   LEU A  87       4.520   5.217   4.379  1.00 90.63           C
+ATOM    701  CB  LEU A  87       4.449   7.667   3.877  1.00 90.63           C
+ATOM    702  O   LEU A  87       4.736   4.815   5.524  1.00 90.63           O
+ATOM    703  CG  LEU A  87       4.127   8.198   5.274  1.00 90.63           C
+ATOM    704  CD1 LEU A  87       5.400   8.666   5.971  1.00 90.63           C
+ATOM    705  CD2 LEU A  87       3.108   9.330   5.195  1.00 90.63           C
+ATOM    706  N   VAL A  88       3.611   4.770   3.617  1.00 89.50           N
+ATOM    707  CA  VAL A  88       2.818   3.610   4.012  1.00 89.50           C
+ATOM    708  C   VAL A  88       3.741   2.436   4.330  1.00 89.50           C
+ATOM    709  CB  VAL A  88       1.808   3.212   2.913  1.00 89.50           C
+ATOM    710  O   VAL A  88       3.547   1.739   5.328  1.00 89.50           O
+ATOM    711  CG1 VAL A  88       1.118   1.895   3.265  1.00 89.50           C
+ATOM    712  CG2 VAL A  88       0.777   4.321   2.708  1.00 89.50           C
+ATOM    713  N   LEU A  89       4.633   2.181   3.505  1.00 90.95           N
+ATOM    714  CA  LEU A  89       5.629   1.136   3.718  1.00 90.95           C
+ATOM    715  C   LEU A  89       6.348   1.334   5.048  1.00 90.95           C
+ATOM    716  CB  LEU A  89       6.644   1.123   2.572  1.00 90.95           C
+ATOM    717  O   LEU A  89       6.528   0.380   5.809  1.00 90.95           O
+ATOM    718  CG  LEU A  89       7.716   0.033   2.629  1.00 90.95           C
+ATOM    719  CD1 LEU A  89       7.069  -1.348   2.620  1.00 90.95           C
+ATOM    720  CD2 LEU A  89       8.691   0.180   1.466  1.00 90.95           C
+ATOM    721  N   GLU A  90       6.858   2.505   5.268  1.00 91.77           N
+ATOM    722  CA  GLU A  90       7.540   2.813   6.521  1.00 91.77           C
+ATOM    723  C   GLU A  90       6.648   2.516   7.723  1.00 91.77           C
+ATOM    724  CB  GLU A  90       7.985   4.278   6.545  1.00 91.77           C
+ATOM    725  O   GLU A  90       7.113   1.982   8.731  1.00 91.77           O
+ATOM    726  CG  GLU A  90       9.127   4.590   5.589  1.00 91.77           C
+ATOM    727  CD  GLU A  90      10.319   5.241   6.271  1.00 91.77           C
+ATOM    728  OE1 GLU A  90      11.320   4.540   6.544  1.00 91.77           O
+ATOM    729  OE2 GLU A  90      10.252   6.462   6.535  1.00 91.77           O
+ATOM    730  N   ILE A  91       5.411   2.885   7.569  1.00 90.84           N
+ATOM    731  CA  ILE A  91       4.447   2.638   8.635  1.00 90.84           C
+ATOM    732  C   ILE A  91       4.287   1.135   8.849  1.00 90.84           C
+ATOM    733  CB  ILE A  91       3.078   3.283   8.321  1.00 90.84           C
+ATOM    734  O   ILE A  91       4.286   0.660   9.987  1.00 90.84           O
+ATOM    735  CG1 ILE A  91       3.208   4.810   8.263  1.00 90.84           C
+ATOM    736  CG2 ILE A  91       2.031   2.861   9.356  1.00 90.84           C
+ATOM    737  CD1 ILE A  91       1.989   5.514   7.684  1.00 90.84           C
+ATOM    738  N   LEU A  92       4.083   0.438   7.825  1.00 90.22           N
+ATOM    739  CA  LEU A  92       3.929  -1.012   7.890  1.00 90.22           C
+ATOM    740  C   LEU A  92       5.163  -1.662   8.506  1.00 90.22           C
+ATOM    741  CB  LEU A  92       3.677  -1.587   6.494  1.00 90.22           C
+ATOM    742  O   LEU A  92       5.045  -2.579   9.322  1.00 90.22           O
+ATOM    743  CG  LEU A  92       2.300  -1.314   5.887  1.00 90.22           C
+ATOM    744  CD1 LEU A  92       2.262  -1.772   4.432  1.00 90.22           C
+ATOM    745  CD2 LEU A  92       1.211  -2.006   6.699  1.00 90.22           C
+ATOM    746  N   LYS A  93       6.355  -1.270   8.049  1.00 89.96           N
+ATOM    747  CA  LYS A  93       7.611  -1.791   8.582  1.00 89.96           C
+ATOM    748  C   LYS A  93       7.703  -1.568  10.089  1.00 89.96           C
+ATOM    749  CB  LYS A  93       8.803  -1.137   7.881  1.00 89.96           C
+ATOM    750  O   LYS A  93       8.149  -2.450  10.826  1.00 89.96           O
+ATOM    751  CG  LYS A  93       9.068  -1.672   6.481  1.00 89.96           C
+ATOM    752  CD  LYS A  93      10.333  -1.070   5.884  1.00 89.96           C
+ATOM    753  CE  LYS A  93      10.606  -1.615   4.488  1.00 89.96           C
+ATOM    754  NZ  LYS A  93      11.842  -1.022   3.894  1.00 89.96           N
+ATOM    755  N   GLU A  94       7.401  -0.356  10.430  1.00 91.25           N
+ATOM    756  CA  GLU A  94       7.387  -0.032  11.853  1.00 91.25           C
+ATOM    757  C   GLU A  94       6.457  -0.965  12.623  1.00 91.25           C
+ATOM    758  CB  GLU A  94       6.968   1.425  12.069  1.00 91.25           C
+ATOM    759  O   GLU A  94       6.797  -1.429  13.713  1.00 91.25           O
+ATOM    760  CG  GLU A  94       8.067   2.432  11.765  1.00 91.25           C
+ATOM    761  CD  GLU A  94       7.783   3.817  12.324  1.00 91.25           C
+ATOM    762  OE1 GLU A  94       8.221   4.116  13.459  1.00 91.25           O
+ATOM    763  OE2 GLU A  94       7.116   4.610  11.623  1.00 91.25           O
+ATOM    764  N   ARG A  95       5.355  -1.225  12.075  1.00 85.31           N
+ATOM    765  CA  ARG A  95       4.398  -2.127  12.709  1.00 85.31           C
+ATOM    766  C   ARG A  95       4.938  -3.553  12.756  1.00 85.31           C
+ATOM    767  CB  ARG A  95       3.059  -2.098  11.969  1.00 85.31           C
+ATOM    768  O   ARG A  95       4.712  -4.276  13.728  1.00 85.31           O
+ATOM    769  CG  ARG A  95       2.304  -0.786  12.115  1.00 85.31           C
+ATOM    770  CD  ARG A  95       1.648  -0.662  13.483  1.00 85.31           C
+ATOM    771  NE  ARG A  95       0.780   0.509  13.560  1.00 85.31           N
+ATOM    772  NH1 ARG A  95      -1.032  -0.634  14.424  1.00 85.31           N
+ATOM    773  NH2 ARG A  95      -1.174   1.620  14.033  1.00 85.31           N
+ATOM    774  CZ  ARG A  95      -0.474   0.496  14.006  1.00 85.31           C
+ATOM    775  N   LEU A  96       5.431  -3.928  11.737  1.00 87.53           N
+ATOM    776  CA  LEU A  96       6.039  -5.251  11.646  1.00 87.53           C
+ATOM    777  C   LEU A  96       7.142  -5.415  12.687  1.00 87.53           C
+ATOM    778  CB  LEU A  96       6.605  -5.486  10.244  1.00 87.53           C
+ATOM    779  O   LEU A  96       7.260  -6.471  13.311  1.00 87.53           O
+ATOM    780  CG  LEU A  96       7.106  -6.899   9.943  1.00 87.53           C
+ATOM    781  CD1 LEU A  96       5.938  -7.879   9.903  1.00 87.53           C
+ATOM    782  CD2 LEU A  96       7.877  -6.925   8.627  1.00 87.53           C
+ATOM    783  N   LYS A  97       8.035  -4.458  12.855  1.00 87.68           N
+ATOM    784  CA  LYS A  97       9.111  -4.470  13.842  1.00 87.68           C
+ATOM    785  C   LYS A  97       8.555  -4.573  15.260  1.00 87.68           C
+ATOM    786  CB  LYS A  97       9.976  -3.216  13.709  1.00 87.68           C
+ATOM    787  O   LYS A  97       9.131  -5.256  16.109  1.00 87.68           O
+ATOM    788  CG  LYS A  97      10.961  -3.264  12.550  1.00 87.68           C
+ATOM    789  CD  LYS A  97      11.875  -2.045  12.542  1.00 87.68           C
+ATOM    790  CE  LYS A  97      12.840  -2.076  11.365  1.00 87.68           C
+ATOM    791  NZ  LYS A  97      13.742  -0.886  11.356  1.00 87.68           N
+ATOM    792  N   GLU A  98       7.395  -3.949  15.535  1.00 85.16           N
+ATOM    793  CA  GLU A  98       6.766  -3.985  16.852  1.00 85.16           C
+ATOM    794  C   GLU A  98       6.185  -5.364  17.149  1.00 85.16           C
+ATOM    795  CB  GLU A  98       5.671  -2.920  16.954  1.00 85.16           C
+ATOM    796  O   GLU A  98       6.174  -5.804  18.300  1.00 85.16           O
+ATOM    797  CG  GLU A  98       6.201  -1.494  16.993  1.00 85.16           C
+ATOM    798  CD  GLU A  98       5.199  -0.496  17.550  1.00 85.16           C
+ATOM    799  OE1 GLU A  98       5.207  -0.247  18.777  1.00 85.16           O
+ATOM    800  OE2 GLU A  98       4.397   0.041  16.753  1.00 85.16           O
+ATOM    801  N   LYS A  99       5.862  -6.201  16.145  1.00 71.59           N
+ATOM    802  CA  LYS A  99       5.236  -7.516  16.249  1.00 71.59           C
+ATOM    803  C   LYS A  99       6.285  -8.620  16.338  1.00 71.59           C
+ATOM    804  CB  LYS A  99       4.311  -7.766  15.057  1.00 71.59           C
+ATOM    805  O   LYS A  99       6.031  -9.682  16.910  1.00 71.59           O
+ATOM    806  CG  LYS A  99       2.886  -7.276  15.266  1.00 71.59           C
+ATOM    807  CD  LYS A  99       1.932  -7.876  14.240  1.00 71.59           C
+ATOM    808  CE  LYS A  99       0.499  -7.420  14.474  1.00 71.59           C
+ATOM    809  NZ  LYS A  99      -0.480  -8.264  13.726  1.00 71.59           N
+ATOM    810  N   GLU A 100       7.534  -8.377  16.016  1.00 69.93           N
+ATOM    811  CA  GLU A 100       8.637  -9.325  16.142  1.00 69.93           C
+ATOM    812  C   GLU A 100       9.233  -9.296  17.546  1.00 69.93           C
+ATOM    813  CB  GLU A 100       9.723  -9.028  15.104  1.00 69.93           C
+ATOM    814  O   GLU A 100       9.551 -10.343  18.113  1.00 69.93           O
+ATOM    815  CG  GLU A 100       9.683  -9.948  13.892  1.00 69.93           C
+ATOM    816  CD  GLU A 100      10.905  -9.814  12.998  1.00 69.93           C
+ATOM    817  OE1 GLU A 100      11.866 -10.601  13.160  1.00 69.93           O
+ATOM    818  OE2 GLU A 100      10.903  -8.915  12.128  1.00 69.93           O
+ENDMDL
+END

test/matrix-test.cpp

@@ -0,0 +1,103 @@
+/*-
+ * SPDX-License-Identifier: BSD-2-Clause
+ *
+ * Copyright (c) 2025 NKI/AVL, Netherlands Cancer Institute
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * 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
+ * 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 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.
+ */
+
+#include "cif++/matrix.hpp"
+#include "test-main.hpp"
+
+#include <catch2/catch_test_macros.hpp>
+#include <cif++.hpp>
+
+TEST_CASE("m1")
+{
+	cif::matrix3x3<int> m = cif::identity_matrix<int>(3);
+
+	CHECK(cif::determinant(m) == 1);
+}
+
+TEST_CASE("m2")
+{
+	cif::matrix4x4<int> m = cif::identity_matrix<int>(4);
+
+	cif::sub_matrix<cif::matrix4x4<int>> ms(m, 1, 1);
+	CHECK(ms == cif::identity_matrix<int>(3));
+}
+
+TEST_CASE("m3")
+{
+	cif::matrix4x4<int> m{
+		{ 1, 2, 3, 4,      //
+			5, 6, 7, 8,    //
+			9, 10, 11, 12, //
+			13, 14, 15, 16 }
+	};
+	cif::sub_matrix<cif::matrix4x4<int>> ms(m, 1, 1);
+
+	cif::matrix3x3<int> t{
+		{ 1, 3, 4, 9, 11, 12, 13, 15, 16 }
+	};
+
+	CHECK(ms == t);
+}
+
+TEST_CASE("m4")
+{
+	cif::matrix4x4<int> m{
+		{
+			-2,
+			3,
+			1,
+			0,
+			4,
+			1,
+			-3,
+			2,
+			0,
+			-1,
+			2,
+			5,
+			3,
+			2,
+			0,
+			-4,
+		}
+	};
+
+	// std::cout << m << "\n\n";
+
+	// std::cout << cif::matrix3x3<int>(cif::sub_matrix<decltype(m)>(m, 0, 0)) << "\n\n";
+	// std::cout << cif::matrix3x3<int>(cif::sub_matrix<decltype(m)>(m, 0, 1)) << "\n\n";
+	// std::cout << cif::matrix3x3<int>(cif::sub_matrix<decltype(m)>(m, 0, 2)) << "\n\n";
+	// std::cout << cif::matrix3x3<int>(cif::sub_matrix<decltype(m)>(m, 0, 3)) << "\n\n";
+
+	// std::cout << cif::determinant(cif::matrix3x3<int>(cif::sub_matrix<decltype(m)>(m, 0, 0))) << "\n\n";
+	// std::cout << cif::determinant(cif::matrix3x3<int>(cif::sub_matrix<decltype(m)>(m, 0, 1))) << "\n\n";
+	// std::cout << cif::determinant(cif::matrix3x3<int>(cif::sub_matrix<decltype(m)>(m, 0, 2))) << "\n\n";
+	// std::cout << cif::determinant(cif::matrix3x3<int>(cif::sub_matrix<decltype(m)>(m, 0, 3))) << "\n\n";
+
+	CHECK(cif::determinant(m) == 332);
+}
+
+

test/model-test.cpp

@@ -32,11 +32,11 @@
 
 // --------------------------------------------------------------------
 
-cif::file operator""_cf(const char *text, size_t length)
+cif::file operator""_cf(const char *text, std::size_t length)
 {
 	struct membuf : public std::streambuf
 	{
-		membuf(char *text, size_t length)
+		membuf(char *text, std::size_t length)
 		{
 			this->setg(text, text, text + length);
 		}
@@ -53,8 +53,8 @@ TEST_CASE("create_nonpoly_1")
 	cif::VERBOSE = 1;
 
 	cif::file file;
-	file.load_dictionary("mmcif_pdbx.dic");
-	file.emplace("TEST"); // create a datablock
+	auto &&[dbi, ignore] = file.emplace("TEST"); // create a datablock
+	dbi->set_validator(&cif::validator_factory::instance().get("mmcif_pdbx.dic"));
 
 	cif::mm::structure structure(file);
 
@@ -82,7 +82,7 @@ _atom_site.pdbx_formal_charge
 # that's enough to test with
 )"_cf;
 
-	atoms.load_dictionary("mmcif_pdbx.dic");
+	atoms.front().set_validator(&cif::validator_factory::instance().get("mmcif_pdbx.dic"));
 
 	auto &hem_data = atoms["HEM"];
 	auto &atom_site = hem_data["atom_site"];
@@ -159,14 +159,14 @@ _struct_asym.details                       ?
 _atom_type.symbol   C
 )"_cf;
 
-	expected.load_dictionary("mmcif_pdbx.dic");
+	expected.front().set_validator(&cif::validator_factory::instance().get("mmcif_pdbx.dic"));
 
 	if (not(expected.front() == structure.get_datablock()))
 	{
-		REQUIRE(false);
-		std::cout << expected.front() << '\n'
+		std::cerr << expected.front() << '\n'
 				  << '\n'
 				  << structure.get_datablock() << '\n';
+		REQUIRE(false);
 	}
 }
 
@@ -177,8 +177,8 @@ TEST_CASE("create_nonpoly_2")
 	cif::VERBOSE = 1;
 
 	cif::file file;
-	file.load_dictionary("mmcif_pdbx.dic");
-	file.emplace("TEST"); // create a datablock
+	auto &&[dbi, ignore] = file.emplace("TEST"); // create a datablock
+	dbi->set_validator(&cif::validator_factory::instance().get("mmcif_pdbx.dic"));
 
 	cif::mm::structure structure(file);
 
@@ -270,7 +270,7 @@ _struct_asym.details                       ?
 _atom_type.symbol   C
 )"_cf;
 
-	expected.load_dictionary("mmcif_pdbx.dic");
+	expected.front().set_validator(&cif::validator_factory::instance().get("mmcif_pdbx.dic"));
 
 	REQUIRE(expected.front() == structure.get_datablock());
 
@@ -354,7 +354,7 @@ _struct_asym.details                       ?
 #
 )"_cf;
 
-	data.load_dictionary("mmcif_pdbx.dic");
+	data.front().set_validator(&cif::validator_factory::instance().get("mmcif_pdbx.dic"));
 
 	cif::mm::structure s(data);
 
@@ -431,3 +431,169 @@ TEST_CASE("remove_residue_1")
 
 	REQUIRE_NOTHROW(s.validate_atoms());
 }
+
+// --------------------------------------------------------------------
+// Tests for structure_open_options
+
+TEST_CASE("options_1")
+{
+	using namespace cif::literals;
+
+	const std::filesystem::path example(gTestDir / ".." / "examples" / "1cbs.cif.gz");
+	cif::file file(example.string());
+
+	auto &cf = cif::compound_factory::instance();
+
+	SECTION("skip_water")
+	{
+		cif::mm::structure s(file, 1, { .skip_water = true });
+
+		REQUIRE_NOTHROW(s.validate_atoms());
+
+		for (auto a : s.atoms())
+			CHECK_FALSE(a.is_water());
+	}
+
+	SECTION("skip_hetatom")
+	{
+		cif::mm::structure s(file, 1, { .skip_hetatom = true });
+
+		REQUIRE_NOTHROW(s.validate_atoms());
+
+		for (auto a : s.atoms())
+			CHECK((a.is_water() or cf.is_peptide(a.get_label_comp_id()) or cf.is_base(a.get_label_comp_id())));
+	}
+
+	SECTION("selected_asyms")
+	{
+		cif::mm::structure s(file, 1, { .asyms = { "A" } });
+
+		REQUIRE_NOTHROW(s.validate_atoms());
+
+		for (auto a : s.atoms())
+			CHECK(a.get_label_asym_id() == "A");
+	}
+
+	SECTION("min-b-factor")
+	{
+		cif::mm::structure s(file, 1, { .min_b_factor = 20.f });
+
+		REQUIRE_NOTHROW(s.validate_atoms());
+
+		for (auto a : s.atoms())
+			CHECK(a.get_property_float("B_iso_or_equiv") >= 20.f);
+	}
+
+	SECTION("max-b-factor")
+	{
+		cif::mm::structure s(file, 1, { .max_b_factor = 20.f });
+
+		REQUIRE_NOTHROW(s.validate_atoms());
+
+		for (auto a : s.atoms())
+			CHECK(a.get_property_float("B_iso_or_equiv") <= 20.f);
+	}
+}
+
+TEST_CASE("options_2")
+{
+
+	auto data = R"(
+data_TEST
+# 
+_pdbx_nonpoly_scheme.asym_id         A 
+_pdbx_nonpoly_scheme.ndb_seq_num     1 
+_pdbx_nonpoly_scheme.entity_id       1 
+_pdbx_nonpoly_scheme.mon_id          HEM 
+_pdbx_nonpoly_scheme.pdb_seq_num     1 
+_pdbx_nonpoly_scheme.auth_seq_num    1 
+_pdbx_nonpoly_scheme.pdb_mon_id      HEM 
+_pdbx_nonpoly_scheme.auth_mon_id     HEM 
+_pdbx_nonpoly_scheme.pdb_strand_id   A 
+_pdbx_nonpoly_scheme.pdb_ins_code    . 
+#
+loop_
+_atom_site.id
+_atom_site.auth_asym_id
+_atom_site.label_alt_id
+_atom_site.label_asym_id
+_atom_site.label_atom_id
+_atom_site.label_comp_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.type_symbol
+_atom_site.group_PDB
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.B_iso_or_equiv
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_comp_id
+_atom_site.auth_atom_id
+_atom_site.pdbx_PDB_model_num
+1 A A A CHA HEM 1 . C HETATM ? -5.248 39.769 -0.250 0.75 7.67 ? 1 HEM CHA 1
+3 A A A CHB HEM 1 . C HETATM ? -3.774 36.790 3.280  0.75 7.05 ? 1 HEM CHB 1
+2 A A A CHC HEM 1 . C HETATM ? -2.879 33.328 0.013  0.75 7.69 ? 1 HEM CHC 1
+4 A A A CHD HEM 1 . C HETATM ? -4.342 36.262 -3.536 0.75 8.00 ? 1 HEM CHD 1
+5 A B A CHA HEM 1 . C HETATM ? -5.248 39.769 -0.250 0.25 7.67 ? 1 HEM CHA 1
+6 A B A CHB HEM 1 . C HETATM ? -3.774 36.790 3.280  0.25 7.05 ? 1 HEM CHB 1
+7 A B A CHC HEM 1 . C HETATM ? -2.879 33.328 0.013  0.25 7.69 ? 1 HEM CHC 1
+8 A B A CHD HEM 1 . C HETATM ? -4.342 36.262 -3.536 0.25 8.00 ? 1 HEM CHD 1
+#
+_chem_comp.id               HEM
+_chem_comp.type             NON-POLYMER
+_chem_comp.name             'PROTOPORPHYRIN IX CONTAINING FE'
+_chem_comp.formula          'C34 H32 Fe N4 O4'
+_chem_comp.formula_weight   616.487000
+#
+_pdbx_entity_nonpoly.entity_id   1
+_pdbx_entity_nonpoly.name        'PROTOPORPHYRIN IX CONTAINING FE'
+_pdbx_entity_nonpoly.comp_id     HEM
+#
+_entity.id                 1
+_entity.type               non-polymer
+_entity.pdbx_description   'PROTOPORPHYRIN IX CONTAINING FE'
+_entity.formula_weight     616.487000
+#
+_struct_asym.id                            A
+_struct_asym.entity_id                     1
+_struct_asym.pdbx_blank_PDB_chainid_flag   N
+_struct_asym.pdbx_modified                 N
+_struct_asym.details                       ?
+#
+)"_cf;
+
+	data.front().set_validator(&cif::validator_factory::instance().get("mmcif_pdbx.dic"));
+
+	SECTION("max")
+	{
+		cif::mm::structure s(data, 1, {
+			.occupancy_mode = cif::mm::occupancy_policy::MAX
+		});
+
+		REQUIRE(s.atoms().size() == 4);
+		CHECK(s.atoms().front().get_label_alt_id() == "A");
+	}
+
+	SECTION("min")
+	{
+		cif::mm::structure s(data, 1, {
+			.occupancy_mode = cif::mm::occupancy_policy::MIN
+		});
+
+		REQUIRE(s.atoms().size() == 4);
+		CHECK(s.atoms().front().get_label_alt_id() == "B");
+	}
+
+	SECTION("unoccupied")
+	{
+		cif::mm::structure s(data, 1, {
+			.occupancy_mode = cif::mm::occupancy_policy::UNOCCUPIED
+		});
+
+		CHECK(s.atoms().empty());
+	}
+}

test/query-test.cpp

@@ -1,17 +1,17 @@
 /*-
  * SPDX-License-Identifier: BSD-2-Clause
- *
- * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
- *
+ * 
+ * Copyright (c) 2025 NKI/AVL, Netherlands Cancer Institute
+ * 
  * Redistribution and use in source and binary forms, with or without
  * 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
  * 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 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
@@ -24,38 +24,29 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-
 #include "test-main.hpp"
 
-#include <stdexcept>
-
 #include <cif++.hpp>
 
-// --------------------------------------------------------------------
+#include <iostream>
+#include <fstream>
 
-TEST_CASE("fmt_1")
+TEST_CASE("q-1")
 {
-	std::ostringstream os;
+	using namespace cif::literals;
 
-	std::string world("world");
-	os << cif::format("Hello, %-10.10s, the magic number is %d and pi is %g", world, 42, cif::kPI);
-	REQUIRE(os.str() == "Hello, world     , the magic number is 42 and pi is 3.14159");
+	cif::compound_factory::instance().push_dictionary(gTestDir / "REA.cif");
 
-	REQUIRE(cif::format("Hello, %-10.10s, the magic number is %d and pi is %g", world, 42, cif::kPI).str() ==
-		"Hello, world     , the magic number is 42 and pi is 3.14159");
+	cif::file a = cif::pdb::read(gTestDir / "pdb1cbs.ent.gz");
+	auto &pdbx_poly_seq_scheme = a.front()["pdbx_poly_seq_scheme"];
+	REQUIRE_FALSE(pdbx_poly_seq_scheme.empty());
+
+	SECTION("s-11")
+	{
+		CHECK(pdbx_poly_seq_scheme.count("asym_id"_key == "A") == 137);
+
+		CHECK(pdbx_poly_seq_scheme.count("asym_id"_key == "A" and "entity_id"_key == 1 and "seq_id"_key == 1 and "mon_id"_key == "PRO") == 1);
+
+		CHECK(pdbx_poly_seq_scheme.count("asym_id"_key == "A" and "entity_id"_key == 1 and "seq_id"_key == 1 and "mon_id"_key == "PRO" and "hetero"_key == false) == 1);
+	}
 }
-
-// --------------------------------------------------------------------
-
-TEST_CASE("clr_1")
-{
-	using namespace cif::colour;
-
-	std::cout << "Hello, " << cif::coloured("world!", white, red, cif::colour::regular) << '\n'
-			  << "Hello, " << cif::coloured("world!", white, red, bold) << '\n'
-			  << "Hello, " << cif::coloured("world!", black, red) << '\n'
-			  << "Hello, " << cif::coloured("world!", white, green) << '\n'
-			  << "Hello, " << cif::coloured("world!", white, blue) << '\n'
-			  << "Hello, " << cif::coloured("world!", blue, white) << '\n'
-			  << "Hello, " << cif::coloured("world!", red, white, bold) << '\n';
-}

test/reconstruction-test.cpp

@@ -28,6 +28,7 @@
 
 #include <cif++.hpp>
 
+#include <filesystem>
 #include <iostream>
 #include <fstream>
 
@@ -54,7 +55,7 @@ TEST_CASE("reconstruct")
 
 			std::error_code ec;
 			CHECK_FALSE(cif::pdb::is_valid_pdbx_file(f, ec));
-			CHECK(ec != std::errc{});
+			CHECK((bool)ec);
 
 			CHECK(cif::pdb::reconstruct_pdbx(f));
 		}

test/sugar-test.cpp

@@ -32,11 +32,11 @@
 
 // --------------------------------------------------------------------
 
-cif::file operator""_cf(const char* text, size_t length)
+cif::file operator""_cf(const char* text, std::size_t length)
 {
     struct membuf : public std::streambuf
     {
-        membuf(char* text, size_t length)
+        membuf(char* text, std::size_t length)
         {
             this->setg(text, text, text + length);
         }
@@ -131,7 +131,7 @@ TEST_CASE("sugar_name_1")
 // 	auto &db = s.get_datablock();
 // 	auto &as = db["atom_site"];
 
-// 	for (size_t i = 0; i < 2; ++i)
+// 	for (std::size_t i = 0; i < 2; ++i)
 // 	{
 // 		for (auto r : as.find("label_asym_id"_key == "H" and "auth_seq_id"_key == i + 1))
 // 			/*auto &ri = */ai[i].emplace_back(r);

test/test-main.cpp

@@ -11,12 +11,7 @@ int main(int argc, char *argv[])
 	Catch::Session session; // There must be exactly one instance
 
 	// Build a new parser on top of Catch2's
-#if CATCH22
-	using namespace Catch::clara;
-#else
-	// Build a new parser on top of Catch2's
 	using namespace Catch::Clara;
-#endif
 
 	auto cli = session.cli()                               // Get Catch2's command line parser
 	           | Opt(gTestDir, "data-dir")                 // bind variable to a new option, with a hint string

test/test-main.hpp

@@ -1,17 +1,17 @@
 /*-
  * SPDX-License-Identifier: BSD-2-Clause
- * 
+ *
  * Copyright (c) 2024 NKI/AVL, Netherlands Cancer Institute
- * 
+ *
  * Redistribution and use in source and binary forms, with or without
  * 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
  * 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 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
@@ -26,11 +26,7 @@
 
 #pragma once
 
-#if CATCH22
-#include <catch2/catch.hpp>
-#else
 #include <catch2/catch_all.hpp>
-#endif
 
 #include <filesystem>
 

test/unit-3d-test.cpp

@@ -24,21 +24,28 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
+#include "cif++/point.hpp"
 #include "test-main.hpp"
 
+#include <catch2/catch_test_macros.hpp>
+#include <catch2/matchers/catch_matchers_floating_point.hpp>
+#include <cif++.hpp>
 #include <stdexcept>
 
-#include <cif++.hpp>
+#if defined(_MSC_VER)
+# pragma warning(disable : 5054) // warning C5054: operator '&': deprecated between enumerations of different types
+# pragma warning(disable : 4127) // conditional expression is constant
+#endif
 
 #include <Eigen/Eigenvalues>
 
 // --------------------------------------------------------------------
 
-cif::file operator""_cf(const char *text, size_t length)
+cif::file operator""_cf(const char *text, std::size_t length)
 {
 	struct membuf : public std::streambuf
 	{
-		membuf(char *text, size_t length)
+		membuf(char *text, std::size_t length)
 		{
 			this->setg(text, text, text + length);
 		}
@@ -90,7 +97,7 @@ TEST_CASE("t1")
 
 	const auto &&[angle, axis] = cif::quaternion_to_angle_axis(q2);
 
-	REQUIRE_THAT(std::fmod(360 + angle, 360), Catch::Matchers::WithinRel(std::fmod(360 - angle0, 360), 0.01));
+	CHECK_THAT(std::fmod(360 + angle, 360), Catch::Matchers::WithinRel(std::fmod(360 - angle0, 360), 0.01));
 
 	for (auto &p : p1)
 		p.rotate(q2);
@@ -116,7 +123,7 @@ TEST_CASE("t2")
 
 	auto &&[angle, axis] = cif::quaternion_to_angle_axis(q);
 
-	REQUIRE_THAT(angle, Catch::Matchers::WithinRel(45.f, 0.01f));
+	CHECK_THAT(angle, Catch::Matchers::WithinRel(45.f, 0.01f));
 }
 
 TEST_CASE("t3")
@@ -140,7 +147,7 @@ TEST_CASE("t3")
 
 	double a = cif::angle(v, p[0], p[1]);
 
-	REQUIRE_THAT(a, Catch::Matchers::WithinRel(45.f, 0.01f));
+	CHECK_THAT(a, Catch::Matchers::WithinRel(45.f, 0.01f));
 }
 
 TEST_CASE("dh_q_0")
@@ -148,39 +155,37 @@ TEST_CASE("dh_q_0")
 	cif::point axis(1, 0, 0);
 
 	cif::point p(1, 1, 0);
-	
-	cif::point t[3] =
-	{
+
+	cif::point t[3] = {
 		{ 0, 1, 0 },
 		{ 0, 0, 0 },
 		{ 1, 0, 0 }
 	};
 
 	auto a = cif::dihedral_angle(t[0], t[1], t[2], p);
-	REQUIRE_THAT(a, Catch::Matchers::WithinRel(0, 0.01f));
+	CHECK_THAT(a, Catch::Matchers::WithinRel(0.f, 0.01f));
 
 	auto q = cif::construct_from_angle_axis(90, axis);
 
 	p.rotate(q);
 
-	REQUIRE_THAT(p.m_x, Catch::Matchers::WithinRel(1, 0.01f));
-	REQUIRE_THAT(p.m_y, Catch::Matchers::WithinRel(0, 0.01f));
-	REQUIRE_THAT(p.m_z, Catch::Matchers::WithinRel(1, 0.01f));
+	REQUIRE(std::abs(p.m_x - 1.f) < 0.01f);
+	REQUIRE(std::abs(p.m_y - 0.f) < 0.01f);
+	REQUIRE(std::abs(p.m_z - 1.f) < 0.01f);
 
 	a = cif::dihedral_angle(t[0], t[1], t[2], p);
-	REQUIRE_THAT(a, Catch::Matchers::WithinRel(90, 0.01f));
+	REQUIRE(std::abs(a - 90.f) < 0.01f);
 
 	q = cif::construct_from_angle_axis(-90, axis);
 
 	p.rotate(q);
 
-	REQUIRE_THAT(p.m_x, Catch::Matchers::WithinRel(1, 0.01f));
-	REQUIRE_THAT(p.m_y, Catch::Matchers::WithinRel(1, 0.01f));
-	REQUIRE_THAT(p.m_z, Catch::Matchers::WithinRel(0, 0.01f));
+	REQUIRE(std::abs(p.m_x - 1.f) < 0.01f);
+	REQUIRE(std::abs(p.m_y - 1.f) < 0.01f);
+	REQUIRE(std::abs(p.m_z - 0.f) < 0.01f);
 
 	a = cif::dihedral_angle(t[0], t[1], t[2], p);
-	REQUIRE_THAT(a, Catch::Matchers::WithinRel(0, 0.01f));
-
+	REQUIRE(std::abs(a - 0.f) < 0.01f);
 }
 
 TEST_CASE("dh_q_1")
@@ -222,78 +227,117 @@ TEST_CASE("dh_q_1")
 		pts[3].rotate(q, pts[2]);
 
 		auto dh = cif::dihedral_angle(pts[0], pts[1], pts[2], pts[3]);
-		REQUIRE_THAT(dh, Catch::Matchers::WithinRel(angle, 0.1f));
+		CHECK_THAT(dh, Catch::Matchers::WithinRel(angle, 0.1f));
 	}
 }
 
 // --------------------------------------------------------------------
 
-TEST_CASE("m2q_0, *utf::tolerance(0.001f)")
+// TEST_CASE("m2q_0")
+// {
+// 	for (std::size_t i = 0; i < cif::kSymopNrTableSize; ++i)
+// 	{
+// 		auto d = cif::kSymopNrTable[i].symop().data();
+
+// 		cif::matrix3x3<float> rot;
+// 		float Qxx = rot(0, 0) = d[0];
+// 		float Qxy = rot(0, 1) = d[1];
+// 		float Qxz = rot(0, 2) = d[2];
+// 		float Qyx = rot(1, 0) = d[3];
+// 		float Qyy = rot(1, 1) = d[4];
+// 		float Qyz = rot(1, 2) = d[5];
+// 		float Qzx = rot(2, 0) = d[6];
+// 		float Qzy = rot(2, 1) = d[7];
+// 		float Qzz = rot(2, 2) = d[8];
+
+// 		Eigen::Matrix4f em;
+
+// 		em << Qxx - Qyy - Qzz, Qyx + Qxy, Qzx + Qxz, Qzy - Qyz,
+// 			Qyx + Qxy, Qyy - Qxx - Qzz, Qzy + Qyz, Qxz - Qzx,
+// 			Qzx + Qxz, Qzy + Qyz, Qzz - Qxx - Qyy, Qyx - Qxy,
+// 			Qzy - Qyz, Qxz - Qzx, Qyx - Qxy, Qxx + Qyy + Qzz;
+
+// 		Eigen::EigenSolver<Eigen::Matrix4f> es(em / 3);
+
+// 		auto ev = es.eigenvalues();
+
+// 		std::size_t bestJ = 0;
+// 		float bestEV = -1;
+
+// 		for (std::size_t j = 0; j < 4; ++j)
+// 		{
+// 			if (bestEV < ev[j].real())
+// 			{
+// 				bestEV = ev[j].real();
+// 				bestJ = j;
+// 			}
+// 		}
+
+// 		if (std::abs(bestEV - 1) > 0.01)
+// 			continue; // not a rotation matrix
+
+// 		auto col = es.eigenvectors().col(bestJ);
+
+// 		auto q = normalize(cif::quaternion{
+// 			static_cast<float>(col(3).real()),
+// 			static_cast<float>(col(0).real()),
+// 			static_cast<float>(col(1).real()),
+// 			static_cast<float>(col(2).real()) });
+
+// 		cif::point p1{ 1, 1, 1 };
+// 		cif::point p2 = p1;
+// 		p2.rotate(q);
+
+// 		cif::point p3 = rot * p1;
+
+// 		CHECK_THAT(p2.m_x, Catch::Matchers::WithinRel(p3.m_x, 0.01f));
+// 		CHECK_THAT(p2.m_y, Catch::Matchers::WithinRel(p3.m_y, 0.01f));
+// 		CHECK_THAT(p2.m_z, Catch::Matchers::WithinRel(p3.m_z, 0.01f));
+// 	}
+// }
+
+TEST_CASE("m2q_0a")
 {
-	for (size_t i = 0; i < cif::kSymopNrTableSize; ++i)
+	for (std::size_t i = 0; i < cif::kSymopNrTableSize; ++i)
 	{
 		auto d = cif::kSymopNrTable[i].symop().data();
 
-		cif::matrix3x3<float> rot;
-		float Qxx = rot(0, 0) = d[0];
-		float Qxy = rot(0, 1) = d[1];
-		float Qxz = rot(0, 2) = d[2];
-		float Qyx = rot(1, 0) = d[3];
-		float Qyy = rot(1, 1) = d[4];
-		float Qyz = rot(1, 2) = d[5];
-		float Qzx = rot(2, 0) = d[6];
-		float Qzy = rot(2, 1) = d[7];
-		float Qzz = rot(2, 2) = d[8];
+		Eigen::Matrix3f rot;
+		rot << static_cast<float>(d[0]), static_cast<float>(d[1]), static_cast<float>(d[2]), static_cast<float>(d[3]), static_cast<float>(d[4]), static_cast<float>(d[5]), static_cast<float>(d[6]), static_cast<float>(d[7]), static_cast<float>(d[8]);
 
-		Eigen::Matrix4f em;
+		// check to see if this matrix contains a true rotation
+		if (rot * rot.transpose() != Eigen::Matrix3f::Identity() or rot.determinant() != 1)
+			continue;
 
-		em << Qxx - Qyy - Qzz, Qyx + Qxy, Qzx + Qxz, Qzy - Qyz,
-		      Qyx + Qxy, Qyy - Qxx - Qzz, Qzy + Qyz, Qxz - Qzx,
-			  Qzx + Qxz, Qzy + Qyz, Qzz - Qxx - Qyy, Qyx - Qxy,
-			  Qzy - Qyz, Qxz - Qzx, Qyx - Qxy, Qxx + Qyy + Qzz;
+		Eigen::Quaternionf qe(rot);
 
-		Eigen::EigenSolver<Eigen::Matrix4f> es(em / 3);
+		auto q = normalize(cif::quaternion{ qe.w(), qe.x(), qe.y(), qe.z() });
 
-		auto ev = es.eigenvalues();
-
-		size_t bestJ = 0;
-		float bestEV = -1;
-
-		for (size_t j = 0; j < 4; ++j)
-		{
-			if (bestEV < ev[j].real())
-			{
-				bestEV = ev[j].real();
-				bestJ = j;
-			}
-		}
-
-		if (std::abs(bestEV - 1) > 0.01)
-			continue; // not a rotation matrix
-
-		auto col = es.eigenvectors().col(bestJ);
-
-		auto q = normalize(cif::quaternion{
-			static_cast<float>(col(3).real()),
-			static_cast<float>(col(0).real()),
-			static_cast<float>(col(1).real()),
-			static_cast<float>(col(2).real()) });
-		
 		cif::point p1{ 1, 1, 1 };
 		cif::point p2 = p1;
 		p2.rotate(q);
 
-		cif::point p3 = rot * p1;
+		cif::matrix3x3<float> rot_c({ static_cast<float>(d[0]),
+			static_cast<float>(d[1]),
+			static_cast<float>(d[2]),
+			static_cast<float>(d[3]),
+			static_cast<float>(d[4]),
+			static_cast<float>(d[5]),
+			static_cast<float>(d[6]),
+			static_cast<float>(d[7]),
+			static_cast<float>(d[8]) });
 
-		REQUIRE_THAT(p2.m_x, Catch::Matchers::WithinRel(p3.m_x, 0.01f));
-		REQUIRE_THAT(p2.m_y, Catch::Matchers::WithinRel(p3.m_y, 0.01f));
-		REQUIRE_THAT(p2.m_z, Catch::Matchers::WithinRel(p3.m_z, 0.01f));
+		cif::point p3 = rot_c * p1;
+
+		CHECK_THAT(p2.m_x, Catch::Matchers::WithinRel(p3.m_x, 0.01f));
+		CHECK_THAT(p2.m_y, Catch::Matchers::WithinRel(p3.m_y, 0.01f));
+		CHECK_THAT(p2.m_z, Catch::Matchers::WithinRel(p3.m_z, 0.01f));
 	}
 }
 
-// "TEST_CASE(m2q_1, *utf::tolerance(0.001f)")
+// "TEST_CASE(m2q_1")
 // {
-// 	for (size_t i = 0; i < cif::kSymopNrTableSize; ++i)
+// 	for (std::size_t i = 0; i < cif::kSymopNrTableSize; ++i)
 // 	{
 // 		auto d = cif::kSymopNrTable[i].symop().data();
 
@@ -317,10 +361,10 @@ TEST_CASE("m2q_0, *utf::tolerance(0.001f)")
 
 // 		auto &&[ev, em] = cif::eigen(m * (1/3.0f), false);
 
-// 		size_t bestJ = 0;
+// 		std::size_t bestJ = 0;
 // 		float bestEV = -1;
 
-// 		for (size_t j = 0; j < 4; ++j)
+// 		for (std::size_t j = 0; j < 4; ++j)
 // 		{
 // 			if (bestEV < ev[j])
 // 			{
@@ -337,7 +381,7 @@ TEST_CASE("m2q_0, *utf::tolerance(0.001f)")
 // 			static_cast<float>(em(bestJ, 0)),
 // 			static_cast<float>(em(bestJ, 1)),
 // 			static_cast<float>(em(bestJ, 2)) });
-		
+
 // 		cif::point p1{ 1, 1, 1 };
 // 		cif::point p2 = p1;
 // 		p2.rotate(q);
@@ -360,15 +404,15 @@ TEST_CASE("symm_1")
 
 	cif::point f = fractional(p, c);
 
-	REQUIRE_THAT(f.m_x, Catch::Matchers::WithinRel(0.1f, 0.01f));
-	REQUIRE_THAT(f.m_y, Catch::Matchers::WithinRel(0.1f, 0.01f));
-	REQUIRE_THAT(f.m_z, Catch::Matchers::WithinRel(0.1f, 0.01f));
+	CHECK_THAT(f.m_x, Catch::Matchers::WithinRel(0.1f, 0.01f));
+	CHECK_THAT(f.m_y, Catch::Matchers::WithinRel(0.1f, 0.01f));
+	CHECK_THAT(f.m_z, Catch::Matchers::WithinRel(0.1f, 0.01f));
 
 	cif::point o = orthogonal(f, c);
 
-	REQUIRE_THAT(o.m_x, Catch::Matchers::WithinRel(1.f, 0.01f));
-	REQUIRE_THAT(o.m_y, Catch::Matchers::WithinRel(1.f, 0.01f));
-	REQUIRE_THAT(o.m_z, Catch::Matchers::WithinRel(1.f, 0.01f));
+	CHECK_THAT(o.m_x, Catch::Matchers::WithinRel(1.f, 0.01f));
+	CHECK_THAT(o.m_y, Catch::Matchers::WithinRel(1.f, 0.01f));
+	CHECK_THAT(o.m_z, Catch::Matchers::WithinRel(1.f, 0.01f));
 }
 
 TEST_CASE("symm_2")
@@ -390,33 +434,33 @@ TEST_CASE("symm_3")
 	REQUIRE(sg.get_name() == "P 21 21 2");
 }
 
-TEST_CASE("symm_4, *utf::tolerance(0.1f)")
+TEST_CASE("symm_4")
 {
 	using namespace cif::literals;
 
 	// based on 2b8h
 	auto sg = cif::spacegroup(154); // p 32 2 1
-	auto c = cif::cell(107.516, 107.516, 338.487, 90.00, 90.00, 120.00);
-	
-	cif::point a{   -8.688,  79.351, 10.439 }; // O6 NAG A 500
-	cif::point b{  -35.356,  33.693, -3.236 }; // CG2 THR D 400
-	cif::point sb(  -6.916,   79.34,   3.236); // 4_565 copy of b
+	auto c = cif::cell(107.516f, 107.516f, 338.487f, 90.00f, 90.00f, 120.00f);
 
-	REQUIRE_THAT(distance(a, sg(a, c, "1_455"_symop)), Catch::Matchers::WithinRel(static_cast<float>(c.get_a()), 0.01f));
-	REQUIRE_THAT(distance(a, sg(a, c, "1_545"_symop)), Catch::Matchers::WithinRel(static_cast<float>(c.get_b()), 0.01f));
-	REQUIRE_THAT(distance(a, sg(a, c, "1_554"_symop)), Catch::Matchers::WithinRel(static_cast<float>(c.get_c()), 0.01f));
+	cif::point a{ -8.688f, 79.351f, 10.439f };  // O6 NAG A 500
+	cif::point b{ -35.356f, 33.693f, -3.236f }; // CG2 THR D 400
+	cif::point sb(-6.916f, 79.34f, 3.236f);     // 4_565 copy of b
+
+	CHECK_THAT(distance(a, sg(a, c, "1_455"_symop)), Catch::Matchers::WithinRel(static_cast<float>(c.get_a()), 0.01f));
+	CHECK_THAT(distance(a, sg(a, c, "1_545"_symop)), Catch::Matchers::WithinRel(static_cast<float>(c.get_b()), 0.01f));
+	CHECK_THAT(distance(a, sg(a, c, "1_554"_symop)), Catch::Matchers::WithinRel(static_cast<float>(c.get_c()), 0.01f));
 
 	auto sb2 = sg(b, c, "4_565"_symop);
-	REQUIRE_THAT(sb.m_x, Catch::Matchers::WithinRel(sb2.m_x, 0.01f));
-	REQUIRE_THAT(sb.m_y, Catch::Matchers::WithinRel(sb2.m_y, 0.01f));
-	REQUIRE_THAT(sb.m_z, Catch::Matchers::WithinRel(sb2.m_z, 0.01f));
+	CHECK_THAT(sb.m_x, Catch::Matchers::WithinRel(sb2.m_x, 0.01f));
+	CHECK_THAT(sb.m_y, Catch::Matchers::WithinRel(sb2.m_y, 0.01f));
+	CHECK_THAT(sb.m_z, Catch::Matchers::WithinRel(sb2.m_z, 0.01f));
 
-	REQUIRE_THAT(distance(a, sb2), Catch::Matchers::WithinRel(7.42f, 0.01f));	
+	CHECK_THAT(distance(a, sb2), Catch::Matchers::WithinRel(7.42f, 0.01f));
 }
 
 // --------------------------------------------------------------------
 
-TEST_CASE("symm_4wvp_1, *utf::tolerance(0.1f)")
+TEST_CASE("symm_4wvp_1")
 {
 	using namespace cif::literals;
 
@@ -427,25 +471,24 @@ TEST_CASE("symm_4wvp_1, *utf::tolerance(0.1f)")
 
 	cif::crystal c(db);
 
-	cif::point p{ -78.722, 98.528,  11.994 };
+	cif::point p{ -78.722f, 98.528f, 11.994f };
 	auto a = s.get_residue("A", 10, "").get_atom_by_atom_id("O");
 
 	auto sp1 = c.symmetry_copy(a.get_location(), "2_565"_symop);
-	REQUIRE_THAT(sp1.m_x, Catch::Matchers::WithinAbs(p.m_x, 0.5f));
-	REQUIRE_THAT(sp1.m_y, Catch::Matchers::WithinAbs(p.m_y, 0.5f));
-	REQUIRE_THAT(sp1.m_z, Catch::Matchers::WithinAbs(p.m_z, 0.5f));
+	CHECK_THAT(sp1.m_x, Catch::Matchers::WithinAbs(p.m_x, 0.5f));
+	CHECK_THAT(sp1.m_y, Catch::Matchers::WithinAbs(p.m_y, 0.5f));
+	CHECK_THAT(sp1.m_z, Catch::Matchers::WithinAbs(p.m_z, 0.5f));
 
 	const auto &[d, sp2, so] = c.closest_symmetry_copy(p, a.get_location());
 
 	REQUIRE(d < 1);
 
-	REQUIRE_THAT(sp2.m_x, Catch::Matchers::WithinAbs(p.m_x, 0.5f));
-	REQUIRE_THAT(sp2.m_y, Catch::Matchers::WithinAbs(p.m_y, 0.5f));
-	REQUIRE_THAT(sp2.m_z, Catch::Matchers::WithinAbs(p.m_z, 0.5f));
-
+	CHECK_THAT(sp2.m_x, Catch::Matchers::WithinAbs(p.m_x, 0.5f));
+	CHECK_THAT(sp2.m_y, Catch::Matchers::WithinAbs(p.m_y, 0.5f));
+	CHECK_THAT(sp2.m_z, Catch::Matchers::WithinAbs(p.m_z, 0.5f));
 }
 
-TEST_CASE("symm_2bi3_1, *utf::tolerance(0.1f)")
+TEST_CASE("symm_2bi3_1")
 {
 	cif::file f(gTestDir / "2bi3.cif.gz");
 
@@ -455,18 +498,15 @@ TEST_CASE("symm_2bi3_1, *utf::tolerance(0.1f)")
 	cif::crystal c(db);
 
 	auto struct_conn = db["struct_conn"];
-	for (const auto &[
-			asym1, seqid1, authseqid1, atomid1, symm1,
-			asym2, seqid2, authseqid2, atomid2, symm2,
-			dist] : struct_conn.find<
-				std::string,int,std::string,std::string,std::string,
-				std::string,int,std::string,std::string,std::string,
-				float>(
-			cif::key("ptnr1_symmetry") != "1_555" or cif::key("ptnr2_symmetry") != "1_555",
-			"ptnr1_label_asym_id", "ptnr1_label_seq_id", "ptnr1_auth_seq_id", "ptnr1_label_atom_id", "ptnr1_symmetry", 
-			"ptnr2_label_asym_id", "ptnr2_label_seq_id", "ptnr2_auth_seq_id", "ptnr2_label_atom_id", "ptnr2_symmetry", 
-			"pdbx_dist_value"
-		))
+	for (const auto &[asym1, seqid1, authseqid1, atomid1, symm1,
+			 asym2, seqid2, authseqid2, atomid2, symm2,
+			 dist] : struct_conn.find<std::string, int, std::string, std::string, std::string,
+			 std::string, int, std::string, std::string, std::string,
+			 float>(
+			 cif::key("ptnr1_symmetry") != "1_555" or cif::key("ptnr2_symmetry") != "1_555",
+			 "ptnr1_label_asym_id", "ptnr1_label_seq_id", "ptnr1_auth_seq_id", "ptnr1_label_atom_id", "ptnr1_symmetry",
+			 "ptnr2_label_asym_id", "ptnr2_label_seq_id", "ptnr2_auth_seq_id", "ptnr2_label_atom_id", "ptnr2_symmetry",
+			 "pdbx_dist_value"))
 	{
 		auto &r1 = s.get_residue(asym1, seqid1, authseqid1);
 		auto &r2 = s.get_residue(asym2, seqid2, authseqid2);
@@ -477,22 +517,22 @@ TEST_CASE("symm_2bi3_1, *utf::tolerance(0.1f)")
 		auto sa1 = c.symmetry_copy(a1.get_location(), cif::sym_op(symm1));
 		auto sa2 = c.symmetry_copy(a2.get_location(), cif::sym_op(symm2));
 
-		REQUIRE_THAT(cif::distance(sa1, sa2), Catch::Matchers::WithinAbs(dist, 0.5f));
+		CHECK_THAT(cif::distance(sa1, sa2), Catch::Matchers::WithinAbs(dist, 0.5f));
 
 		auto pa1 = a1.get_location();
 
 		const auto &[d, p, so] = c.closest_symmetry_copy(pa1, a2.get_location());
 
-		REQUIRE_THAT(p.m_x, Catch::Matchers::WithinAbs(sa2.m_x, 0.5f));
-		REQUIRE_THAT(p.m_y, Catch::Matchers::WithinAbs(sa2.m_y, 0.5f));
-		REQUIRE_THAT(p.m_z, Catch::Matchers::WithinAbs(sa2.m_z, 0.5f));
+		CHECK_THAT(p.m_x, Catch::Matchers::WithinAbs(sa2.m_x, 0.5f));
+		CHECK_THAT(p.m_y, Catch::Matchers::WithinAbs(sa2.m_y, 0.5f));
+		CHECK_THAT(p.m_z, Catch::Matchers::WithinAbs(sa2.m_z, 0.5f));
 
-		REQUIRE_THAT(d, Catch::Matchers::WithinAbs(dist, 0.5f));
+		CHECK_THAT(d, Catch::Matchers::WithinAbs(dist, 0.5f));
 		REQUIRE(so.string() == symm2);
 	}
 }
 
-TEST_CASE("symm_2bi3_1a, *utf::tolerance(0.1f)")
+TEST_CASE("symm_2bi3_1a")
 {
 	using namespace cif::literals;
 
@@ -504,43 +544,40 @@ TEST_CASE("symm_2bi3_1a, *utf::tolerance(0.1f)")
 	auto struct_conn = db["struct_conn"];
 	auto atom_site = db["atom_site"];
 
-	for (const auto &[
-			asym1, seqid1, authseqid1, atomid1, symm1,
-			asym2, seqid2, authseqid2, atomid2, symm2,
-			dist] : struct_conn.find<
-				std::string,std::optional<int>,std::string,std::string,std::string,
-				std::string,std::optional<int>,std::string,std::string,std::string,
-				float>(
-			cif::key("ptnr1_symmetry") != "1_555" or cif::key("ptnr2_symmetry") != "1_555",
-			"ptnr1_label_asym_id", "ptnr1_label_seq_id", "ptnr1_auth_seq_id", "ptnr1_label_atom_id", "ptnr1_symmetry", 
-			"ptnr2_label_asym_id", "ptnr2_label_seq_id", "ptnr2_auth_seq_id", "ptnr2_label_atom_id", "ptnr2_symmetry", 
-			"pdbx_dist_value"
-		))
+	for (const auto &[asym1, seqid1, authseqid1, atomid1, symm1,
+			 asym2, seqid2, authseqid2, atomid2, symm2,
+			 dist] : struct_conn.find<std::string, std::optional<int>, std::string, std::string, std::string,
+			 std::string, std::optional<int>, std::string, std::string, std::string,
+			 float>(
+			 cif::key("ptnr1_symmetry") != "1_555" or cif::key("ptnr2_symmetry") != "1_555",
+			 "ptnr1_label_asym_id", "ptnr1_label_seq_id", "ptnr1_auth_seq_id", "ptnr1_label_atom_id", "ptnr1_symmetry",
+			 "ptnr2_label_asym_id", "ptnr2_label_seq_id", "ptnr2_auth_seq_id", "ptnr2_label_atom_id", "ptnr2_symmetry",
+			 "pdbx_dist_value"))
 	{
-		cif::point p1 = atom_site.find1<float,float,float>(
+		cif::point p1 = atom_site.find1<float, float, float>(
 			"label_asym_id"_key == asym1 and "label_seq_id"_key == seqid1 and "auth_seq_id"_key == authseqid1 and "label_atom_id"_key == atomid1,
 			"cartn_x", "cartn_y", "cartn_z");
-		cif::point p2 = atom_site.find1<float,float,float>(
+		cif::point p2 = atom_site.find1<float, float, float>(
 			"label_asym_id"_key == asym2 and "label_seq_id"_key == seqid2 and "auth_seq_id"_key == authseqid2 and "label_atom_id"_key == atomid2,
 			"cartn_x", "cartn_y", "cartn_z");
 
 		auto sa1 = c.symmetry_copy(p1, cif::sym_op(symm1));
 		auto sa2 = c.symmetry_copy(p2, cif::sym_op(symm2));
 
-		REQUIRE_THAT(cif::distance(sa1, sa2), Catch::Matchers::WithinAbs(dist, 0.5f));
+		CHECK_THAT(cif::distance(sa1, sa2), Catch::Matchers::WithinAbs(dist, 0.5f));
 
 		const auto &[d, p, so] = c.closest_symmetry_copy(p1, p2);
 
-		REQUIRE_THAT(p.m_x, Catch::Matchers::WithinAbs(sa2.m_x, 0.5f));
-		REQUIRE_THAT(p.m_y, Catch::Matchers::WithinAbs(sa2.m_y, 0.5f));
-		REQUIRE_THAT(p.m_z, Catch::Matchers::WithinAbs(sa2.m_z, 0.5f));
+		CHECK_THAT(p.m_x, Catch::Matchers::WithinAbs(sa2.m_x, 0.5f));
+		CHECK_THAT(p.m_y, Catch::Matchers::WithinAbs(sa2.m_y, 0.5f));
+		CHECK_THAT(p.m_z, Catch::Matchers::WithinAbs(sa2.m_z, 0.5f));
 
-		REQUIRE_THAT(d, Catch::Matchers::WithinAbs(dist, 0.5f));
+		CHECK_THAT(d, Catch::Matchers::WithinAbs(dist, 0.5f));
 		REQUIRE(so.string() == symm2);
 	}
 }
 
-TEST_CASE("symm_3bwh_1, *utf::tolerance(0.1f)")
+TEST_CASE("symm_3bwh_1")
 {
 	cif::file f(gTestDir / "3bwh.cif.gz");
 
@@ -555,15 +592,15 @@ TEST_CASE("symm_3bwh_1, *utf::tolerance(0.1f)")
 		{
 			if (a1 == a2)
 				continue;
-			
-			const auto&[ d, p, so ] = c.closest_symmetry_copy(a1.get_location(), a2.get_location());
 
-			REQUIRE_THAT(d, Catch::Matchers::WithinAbs(distance(a1.get_location(), p), 0.5f));
+			const auto &[d, p, so] = c.closest_symmetry_copy(a1.get_location(), a2.get_location());
+
+			CHECK_THAT(d, Catch::Matchers::WithinAbs(distance(a1.get_location(), p), 0.5f));
 		}
 	}
 }
 
-TEST_CASE("volume_3bwh_1, *utf::tolerance(0.1f)")
+TEST_CASE("volume_3bwh_1")
 {
 	cif::file f(gTestDir / "1juh.cif.gz");
 
@@ -571,6 +608,42 @@ TEST_CASE("volume_3bwh_1, *utf::tolerance(0.1f)")
 
 	cif::crystal c(db);
 
-	REQUIRE_THAT(c.get_cell().get_volume(), Catch::Matchers::WithinRel(741009.625f, 0.01f));
+	CHECK_THAT(c.get_cell().get_volume(), Catch::Matchers::WithinRel(741009.625f, 0.01f));
 }
 
+// --------------------------------------------------------------------
+
+TEST_CASE("smallest_sphere-1")
+{
+	std::vector<cif::point> pts{
+		{ 0.9295, 4.9006, 46.9706 },
+		{ -0.1215, 5.5936, 46.0726 },
+		{ -0.7975, 4.7046, 45.0796 },
+		{ -1.4875, 3.5486, 45.7196 },
+		{ -0.6535, 2.8816, 46.8186 },
+		{ 0.3825, 3.5156, 47.4496 },
+		{ 1.1995, 2.9206, 48.5286 },
+		{ 0.8255, 2.0466, 49.4716 },
+		{ 1.6625, 1.5036, 50.5176 },
+		{ 1.1165, 0.6056, 51.3626 },
+		{ 1.8325, -0.0064, 52.4656 },
+		{ 1.1945, -0.9044, 53.2216 },
+		{ 1.8135, -1.5534, 54.3566 },
+		{ 1.0925, -2.4574, 55.0656 },
+		{ 1.5205, -3.2204, 56.2476 },
+		{ 1.1955, 5.8066, 48.1796 },
+		{ 2.2495, 4.6896, 46.1796 },
+		{ -1.2515, 1.5186, 47.1786 },
+		{ 3.1385, 1.9106, 50.6166 },
+		{ 3.2605, -1.1834, 54.7206 },
+		{ 2.5975, -3.8554, 56.2096 },
+		{ 0.7975, -3.2184, 57.2686 }
+	};
+
+	for (int i = 0; i < 1000; ++i)
+	{
+		auto [c, r] = cif::smallest_sphere_around_points(pts);
+		CHECK_THAT(cif::distance(c, cif::point{ 0, 0.743099928, 51.1741028 }), Catch::Matchers::WithinAbs(0.f, 0.01f));
+		CHECK_THAT(r, Catch::Matchers::WithinAbs(7.31248331f, 0.01f));
+	}
+}

test/validate-pdbx-test.cpp

@@ -32,11 +32,11 @@
 
 // --------------------------------------------------------------------
 
-cif::file operator""_cf(const char *text, size_t length)
+cif::file operator""_cf(const char *text, std::size_t length)
 {
 	struct membuf : public std::streambuf
 	{
-		membuf(char *text, size_t length)
+		membuf(char *text, std::size_t length)
 		{
 			this->setg(text, text, text + length);
 		}
@@ -279,6 +279,20 @@ A 1 5   GLY 5   5   5   GLY GLY A . n
 
 		REQUIRE_FALSE(cif::pdb::is_valid_pdbx_file(f));
 	}
-
-
+}
+
+TEST_CASE("extended-dictionary-1")
+{
+	cif::add_file_resource("dssp-extension.dic", gTestDir / "dssp-extension.dic");
+
+	cif::VERBOSE = 2;
+
+	auto f = cif::pdb::read(gTestDir / "1cbs-dssp.cif");
+	CHECK(f.is_valid());
+}
+
+TEST_CASE("brak")
+{
+	auto f = cif::pdb::read(gTestDir / "brak.pdb");
+	CHECK(f.is_valid());
 }

tools/depends.cmd

@@ -5,6 +5,8 @@ IF NOT EXIST build_ci\libs (
   MKDIR build_ci\libs
 )
 CD build_ci\libs
+
+@REM Install ZLib
 IF NOT EXIST zlib-%ZLIB_VERSION%.zip (
   ECHO Downloading https://github.com/libarchive/zlib/archive/v%ZLIB_VERSION%.zip
   curl -L -o zlib-%ZLIB_VERSION%.zip https://github.com/libarchive/zlib/archive/v%ZLIB_VERSION%.zip || EXIT /b 1
@@ -14,9 +16,9 @@ IF NOT EXIST zlib-%ZLIB_VERSION% (
   C:\windows\system32\tar.exe -x -f zlib-%ZLIB_VERSION%.zip || EXIT /b 1
 )
 CD zlib-%ZLIB_VERSION%
-cmake -G "Visual Studio 17 2022" . || EXIT /b 1
-cmake --build . --target ALL_BUILD --config Release || EXIT /b 1
-cmake --build . --target RUN_TESTS --config Release || EXIT /b 1
-cmake --build . --target INSTALL --config Release || EXIT /b 1
+cmake -B build || EXIT /b 1
+cmake --build build --target ALL_BUILD --config Release || EXIT /b 1
+cmake --build build --target RUN_TESTS --config Release || EXIT /b 1
+cmake --build build --target INSTALL --config Release || EXIT /b 1
 
 @EXIT /b 0

tools/update-libcifpp-data.in

@@ -63,7 +63,7 @@ update_dictionary() {
 
 update_dictionary "@CIFPP_CACHE_DIR@/components.cif" "https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz"
 update_dictionary "@CIFPP_CACHE_DIR@/mmcif_pdbx.dic" "https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz"
-update_dictionary "@CIFPP_CACHE_DIR@/mmcif_ma.dic" "https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic"
+update_dictionary "@CIFPP_CACHE_DIR@/mmcif_ma.dic" "https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_ma.dic"
 
 # notify subscribers, using find instead of run-parts to make it work on FreeBSD as well