Fixing pdb2cif, and sequence checking

- Add audit_conform only if file is really valid
- Added reconstruction code for PDBx

.github/workflows/build-documentation.yml

@@ -0,0 +1,65 @@
+# This starter workflow is for a CMake project running on multiple platforms. There is a different starter workflow if you just want a single platform.
+# See: https://github.com/actions/starter-workflows/blob/main/ci/cmake-single-platform.yml
+name: publish docs
+
+on:
+  push:
+    branches: [ "trunk" ]
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+
+    - 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.
+      id: strings
+      shell: bash
+      run: |
+        echo "build-output-dir=${{ github.workspace }}/build" >> "$GITHUB_OUTPUT"
+
+    - name: Install dependencies Ubuntu
+      run: sudo apt-get update && sudo apt-get install cmake doxygen
+
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+        cache: 'pip' # caching pip dependencies
+    - run: pip install -r docs/requirements.txt
+
+    - name: Configure CMake
+      run: cmake -S . -B ${{ steps.strings.outputs.build-output-dir }} -DBUILD_DOCUMENTATION=ON -DBUILD_TESTING=OFF
+
+    - name: Run Sphinx
+      run: |
+        cmake --build ${{ steps.strings.outputs.build-output-dir }} --target Sphinx-libcifpp
+        ls -l ${{ steps.strings.outputs.build-output-dir }}
+        ls -l ${{ steps.strings.outputs.build-output-dir }}/docs/sphinx
+
+    - name: Upload artifact
+      uses: actions/upload-pages-artifact@v2
+      with:
+        path: ${{ steps.strings.outputs.build-output-dir }}/docs/sphinx
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    runs-on: ubuntu-latest
+    needs: docs
+
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2

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

@@ -45,13 +45,15 @@ jobs:
         cmake -B ${{ steps.strings.outputs.build-output-dir }}
         -DCMAKE_CXX_COMPILER=${{ matrix.cpp_compiler }}
         -DCMAKE_BUILD_TYPE=Release
-        -DCIFPP_DOWNLOAD_CCD=OFF
         -S ${{ github.workspace }}
         
     - name: Build
       run: cmake --build ${{ steps.strings.outputs.build-output-dir }} --config Release
-
+      
     - name: Test
       working-directory: ${{ steps.strings.outputs.build-output-dir }}
       run: ctest --build-config Release --output-on-failure
 
+    - name: Install
+      if: matrix.os != 'windows-latest'
+      run: sudo cmake --install ${{ steps.strings.outputs.build-output-dir }} --config Release

.gitignore

@@ -2,7 +2,7 @@ build/
 .vscode/
 .vs/
 tools/update-libcifpp-data
-data/components.cif*
+rsrc/components.cif*
 CMakeSettings.json
 msvc/
 src/revision.hpp
@@ -11,4 +11,5 @@ Testing/
 include/cif++/exports.hpp
 docs/api
 docs/conf.py
-build_ci/
+build_ci/
+data/components.cif

CMakeLists.txt

@@ -11,21 +11,24 @@
 # this list of conditions and the following disclaimer in the documentation
 # and/or other materials provided with the distribution.
 
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 cmake_minimum_required(VERSION 3.16)
 
 # set the project name
-project(libcifpp VERSION 6.0.0 LANGUAGES CXX)
+project(
+	libcifpp
+	VERSION 7.0.0
+	LANGUAGES CXX)
 
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 
@@ -50,7 +53,9 @@ if(CMAKE_GENERATOR STREQUAL "Ninja Multi-Config")
 endif()
 
 if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers")
+	set(CMAKE_CXX_FLAGS
+		"${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers"
+	)
 elseif(MSVC)
 	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4")
 endif()
@@ -66,25 +71,26 @@ if(NOT(BUILD_FOR_CCP4 AND WIN32))
 	option(BUILD_SHARED_LIBS "Build a shared library instead of a static one" OFF)
 endif()
 
-# Lots of code depend on the availability of the components.cif file
-option(CIFPP_DOWNLOAD_CCD "Download the CCD file components.cif during installation" ON)
+if(BUILD_FOR_CCP4)
+	unset(CIFPP_DOWNLOAD_CCD)
+	unset(CIFPP_INSTALL_UPDATE_SCRIPT)
+else()
+	# Lots of code depend on the availability of the components.cif file
+	option(CIFPP_DOWNLOAD_CCD
+		"Download the CCD file components.cif during installation" ON)
 
-# An optional cron script can be installed to keep the data files up-to-date
-if("${CMAKE_SYSTEM_NAME}" STREQUAL "Linux" AND NOT BUILD_FOR_CCP4)
-	option(CIFPP_INSTALL_UPDATE_SCRIPT "Install the script to update CCD and dictionary files" ON)
+	# An optional cron script can be installed to keep the data files up-to-date
+	if(UNIX AND NOT APPLE)
+		option(CIFPP_INSTALL_UPDATE_SCRIPT
+			"Install the script to update CCD and dictionary files" ON)
+	endif()
 endif()
 
-# When CCP4 is sourced in the environment, we can recreate the symmetry operations table
-if(EXISTS "$ENV{CCP4}")
-	if(EXISTS "$ENV{CCP4}/lib/data/syminfo.lib")
-		option(CIFPP_RECREATE_SYMOP_DATA "Recreate SymOp data table in case it is out of date" ON)
-	else()
-		set(CIFPP_RECREATE_SYMOP_DATA OFF)
-		message(WARNING "Symop data table recreation requested, but file syminfo.lib was not found in $ENV{CLIBD}")
-	endif()
-else()
-	set(CIFPP_RECREATE_SYMOP_DATA OFF)
-	message("Not trying to recreate symop_table_data.hpp since CCP4 is not defined")
+# When CCP4 is sourced in the environment, we can recreate the symmetry
+# operations table
+if(EXISTS "$ENV{CCP4}/lib/data/syminfo.lib")
+	option(CIFPP_RECREATE_SYMOP_DATA
+		"Recreate SymOp data table in case it is out of date" ON)
 endif()
 
 # CCP4 build
@@ -141,23 +147,30 @@ endif()
 # Libraries
 
 # Start by finding out if std:regex is usable. Note that the current
-# implementation in GCC is not acceptable, it crashes on long lines.
-# The implementation in libc++ (clang) and MSVC seem to be OK.
-check_cxx_source_compiles("
+# implementation in GCC is not acceptable, it crashes on long lines. The
+# implementation in libc++ (clang) and MSVC seem to be OK.
+check_cxx_source_compiles(
+	"
 #include <iostream>
 #ifndef __GLIBCXX__
 #error
 #endif
-int main(int argc, char *argv[]) { return 0; }" GXX_LIBSTDCPP)
+int main(int argc, char *argv[]) { return 0; }"
+	GXX_LIBSTDCPP)
 
 if(GXX_LIBSTDCPP)
-	message(STATUS "Testing for known regex bug, since you're using GNU libstdc++")
+	message(
+		STATUS "Testing for known regex bug, since you're using GNU libstdc++")
 
 	try_run(STD_REGEX_RUNNING STD_REGEX_COMPILING
-		${CMAKE_CURRENT_BINARY_DIR}/test ${PROJECT_SOURCE_DIR}/cmake/test-rx.cpp)
+		${CMAKE_CURRENT_BINARY_DIR}/test
+		${PROJECT_SOURCE_DIR}/cmake/test-rx.cpp)
 
 	if(STD_REGEX_RUNNING STREQUAL FAILED_TO_RUN)
-		message(STATUS "You are probably trying to compile using the g++ standard library which contains a crashing std::regex implementation. Will use boost::regex instead")
+		message(
+			STATUS
+			"You are probably trying to compile using the g++ standard library which contains a crashing std::regex implementation. Will use boost::regex instead"
+		)
 
 		find_package(Boost 1.80 QUIET COMPONENTS regex)
 
@@ -167,8 +180,7 @@ if(GXX_LIBSTDCPP)
 			FetchContent_Declare(
 				boost-rx
 				GIT_REPOSITORY https://github.com/boostorg/regex
-				GIT_TAG boost-1.83.0
-			)
+				GIT_TAG boost-1.83.0)
 
 			FetchContent_MakeAvailable(boost-rx)
 		endif()
@@ -182,8 +194,8 @@ set(THREADS_PREFER_PTHREAD_FLAG)
 find_package(Threads)
 
 if(MSVC)
-	# Avoid linking the shared library of zlib
-	# Search ZLIB_ROOT first if it is set.
+	# Avoid linking the shared library of zlib Search ZLIB_ROOT first if it is
+	# set.
 	if(ZLIB_ROOT)
 		set(_ZLIB_SEARCH_ROOT PATHS ${ZLIB_ROOT} NO_DEFAULT_PATH)
 		list(APPEND _ZLIB_SEARCHES _ZLIB_SEARCH_ROOT)
@@ -193,8 +205,7 @@ if(MSVC)
 	set(_ZLIB_x86 "(x86)")
 	set(_ZLIB_SEARCH_NORMAL
 		PATHS "[HKEY_LOCAL_MACHINE\\SOFTWARE\\GnuWin32\\Zlib;InstallPath]"
-		"$ENV{ProgramFiles}/zlib"
-		"$ENV{ProgramFiles${_ZLIB_x86}}/zlib")
+		"$ENV{ProgramFiles}/zlib" "$ENV{ProgramFiles${_ZLIB_x86}}/zlib")
 	unset(_ZLIB_x86)
 	list(APPEND _ZLIB_SEARCHES _ZLIB_SEARCH_NORMAL)
 
@@ -203,26 +214,37 @@ if(MSVC)
 	endif()
 
 	foreach(search ${_ZLIB_SEARCHES})
-		find_library(ZLIB_LIBRARY NAMES zlibstatic NAMES_PER_DIR ${${search}} PATH_SUFFIXES lib)
+		find_library(
+			ZLIB_LIBRARY
+			NAMES zlibstatic NAMES_PER_DIR ${${search}}
+			PATH_SUFFIXES lib)
 	endforeach()
 endif()
 
 find_package(ZLIB REQUIRED)
 
-find_package(Eigen3 QUIET)
+# Using Eigen3 is a bit of a thing. We don't want to build it completely since
+# we only need a couple of header files. Nothing special. But often, eigen3 is
+# already installed and then we prefer that.
+find_package(Eigen3 3.4 QUIET)
 
-if(Eigen3_FOUND)
-	get_target_property(EIGEN_INCLUDE_DIR Eigen3::Eigen INTERFACE_INCLUDE_DIRECTORIES)
+if(Eigen3_FOUND AND TARGET Eigen3::Eigen)
+	get_target_property(EIGEN_INCLUDE_DIR Eigen3::Eigen
+		INTERFACE_INCLUDE_DIRECTORIES)
 else()
-	ExternalProject_Add(
-		local_Eigen3
+	# 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
-		CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/external
-	)
+		GIT_TAG 3.4.0)
 
-	set(EIGEN3_D local_Eigen3)
-	set(EIGEN_INCLUDE_DIR ${CMAKE_CURRENT_BINARY_DIR}/external/include/eigen3)
+	FetchContent_GetProperties(my-eigen3)
+
+	if(NOT my-eigen3_POPULATED)
+		FetchContent_Populate(my-eigen3)
+	endif()
+
+	set(EIGEN_INCLUDE_DIR ${my-eigen3_SOURCE_DIR})
 endif()
 
 include(FindFilesystem)
@@ -238,17 +260,20 @@ write_version_header(${PROJECT_SOURCE_DIR}/src/ LIB_NAME "LibCIFPP")
 # SymOp data table
 if(CIFPP_RECREATE_SYMOP_DATA)
 	# The tool to create the table
-	add_executable(symop-map-generator "${PROJECT_SOURCE_DIR}/src/symop-map-generator.cpp")
+	add_executable(symop-map-generator
+		"${PROJECT_SOURCE_DIR}/src/symop-map-generator.cpp")
 
 	add_custom_command(
 		OUTPUT ${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp
-		COMMAND $<TARGET_FILE:symop-map-generator> $ENV{CLIBD}/syminfo.lib $ENV{CLIBD}/symop.lib ${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp
-	)
+		COMMAND
+		$<TARGET_FILE:symop-map-generator> $ENV{CLIBD}/syminfo.lib
+		$ENV{CLIBD}/symop.lib ${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp)
 
 	add_custom_target(
-		OUTPUT ${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp
-		DEPENDS symop-map-generator "$ENV{CLIBD}/syminfo.lib" "$ENV{CLIBD}/symop.lib"
-	)
+		OUTPUT
+		${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp
+		DEPENDS symop-map-generator "$ENV{CLIBD}/syminfo.lib"
+		"$ENV{CLIBD}/symop.lib")
 endif()
 
 # Sources
@@ -264,19 +289,18 @@ set(project_sources
 	${PROJECT_SOURCE_DIR}/src/validate.cpp
 	${PROJECT_SOURCE_DIR}/src/text.cpp
 	${PROJECT_SOURCE_DIR}/src/utilities.cpp
-
 	${PROJECT_SOURCE_DIR}/src/atom_type.cpp
 	${PROJECT_SOURCE_DIR}/src/compound.cpp
 	${PROJECT_SOURCE_DIR}/src/point.cpp
 	${PROJECT_SOURCE_DIR}/src/symmetry.cpp
-
 	${PROJECT_SOURCE_DIR}/src/model.cpp
-
 	${PROJECT_SOURCE_DIR}/src/pdb/cif2pdb.cpp
 	${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif.cpp
 	${PROJECT_SOURCE_DIR}/src/pdb/pdb_record.hpp
 	${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif_remark_3.hpp
 	${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif_remark_3.cpp
+	${PROJECT_SOURCE_DIR}/src/pdb/reconstruct.cpp
+	${PROJECT_SOURCE_DIR}/src/pdb/validate-pdbx.cpp
 )
 
 set(project_headers
@@ -293,33 +317,32 @@ set(project_headers
 	${PROJECT_SOURCE_DIR}/include/cif++/condition.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/category.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/row.hpp
-
 	${PROJECT_SOURCE_DIR}/include/cif++/atom_type.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/compound.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/point.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/symmetry.hpp
-
 	${PROJECT_SOURCE_DIR}/include/cif++/model.hpp
-
 	${PROJECT_SOURCE_DIR}/include/cif++/pdb.hpp
-
 	${PROJECT_SOURCE_DIR}/include/cif++/pdb/cif2pdb.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/pdb/io.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/pdb/pdb2cif.hpp
-	${PROJECT_SOURCE_DIR}/include/cif++/pdb/tls.hpp
-)
+	${PROJECT_SOURCE_DIR}/include/cif++/pdb/tls.hpp)
 
-add_library(cifpp ${project_sources} ${project_headers} ${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp)
+add_library(cifpp ${project_sources} ${project_headers}
+	${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp)
 add_library(cifpp::cifpp ALIAS cifpp)
 
 set(CMAKE_DEBUG_POSTFIX d)
 set_target_properties(cifpp PROPERTIES DEBUG_POSTFIX "d")
 
-generate_export_header(cifpp EXPORT_FILE_NAME ${PROJECT_SOURCE_DIR}/include/cif++/exports.hpp)
+generate_export_header(cifpp EXPORT_FILE_NAME
+	${PROJECT_SOURCE_DIR}/include/cif++/exports.hpp)
 
 if(BOOST_REGEX)
-	target_compile_definitions(cifpp PRIVATE USE_BOOST_REGEX=1 BOOST_REGEX_STANDALONE=1)
-	get_target_property(BOOST_REGEX_INCLUDE_DIR Boost::regex INTERFACE_INCLUDE_DIRECTORIES)
+	target_compile_definitions(cifpp PRIVATE USE_BOOST_REGEX=1
+		BOOST_REGEX_STANDALONE=1)
+	get_target_property(BOOST_REGEX_INCLUDE_DIR Boost::regex
+		INTERFACE_INCLUDE_DIRECTORIES)
 endif()
 
 if(MSVC)
@@ -328,20 +351,14 @@ endif()
 
 set_target_properties(cifpp PROPERTIES POSITION_INDEPENDENT_CODE ON)
 
-target_include_directories(cifpp
-	PUBLIC
-	"$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>"
+target_include_directories(
+	cifpp
+	PUBLIC "$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>"
 	"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
-	PRIVATE
-	"${EIGEN_INCLUDE_DIR}"
-	"${BOOST_REGEX_INCLUDE_DIR}"
-)
+	PRIVATE "${BOOST_REGEX_INCLUDE_DIR}" "${EIGEN_INCLUDE_DIR}")
 
-target_link_libraries(cifpp PUBLIC Threads::Threads ZLIB::ZLIB ${CIFPP_REQUIRED_LIBRARIES})
-
-if(${EIGEN3_D})
-	add_dependencies(cifpp ${EIGEN3_D})
-endif()
+target_link_libraries(cifpp PUBLIC Threads::Threads ZLIB::ZLIB
+	${CIFPP_REQUIRED_LIBRARIES})
 
 if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
 	target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
@@ -349,7 +366,7 @@ endif(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
 
 if(CIFPP_DOWNLOAD_CCD)
 	# download the components.cif file from CCD
-	set(COMPONENTS_CIF ${PROJECT_SOURCE_DIR}/data/components.cif)
+	set(COMPONENTS_CIF ${PROJECT_SOURCE_DIR}/rsrc/components.cif)
 
 	if(EXISTS ${COMPONENTS_CIF})
 		file(SIZE ${COMPONENTS_CIF} CCD_FILE_SIZE)
@@ -361,70 +378,88 @@ if(CIFPP_DOWNLOAD_CCD)
 	endif()
 
 	if(NOT EXISTS ${COMPONENTS_CIF})
-		if(NOT EXISTS ${PROJECT_SOURCE_DIR}/data)
-			file(MAKE_DIRECTORY ${PROJECT_SOURCE_DIR}/data/)
-		endif()
-
-		# Since the file(DOWNLOAD) command in cmake does not use
-		# compression, we try to download the gzipped version and
-		# decompress it ourselves.
+		# Since the file(DOWNLOAD) command in cmake does not use compression, we try
+		# to download the gzipped version and decompress it ourselves.
 		find_program(GUNZIP gunzip)
 
-		if(GUNZIP)
+		if(WIN32 OR GUNZIP STREQUAL "GUNZIP-NOTFOUND")
+			file(
+				DOWNLOAD https://files.wwpdb.org/pub/pdb/data/monomers/components.cif
+				${COMPONENTS_CIF}
+				SHOW_PROGRESS
+				STATUS CCD_FETCH_STATUS)
+		else()
 			if(NOT EXISTS "${COMPONENTS_CIF}.gz")
-				file(DOWNLOAD https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz ${COMPONENTS_CIF}.gz
-					SHOW_PROGRESS STATUS CCD_FETCH_STATUS)
+				file(
+					DOWNLOAD
+					https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
+					${COMPONENTS_CIF}.gz
+					SHOW_PROGRESS
+					STATUS CCD_FETCH_STATUS)
 			endif()
 
-			add_custom_command(OUTPUT ${COMPONENTS_CIF}
-				COMMAND ${GUNZIP} ${COMPONENTS_CIF}.gz
-				WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/data/)
-		else()
-			file(DOWNLOAD https://files.wwpdb.org/pub/pdb/data/monomers/components.cif ${COMPONENTS_CIF}
-				SHOW_PROGRESS STATUS CCD_FETCH_STATUS)
+			add_custom_command(
+				OUTPUT ${COMPONENTS_CIF}
+				COMMAND "${GUNZIP}" ${COMPONENTS_CIF}.gz
+				WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/rsrc/)
+
+			add_custom_target(COMPONENTS ALL DEPENDS ${COMPONENTS_CIF})
 		endif()
 
 		# Do not continue if downloading went wrong
 		list(POP_FRONT CCD_FETCH_STATUS CCD_FETCH_STATUS_CODE)
 
 		if(CCD_FETCH_STATUS_CODE)
-			message(FATAL_ERROR "Error trying to download CCD file: ${CCD_FETCH_STATUS}")
+			message(
+				FATAL_ERROR "Error trying to download CCD file: ${CCD_FETCH_STATUS}")
 		endif()
 	endif()
-
-	add_custom_target(COMPONENTS ALL DEPENDS ${COMPONENTS_CIF})
 endif()
 
 # Installation directories
 if(BUILD_FOR_CCP4)
-	set(CIFPP_DATA_DIR "$ENV{CCP4}/share/libcifpp" CACHE PATH "Directory where dictionary and other static data is stored")
+	set(CIFPP_DATA_DIR
+		"$ENV{CCP4}/share/libcifpp"
+		CACHE PATH "Directory where dictionary and other static data is stored")
 else()
-	set(CIFPP_DATA_DIR "${CMAKE_INSTALL_FULL_DATADIR}/libcifpp" CACHE PATH "Directory where dictionary and other static data is stored")
+	set(CIFPP_DATA_DIR
+		"${CMAKE_INSTALL_FULL_DATADIR}/libcifpp"
+		CACHE PATH "Directory where dictionary and other static data is stored")
 endif()
 
-target_compile_definitions(cifpp PUBLIC DATA_DIR="${CIFPP_DATA_DIR}")
+if(CIFPP_DATA_DIR)
+	target_compile_definitions(cifpp PUBLIC DATA_DIR="${CIFPP_DATA_DIR}")
+endif()
 
 if(UNIX AND NOT BUILD_FOR_CCP4)
 	if("${CMAKE_INSTALL_PREFIX}" STREQUAL "/usr/local")
-		set(CIFPP_CACHE_DIR "/var/cache/libcifpp" CACHE PATH "The directory where downloaded data files are stored")
+		set(CIFPP_CACHE_DIR
+			"/var/cache/libcifpp"
+			CACHE PATH "The directory where downloaded data files are stored")
 	else()
-		set(CIFPP_CACHE_DIR "${CMAKE_INSTALL_FULL_LOCALSTATEDIR}/cache/libcifpp" CACHE PATH "The directory where downloaded data files are stored")
+		set(CIFPP_CACHE_DIR
+			"${CMAKE_INSTALL_FULL_LOCALSTATEDIR}/cache/libcifpp"
+			CACHE PATH "The directory where downloaded data files are stored")
 	endif()
 
 	target_compile_definitions(cifpp PUBLIC CACHE_DIR="${CIFPP_CACHE_DIR}")
 
-	set(CIFPP_ETC_DIR "${CMAKE_INSTALL_FULL_SYSCONFDIR}" CACHE PATH "The directory where the update configuration file is stored")
+	set(CIFPP_ETC_DIR
+		"${CMAKE_INSTALL_FULL_SYSCONFDIR}"
+		CACHE PATH "The directory where the update configuration file is stored")
 else()
 	unset(CIFPP_CACHE_DIR)
 endif()
 
 # Install rules
-install(TARGETS cifpp
+install(
+	TARGETS cifpp
 	EXPORT cifpp-targets
 	ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
 	LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
 	RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-	INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+	INCLUDES
+	DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 
 if(MSVC AND BUILD_SHARED_LIBS)
 	install(
@@ -439,89 +474,89 @@ file(GLOB OLD_CONFIG_FILES
 	${CMAKE_INSTALL_FULL_LIBDIR}/cmake/cifpp/cifppTargets*.cmake)
 
 if(OLD_CONFIG_FILES)
-	message(STATUS "Installation will remove old config files: ${OLD_CONFIG_FILES}")
+	message(
+		STATUS "Installation will remove old config files: ${OLD_CONFIG_FILES}")
 	install(CODE "file(REMOVE ${OLD_CONFIG_FILES})")
 endif()
 
-install(EXPORT cifpp-targets
+install(
+	EXPORT cifpp-targets
 	FILE "cifpp-targets.cmake"
 	NAMESPACE cifpp::
-	DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cifpp
-)
+	DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cifpp)
 
 install(
 	DIRECTORY include/cif++
 	DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
-	COMPONENT Devel
-)
+	COMPONENT Devel)
 
 install(
 	FILES include/cif++.hpp
 	DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
-	COMPONENT Devel
-)
+	COMPONENT Devel)
 
-install(FILES
-	${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
-	${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx.dic
-	${PROJECT_SOURCE_DIR}/rsrc/mmcif_ma.dic
-	${COMPONENTS_CIF}
-	DESTINATION ${CIFPP_DATA_DIR}
-)
+if(CIFPP_DATA_DIR)
+	install(
+		FILES ${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
+		${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx.dic
+		${PROJECT_SOURCE_DIR}/rsrc/mmcif_ma.dic ${COMPONENTS_CIF}
+		DESTINATION ${CIFPP_DATA_DIR})
+endif()
 
 if(CIFPP_CACHE_DIR)
-	install(FILES
-		${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
+	install(
+		FILES ${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
 		${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx.dic
-		${PROJECT_SOURCE_DIR}/rsrc/mmcif_ma.dic
-		${COMPONENTS_CIF}
-		DESTINATION ${CIFPP_CACHE_DIR}
-	)
+		${PROJECT_SOURCE_DIR}/rsrc/mmcif_ma.dic ${COMPONENTS_CIF}
+		DESTINATION ${CIFPP_CACHE_DIR})
 endif()
 
 set(CONFIG_TEMPLATE_FILE ${PROJECT_SOURCE_DIR}/cmake/cifpp-config.cmake.in)
 
 configure_package_config_file(
-	${CONFIG_TEMPLATE_FILE}
-	${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config.cmake
+	${CONFIG_TEMPLATE_FILE} ${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config.cmake
 	INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cifpp
-	PATH_VARS CIFPP_DATA_DIR
-)
+	PATH_VARS CIFPP_DATA_DIR)
 
-install(FILES
-	"${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config.cmake"
+install(
+	FILES "${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config.cmake"
 	"${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config-version.cmake"
 	DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cifpp
-	COMPONENT Devel
-)
+	COMPONENT Devel)
 
-set_target_properties(cifpp PROPERTIES
-	VERSION ${PROJECT_VERSION}
+set_target_properties(
+	cifpp
+	PROPERTIES VERSION ${PROJECT_VERSION}
 	SOVERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}"
 	INTERFACE_cifpp_MAJOR_VERSION ${PROJECT_VERSION_MAJOR})
 
-set_property(TARGET cifpp APPEND PROPERTY
-	COMPATIBLE_INTERFACE_STRING cifpp_MAJOR_VERSION
-)
+set_property(
+	TARGET cifpp
+	APPEND
+	PROPERTY COMPATIBLE_INTERFACE_STRING cifpp_MAJOR_VERSION)
 
 write_basic_package_version_file(
 	"${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config-version.cmake"
 	VERSION ${PROJECT_VERSION}
-	COMPATIBILITY AnyNewerVersion
-)
+	COMPATIBILITY AnyNewerVersion)
+
+# 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)
-
 	# We're using the older version 2 of Catch2
 	FetchContent_Declare(
 		Catch2
 		GIT_REPOSITORY https://github.com/catchorg/Catch2.git
-		GIT_TAG v2.13.9
-	)
+		GIT_TAG v2.13.9)
 
 	FetchContent_MakeAvailable(Catch2)
 
-	list(APPEND CIFPP_tests
+	list(
+		APPEND
+		CIFPP_tests
 		unit-v2
 		unit-3d
 		format
@@ -529,63 +564,83 @@ if(BUILD_TESTING)
 		rename-compound
 		sugar
 		spinner
-	)
+		reconstruction
+		validate-pdbx)
 
 	foreach(CIFPP_TEST IN LISTS CIFPP_tests)
 		set(CIFPP_TEST "${CIFPP_TEST}-test")
 		set(CIFPP_TEST_SOURCE "${CMAKE_CURRENT_SOURCE_DIR}/test/${CIFPP_TEST}.cpp")
 
-		add_executable(${CIFPP_TEST} ${CIFPP_TEST_SOURCE} "${CMAKE_CURRENT_SOURCE_DIR}/test/test-main.cpp")
+		add_executable(
+			${CIFPP_TEST} ${CIFPP_TEST_SOURCE}
+			"${CMAKE_CURRENT_SOURCE_DIR}/test/test-main.cpp")
 
-		target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp::cifpp Catch2::Catch2)
-		target_include_directories(${CIFPP_TEST} PRIVATE ${EIGEN_INCLUDE_DIR})
+		target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp::cifpp
+			Catch2::Catch2)
+		target_include_directories(${CIFPP_TEST} PRIVATE "${EIGEN_INCLUDE_DIR}")
 
 		if(MSVC)
 			# Specify unwind semantics so that MSVC knowns how to handle exceptions
 			target_compile_options(${CIFPP_TEST} PRIVATE /EHsc)
 		endif()
 
-		add_custom_target("run-${CIFPP_TEST}" DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch ${CIFPP_TEST})
+		add_custom_target(
+			"run-${CIFPP_TEST}"
+			DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch ${CIFPP_TEST})
 
 		add_custom_command(
 			OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch
-			COMMAND $<TARGET_FILE:${CIFPP_TEST}> --data-dir ${CMAKE_CURRENT_SOURCE_DIR}/test)
+			COMMAND $<TARGET_FILE:${CIFPP_TEST}> --data-dir
+			${CMAKE_CURRENT_SOURCE_DIR}/test)
 
-		add_test(NAME ${CIFPP_TEST}
-			COMMAND $<TARGET_FILE:${CIFPP_TEST}> --data-dir ${CMAKE_CURRENT_SOURCE_DIR}/test)
+		add_test(NAME ${CIFPP_TEST} COMMAND $<TARGET_FILE:${CIFPP_TEST}> --data-dir
+			${CMAKE_CURRENT_SOURCE_DIR}/test)
 	endforeach()
 endif()
 
 # Optionally install the update scripts for CCD and dictionary files
 if(CIFPP_INSTALL_UPDATE_SCRIPT)
-	if(${CMAKE_SYSTEM_NAME} STREQUAL "Linux" OR ${CMAKE_SYSTEM_NAME} STREQUAL "GNU")
+	if(${CMAKE_SYSTEM_NAME} STREQUAL "Linux" OR ${CMAKE_SYSTEM_NAME} STREQUAL
+		"GNU")
 		if("${CMAKE_INSTALL_PREFIX}" STREQUAL "/usr/local")
-			set(CIFPP_CRON_DIR "/etc/cron.weekly" CACHE PATH "The cron directory, for the update script")
+			set(CIFPP_CRON_DIR
+				"/etc/cron.weekly"
+				CACHE PATH "The cron directory, for the update script")
 		else()
-			set(CIFPP_CRON_DIR "${CIFPP_ETC_DIR}/cron.weekly" CACHE PATH "The cron directory, for the update script")
+			set(CIFPP_CRON_DIR
+				"${CIFPP_ETC_DIR}/cron.weekly"
+				CACHE PATH "The cron directory, for the update script")
 		endif()
-	elseif(UNIX) # assume all others are like FreeBSD...
-		set(CIFPP_CRON_DIR "${CIFPP_ETC_DIR}/periodic/weekly" CACHE PATH "The cron directory, for the update script")
+	elseif(${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD")
+		set(CIFPP_CRON_DIR
+			"${CIFPP_ETC_DIR}/periodic/weekly"
+			CACHE PATH "The cron directory, for the update script")
 	else()
 		message(FATAL_ERROR "Don't know where to install the update script")
 	endif()
 
-	configure_file(${PROJECT_SOURCE_DIR}/tools/update-libcifpp-data.in update-libcifpp-data @ONLY)
+	configure_file(${PROJECT_SOURCE_DIR}/tools/update-libcifpp-data.in
+		update-libcifpp-data @ONLY)
 	install(
 		FILES ${CMAKE_CURRENT_BINARY_DIR}/update-libcifpp-data
 		DESTINATION ${CIFPP_CRON_DIR}
-		PERMISSIONS OWNER_EXECUTE OWNER_READ GROUP_EXECUTE GROUP_READ WORLD_EXECUTE WORLD_READ
-	)
+		PERMISSIONS OWNER_EXECUTE OWNER_READ GROUP_EXECUTE GROUP_READ WORLD_EXECUTE
+		WORLD_READ)
 
 	install(DIRECTORY DESTINATION ${CIFPP_CACHE_DIR})
 
 	# a config file, to make it complete
 	if(NOT EXISTS "${CIFPP_ETC_DIR}/libcifpp.conf")
-		file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf [[# Uncomment the next line to enable automatic updates
+		file(
+			WRITE ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf
+			[[# Uncomment the next line to enable automatic updates
 # update=true
 ]])
-		install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf DESTINATION "${CIFPP_ETC_DIR}")
-		install(CODE "message(\"A configuration file has been written to ${CIFPP_ETC_DIR}/libcifpp.conf, please edit this file to enable automatic updates\")")
+		install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf
+			DESTINATION "${CIFPP_ETC_DIR}")
+		install(
+			CODE "message(\"A configuration file has been written to ${CIFPP_ETC_DIR}/libcifpp.conf, please edit this file to enable automatic updates\")"
+		)
 
 		install(DIRECTORY DESTINATION "${CIFPP_ETC_DIR}/libcifpp/cache-update.d")
 	endif()
@@ -602,7 +657,7 @@ set(CPACK_SOURCE_TGZ ON)
 set(CPACK_SOURCE_TBZ2 OFF)
 set(CPACK_SOURCE_TXZ OFF)
 set(CPACK_SOURCE_TZ OFF)
-set(CPACK_SOURCE_IGNORE_FILES "/data/components.cif;/build;/.vscode;/.git")
+set(CPACK_SOURCE_IGNORE_FILES "/rsrc/components.cif;/build;/.vscode;/.git")
 set(CPACK_PACKAGE_FILE_NAME "${PROJECT_NAME}-${PROJECT_VERSION}")
 set(CPACK_SOURCE_PACKAGE_FILE_NAME ${CPACK_PACKAGE_FILE_NAME})
 include(CPack)

README.md

@@ -1,10 +1,34 @@
+[![github CI](https://github.com/pdb-redo/libcifpp/actions/workflows/cmake-multi-platform.yml/badge.svg)](https://github.com/pdb-redo/libcifpp/actions)
+[![GitHub License](https://img.shields.io/github/license/pdb-redo/libcifpp)](https://github.com/pdb-redo/libcifpp/LICENSE)
+
 # libcifpp
 
-This library contains code to work with mmCIF and legacy PDB files.
+As the name implies, this library was originally written to work with mmCIF files
+using C++ as programming language. The design of this library leanes heavily on
+the structure of CIF files. These files can be thought of as a text dump of a
+relational databank with, often but not always, a very strict schema describing
+the data. These schema's are called dictionaries.
+
+Using information from the content of a mmCIF file and an optional schema,
+libcifpp allows you to access the data in the file as a collection of datablock
+each containing a collection of categories with rows of data. The categories can
+be searched for data using queries written in regular C++ syntax. When a dictionary
+was specified, inserted data is checked for validity. Likewise removal of data
+may result in cascaded removal of linked data in other categories using
+parent/child relationship information.
+
+Since there were still many programs using the legacy PDB format at the time
+development started, a layer was added that converts data to and from PDB format
+into mmCIF format. This means you can manipulate PDB files as if they were
+normal mmCIF files.
+
+Apart from this basic functionality, libcifpp also offers code to help with
+symmetry calculations, 3d manipulations and obtaining information from the CCD
+[Chemical Component Dictionary](https://www.wwpdb.org/data/ccd).
 
 ## Documentation
 
-The documentation can be found at https://www.hekkelman.com/libcifpp-doc/
+The documentation can be found at [github.io](https://pdb-redo.github.io/libcifpp/)
 
 ## Synopsis
 
@@ -64,54 +88,138 @@ int main(int argc, char *argv[])
 You might be able to use libcifpp from a package manager used by your
 OS distribution. But most likely this package will be out-of-date.
 Therefore it is recommended to build *libcifpp* from code. It is not
-hard to do.
+hard to do. But it is recommended to read the following instructions
+carefully.
 
 ### Requirements
 
 The code for this library was written in C++17. You therefore need a
-recent compiler to build it. For the development gcc 9.4 and clang 9.0
+recent compiler to build it. For the development gcc >= 9.4 and clang >= 9.0
 have been used as well as MSVC version 2019.
 
-Other requirements are:
+The other requirement you really need to have installed on your computer
+is a version of [CMake](https://cmake.org). For now the minimum version
+is 3.16 but that may soon change into a higher version. You should also
+install the gui version of CMake to set build options easily, on Debian
+I prefer to use the curses version installed with `cmake-curses-gui`.
+
+It is very useful to have [mrc](https://github.com/mhekkel/mrc) available.
+However, this is only an option if you use Windows or an operating system
+using the ELF executable format (i.e. Linux or FreeBSD). MRC is a resource
+compiler that allows including data files into the executable making them
+easier to install.
+
+Other libraries you might want to install beforehand are:
 
-- [cmake](https://cmake.org) A build tool.
-- [mrc](https://github.com/mhekkel/mrc), a resource compiler that
-  allows including data files into the executable making them easier to
-  install. Strictly speaking this is optional, but at the expense of
-  functionality.
 - [libeigen](https://eigen.tuxfamily.org/index.php?title=Main_Page), a
   library to do amongst others matrix calculations. This usually can be
   installed using your package manager, in Debian/Ubuntu it is called
   `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).
-
-The Boost libraries are only needed in case you want to build the test
-code or if you are using GCC. That last condition is due to a long
-standing bug in the 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.
+- [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.
 
 ### Building
 
-Building the code is as simple as typing:
+First you need to download the code:
 
 ```console
- git clone https://github.com/PDB-REDO/libcifpp.git --recurse-submodules
+ git clone https://github.com/PDB-REDO/libcifpp.git
  cd libcifpp
- cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$HOME/.local -DCMAKE_BUILD_TYPE=Release
- cmake --build build
- cmake --install build
 ```
 
-This checks out the source code from github, creates a new directory
-where cmake stores its files. Run a configure, build the code and then
-it installs the library and auxiliary files.
+You should start by considering where to install libcifpp. If you have
+sufficient permissions on your computer you perhaps should use the
+default but libcifpp can be configured to be installed anywhere
+including e.g. *$HOME/.local*.
+
+Next step is to configure, for this use the CMake gui application. If you
+installed the curses version of cmake you can type `ccmake`. On Windows
+you can use `cmake-gui.exe`.
+
+To install in the default location:
+
+```console
+ccmake -S . -B build
+```
+
+To install elsewhere, e.g. *$HOME/.local*:
+
+```console
+ccmake -S . -B build -DCMAKE_INSTALL_PREFIX=$HOME/.local
+```
+
+In the cmake window, start the configure command (use button or press 'c').
+After the first configure step you will see a list of settable options.
+Alter these to match your preferences. Most options are self explaining
+and contain a description. Some may need a bit more explanation:
+
+- CIFPP_DATA_DIR, this directory will be used to store initial versions
+  of the mmcif_pdbx dictionary as well as the optional CCD file.
+
+- CIFPP_DOWNLOAD_CCD
+
+  The CCD file is huge and perhaps you think you don't
+  need it. In that case you can leave this OFF. But that will limit the
+  use cases.
+
+- CIFPP_INSTALL_UPDATE_SCRIPT
+  
+  The files in CIFPP_DATA_DIR are quickly becoming out of date. On
+  FreeBSD and Linux you can install a script that updates these files
+  on a weekly basis.
+
+- CIFPP_CRON_DIR
+  
+  The directory where the update script is to be installed.
+
+- CIFPP_ETC_DIR
+  
+  The update script will only work if the file called *libcifpp.conf*
+  in this *etc* directory will contain an uncommented line with
+
+```console
+update=true
+```
+
+- CIFPP_CACHE_DIR
+
+  When you installed and enabled the update script, new files are
+  written to this directory.
+
+- CIFPP_RECREATE_SYMOP_DATA
+  
+  If you had CCP4 sourced into your environment, this option allows
+  you to recreate the symop data file.
+
+- BUILD_FOR_CCP4
+  
+  Build a special version of libcifpp to be installed in the CCP4
+  environment.
+
+After setting these options you can run the configure step again and
+then use generate to create the makefiles.
+
+Building and installing is then as simple as:
+
+```console
+cmake --build build
+cmake --install build
+```
+
+If this fails due to lack of permissions, you can try:
+
+```console
+sudo cmake --install build
+```
 
 Tests are created by default, and to test the code you can run:
 
 ```console
- cmake --build build
- ctest --test-dir build
+ctest --test-dir build
 ```

changelog

@@ -1,3 +1,20 @@
+Version 7.0.0
+- Renaming many methods and parameters to be more
+  consistent with the mmCIF dictionaries.
+  (Most notably, item used to be called column or
+  tag sometimes).
+- validation_error is now a std::system_error error
+  value. The exception is gone.
+- Added repairSequenceInfo to repair invalid files
+
+Version 6.1.0
+- Add formula weight to entity in pdb2cif
+- Change order of categories inside a datablock to match order in file
+- Change default order to write out categories in a file based on
+  parent/child relationship
+- Added validate_pdbx and recover_pdbx
+- Fixed a serious bug in category_index when moving categories
+
 Version 6.0.0
 - Drop the use of CCP4's monomer library for compound information
 

docs/resources.rst

@@ -18,7 +18,7 @@ Loading Resources
 
 No matter where the resource is located, you should always use the single libcifpp API call :cpp:func:`cif::load_resource` to load them. This function returns a *std::istream* wrapped inside a *std::unique_ptr*. 
 
-The order in which resources are search for is:
+The order in which resources are searched for is:
 
 * Use the resource that was defined by calling :cpp:func:`cif::add_file_resource`
   for this name.

include/cif++/category.hpp

@@ -31,22 +31,22 @@
 #include "cif++/condition.hpp"
 #include "cif++/iterator.hpp"
 #include "cif++/row.hpp"
-#include "cif++/validate.hpp"
 #include "cif++/text.hpp"
+#include "cif++/validate.hpp"
 
 #include <array>
 
 /** \file category.hpp
-  * Documentation for the cif::category class
-  *
-  * The category class should meet the requirements of Container and
-  * SequenceContainer.
-  * 
-  * TODO: implement all of:
-  * https://en.cppreference.com/w/cpp/named_req/Container
-  * https://en.cppreference.com/w/cpp/named_req/SequenceContainer
-  * and more?
-  */
+ * Documentation for the cif::category class
+ *
+ * The category class should meet the requirements of Container and
+ * SequenceContainer.
+ *
+ * TODO: implement all of:
+ * https://en.cppreference.com/w/cpp/named_req/Container
+ * https://en.cppreference.com/w/cpp/named_req/SequenceContainer
+ * and more?
+ */
 
 namespace cif
 {
@@ -61,23 +61,43 @@ namespace cif
 class duplicate_key_error : public std::runtime_error
 {
   public:
-    /**
-     * @brief Construct a new duplicate key error object
-     */
+	/**
+	 * @brief Construct a new duplicate key error object
+	 */
 	duplicate_key_error(const std::string &msg)
 		: std::runtime_error(msg)
 	{
 	}
 };
 
+/// @brief A missing_key_error is thrown when an attempt is made
+/// to create an index when one of the key items is missing.
+class missing_key_error : public std::runtime_error
+{
+  public:
+	/**
+	 * @brief Construct a new duplicate key error object
+	 */
+	missing_key_error(const std::string &msg, const std::string &key)
+		: std::runtime_error(msg)
+		, m_key(key)
+	{
+	}
+
+	const std::string &get_key() const noexcept { return m_key; }
+
+  private:
+	std::string m_key;
+};
+
 /// @brief A multiple_results_error is throw when you request a single
 /// row using a query but the query contains more than exactly one row.
 class multiple_results_error : public std::runtime_error
 {
   public:
-    /**
-     * @brief Construct a new multiple results error object
-     */
+	/**
+	 * @brief Construct a new multiple results error object
+	 */
 	multiple_results_error()
 		: std::runtime_error("query should have returned exactly one row")
 	{
@@ -136,8 +156,16 @@ class category
 	// --------------------------------------------------------------------
 
 	const std::string &name() const { return m_name; } ///< Returns the name of the category
-	iset key_fields() const; ///< Returns the cif::iset of key field names. Retrieved from the @ref category_validator for this category
-	std::set<uint16_t> key_field_indices() const; ///< Returns a set of indices for the key fields.
+
+	[[deprecated("use key_items instead")]]
+	iset key_fields() const;                           ///< Returns the cif::iset of key item names. Retrieved from the @ref category_validator for this category
+
+	iset key_items() const;                           ///< Returns the cif::iset of key item names. Retrieved from the @ref category_validator for this category
+
+	[[deprecated("use key_item_indices instead")]]
+	std::set<uint16_t> key_field_indices() const;      ///< Returns a set of indices for the key items.
+
+	std::set<uint16_t> key_item_indices() const;      ///< Returns a set of indices for the key items.
 
 	/// @brief Set the validator for this category to @a v
 	/// @param v The category_validator to assign. A nullptr value is allowed.
@@ -162,7 +190,7 @@ class category
 
 	/// @brief Validate links, that means, values in this category should have an
 	/// accompanying value in parent categories.
-	/// 
+	///
 	/// @note
 	/// The code makes one exception when validating missing links and that's between
 	/// *atom_site* and a parent *pdbx_poly_seq_scheme* or *entity_poly_seq*.
@@ -265,7 +293,7 @@ class category
 	/// Return the theoretical maximum number or rows that can be stored
 	size_t max_size() const
 	{
-		return std::numeric_limits<size_t>::max();	// this is a bit optimistic, I guess
+		return std::numeric_limits<size_t>::max(); // this is a bit optimistic, I guess
 	}
 
 	/// Return true if the category is empty
@@ -281,12 +309,12 @@ class category
 	using key_type = row_initializer;
 
 	/// @brief Return a row_handle for the row specified by \a key
-	/// @param key The value for the key, fields specified in the dictionary should have a value
+	/// @param key The value for the key, items specified in the dictionary should have a value
 	/// @return The row found in the index, or an undefined row_handle
 	row_handle operator[](const key_type &key);
 
 	/// @brief Return a const row_handle for the row specified by \a key
-	/// @param key The value for the key, fields specified in the dictionary should have a value
+	/// @param key The value for the key, items specified in the dictionary should have a value
 	/// @return The row found in the index, or an undefined row_handle
 	const row_handle operator[](const key_type &key) const
 	{
@@ -301,15 +329,15 @@ class category
 	/// @code{.cpp}
 	/// for (const auto &[name, value] : cat.rows<std::string,int>("item_name", "item_value"))
 	///   std::cout << name << ": " << value << '\n';
-	/// @endcode 
+	/// @endcode
 	///
-	/// @tparam Ts The types for the columns requested
-	/// @param names The names for the columns requested
+	/// @tparam Ts The types for the items requested
+	/// @param names The names for the items requested
 
 	template <typename... Ts, typename... Ns>
 	iterator_proxy<const category, Ts...> rows(Ns... names) const
 	{
-		static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of column titles should be equal to the number of types to return");
+		static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of item names should be equal to the number of types to return");
 		return iterator_proxy<const category, Ts...>(*this, begin(), { names... });
 	}
 
@@ -320,19 +348,19 @@ class category
 	/// for (const auto &[name, value] : cat.rows<std::string,int>("item_name", "item_value"))
 	///   std::cout << name << ": " << value << '\n';
 	///
-	/// // or in case we only need one column:
+	/// // or in case we only need one item:
 	///
 	/// for (int id : cat.rows<int>("id"))
 	///   std::cout << id << '\n';
-	/// @endcode 
+	/// @endcode
 	///
-	/// @tparam Ts The types for the columns requested
-	/// @param names The names for the columns requested
+	/// @tparam Ts The types for the items requested
+	/// @param names The names for the items requested
 
 	template <typename... Ts, typename... Ns>
 	iterator_proxy<category, Ts...> rows(Ns... names)
 	{
-		static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of column titles should be equal to the number of types to return");
+		static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of item names should be equal to the number of types to return");
 		return iterator_proxy<category, Ts...>(*this, begin(), { names... });
 	}
 
@@ -343,7 +371,7 @@ class category
 	/// @code{.cpp}
 	/// for (row_handle rh : cat.find(cif::key("first_name") == "John" and cif::key("last_name") == "Doe"))
 	///    .. // do something with rh
-	/// @endcode 
+	/// @endcode
 	///
 	/// @param cond The condition for the query
 	/// @return A special iterator that loops over all elements that match. The iterator can be dereferenced
@@ -397,17 +425,17 @@ class category
 	/// @code{.cpp}
 	/// for (const auto &[name, value] : cat.find<std::string,int>(cif::key("item_value") > 10, "item_name", "item_value"))
 	///    std::cout << name << ": " << value << '\n';
-	/// @endcode 
+	/// @endcode
 	///
 	/// @param cond The condition for the query
-	/// @tparam Ts The types for the columns requested
-	/// @param names The names for the columns requested
+	/// @tparam Ts The types for the items requested
+	/// @param names The names for the items requested
 	/// @return A special iterator that loops over all elements that match.
 
 	template <typename... Ts, typename... Ns>
 	conditional_iterator_proxy<category, Ts...> find(condition &&cond, Ns... names)
 	{
-		static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of column titles should be equal to the number of types to return");
+		static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of item names should be equal to the number of types to return");
 		return find<Ts...>(cbegin(), std::move(cond), std::forward<Ns>(names)...);
 	}
 
@@ -415,14 +443,14 @@ class category
 	/// iterator can be used in a structured binding context.
 	///
 	/// @param cond The condition for the query
-	/// @tparam Ts The types for the columns requested
-	/// @param names The names for the columns requested
+	/// @tparam Ts The types for the items requested
+	/// @param names The names for the items requested
 	/// @return A special iterator that loops over all elements that match.
 
 	template <typename... Ts, typename... Ns>
 	conditional_iterator_proxy<const category, Ts...> find(condition &&cond, Ns... names) const
 	{
-		static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of column titles should be equal to the number of types to return");
+		static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of item names should be equal to the number of types to return");
 		return find<Ts...>(cbegin(), std::move(cond), std::forward<Ns>(names)...);
 	}
 
@@ -431,14 +459,14 @@ class category
 	///
 	/// @param pos Iterator pointing to the location where to start
 	/// @param cond The condition for the query
-	/// @tparam Ts The types for the columns requested
-	/// @param names The names for the columns requested
+	/// @tparam Ts The types for the items requested
+	/// @param names The names for the items requested
 	/// @return A special iterator that loops over all elements that match.
 
 	template <typename... Ts, typename... Ns>
 	conditional_iterator_proxy<category, Ts...> find(const_iterator pos, condition &&cond, Ns... names)
 	{
-		static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of column titles should be equal to the number of types to return");
+		static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of item names should be equal to the number of types to return");
 		return { *this, pos, std::move(cond), std::forward<Ns>(names)... };
 	}
 
@@ -447,14 +475,14 @@ class category
 	///
 	/// @param pos Iterator pointing to the location where to start
 	/// @param cond The condition for the query
-	/// @tparam Ts The types for the columns requested
-	/// @param names The names for the columns requested
+	/// @tparam Ts The types for the items requested
+	/// @param names The names for the items requested
 	/// @return A special iterator that loops over all elements that match.
 
 	template <typename... Ts, typename... Ns>
 	conditional_iterator_proxy<const category, Ts...> find(const_iterator pos, condition &&cond, Ns... names) const
 	{
-		static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of column titles should be equal to the number of types to return");
+		static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of item names should be equal to the number of types to return");
 		return { *this, pos, std::move(cond), std::forward<Ns>(names)... };
 	}
 
@@ -509,30 +537,30 @@ class category
 		return *h.begin();
 	}
 
-	/// @brief Return value for the column named @a column for the single row that
+	/// @brief Return value for the item named @a item for the single row that
 	/// matches @a cond. Throws @a multiple_results_error if there are is not exactly one row
 	/// @tparam The type to use for the result
 	/// @param cond The condition to search for
-	/// @param column The name of the column to return the value for
+	/// @param item The name of the item to return the value for
 	/// @return The value found
 	template <typename T>
-	T find1(condition &&cond, const char *column) const
+	T find1(condition &&cond, std::string_view item) const
 	{
-		return find1<T>(cbegin(), std::move(cond), column);
+		return find1<T>(cbegin(), std::move(cond), item);
 	}
 
-	/// @brief Return value for the column named @a column for the single row that
+	/// @brief Return value for the item named @a item for the single row that
 	/// matches @a cond when starting to search at @a pos.
 	/// Throws @a multiple_results_error if there are is not exactly one row
 	/// @tparam The type to use for the result
 	/// @param pos The location to start the search
 	/// @param cond The condition to search for
-	/// @param column The name of the column to return the value for
+	/// @param item The name of the item to return the value for
 	/// @return The value found
 	template <typename T, std::enable_if_t<not is_optional_v<T>, int> = 0>
-	T find1(const_iterator pos, condition &&cond, const char *column) const
+	T find1(const_iterator pos, condition &&cond, std::string_view item) const
 	{
-		auto h = find<T>(pos, std::move(cond), column);
+		auto h = find<T>(pos, std::move(cond), item);
 
 		if (h.size() != 1)
 			throw multiple_results_error();
@@ -540,18 +568,18 @@ class category
 		return *h.begin();
 	}
 
-	/// @brief Return a value of type std::optional<T> for the column named @a column for the single row that
+	/// @brief Return a value of type std::optional<T> for the item named @a item for the single row that
 	/// matches @a cond when starting to search at @a pos.
 	/// If the row was not found, an empty value is returned.
 	/// @tparam The type to use for the result
 	/// @param pos The location to start the search
 	/// @param cond The condition to search for
-	/// @param column The name of the column to return the value for
+	/// @param item The name of the item to return the value for
 	/// @return The value found, can be empty if no row matches the condition
 	template <typename T, std::enable_if_t<is_optional_v<T>, int> = 0>
-	T find1(const_iterator pos, condition &&cond, const char *column) const
+	T find1(const_iterator pos, condition &&cond, std::string_view item) const
 	{
-		auto h = find<typename T::value_type>(pos, std::move(cond), column);
+		auto h = find<typename T::value_type>(pos, std::move(cond), item);
 
 		if (h.size() > 1)
 			throw multiple_results_error();
@@ -562,34 +590,34 @@ class category
 		return *h.begin();
 	}
 
-	/// @brief Return a std::tuple for the values for the columns named in @a columns
+	/// @brief Return a std::tuple for the values for the items named in @a items
 	/// for the single row that matches @a cond
 	/// Throws @a multiple_results_error if there are is not exactly one row
 	/// @tparam The types to use for the resulting tuple
 	/// @param cond The condition to search for
-	/// @param columns The names of the columns to return the value for
+	/// @param items The names of the items to return the value for
 	/// @return The values found as a single tuple of type std::tuple<Ts...>
 	template <typename... Ts, typename... Cs, typename U = std::enable_if_t<sizeof...(Ts) != 1>>
-	std::tuple<Ts...> find1(condition &&cond, Cs... columns) const
+	std::tuple<Ts...> find1(condition &&cond, Cs... items) const
 	{
-		static_assert(sizeof...(Ts) == sizeof...(Cs), "The number of column titles should be equal to the number of types to return");
-		// static_assert(std::is_same_v<Cs, const char*>..., "The column names should be const char");
-		return find1<Ts...>(cbegin(), std::move(cond), std::forward<Cs>(columns)...);
+		static_assert(sizeof...(Ts) == sizeof...(Cs), "The number of item names should be equal to the number of types to return");
+		// static_assert(std::is_same_v<Cs, const char*>..., "The item names should be const char");
+		return find1<Ts...>(cbegin(), std::move(cond), std::forward<Cs>(items)...);
 	}
 
-	/// @brief Return a std::tuple for the values for the columns named in @a columns
+	/// @brief Return a std::tuple for the values for the items named in @a items
 	/// for the single row that matches @a cond when starting to search at @a pos
 	/// Throws @a multiple_results_error if there are is not exactly one row
 	/// @tparam The types to use for the resulting tuple
 	/// @param pos The location to start the search
 	/// @param cond The condition to search for
-	/// @param columns The names of the columns to return the value for
+	/// @param items The names of the items to return the value for
 	/// @return The values found as a single tuple of type std::tuple<Ts...>
 	template <typename... Ts, typename... Cs, typename U = std::enable_if_t<sizeof...(Ts) != 1>>
-	std::tuple<Ts...> find1(const_iterator pos, condition &&cond, Cs... columns) const
+	std::tuple<Ts...> find1(const_iterator pos, condition &&cond, Cs... items) const
 	{
-		static_assert(sizeof...(Ts) == sizeof...(Cs), "The number of column titles should be equal to the number of types to return");
-		auto h = find<Ts...>(pos, std::move(cond), std::forward<Cs>(columns)...);
+		static_assert(sizeof...(Ts) == sizeof...(Cs), "The number of item names should be equal to the number of types to return");
+		auto h = find<Ts...>(pos, std::move(cond), std::forward<Cs>(items)...);
 
 		if (h.size() != 1)
 			throw multiple_results_error();
@@ -638,74 +666,74 @@ class category
 		return h.empty() ? row_handle{} : *h.begin();
 	}
 
-	/// @brief Return the value for column @a column for the first row that matches condition @a cond
+	/// @brief Return the value for item @a item for the first row that matches condition @a cond
 	/// @tparam The type of the value to return
 	/// @param cond The condition to search for
-	/// @param column The column for which the value should be returned
+	/// @param item The item for which the value should be returned
 	/// @return The value found or a default constructed value if not found
 	template <typename T>
-	T find_first(condition &&cond, const char *column) const
+	T find_first(condition &&cond, std::string_view item) const
 	{
-		return find_first<T>(cbegin(), std::move(cond), column);
+		return find_first<T>(cbegin(), std::move(cond), item);
 	}
 
-	/// @brief Return the value for column @a column for the first row that matches condition @a cond
+	/// @brief Return the value for item @a item for the first row that matches condition @a cond
 	/// when starting the search at @a pos
 	/// @tparam The type of the value to return
 	/// @param pos The location to start searching
 	/// @param cond The condition to search for
-	/// @param column The column for which the value should be returned
+	/// @param item The item for which the value should be returned
 	/// @return The value found or a default constructed value if not found
 	template <typename T>
-	T find_first(const_iterator pos, condition &&cond, const char *column) const
+	T find_first(const_iterator pos, condition &&cond, std::string_view item) const
 	{
-		auto h = find<T>(pos, std::move(cond), column);
+		auto h = find<T>(pos, std::move(cond), item);
 
 		return h.empty() ? T{} : *h.begin();
 	}
 
-	/// @brief Return a tuple containing the values for the columns @a columns for the first row that matches condition @a cond
+	/// @brief Return a tuple containing the values for the items @a items for the first row that matches condition @a cond
 	/// @tparam The types of the values to return
 	/// @param cond The condition to search for
-	/// @param columns The columns for which the values should be returned
+	/// @param items The items for which the values should be returned
 	/// @return The values found or default constructed values if not found
 	template <typename... Ts, typename... Cs, typename U = std::enable_if_t<sizeof...(Ts) != 1>>
-	std::tuple<Ts...> find_first(condition &&cond, Cs... columns) const
+	std::tuple<Ts...> find_first(condition &&cond, Cs... items) const
 	{
-		static_assert(sizeof...(Ts) == sizeof...(Cs), "The number of column titles should be equal to the number of types to return");
-		// static_assert(std::is_same_v<Cs, const char*>..., "The column names should be const char");
-		return find_first<Ts...>(cbegin(), std::move(cond), std::forward<Cs>(columns)...);
+		static_assert(sizeof...(Ts) == sizeof...(Cs), "The number of item names should be equal to the number of types to return");
+		// static_assert(std::is_same_v<Cs, const char*>..., "The item names should be const char");
+		return find_first<Ts...>(cbegin(), std::move(cond), std::forward<Cs>(items)...);
 	}
 
-	/// @brief Return a tuple containing the values for the columns @a columns for the first row that matches condition @a cond
+	/// @brief Return a tuple containing the values for the items @a items for the first row that matches condition @a cond
 	/// when starting the search at @a pos
 	/// @tparam The types of the values to return
 	/// @param pos The location to start searching
 	/// @param cond The condition to search for
-	/// @param columns The columns for which the values should be returned
+	/// @param items The items for which the values should be returned
 	/// @return The values found or default constructed values if not found
 	template <typename... Ts, typename... Cs, typename U = std::enable_if_t<sizeof...(Ts) != 1>>
-	std::tuple<Ts...> find_first(const_iterator pos, condition &&cond, Cs... columns) const
+	std::tuple<Ts...> find_first(const_iterator pos, condition &&cond, Cs... items) const
 	{
-		static_assert(sizeof...(Ts) == sizeof...(Cs), "The number of column titles should be equal to the number of types to return");
-		auto h = find<Ts...>(pos, std::move(cond), std::forward<Cs>(columns)...);
+		static_assert(sizeof...(Ts) == sizeof...(Cs), "The number of item names should be equal to the number of types to return");
+		auto h = find<Ts...>(pos, std::move(cond), std::forward<Cs>(items)...);
 
 		return h.empty() ? std::tuple<Ts...>{} : *h.begin();
 	}
 
 	// --------------------------------------------------------------------
 
-	/// @brief Return the maximum value for column @a column for all rows that match condition @a cond
+	/// @brief Return the maximum value for item @a item for all rows that match condition @a cond
 	/// @tparam The type of the value to return
-	/// @param column The column to use for the value
+	/// @param item The item to use for the value
 	/// @param cond The condition to search for
 	/// @return The value found or the minimal value for the type
 	template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0>
-	T find_max(const char *column, condition &&cond) const
+	T find_max(std::string_view item, condition &&cond) const
 	{
 		T result = std::numeric_limits<T>::min();
 
-		for (auto v : find<T>(std::move(cond), column))
+		for (auto v : find<T>(std::move(cond), item))
 		{
 			if (result < v)
 				result = v;
@@ -714,27 +742,27 @@ class category
 		return result;
 	}
 
-	/// @brief Return the maximum value for column @a column for all rows
+	/// @brief Return the maximum value for item @a item for all rows
 	/// @tparam The type of the value to return
-	/// @param column The column to use for the value
+	/// @param item The item to use for the value
 	/// @return The value found or the minimal value for the type
 	template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0>
-	T find_max(const char *column) const
+	T find_max(std::string_view item) const
 	{
-		return find_max<T>(column, all());
+		return find_max<T>(item, all());
 	}
 
-	/// @brief Return the minimum value for column @a column for all rows that match condition @a cond
+	/// @brief Return the minimum value for item @a item for all rows that match condition @a cond
 	/// @tparam The type of the value to return
-	/// @param column The column to use for the value
+	/// @param item The item to use for the value
 	/// @param cond The condition to search for
 	/// @return The value found or the maximum value for the type
 	template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0>
-	T find_min(const char *column, condition &&cond) const
+	T find_min(std::string_view item, condition &&cond) const
 	{
 		T result = std::numeric_limits<T>::max();
 
-		for (auto v : find<T>(std::move(cond), column))
+		for (auto v : find<T>(std::move(cond), item))
 		{
 			if (result > v)
 				result = v;
@@ -743,20 +771,28 @@ class category
 		return result;
 	}
 
-	/// @brief Return the maximum value for column @a column for all rows
+	/// @brief Return the maximum value for item @a item for all rows
 	/// @tparam The type of the value to return
-	/// @param column The column to use for the value
+	/// @param item The item to use for the value
 	/// @return The value found or the maximum value for the type
 	template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0>
-	T find_min(const char *column) const
+	T find_min(std::string_view item) const
 	{
-		return find_min<T>(column, all());
+		return find_min<T>(item, all());
 	}
 
 	/// @brief Return whether a row exists that matches condition @a cond
 	/// @param cond The condition to match
 	/// @return True if a row exists
-	bool exists(condition &&cond) const
+	[[deprecated("Use contains instead")]] bool exists(condition &&cond) const
+	{
+		return contains(std::move(cond));
+	}
+
+	/// @brief Return whether a row exists that matches condition @a cond
+	/// @param cond The condition to match
+	/// @return True if a row exists
+	bool contains(condition &&cond) const
 	{
 		bool result = false;
 
@@ -846,7 +882,7 @@ class category
 	// 	insert_impl(pos, std::move(row));
 	// }
 
-	/// Erase the row pointed to by @a pos and return the iterator to the 
+	/// Erase the row pointed to by @a pos and return the iterator to the
 	/// row following pos.
 	iterator erase(iterator pos);
 
@@ -890,7 +926,7 @@ class category
 			for (auto i = b; i != e; ++i)
 			{
 				// item_value *new_item = this->create_item(*i);
-				r->append(add_column(i->name()), { i->value() });
+				r->append(add_item(i->name()), { i->value() });
 			}
 		}
 		catch (...)
@@ -912,7 +948,6 @@ class category
 	/// result is unique in the context of this category
 	std::string get_unique_id(std::function<std::string(int)> generator = cif::cif_id_for_number);
 
-
 	/// @brief Generate a new, unique ID based on a string prefix followed by a number
 	/// @param prefix The string prefix
 	/// @return a new unique ID
@@ -922,98 +957,172 @@ class category
 			{ return prefix + std::to_string(nr + 1); });
 	}
 
+	/// @brief Generate a new, unique value for a item named @a item_name
+	/// @param item_name The name of the item
+	/// @return a new unique value
+	std::string get_unique_value(std::string_view item_name);
+
 	// --------------------------------------------------------------------
 
-	/// \brief Update a single column named @a tag in the rows that match \a cond to value \a value
+	/// \brief Update a single item named @a item_name in the rows that match \a cond to value \a value
 	/// making sure the linked categories are updated according to the link.
 	/// That means, child categories are updated if the links are absolute
 	/// and unique. If they are not, the child category rows are split.
 
-	void update_value(condition &&cond, std::string_view tag, std::string_view value)
+	void update_value(condition &&cond, std::string_view item_name, std::string_view value)
 	{
 		auto rs = find(std::move(cond));
 		std::vector<row_handle> rows;
 		std::copy(rs.begin(), rs.end(), std::back_inserter(rows));
-		update_value(rows, tag, value);
+		update_value(rows, item_name, value);
 	}
 
-	/// \brief Update a single column named @a tag in @a rows to value \a value
+	/// \brief Update a single item named @a item_name in @a rows to value \a value
 	/// making sure the linked categories are updated according to the link.
 	/// That means, child categories are updated if the links are absolute
 	/// and unique. If they are not, the child category rows are split.
 
-	void update_value(const std::vector<row_handle> &rows, std::string_view tag, std::string_view value);
+	void update_value(const std::vector<row_handle> &rows, std::string_view item_name, std::string_view value);
 
 	// --------------------------------------------------------------------
-	/// \brief Return the index number for \a column_name
+	// Naming used to be very inconsistent. For backward compatibility,
+	// the old function names are here as deprecated variants.
 
+	/// \brief Return the index number for \a column_name
+	[[deprecated("Use get_item_ix instead")]]
 	uint16_t get_column_ix(std::string_view column_name) const
 	{
-		uint16_t result;
-
-		for (result = 0; result < m_columns.size(); ++result)
-		{
-			if (iequals(column_name, m_columns[result].m_name))
-				break;
-		}
-
-		if (VERBOSE > 0 and result == m_columns.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(column_name);
-			if (iv == nullptr)
-				std::cerr << "Invalid name used '" << column_name << "' is not a known column in " + m_name << '\n';
-		}
-
-		return result;
+		return get_item_ix(column_name);
 	}
 
 	/// @brief Return the name for column with index @a ix
 	/// @param ix The index number
 	/// @return The name of the column
+	[[deprecated("use get_item_name instead")]]
 	std::string_view get_column_name(uint16_t ix) const
 	{
-		if (ix >= m_columns.size())
-			throw std::out_of_range("column index is out of range");
-
-		return m_columns[ix].m_name;
+		return get_item_name(ix);
 	}
 
-	/// @brief Make sure a column with name @a column_name is known and return its index number
-	/// @param column_name The name of the column
-	/// @return The index number of the column
-	uint16_t add_column(std::string_view column_name)
+	/// @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
+	[[deprecated("use add_item instead")]]
+	uint16_t add_column(std::string_view item_name)
 	{
-		using namespace std::literals;
+		return add_item(item_name);
+	}
 
-		uint16_t result = get_column_ix(column_name);
+	/** @brief Remove column name @a colum_name
+	 * @param column_name The column to be removed
+	 */
+	[[deprecated("use remove_item instead")]]
+	void remove_column(std::string_view column_name)
+	{
+		remove_item(column_name);
+	}
 
-		if (result == m_columns.size())
-		{
-			const item_validator *item_validator = nullptr;
-
-			if (m_cat_validator != nullptr)
-			{
-				item_validator = m_cat_validator->get_validator_for_item(column_name);
-				if (item_validator == nullptr)
-					m_validator->report_error("tag " + std::string(column_name) + " not allowed in category " + m_name, false);
-			}
-
-			m_columns.emplace_back(column_name, item_validator);
-		}
-
-		return result;
+	/** @brief Rename column @a from_name to @a to_name */
+	[[deprecated("use rename_item instead")]]
+	void rename_column(std::string_view from_name, std::string_view to_name)
+	{
+		rename_item(from_name, to_name);
 	}
 
 	/// @brief Return whether a column with name @a name exists in this category
 	/// @param name The name of the column
 	/// @return True if the column exists
+	[[deprecated("use has_item instead")]]
 	bool has_column(std::string_view name) const
 	{
-		return get_column_ix(name) < m_columns.size();
+		return has_item(name);
 	}
 
 	/// @brief Return the cif::iset of columns in this category
-	iset get_columns() const;
+	[[deprecated("use get_items instead")]]
+	iset get_columns() const
+	{
+		return get_items();
+	}
+
+	// --------------------------------------------------------------------
+	/// \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;
+	}
+
+	/// @brief Return the name for item with index @a ix
+	/// @param ix The index number
+	/// @return The name of the item
+	std::string_view get_item_name(uint16_t ix) const
+	{
+		if (ix >= m_items.size())
+			throw std::out_of_range("item index is out of range");
+
+		return m_items[ix].m_name;
+	}
+
+	/// @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;
+	}
+
+	/** @brief Remove item name @a colum_name
+	 * @param item_name The item to be removed
+	 */
+	void remove_item(std::string_view item_name);
+
+	/** @brief Rename item @a from_name to @a to_name */
+	void rename_item(std::string_view from_name, std::string_view to_name);
+
+	/// @brief Return whether a item with name @a name exists in this category
+	/// @param name The name of the item
+	/// @return True if the item exists
+	bool has_item(std::string_view name) const
+	{
+		return get_item_ix(name) < m_items.size();
+	}
+
+	/// @brief Return the cif::iset of items in this category
+	iset get_items() const;
 
 	// --------------------------------------------------------------------
 
@@ -1029,30 +1138,37 @@ class category
 
 	// --------------------------------------------------------------------
 
-	/// This function returns effectively the list of fully qualified column
-	/// names, that is category_name + '.' + column_name for each column
-	std::vector<std::string> get_tag_order() const;
+	/// This function returns effectively the list of fully qualified item
+	/// names, that is category_name + '.' + item_name for each item
+	[[deprecated("use get_item_order instead")]]
+	std::vector<std::string> get_tag_order() const
+	{
+		return get_item_order();
+	}
+
+	/// This function returns effectively the list of fully qualified item
+	/// names, that is category_name + '.' + item_name for each item
+	std::vector<std::string> get_item_order() const;
 
 	/// Write the contents of the category to the std::ostream @a os
 	void write(std::ostream &os) const;
 
 	/// @brief Write the contents of the category to the std::ostream @a os and
-	/// use @a order as the order of the columns. If @a addMissingColumns is
-	/// false, columns that do not contain any value will be suppressed
+	/// use @a order as the order of the items. If @a addMissingItems is
+	/// false, items that do not contain any value will be suppressed
 	/// @param os The std::ostream to write to
-	/// @param order The order in which the columns should appear
-	/// @param addMissingColumns When false, empty columns are suppressed from the output
-	void write(std::ostream &os, const std::vector<std::string> &order, bool addMissingColumns = true);
+	/// @param order The order in which the items should appear
+	/// @param addMissingItems When false, empty items are suppressed from the output
+	void write(std::ostream &os, const std::vector<std::string> &order, bool addMissingItems = true);
 
   private:
-	void write(std::ostream &os, const std::vector<uint16_t> &order, bool includeEmptyColumns) const;
+	void write(std::ostream &os, const std::vector<uint16_t> &order, bool includeEmptyItems) const;
 
   public:
-
 	/// friend function to make it possible to do:
 	/// @code {.cpp}
 	/// std::cout << my_category;
-	/// @endcode 
+	/// @endcode
 	friend std::ostream &operator<<(std::ostream &os, const category &cat)
 	{
 		cat.write(os);
@@ -1060,7 +1176,7 @@ class category
 	}
 
   private:
-	void update_value(row *row, uint16_t column, std::string_view value, bool updateLinked, bool validate = true);
+	void update_value(row *row, uint16_t item, std::string_view value, bool updateLinked, bool validate = true);
 
 	void erase_orphans(condition &&cond, category &parent);
 
@@ -1097,12 +1213,12 @@ class category
 
 	row_handle create_copy(row_handle r);
 
-	struct item_column
+	struct item_entry
 	{
 		std::string m_name;
 		const item_validator *m_validator;
 
-		item_column(std::string_view name, const item_validator *validator)
+		item_entry(std::string_view name, const item_validator *validator)
 			: m_name(name)
 			, m_validator(validator)
 		{
@@ -1132,12 +1248,12 @@ class category
 
 	// --------------------------------------------------------------------
 
-	void swap_item(uint16_t column_ix, row_handle &a, row_handle &b);
+	void swap_item(uint16_t item_ix, row_handle &a, row_handle &b);
 
 	// --------------------------------------------------------------------
 
 	std::string m_name;
-	std::vector<item_column> m_columns;
+	std::vector<item_entry> m_items;
 	const validator *m_validator = nullptr;
 	const category_validator *m_cat_validator = nullptr;
 	std::vector<link> m_parent_links, m_child_links;

include/cif++/compound.hpp

@@ -166,17 +166,28 @@ class compound
 		return m_id == "HOH" or m_id == "H2O" or m_id == "WAT";
 	}
 
+	/** \brief Return whether this compound has a type of either 'peptide linking' or 'L-peptide linking' */
+	bool is_peptide() const;
+
+	/** \brief Return whether this compound has a type of either 'DNA linking' or 'RNA linking' */
+	bool is_base() const;
+
+	char one_letter_code() const { return m_one_letter_code; }; ///< Return the one letter code to use in a canonical sequence. If unknown the value '\0' is returned
+	std::string parent_id() const { return m_parent_id; };      ///< Return the parent id code in case a parent is specified (e.g. MET for MSE)
+
   private:
 	friend class compound_factory_impl;
+	friend class local_compound_factory_impl;
 
 	compound(cif::datablock &db);
-	compound(cif::datablock &db, const std::string &id, const std::string &name, const std::string &type, const std::string &group);
+	compound(cif::datablock &db, int);
 
 	std::string m_id;
 	std::string m_name;
 	std::string m_type;
-	std::string m_group;
 	std::string m_formula;
+	char m_one_letter_code = 0;
+	std::string m_parent_id;
 	float m_formula_weight = 0;
 	int m_formal_charge = 0;
 	std::vector<compound_atom> m_atoms;
@@ -214,29 +225,71 @@ class compound_factory
 	/// Override any previously loaded dictionary with @a inDictFile
 	void push_dictionary(const std::filesystem::path &inDictFile);
 
+	/** @brief Override any previously loaded dictionary with the data in @a file
+	 *
+	 * @note experimental feature
+	 *
+	 * Load the file @a file as a source for compound information. This may
+	 * be e.g. a regular mmCIF file with extra files containing compound
+	 * information.
+	 *
+	 * Be carefull to remove the block again, best use @ref cif::compound_source
+	 * as a stack based object.
+	 */
+
+	void push_dictionary(const file &file);
+
 	/// Remove the last pushed dictionary
 	void pop_dictionary();
 
 	/// Return whether @a res_name is a valid and known peptide
+	[[deprecated("use is_peptide or is_std_peptide instead)")]]
 	bool is_known_peptide(const std::string &res_name) const;
 
 	/// Return whether @a res_name is a valid and known base
+	[[deprecated("use is_base or is_std_base instead)")]]
 	bool is_known_base(const std::string &res_name) const;
 
+	/// Return whether @a res_name is a peptide
+	bool is_peptide(std::string_view res_name) const;
+
+	/// Return whether @a res_name is a base
+	bool is_base(std::string_view res_name) const;
+
+	/// Return whether @a res_name is one of the standard peptides
+	bool is_std_peptide(std::string_view res_name) const;
+
+	/// Return whether @a res_name is one of the standard bases
+	bool is_std_base(std::string_view res_name) const;
+
+	/// Return whether @a res_name is a monomer (either base or peptide)
+	bool is_monomer(std::string_view res_name) const;
+
+	/// Return whether @a res_name is one of the standard bases or peptides
+	bool is_std_monomer(std::string_view res_name) const
+	{
+		return is_std_base(res_name) or is_std_peptide(res_name);
+	}
+
+	bool is_water(std::string_view res_name) const
+	{
+		return res_name == "HOH" or res_name == "H2O" or res_name == "WAT";
+	}
+
 	/// \brief Create the compound object for \a id
 	///
 	/// This will create the compound instance for \a id if it doesn't exist already.
 	/// The result is owned by this factory and should not be deleted by the user.
 	/// \param id	The compound ID, a three letter code usually
 	/// \result		The compound, or nullptr if it could not be created (missing info)
-	const compound *create(std::string id);
+	const compound *create(std::string_view id);
 
 	~compound_factory();
 
 	CIFPP_EXPORT static const std::map<std::string, char> kAAMap, ///< Globally accessible static list of the default amino acids
 		kBaseMap;                                                 ///< Globally accessible static list of the default bases
 
-	void report_missing_compound(const std::string &compound_id);
+	void report_missing_compound(std::string_view compound_id);
 
   private:
 	compound_factory();
@@ -251,4 +304,35 @@ class compound_factory
 	std::shared_ptr<compound_factory_impl> m_impl;
 };
 
+// --------------------------------------------------------------------
+
+/**
+ * @brief Stack based source for compound info.
+ *
+ * Use this class to temporarily add a compound source to the
+ * compound_factory.
+ *
+ * @code{.cpp}
+ * cif::file f("1cbs-with-custom-rea.cif");
+ * cif::compound_source cs(f);
+ *
+ * auto &cf = cif::compound_factory::instance();
+ * auto rea_compound = cf.create("REA");
+ * @endcode
+ */
+
+class compound_source
+{
+  public:
+	compound_source(const cif::file &file)
+	{
+		cif::compound_factory::instance().push_dictionary(file);
+	}
+
+	~compound_source()
+	{
+		cif::compound_factory::instance().pop_dictionary();
+	}
+};
+
 } // namespace cif

include/cif++/condition.hpp

@@ -39,17 +39,17 @@
  * query you can use to find rows in a @ref cif::category
  *
  * Conditions are created as standard C++ expressions. That means
- * you can use the standard comparison operators to compare field
+ * you can use the standard comparison operators to compare item
  * contents with a value and boolean operators to chain everything
  * together.
  *
- * To create a query that simply compares one field with one value:
+ * To create a query that simply compares one item with one value:
  *
  * @code {.cpp}
  * cif::condition c = cif::key("id") == 1;
  * @endcode
  * 
- * That will find rows where the ID field contains the number 1. If
+ * 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}
@@ -64,7 +64,7 @@
  * auto c3 = "id"_key == 1 or "id"_key == 2;
  * @endcode
  * 
- * There are some special values you can use. To find rows with field that
+ * There are some special values you can use. To find rows with item that
  * do not have a value:
  * 
  * @code{.cpp}
@@ -83,7 +83,7 @@
  * auto c6 = cif::all;
  * @endcode
  * 
- * And when you want to search for any column containing the value 'foo':
+ * And when you want to search for any item containing the value 'foo':
  * 
  * @code{.cpp}
  * auto c7 = cif::any == "foo";
@@ -104,31 +104,40 @@ namespace cif
 /// we declare a function to access its contents
 
 /**
- * @brief Get the fields that can be used as key in conditions for a category
+ * @brief Get the items that can be used as key in conditions for a category
  * 
- * @param cat The category whose fields to return
- * @return iset The set of key field names
+ * @param cat The category whose items to return
+ * @return iset The set of key item names
  */
+[[deprecated("use get_category_items instead")]]
 iset get_category_fields(const category &cat);
 
 /**
- * @brief Get the column index for column @a col in category @a cat
+ * @brief Get the items that can be used as key in conditions for a category
  * 
- * @param cat The category
- * @param col The name of the column
- * @return uint16_t The index
+ * @param cat The category whose items to return
+ * @return iset The set of key field names
  */
-uint16_t get_column_ix(const category &cat, std::string_view col);
+iset get_category_items(const category &cat);
 
 /**
- * @brief Return whether the column @a col in category @a cat has a primitive type of *uchar*
+ * @brief Get the item index for item @a col in category @a cat
  * 
  * @param cat The category
- * @param col The column name
+ * @param col The name of the item
+ * @return uint16_t The index
+ */
+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*
  * @return false If the primitive type is not of type *uchar*
  */
-bool is_column_type_uchar(const category &cat, std::string_view col);
+bool is_item_type_uchar(const category &cat, std::string_view col);
 
 // --------------------------------------------------------------------
 // some more templates to be able to do querying
@@ -219,7 +228,7 @@ class condition
 
 	/**
 	 * @brief Prepare the condition to be used on category @a c. This will
-	 * take care of setting the correct indices for fields e.g.
+	 * take care of setting the correct indices for items e.g.
 	 * 
 	 * @param c The category this query should act upon
 	 */
@@ -305,14 +314,14 @@ namespace detail
 {
 	struct key_is_empty_condition_impl : public condition_impl
 	{
-		key_is_empty_condition_impl(const std::string &item_tag)
-			: m_item_tag(item_tag)
+		key_is_empty_condition_impl(const std::string &item_name)
+			: m_item_name(item_name)
 		{
 		}
 
 		condition_impl *prepare(const category &c) override
 		{
-			m_item_ix = get_column_ix(c, m_item_tag);
+			m_item_ix = get_item_ix(c, m_item_name);
 			return this;
 		}
 
@@ -323,23 +332,23 @@ namespace detail
 
 		void str(std::ostream &os) const override
 		{
-			os << m_item_tag << " IS NULL";
+			os << m_item_name << " IS NULL";
 		}
 
-		std::string m_item_tag;
+		std::string m_item_name;
 		uint16_t m_item_ix = 0;
 	};
 
 	struct key_is_not_empty_condition_impl : public condition_impl
 	{
-		key_is_not_empty_condition_impl(const std::string &item_tag)
-			: m_item_tag(item_tag)
+		key_is_not_empty_condition_impl(const std::string &item_name)
+			: m_item_name(item_name)
 		{
 		}
 
 		condition_impl *prepare(const category &c) override
 		{
-			m_item_ix = get_column_ix(c, m_item_tag);
+			m_item_ix = get_item_ix(c, m_item_name);
 			return this;
 		}
 
@@ -350,17 +359,17 @@ namespace detail
 
 		void str(std::ostream &os) const override
 		{
-			os << m_item_tag << " IS NOT NULL";
+			os << m_item_name << " IS NOT NULL";
 		}
 
-		std::string m_item_tag;
+		std::string m_item_name;
 		uint16_t m_item_ix = 0;
 	};
 
 	struct key_equals_condition_impl : public condition_impl
 	{
 		key_equals_condition_impl(item &&i)
-			: m_item_tag(i.name())
+			: m_item_name(i.name())
 			, m_value(i.value())
 		{
 		}
@@ -374,7 +383,7 @@ namespace detail
 
 		void str(std::ostream &os) const override
 		{
-			os << m_item_tag << (m_icase ? "^ " : " ") << " == " << m_value;
+			os << m_item_name << (m_icase ? "^ " : " ") << " == " << m_value;
 		}
 
 		virtual std::optional<row_handle> single() const override
@@ -390,13 +399,13 @@ namespace detail
 				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 tags 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_tag == ri->m_item_tag;
+					// 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_tag;
+		std::string m_item_name;
 		uint16_t m_item_ix = 0;
 		bool m_icase = false;
 		std::string m_value;
@@ -406,7 +415,7 @@ namespace detail
 	struct key_equals_or_empty_condition_impl : public condition_impl
 	{
 		key_equals_or_empty_condition_impl(key_equals_condition_impl *equals)
-			: m_item_tag(equals->m_item_tag)
+			: m_item_name(equals->m_item_name)
 			, m_value(equals->m_value)
 			, m_icase(equals->m_icase)
 			, m_single_hit(equals->m_single_hit)
@@ -415,8 +424,8 @@ namespace detail
 
 		condition_impl *prepare(const category &c) override
 		{
-			m_item_ix = get_column_ix(c, m_item_tag);
-			m_icase = is_column_type_uchar(c, m_item_tag);
+			m_item_ix = get_item_ix(c, m_item_name);
+			m_icase = is_item_type_uchar(c, m_item_name);
 			return this;
 		}
 
@@ -432,7 +441,7 @@ namespace detail
 
 		void str(std::ostream &os) const override
 		{
-			os << '(' << m_item_tag << (m_icase ? "^ " : " ") << " == " << m_value << " OR " << m_item_tag << " IS NULL)";
+			os << '(' << m_item_name << (m_icase ? "^ " : " ") << " == " << m_value << " OR " << m_item_name << " IS NULL)";
 		}
 
 		virtual std::optional<row_handle> single() const override
@@ -448,13 +457,13 @@ namespace detail
 				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 tags 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_tag == ri->m_item_tag;
+					// 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_tag;
+		std::string m_item_name;
 		uint16_t m_item_ix = 0;
 		std::string m_value;
 		bool m_icase = false;
@@ -464,8 +473,8 @@ namespace detail
 	struct key_compare_condition_impl : public condition_impl
 	{
 		template <typename COMP>
-		key_compare_condition_impl(const std::string &item_tag, COMP &&comp, const std::string &s)
-			: m_item_tag(item_tag)
+		key_compare_condition_impl(const std::string &item_name, COMP &&comp, const std::string &s)
+			: m_item_name(item_name)
 			, m_compare(std::move(comp))
 			, m_str(s)
 		{
@@ -473,8 +482,8 @@ namespace detail
 
 		condition_impl *prepare(const category &c) override
 		{
-			m_item_ix = get_column_ix(c, m_item_tag);
-			m_icase = is_column_type_uchar(c, m_item_tag);
+			m_item_ix = get_item_ix(c, m_item_name);
+			m_icase = is_item_type_uchar(c, m_item_name);
 			return this;
 		}
 
@@ -485,10 +494,10 @@ namespace detail
 
 		void str(std::ostream &os) const override
 		{
-			os << m_item_tag << (m_icase ? "^ " : " ") << m_str;
+			os << m_item_name << (m_icase ? "^ " : " ") << m_str;
 		}
 
-		std::string m_item_tag;
+		std::string m_item_name;
 		uint16_t m_item_ix = 0;
 		bool m_icase = false;
 		std::function<bool(row_handle, bool)> m_compare;
@@ -497,8 +506,8 @@ namespace detail
 
 	struct key_matches_condition_impl : public condition_impl
 	{
-		key_matches_condition_impl(const std::string &item_tag, const std::regex &rx)
-			: m_item_tag(item_tag)
+		key_matches_condition_impl(const std::string &item_name, const std::regex &rx)
+			: m_item_name(item_name)
 			, m_item_ix(0)
 			, mRx(rx)
 		{
@@ -506,7 +515,7 @@ namespace detail
 
 		condition_impl *prepare(const category &c) override
 		{
-			m_item_ix = get_column_ix(c, m_item_tag);
+			m_item_ix = get_item_ix(c, m_item_name);
 			return this;
 		}
 
@@ -518,10 +527,10 @@ namespace detail
 
 		void str(std::ostream &os) const override
 		{
-			os << m_item_tag << " =~ expression";
+			os << m_item_name << " =~ expression";
 		}
 
-		std::string m_item_tag;
+		std::string m_item_name;
 		uint16_t m_item_ix;
 		std::regex mRx;
 	};
@@ -541,7 +550,7 @@ namespace detail
 			auto &c = r.get_category();
 
 			bool result = false;
-			for (auto &f : get_category_fields(c))
+			for (auto &f : get_category_items(c))
 			{
 				try
 				{
@@ -579,7 +588,7 @@ namespace detail
 			auto &c = r.get_category();
 
 			bool result = false;
-			for (auto &f : get_category_fields(c))
+			for (auto &f : get_category_items(c))
 			{
 				try
 				{
@@ -864,7 +873,7 @@ inline condition operator or(condition &&a, condition &&b)
 			auto ci = static_cast<detail::key_equals_condition_impl *>(a.m_impl);
 			auto ce = static_cast<detail::key_is_empty_condition_impl *>(b.m_impl);
 
-			if (ci->m_item_tag == ce->m_item_tag)
+			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
@@ -873,7 +882,7 @@ inline condition operator or(condition &&a, condition &&b)
 			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);
 
-			if (ci->m_item_tag == ce->m_item_tag)
+			if (ci->m_item_name == ce->m_item_name)
 				return condition(new detail::key_equals_or_empty_condition_impl(ci));
 		}
 
@@ -887,7 +896,7 @@ inline condition operator or(condition &&a, condition &&b)
 }
 
 /**
- * @brief A helper class to make it possible to search for empty fields (NULL)
+ * @brief A helper class to make it possible to search for empty items (NULL)
  * 
  * @code{.cpp}
  * "id"_key == cif::empty_type();
@@ -909,35 +918,45 @@ struct empty_type
 inline constexpr empty_type null = empty_type();
 
 /**
- * @brief Class to use in creating conditions, creates a reference to a field or column
+ * @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 itemTag as name
+	 * @brief Construct a new key object using @a item_name as name
 	 * 
-	 * @param itemTag 
+	 * @param item_name 
 	 */
-	explicit key(const std::string &itemTag)
-		: m_item_tag(itemTag)
+	explicit key(const std::string &item_name)
+		: m_item_name(item_name)
 	{
 	}
 
 	/**
-	 * @brief Construct a new key object using @a itemTag as name
+	 * @brief Construct a new key object using @a item_name as name
 	 * 
-	 * @param itemTag 
+	 * @param item_name 
 	 */
-	explicit key(const char *itemTag)
-		: m_item_tag(itemTag)
+	explicit key(const char *item_name)
+		: m_item_name(item_name)
+	{
+	}
+
+	/**
+	 * @brief Construct a new key object using @a item_name as name
+	 * 
+	 * @param item_name 
+	 */
+	explicit key(std::string_view item_name)
+		: m_item_name(item_name)
 	{
 	}
 
 	key(const key &) = delete;
 	key &operator=(const key &) = delete;
 
-	std::string m_item_tag; ///< The column name
+	std::string m_item_name; ///< The item name
 };
 
 /**
@@ -946,7 +965,7 @@ struct key
 template <typename T>
 condition operator==(const key &key, const T &v)
 {
-	return condition(new detail::key_equals_condition_impl({ key.m_item_tag, v }));
+	return condition(new detail::key_equals_condition_impl({ key.m_item_name, v }));
 }
 
 /**
@@ -955,9 +974,9 @@ condition operator==(const key &key, const T &v)
 inline condition operator==(const key &key, std::string_view value)
 {
 	if (not value.empty())
-		return condition(new detail::key_equals_condition_impl({ key.m_item_tag, value }));
+		return condition(new detail::key_equals_condition_impl({ key.m_item_name, value }));
 	else
-		return condition(new detail::key_is_empty_condition_impl(key.m_item_tag));
+		return condition(new detail::key_is_empty_condition_impl(key.m_item_name));
 }
 
 /**
@@ -987,8 +1006,8 @@ condition operator>(const key &key, const T &v)
 	s << " > " << v;
 
 	return condition(new detail::key_compare_condition_impl(
-		key.m_item_tag, [tag = key.m_item_tag, v](row_handle r, bool icase)
-		{ return r[tag].template compare<T>(v, icase) > 0; },
+		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()));
 }
 
@@ -1002,8 +1021,8 @@ condition operator>=(const key &key, const T &v)
 	s << " >= " << v;
 
 	return condition(new detail::key_compare_condition_impl(
-		key.m_item_tag, [tag = key.m_item_tag, v](row_handle r, bool icase)
-		{ return r[tag].template compare<T>(v, icase) >= 0; },
+		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()));
 }
 
@@ -1017,8 +1036,8 @@ condition operator<(const key &key, const T &v)
 	s << " < " << v;
 
 	return condition(new detail::key_compare_condition_impl(
-		key.m_item_tag, [tag = key.m_item_tag, v](row_handle r, bool icase)
-		{ return r[tag].template compare<T>(v, icase) < 0; },
+		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()));
 }
 
@@ -1032,8 +1051,8 @@ condition operator<=(const key &key, const T &v)
 	s << " <= " << v;
 
 	return condition(new detail::key_compare_condition_impl(
-		key.m_item_tag, [tag = key.m_item_tag, v](row_handle r, bool icase)
-		{ return r[tag].template compare<T>(v, icase) <= 0; },
+		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()));
 }
 
@@ -1042,7 +1061,7 @@ condition operator<=(const key &key, const T &v)
  */
 inline condition operator==(const key &key, const std::regex &rx)
 {
-	return condition(new detail::key_matches_condition_impl(key.m_item_tag, rx));
+	return condition(new detail::key_matches_condition_impl(key.m_item_name, rx));
 }
 
 /**
@@ -1050,7 +1069,7 @@ inline condition operator==(const key &key, const std::regex &rx)
  */
 inline condition operator==(const key &key, const empty_type &)
 {
-	return condition(new detail::key_is_empty_condition_impl(key.m_item_tag));
+	return condition(new detail::key_is_empty_condition_impl(key.m_item_name));
 }
 
 /**
@@ -1058,20 +1077,20 @@ inline condition operator==(const key &key, const empty_type &)
  */
 inline condition operator!=(const key &key, const empty_type &)
 {
-	return condition(new detail::key_is_not_empty_condition_impl(key.m_item_tag));
+	return condition(new detail::key_is_not_empty_condition_impl(key.m_item_name));
 }
 
 /**
- * @brief Create a condition to search any column for a value @a v if @a v contains a value
+ * @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::key_equals_condition_impl({ key.m_item_tag, *v }));
+		return condition(new detail::key_equals_condition_impl({ key.m_item_name, *v }));
 	else
-		return condition(new detail::key_is_empty_condition_impl(key.m_item_tag));
+		return condition(new detail::key_is_empty_condition_impl(key.m_item_name));
 }
 
 /**
@@ -1089,12 +1108,12 @@ struct any_type
 /** @endcond */
 
 /**
- * @brief A helper for any field constructs
+ * @brief A helper for any item constructs
  */
 inline constexpr any_type any = any_type{};
 
 /**
- * @brief Create a condition to search any column for a value @a v
+ * @brief Create a condition to search any item for a value @a v
  */
 template <typename T>
 condition operator==(const any_type &, const T &v)
@@ -1103,7 +1122,7 @@ condition operator==(const any_type &, const T &v)
 }
 
 /**
- * @brief Create a condition to search any column for a regular expression @a rx
+ * @brief Create a condition to search any item for a regular expression @a rx
  */
 inline condition operator==(const any_type &, const std::regex &rx)
 {
@@ -1121,9 +1140,9 @@ inline condition all()
 namespace literals
 {
 	/**
-	 * @brief Return a cif::key for the column name @a text
+	 * @brief Return a cif::key for the item name @a text
 	 * 
-	 * @param text The name of the column
+	 * @param text The name of the item
 	 * @param length The length of @a text
 	 * @return key The cif::key created
 	 */

include/cif++/datablock.hpp

@@ -106,6 +106,15 @@ class datablock : public std::list<category>
 	 */
 	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
@@ -169,7 +178,16 @@ class datablock : public std::list<category>
 	/**
 	 * @brief Get the preferred order of the categories when writing them
 	 */
-	std::vector<std::string> get_tag_order() const;
+	[[deprecated("use get_item_order instead")]]
+	std::vector<std::string> get_tag_order() const
+	{
+		return get_item_order();
+	}
+
+	/**
+	 * @brief Get the preferred order of the categories when writing them
+	 */
+	std::vector<std::string> get_item_order() const;
 
 	/**
 	 * @brief Write out the contents to @a os
@@ -177,9 +195,9 @@ class datablock : public std::list<category>
 	void write(std::ostream &os) const;
 
 	/**
-	 * @brief Write out the contents to @a os using the order defined in @a tag_order
+	 * @brief Write out the contents to @a os using the order defined in @a item_name_order
 	 */
-	void write(std::ostream &os, const std::vector<std::string> &tag_order);
+	void write(std::ostream &os, const std::vector<std::string> &item_name_order);
 
 	/**
 	 * @brief Friend operator<< to write datablock @a db to std::ostream @a os

include/cif++/item.hpp

@@ -44,7 +44,7 @@
 /** \file item.hpp
  *
  * This file contains the declaration of item but also the item_value and item_handle
- * These handle the storage of and access to the data for a single data field.
+ * These handle the storage of and access to the data for a single data item.
  */
 
 namespace cif
@@ -227,10 +227,10 @@ class item
 	/// \brief empty means either null or unknown
 	bool empty() const { return m_value.empty(); }
 
-	/// \brief returns true if the field contains '.'
+	/// \brief returns true if the item contains '.'
 	bool is_null() const { return m_value == "."; }
 
-	/// \brief returns true if the field contains '?'
+	/// \brief returns true if the item contains '?'
 	bool is_unknown() const { return m_value == "?"; }
 
 	/// \brief the length of the value string
@@ -464,14 +464,14 @@ struct item_handle
 	/** Easy way to test for an empty item */
 	explicit operator bool() const { return not empty(); }
 
-	/// is_null return true if the field contains '.'
+	/// is_null return true if the item contains '.'
 	bool is_null() const
 	{
 		auto txt = text();
 		return txt.length() == 1 and txt.front() == '.';
 	}
 
-	/// is_unknown returns true if the field contains '?'
+	/// is_unknown returns true if the item contains '?'
 	bool is_unknown() const
 	{
 		auto txt = text();
@@ -484,11 +484,11 @@ struct item_handle
 	/**
 	 * @brief Construct a new item handle object
 	 *
-	 * @param column Column index
+	 * @param item Item index
 	 * @param row Reference to the row
 	 */
-	item_handle(uint16_t column, row_handle &row)
-		: m_column(column)
+	item_handle(uint16_t item, row_handle &row)
+		: m_item_ix(item)
 		, m_row_handle(row)
 	{
 	}
@@ -505,7 +505,7 @@ struct item_handle
   private:
 	item_handle();
 
-	uint16_t m_column;
+	uint16_t m_item_ix;
 	row_handle &m_row_handle;
 
 	void assign_value(const item &value);
@@ -556,7 +556,7 @@ struct item_handle::item_value_as<T, std::enable_if_t<std::is_arithmetic_v<T> an
 
 		auto txt = ref.text();
 
-		if (txt.empty())
+		if (ref.empty())
 			result = 1;
 		else
 		{

include/cif++/iterator.hpp

@@ -90,7 +90,7 @@ class iterator_impl
 		: m_category(rhs.m_category)
 		, m_current(rhs.m_current)
 		, m_value(rhs.m_value)
-		, m_column_ix(rhs.m_column_ix)
+		, m_item_ix(rhs.m_item_ix)
 	{
 	}
 
@@ -99,7 +99,7 @@ class iterator_impl
 		: m_category(rhs.m_category)
 		, m_current(const_cast<row_type *>(rhs.m_current))
 		, m_value(rhs.m_value)
-		, m_column_ix(rhs.m_column_ix)
+		, m_item_ix(rhs.m_item_ix)
 	{
 		m_value = get(std::make_index_sequence<N>());
 	}
@@ -108,7 +108,7 @@ class iterator_impl
 	iterator_impl(const iterator_impl<IRowType> &rhs, const std::array<uint16_t, N> &cix)
 		: m_category(rhs.m_category)
 		, m_current(rhs.m_current)
-		, m_column_ix(cix)
+		, m_item_ix(cix)
 	{
 		m_value = get(std::make_index_sequence<N>());
 	}
@@ -117,7 +117,7 @@ class iterator_impl
 	{
 		m_category = i.m_category;
 		m_current = i.m_current;
-		m_column_ix = i.m_column_ix;
+		m_item_ix = i.m_item_ix;
 		m_value = i.m_value;
 		return *this;
 	}
@@ -185,7 +185,7 @@ class iterator_impl
 		if (m_current != nullptr)
 		{
 			row_handle rh{ *m_category, *m_current };
-			return tuple_type{ rh[m_column_ix[Is]].template as<Ts>()... };
+			return tuple_type{ rh[m_item_ix[Is]].template as<Ts>()... };
 		}
 
 		return {};
@@ -194,7 +194,7 @@ class iterator_impl
 	category_type *m_category = nullptr;
 	row_type *m_current = nullptr;
 	value_type m_value;
-	std::array<uint16_t, N> m_column_ix;
+	std::array<uint16_t, N> m_item_ix;
 };
 
 /**
@@ -348,7 +348,7 @@ class iterator_impl<Category, T>
 		: m_category(rhs.m_category)
 		, m_current(rhs.m_current)
 		, m_value(rhs.m_value)
-		, m_column_ix(rhs.m_column_ix)
+		, m_item_ix(rhs.m_item_ix)
 	{
 	}
 
@@ -357,7 +357,7 @@ class iterator_impl<Category, T>
 		: m_category(rhs.m_category)
 		, m_current(const_cast<row_type *>(rhs.m_current))
 		, m_value(rhs.m_value)
-		, m_column_ix(rhs.m_column_ix)
+		, m_item_ix(rhs.m_item_ix)
 	{
 		m_value = get(m_current);
 	}
@@ -366,7 +366,7 @@ class iterator_impl<Category, T>
 	iterator_impl(const iterator_impl<IRowType> &rhs, const std::array<uint16_t, 1> &cix)
 		: m_category(rhs.m_category)
 		, m_current(rhs.m_current)
-		, m_column_ix(cix[0])
+		, m_item_ix(cix[0])
 	{
 		m_value = get();
 	}
@@ -375,7 +375,7 @@ class iterator_impl<Category, T>
 	{
 		m_category = i.m_category;
 		m_current = i.m_current;
-		m_column_ix = i.m_column_ix;
+		m_item_ix = i.m_item_ix;
 		m_value = i.m_value;
 		return *this;
 	}
@@ -442,7 +442,7 @@ class iterator_impl<Category, T>
 		if (m_current != nullptr)
 		{
 			row_handle rh{ *m_category, *m_current };
-			return rh[m_column_ix].template as<T>();
+			return rh[m_item_ix].template as<T>();
 		}
 
 		return {};
@@ -451,7 +451,7 @@ class iterator_impl<Category, T>
 	category_type *m_category = nullptr;
 	row_type *m_current = nullptr;
 	value_type m_value;
-	uint16_t m_column_ix;
+	uint16_t m_item_ix;
 };
 
 // --------------------------------------------------------------------
@@ -482,8 +482,8 @@ class iterator_proxy
 	using iterator = iterator_impl<category_type, Ts...>;
 	using row_iterator = iterator_impl<category_type>;
 
-	iterator_proxy(category_type &cat, row_iterator pos, char const *const columns[N]);
-	iterator_proxy(category_type &cat, row_iterator pos, std::initializer_list<char const *> columns);
+	iterator_proxy(category_type &cat, row_iterator pos, char const *const items[N]);
+	iterator_proxy(category_type &cat, row_iterator pos, std::initializer_list<char const *> items);
 
 	iterator_proxy(iterator_proxy &&p);
 	iterator_proxy &operator=(iterator_proxy &&p);
@@ -492,8 +492,8 @@ class iterator_proxy
 	iterator_proxy &operator=(const iterator_proxy &) = delete;
 	/** @endcond */
 
-	iterator begin() const { return iterator(m_begin, m_column_ix); } ///< Return the iterator pointing to the first row
-	iterator end() const { return iterator(m_end, m_column_ix); }     ///< Return the iterator pointing past the last row
+	iterator begin() const { return iterator(m_begin, m_item_ix); } ///< Return the iterator pointing to the first row
+	iterator end() const { return iterator(m_end, m_item_ix); }     ///< Return the iterator pointing past the last row
 
 	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
@@ -510,13 +510,13 @@ class iterator_proxy
 		std::swap(m_category, rhs.m_category);
 		std::swap(m_begin, rhs.m_begin);
 		std::swap(m_end, rhs.m_end);
-		std::swap(m_column_ix, rhs.m_column_ix);
+		std::swap(m_item_ix, rhs.m_item_ix);
 	}
 
   private:
 	category_type *m_category;
 	row_iterator m_begin, m_end;
-	std::array<uint16_t, N> m_column_ix;
+	std::array<uint16_t, N> m_item_ix;
 };
 
 // --------------------------------------------------------------------
@@ -562,22 +562,23 @@ class conditional_iterator_proxy
 
 		reference operator*()
 		{
-			return *mBegin;
+			return *m_begin;
 		}
 
 		pointer operator->()
 		{
-			return &*mBegin;
+			m_current = *m_begin;
+			return &m_current;
 		}
 
 		conditional_iterator_impl &operator++()
 		{
-			while (mBegin != mEnd)
+			while (m_begin != m_end)
 			{
-				if (++mBegin == mEnd)
+				if (++m_begin == m_end)
 					break;
 				
-				if (m_condition->operator()(mBegin))
+				if (m_condition->operator()(m_begin))
 					break;
 			}
 
@@ -591,18 +592,22 @@ class conditional_iterator_proxy
 			return result;
 		}
 
-		bool operator==(const conditional_iterator_impl &rhs) const { return mBegin == rhs.mBegin; }
-		bool operator!=(const conditional_iterator_impl &rhs) const { return mBegin != rhs.mBegin; }
+		bool operator==(const conditional_iterator_impl &rhs) const { return m_begin == rhs.m_begin; }
+		bool operator!=(const conditional_iterator_impl &rhs) const { return m_begin != rhs.m_begin; }
+
+		bool operator==(const row_iterator &rhs) const { return m_begin == rhs; }
+		bool operator!=(const row_iterator &rhs) const { return m_begin != rhs; }
 
 		template <typename IRowType, typename... ITs>
-		bool operator==(const iterator_impl<IRowType, ITs...> &rhs) const { return mBegin == rhs; }
+		bool operator==(const iterator_impl<IRowType, ITs...> &rhs) const { return m_begin == rhs; }
 
 		template <typename IRowType, typename... ITs>
-		bool operator!=(const iterator_impl<IRowType, ITs...> &rhs) const { return mBegin != rhs; }
+		bool operator!=(const iterator_impl<IRowType, ITs...> &rhs) const { return m_begin != rhs; }
 
 	  private:
-		CategoryType *mCat;
-		base_iterator mBegin, mEnd;
+		CategoryType *m_cat;
+		base_iterator m_begin, m_end;
+		value_type m_current;
 		const condition *m_condition;
 	};
 
@@ -646,26 +651,26 @@ class conditional_iterator_proxy
 
 /** @cond */
 template <typename Category, typename... Ts>
-iterator_proxy<Category, Ts...>::iterator_proxy(Category &cat, row_iterator pos, char const *const columns[N])
+iterator_proxy<Category, Ts...>::iterator_proxy(Category &cat, row_iterator pos, char const *const items[N])
 	: m_category(&cat)
 	, m_begin(pos)
 	, m_end(cat.end())
 {
 	for (uint16_t i = 0; i < N; ++i)
-		m_column_ix[i] = m_category->get_column_ix(columns[i]);
+		m_item_ix[i] = m_category->get_item_ix(items[i]);
 }
 
 template <typename Category, typename... Ts>
-iterator_proxy<Category, Ts...>::iterator_proxy(Category &cat, row_iterator pos, std::initializer_list<char const *> columns)
+iterator_proxy<Category, Ts...>::iterator_proxy(Category &cat, row_iterator pos, std::initializer_list<char const *> items)
 	: m_category(&cat)
 	, m_begin(pos)
 	, m_end(cat.end())
 {
-	// static_assert(columns.size() == N, "The list of column names should be exactly the same as the list of requested columns");
+	// static_assert(items.size() == N, "The list of item names should be exactly the same as the list of requested items");
 
 	std::uint16_t i = 0;
-	for (auto column : columns)
-		m_column_ix[i++] = m_category->get_column_ix(column);
+	for (auto item : items)
+		m_item_ix[i++] = m_category->get_item_ix(item);
 }
 
 // --------------------------------------------------------------------
@@ -673,13 +678,13 @@ iterator_proxy<Category, Ts...>::iterator_proxy(Category &cat, row_iterator pos,
 template <typename Category, typename... Ts>
 conditional_iterator_proxy<Category, Ts...>::conditional_iterator_impl::conditional_iterator_impl(
 	Category &cat, row_iterator pos, const condition &cond, const std::array<uint16_t, N> &cix)
-	: mCat(&cat)
-	, mBegin(pos, cix)
-	, mEnd(cat.end(), cix)
+	: m_cat(&cat)
+	, m_begin(pos, cix)
+	, m_end(cat.end(), cix)
 	, m_condition(&cond)
 {
 	if (m_condition == nullptr or m_condition->empty())
-		mBegin = mEnd;
+		m_begin = m_end;
 }
 
 template <typename Category, typename... Ts>
@@ -702,7 +707,7 @@ conditional_iterator_proxy<Category, Ts...>::conditional_iterator_proxy(Category
 	, mCBegin(pos)
 	, mCEnd(cat.end())
 {
-	static_assert(sizeof...(Ts) == sizeof...(Ns), "Number of column names should be equal to number of requested value types");
+	static_assert(sizeof...(Ts) == sizeof...(Ns), "Number of item names should be equal to number of requested value types");
 
 	if (m_condition)
 	{
@@ -715,7 +720,7 @@ conditional_iterator_proxy<Category, Ts...>::conditional_iterator_proxy(Category
 		mCBegin = mCEnd;
 
 	uint16_t i = 0;
-	((mCix[i++] = m_cat->get_column_ix(names)), ...);
+	((mCix[i++] = m_cat->get_item_ix(names)), ...);
 }
 
 template <typename Category, typename... Ts>

include/cif++/model.hpp

@@ -72,7 +72,7 @@ class structure;
  *
  * The class atom is a kind of flyweight class. It can be copied
  * with low overhead. All data is stored in the underlying mmCIF
- * categories but some very often used fields are cached in the
+ * categories but some very often used items are cached in the
  * impl.
  *
  * It is also possible to have symmetry copies of atoms. They
@@ -207,7 +207,7 @@ class atom
 	/// \brief Copy assignement operator
 	atom &operator=(const atom &rhs) = default;
 
-	/// \brief Return the field named @a name in the _atom_site category for this atom
+	/// \brief Return the item named @a name in the _atom_site category for this atom
 	std::string get_property(std::string_view name) const
 	{
 		if (not m_impl)
@@ -215,7 +215,7 @@ class atom
 		return m_impl->get_property(name);
 	}
 
-	/// \brief Return the field named @a name in the _atom_site category for this atom cast to an int
+	/// \brief Return the item named @a name in the _atom_site category for this atom cast to an int
 	int get_property_int(std::string_view name) const
 	{
 		if (not m_impl)
@@ -223,7 +223,7 @@ class atom
 		return m_impl->get_property_int(name);
 	}
 
-	/// \brief Return the field named @a name in the _atom_site category for this atom cast to a float
+	/// \brief Return the item named @a name in the _atom_site category for this atom cast to a float
 	float get_property_float(std::string_view name) const
 	{
 		if (not m_impl)
@@ -231,7 +231,7 @@ class atom
 		return m_impl->get_property_float(name);
 	}
 
-	/// \brief Set value for the field named @a name in the _atom_site category to @a value
+	/// \brief Set value for the item named @a name in the _atom_site category to @a value
 	void set_property(const std::string_view name, const std::string &value)
 	{
 		if (not m_impl)
@@ -239,7 +239,7 @@ class atom
 		m_impl->set_property(name, value);
 	}
 
-	/// \brief Set value for the field named @a name in the _atom_site category to @a value
+	/// \brief Set value for the item named @a name in the _atom_site category to @a value
 	template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0>
 	void set_property(const std::string_view name, const T &value)
 	{
@@ -730,7 +730,7 @@ class sugar : public residue
 	/**
 	 * @brief Return the sugar number in the glycosylation tree
 	 *
-	 * To store the sugar number, the auth_seq_id field has been overloaded
+	 * To store the sugar number, the auth_seq_id item has been overloaded
 	 * in the specification. But since a sugar number should be, ehm, a number
 	 * and auth_seq_id is specified to contain a string, we do a check here
 	 * to see if it really is a number.
@@ -1115,11 +1115,4 @@ class structure
 	std::vector<residue> m_non_polymers;
 };
 
-// --------------------------------------------------------------------
-
-/// \brief Reconstruct all missing categories for an assumed PDBx file.
-/// Some people believe that simply dumping some atom records is enough.
-/// \param db The cif::datablock that hopefully contains some valid data
-void reconstruct_pdbx(datablock &db);
-
 } // namespace cif::mm

include/cif++/parser.hpp

@@ -143,9 +143,9 @@ class sac_parser
 
 	enum class CIFToken
 	{
-		Unknown,
+		UNKNOWN,
 
-		Eof,
+		END_OF_FILE,
 
 		DATA,
 		LOOP,
@@ -153,24 +153,24 @@ class sac_parser
 		SAVE_,
 		SAVE_NAME,
 		STOP,
-		Tag,
-		Value
+		ITEM_NAME,
+		VALUE
 	};
 
 	static constexpr const char *get_token_name(CIFToken token)
 	{
 		switch (token)
 		{
-			case CIFToken::Unknown: return "Unknown";
-			case CIFToken::Eof: return "Eof";
+			case CIFToken::UNKNOWN: return "Unknown";
+			case CIFToken::END_OF_FILE: return "Eof";
 			case CIFToken::DATA: return "DATA";
 			case CIFToken::LOOP: return "LOOP";
 			case CIFToken::GLOBAL: return "GLOBAL";
 			case CIFToken::SAVE_: return "SAVE";
 			case CIFToken::SAVE_NAME: return "SAVE+name";
 			case CIFToken::STOP: return "STOP";
-			case CIFToken::Tag: return "Tag";
-			case CIFToken::Value: return "Value";
+			case CIFToken::ITEM_NAME: return "Tag";
+			case CIFToken::VALUE: return "Value";
 			default: return "Invalid token parameter";
 		}
 	}
@@ -267,9 +267,9 @@ class sac_parser
 		QuotedString,
 		QuotedStringQuote,
 		UnquotedString,
-		Tag,
-		TextField,
-		TextFieldNL,
+		ItemName,
+		TextItem,
+		TextItemNL,
 		Reserved,
 		Value
 	};

include/cif++/pdb.hpp

@@ -1,17 +1,17 @@
 /*-
  * SPDX-License-Identifier: BSD-2-Clause
- * 
+ *
  * Copyright (c) 2023 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
@@ -28,15 +28,17 @@
 
 #include "cif++/file.hpp"
 
+#include <system_error>
+
 /**
  * @file pdb.hpp
- * 
+ *
  * This file presents the API to read and write files in the
  * legacy and ancient PDB format.
- * 
+ *
  * The code works on the basis of best effort since it is
  * impossible to have correct round trip fidelity.
- * 
+ *
  */
 
 namespace cif::pdb
@@ -81,7 +83,7 @@ inline void write(std::ostream &os, const file &f)
 /** @brief Write out the data in @a db to file @a file
  * in legacy PDB format or mmCIF format, depending on the
  * filename extension.
- * 
+ *
  * If extension of @a file is *.gz* the resulting file will
  * be written in gzip compressed format.
  */
@@ -90,7 +92,7 @@ void write(const std::filesystem::path &file, const datablock &db);
 /** @brief Write out the data in @a f to file @a file
  * in legacy PDB format or mmCIF format, depending on the
  * filename extension.
- * 
+ *
  * If extension of @a file is *.gz* the resulting file will
  * be written in gzip compressed format.
  */
@@ -99,6 +101,74 @@ inline void write(const std::filesystem::path &p, const file &f)
 	write(p, f.front());
 }
 
+// --------------------------------------------------------------------
+
+/** \brief Reconstruct all missing categories for an assumed PDBx file.
+ *
+ * Some people believe that simply dumping some atom records is enough.
+ *
+ * \param file The cif::file that hopefully contains some valid data
+ * \param dictionary The mmcif dictionary to use
+ * \result Returns true if the resulting file is valid
+ */
+
+bool reconstruct_pdbx(file &pdbx_file, std::string_view dictionary = "mmcif_pdbx");
+
+/** \brief This is an extension to cif::validator, use the logic in common
+ * PDBx files to see if the file is internally consistent.
+ *
+ * This function for now checks if the following categories are consistent:
+ *
+ * atom_site -> pdbx_poly_seq_scheme -> entity_poly_seq -> entity_poly -> entity
+ *
+ * Use the common \ref cif::VERBOSE flag to turn on diagnostic messages.
+ * 
+ * This function throws a std::system_error in case of an error
+ *
+ * \param file The input file
+ * \param dictionary The mmcif dictionary 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");
+
+/** \brief This is an extension to cif::validator, use the logic in common
+ * PDBx files to see if the file is internally consistent.
+ *
+ * This function for now checks if the following categories are consistent:
+ *
+ * atom_site -> pdbx_poly_seq_scheme -> entity_poly_seq -> entity_poly -> entity
+ *
+ * Use the common \ref cif::VERBOSE flag to turn on diagnostic messages.
+ * 
+ * The dictionary is assumed to be specified in the file or to be the
+ * 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
+ */
+
+bool is_valid_pdbx_file(const file &pdbx_file, std::error_code &ec);
+
+/** \brief This is an extension to cif::validator, use the logic in common
+ * PDBx files to see if the file is internally consistent.
+ *
+ * This function for now checks if the following categories are consistent:
+ *
+ * atom_site -> pdbx_poly_seq_scheme -> entity_poly_seq -> entity_poly -> entity
+ *
+ * Use the common \ref cif::VERBOSE flag to turn on diagnostic messages.
+ * 
+ * \param file The input file
+ * \param dictionary The dictionary 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,
+	std::error_code &ec);
+
 // --------------------------------------------------------------------
 // Other I/O related routines
 
@@ -106,7 +176,7 @@ inline void write(const std::filesystem::path &p, const file &f)
  *
  * The line returned should be compatible with the legacy PDB
  * format and is e.g. used in the DSSP program.
- * 
+ *
  * @param data The datablock to use as source for the requested data
  * @param truncate_at The maximum length of the line returned
  */
@@ -116,7 +186,7 @@ std::string get_HEADER_line(const datablock &data, std::string::size_type trunca
  *
  * The line returned should be compatible with the legacy PDB
  * format and is e.g. used in the DSSP program.
- * 
+ *
  * @param data The datablock to use as source for the requested data
  * @param truncate_at The maximum length of the line returned
  */
@@ -126,7 +196,7 @@ std::string get_COMPND_line(const datablock &data, std::string::size_type trunca
  *
  * The line returned should be compatible with the legacy PDB
  * format and is e.g. used in the DSSP program.
- * 
+ *
  * @param data The datablock to use as source for the requested data
  * @param truncate_at The maximum length of the line returned
  */
@@ -136,12 +206,11 @@ std::string get_SOURCE_line(const datablock &data, std::string::size_type trunca
  *
  * The line returned should be compatible with the legacy PDB
  * format and is e.g. used in the DSSP program.
- * 
+ *
  * @param data The datablock to use as source for the requested data
  * @param truncate_at The maximum length of the line returned
  */
 
 std::string get_AUTHOR_line(const datablock &data, std::string::size_type truncate_at = 127);
 
-} // namespace pdbx
-
+} // namespace cif::pdb

include/cif++/point.hpp

@@ -35,7 +35,10 @@
 
 #if __has_include(<clipper/core/coords.h>)
 #define HAVE_LIBCLIPPER 1
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wignored-qualifiers"
 #include <clipper/core/coords.h>
+#pragma GCC diagnostic pop
 #endif
 
 /** \file point.hpp

include/cif++/row.hpp

@@ -51,7 +51,7 @@
  * std::string name = rh["label_atom_id"].as<std::string>();
  * 
  * // by index:
- * uint16_t ix = atom_site.get_column_ix("label_atom_id");
+ * uint16_t ix = atom_site.get_item_ix("label_atom_id");
  * assert(rh[ix].as<std::string() == name);
  * @endcode
  * 
@@ -87,15 +87,15 @@ namespace detail
 	{
 		static constexpr size_t N = sizeof...(C);
 
-		get_row_result(const row_handle &r, std::array<uint16_t, N> &&columns)
+		get_row_result(const row_handle &r, std::array<uint16_t, N> &&items)
 			: m_row(r)
-			, m_columns(std::move(columns))
+			, m_items(std::move(items))
 		{
 		}
 
 		const item_handle operator[](uint16_t ix) const
 		{
-			return m_row[m_columns[ix]];
+			return m_row[m_items[ix]];
 		}
 
 		template <typename... Ts, std::enable_if_t<N == sizeof...(Ts), int> = 0>
@@ -107,11 +107,11 @@ namespace detail
 		template <typename... Ts, size_t... Is>
 		std::tuple<Ts...> get(std::index_sequence<Is...>) const
 		{
-			return std::tuple<Ts...>{ m_row[m_columns[Is]].template as<Ts>()... };
+			return std::tuple<Ts...>{ m_row[m_items[Is]].template as<Ts>()... };
 		}
 
 		const row_handle &m_row;
-		std::array<uint16_t, N> m_columns;
+		std::array<uint16_t, N> m_items;
 	};
 
 	// we want to be able to tie some variables to a get_row_result, for this we use tiewraps
@@ -244,63 +244,70 @@ class row_handle
 		return not empty();
 	}
 
-	/// \brief return a cif::item_handle to the item in column @a column_ix
-	item_handle operator[](uint16_t column_ix)
+	/// \brief return a cif::item_handle to the item in item @a item_ix
+	item_handle operator[](uint16_t item_ix)
 	{
-		return empty() ? item_handle::s_null_item : item_handle(column_ix, *this);
+		return empty() ? item_handle::s_null_item : item_handle(item_ix, *this);
 	}
 
-	/// \brief return a const cif::item_handle to the item in column @a column_ix
-	const item_handle operator[](uint16_t column_ix) const
+	/// \brief return a const cif::item_handle to the item in item @a item_ix
+	const item_handle operator[](uint16_t item_ix) const
 	{
-		return empty() ? item_handle::s_null_item : item_handle(column_ix, const_cast<row_handle &>(*this));
+		return empty() ? item_handle::s_null_item : item_handle(item_ix, const_cast<row_handle &>(*this));
 	}
 
-	/// \brief return a cif::item_handle to the item in the column named @a column_name
-	item_handle operator[](std::string_view column_name)
+	/// \brief return a cif::item_handle to the item in the item named @a item_name
+	item_handle operator[](std::string_view item_name)
 	{
-		return empty() ? item_handle::s_null_item : item_handle(add_column(column_name), *this);
+		return empty() ? item_handle::s_null_item : item_handle(add_item(item_name), *this);
 	}
 
-	/// \brief return a const cif::item_handle to the item in the column named @a column_name
-	const item_handle operator[](std::string_view column_name) const
+	/// \brief return a const cif::item_handle to the item in the item named @a item_name
+	const item_handle operator[](std::string_view item_name) const
 	{
-		return empty() ? item_handle::s_null_item : item_handle(get_column_ix(column_name), const_cast<row_handle &>(*this));
+		return empty() ? item_handle::s_null_item : item_handle(get_item_ix(item_name), const_cast<row_handle &>(*this));
 	}
 
 	/// \brief Return an object that can be used in combination with cif::tie
-	/// to assign the values for the columns @a columns
+	/// to assign the values for the items @a items
 	template <typename... C>
-	auto get(C... columns) const
+	auto get(C... items) const
 	{
-		return detail::get_row_result<C...>(*this, { get_column_ix(columns)... });
+		return detail::get_row_result<C...>(*this, { get_item_ix(items)... });
 	}
 
-	/// \brief Return a tuple of values of types @a Ts for the columns @a columns
+	/// \brief Return a tuple of values of types @a Ts for the items @a items
 	template <typename... Ts, typename... C, std::enable_if_t<sizeof...(Ts) == sizeof...(C) and sizeof...(C) != 1, int> = 0>
-	std::tuple<Ts...> get(C... columns) const
+	std::tuple<Ts...> get(C... items) const
 	{
-		return detail::get_row_result<Ts...>(*this, { get_column_ix(columns)... });
+		return detail::get_row_result<Ts...>(*this, { get_item_ix(items)... });
 	}
 
-	/// \brief Get the value of column @a column cast to type @a T
+	/// \brief Get the value of item @a item cast to type @a T
 	template <typename T>
-	T get(const char *column) const
+	T get(const char *item) const
 	{
-		return operator[](get_column_ix(column)).template as<T>();
+		return operator[](get_item_ix(item)).template as<T>();
 	}
 
-	/// \brief assign each of the columns named in @a values to their respective value
+	/// \brief Get the value of item @a item cast to type @a T
+	template <typename T>
+	T get(std::string_view item) const
+	{
+		return operator[](get_item_ix(item)).template as<T>();
+	}
+
+	/// \brief assign each of the items named in @a values to their respective value
 	void assign(const std::vector<item> &values)
 	{
 		for (auto &value : values)
 			assign(value, true);
 	}
 
-	/** \brief assign the value @a value to the column named @a name 
+	/** \brief assign the value @a value to the item named @a name 
 	 * 
 	 * If updateLinked it true, linked records are updated as well.
-	 * That means that if column @a name is part of the link definition
+	 * That means that if item @a name is part of the link definition
 	 * and the link results in a linked record in another category
 	 * this record in the linked category is updated as well.
 	 * 
@@ -310,13 +317,13 @@ class row_handle
 
 	void assign(std::string_view name, std::string_view value, bool updateLinked, bool validate = true)
 	{
-		assign(add_column(name), value, updateLinked, validate);
+		assign(add_item(name), value, updateLinked, validate);
 	}
 
-	/** \brief assign the value @a value to column at index @a column
+	/** \brief assign the value @a value to item at index @a item
 	 * 
 	 * If updateLinked it true, linked records are updated as well.
-	 * That means that if column @a column is part of the link definition
+	 * That means that if item @a item is part of the link definition
 	 * and the link results in a linked record in another category
 	 * this record in the linked category is updated as well.
 	 * 
@@ -324,7 +331,7 @@ class row_handle
 	 * checked to see if it conforms to the rules defined in the dictionary
 	 */
 
-	void assign(uint16_t column, std::string_view value, bool updateLinked, bool validate = true);
+	void assign(uint16_t item, std::string_view value, bool updateLinked, bool validate = true);
 
 	/// \brief compare two rows
 	bool operator==(const row_handle &rhs) const { return m_category == rhs.m_category and m_row == rhs.m_row; }
@@ -333,10 +340,10 @@ class row_handle
 	bool operator!=(const row_handle &rhs) const { return m_category != rhs.m_category or m_row != rhs.m_row; }
 
   private:
-	uint16_t get_column_ix(std::string_view name) const;
-	std::string_view get_column_name(uint16_t ix) const;
+	uint16_t get_item_ix(std::string_view name) const;
+	std::string_view get_item_name(uint16_t ix) const;
 
-	uint16_t add_column(std::string_view name);
+	uint16_t add_item(std::string_view name);
 
 	row *get_row()
 	{
@@ -353,7 +360,7 @@ class row_handle
 		assign(i.name(), i.value(), updateLinked);
 	}
 
-	void swap(uint16_t column, row_handle &r);
+	void swap(uint16_t item, row_handle &r);
 
 	category *m_category = nullptr;
 	row *m_row = nullptr;

include/cif++/text.hpp

@@ -317,7 +317,7 @@ inline char tolower(int ch)
 
 // --------------------------------------------------------------------
 
-/** \brief return a tuple consisting of the category and item name for @a tag
+/** \brief return a tuple consisting of the category and item name for @a item_name
  *
  * The category name is stripped of its leading underscore character.
  *
@@ -325,7 +325,19 @@ inline char tolower(int ch)
  * cif 1.0 formatted data.
  */
 
-std::tuple<std::string, std::string> split_tag_name(std::string_view tag);
+[[deprecated("use split_item_name instead")]]
+std::tuple<std::string, std::string> split_tag_name(std::string_view item_name);
+
+
+/** \brief return a tuple consisting of the category and item name for @a item_name
+ *
+ * The category name is stripped of its leading underscore character.
+ *
+ * If no dot character was found, the category name is empty. That's for
+ * cif 1.0 formatted data.
+ */
+
+std::tuple<std::string, std::string> split_item_name(std::string_view item_name);
 
 // --------------------------------------------------------------------
 

include/cif++/validate.hpp

@@ -28,9 +28,11 @@
 
 #include "cif++/text.hpp"
 
+#include <cassert>
 #include <filesystem>
 #include <list>
 #include <mutex>
+#include <system_error>
 #include <utility>
 
 /**
@@ -49,27 +51,148 @@ namespace cif
 struct category_validator;
 
 // --------------------------------------------------------------------
+// New: error_code
 
 /**
- * @brief The exception thrown when a validation error occurs
+ * @enum validation_error
+ *
+ * @brief A stronly typed class containing the error codes reported by @ref cif::validator and friends
+ */
+enum class validation_error
+{
+	value_does_not_match_rx = 1,      /**< The value of an item does not conform to the regular expression specified for it */
+	value_is_not_in_enumeration_list, /**< The value of an item is not in the list of values allowed */
+	not_a_known_primitive_type,       /**< The type is not a known primitive type */
+	undefined_category,               /**< Category has no definition in the dictionary */
+	unknown_item,                     /**< The item is not defined to be part of the category */
+	incorrect_item_validator,         /**< Incorrectly specified validator for item */
+	missing_mandatory_items,          /**< Missing mandatory items */
+	missing_key_items,                /**< An index could not be constructed due to missing key items */
+	item_not_allowed_in_category,     /**< Requested item allowed in category according to dictionary */
+	empty_file,                       /**< The file contains no datablocks */
+	empty_datablock,                  /**< The datablock contains no categories */
+	empty_category,                   /**< The category is empty */
+	not_valid_pdbx,                   /**< The file is not a valid PDBx file */
+};
+/**
+ * @brief The implementation for @ref validation_category error messages
  *
  */
-class validation_error : public std::exception
+class validation_category_impl : public std::error_category
 {
   public:
-	/// @brief Constructor
-	validation_error(const std::string &msg);
+	/**
+	 * @brief User friendly name
+	 *
+	 * @return const char*
+	 */
 
-	/// @brief Constructor
-	validation_error(const std::string &cat, const std::string &item,
-		const std::string &msg);
+	const char *name() const noexcept override
+	{
+		return "cif::validation";
+	}
 
-	/// @brief The description of the error
-	const char *what() const noexcept { return m_msg.c_str(); }
+	/**
+	 * @brief Provide the error message as a string for the error code @a ev
+	 *
+	 * @param ev The error code
+	 * @return std::string
+	 */
 
-	/// @cond
-	std::string m_msg;
-	/// @endcond
+	std::string message(int ev) const override
+	{
+		switch (static_cast<validation_error>(ev))
+		{
+			case validation_error::value_does_not_match_rx:
+				return "Value in item does not match regular expression";
+			case validation_error::value_is_not_in_enumeration_list:
+				return "Value is not in the enumerated list of valid values";
+			case validation_error::not_a_known_primitive_type:
+				return "The type is not a known primitive type";
+			case validation_error::undefined_category:
+				return "Category has no definition in the dictionary";
+			case validation_error::unknown_item:
+				return "Item is not defined to be part of the category";
+			case validation_error::incorrect_item_validator:
+				return "Incorrectly specified validator for item";
+			case validation_error::missing_mandatory_items:
+				return "Missing mandatory items";
+			case validation_error::missing_key_items:
+				return "An index could not be constructed due to missing key items";
+			case validation_error::item_not_allowed_in_category:
+				return "Requested item allowed in category according to dictionary";
+			case validation_error::empty_file:
+				return "The file contains no datablocks";
+			case validation_error::empty_datablock:
+				return "The datablock contains no categories";
+			case validation_error::empty_category:
+				return "The category is empty";
+			case validation_error::not_valid_pdbx:
+				return "The file is not a valid PDBx file";
+
+			default:
+				assert(false);
+				return "unknown error code";
+		}
+	}
+
+	/**
+	 * @brief Return whether two error codes are equivalent, always false in this case
+	 *
+	 */
+
+	bool equivalent(const std::error_code & /*code*/, int /*condition*/) const noexcept override
+	{
+		return false;
+	}
+};
+
+/**
+ * @brief Return the implementation for the validation_category
+ *
+ * @return std::error_category&
+ */
+inline std::error_category &validation_category()
+{
+	static validation_category_impl instance;
+	return instance;
+}
+
+inline std::error_code make_error_code(validation_error e)
+{
+	return std::error_code(static_cast<int>(e), validation_category());
+}
+
+inline std::error_condition make_error_condition(validation_error e)
+{
+	return std::error_condition(static_cast<int>(e), validation_category());
+}
+
+// --------------------------------------------------------------------
+
+class validation_exception : public std::runtime_error
+{
+  public:
+	validation_exception(validation_error err)
+		: validation_exception(make_error_code(err))
+	{
+	}
+
+	validation_exception(validation_error err, std::string_view category)
+		: validation_exception(make_error_code(err), category)
+	{
+	}
+
+	validation_exception(validation_error err, std::string_view category, std::string_view item)
+		: validation_exception(make_error_code(err), category, item)
+	{
+	}
+
+	validation_exception(std::error_code ec);
+
+	validation_exception(std::error_code ec, std::string_view category);
+
+	validation_exception(std::error_code ec, std::string_view category, std::string_view item);
 };
 
 // --------------------------------------------------------------------
@@ -85,6 +208,9 @@ enum class DDL_PrimitiveType
 /// @brief Return the DDL_PrimitiveType encoded in @a s
 DDL_PrimitiveType map_to_primitive_type(std::string_view s);
 
+/// @brief Return the DDL_PrimitiveType encoded in @a s, error reporting variant
+DDL_PrimitiveType map_to_primitive_type(std::string_view s, std::error_code &ec) noexcept;
+
 struct regex_impl;
 
 /**
@@ -146,6 +272,26 @@ struct type_validator
 	int compare(std::string_view a, std::string_view b) const;
 };
 
+/** @brief Item alias, items can be renamed over time
+ */
+
+struct item_alias
+{
+	item_alias(const std::string &alias_name, const std::string &dictionary, const std::string &version)
+		: m_name(alias_name)
+		, m_dict(dictionary)
+		, m_vers(version)
+	{
+	}
+
+	item_alias(const item_alias &) = default;
+	item_alias &operator=(const item_alias &) = default;
+
+	std::string m_name; ///< The alias_name
+	std::string m_dict; ///< The dictionary in which it was known
+	std::string m_vers; ///< The version of the dictionary
+};
+
 /**
  * @brief An item_validator binds a type_validator to an item in
  * a category along with other information found in the dictionary.
@@ -157,28 +303,32 @@ struct type_validator
  */
 struct item_validator
 {
-	std::string m_tag;                        ///< The item name
+	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
 
 	/// @brief Compare based on the name
 	bool operator<(const item_validator &rhs) const
 	{
-		return icompare(m_tag, rhs.m_tag) < 0;
+		return icompare(m_item_name, rhs.m_item_name) < 0;
 	}
 
 	/// @brief Compare based on the name
 	bool operator==(const item_validator &rhs) const
 	{
-		return iequals(m_tag, rhs.m_tag);
+		return iequals(m_item_name, rhs.m_item_name);
 	}
 
 	/// @brief Validate the value in @a value for this item
-	/// Will throw a validation_error exception if it fails
+	/// Will throw a std::system_error exception if it fails
 	void operator()(std::string_view value) const;
+
+	/// @brief A more gentle version of value validation
+	bool validate_value(std::string_view value, std::error_code &ec) const noexcept;
 };
 
 /**
@@ -191,8 +341,8 @@ struct category_validator
 {
 	std::string m_name;                         ///< The name of the category
 	std::vector<std::string> m_keys;            ///< The list of items that make up the key
-	cif::iset m_groups;							///< The category groups this category belongs to
-	cif::iset m_mandatory_fields;               ///< The mandatory fields for this category
+	cif::iset m_groups;                         ///< The category groups this category belongs to
+	cif::iset m_mandatory_items;                ///< The mandatory items for this category
 	std::set<item_validator> m_item_validators; ///< The item validators for the items in this category
 
 	/// @brief return true if this category sorts before @a rhs
@@ -202,10 +352,13 @@ struct category_validator
 	}
 
 	/// @brief Add item_validator @a v to the list of item validators
-	void addItemValidator(item_validator &&v);
+	void add_item_validator(item_validator &&v);
 
-	/// @brief Return the item_validator for item @a tag, may return nullptr
-	const item_validator *get_validator_for_item(std::string_view tag) const;
+	/// @brief Return the item_validator for item @a item_name, may return nullptr
+	const item_validator *get_validator_for_item(std::string_view item_name) const;
+
+	/// @brief Return the item_validator for an item that has as alias name @a item_name, may return nullptr
+	const item_validator *get_validator_for_aliased_item(std::string_view item_name) const;
 };
 
 /**
@@ -284,7 +437,24 @@ class validator
 	std::vector<const link_validator *> get_links_for_child(std::string_view category) const;
 
 	/// @brief Bottleneck function to report an error in validation
-	void report_error(const std::string &msg, bool fatal) const;
+	void report_error(validation_error err, bool fatal = true) const
+	{
+		report_error(make_error_code(err), fatal);
+	}
+
+	/// @brief Bottleneck function to report an error in validation
+	void report_error(std::error_code ec, bool fatal = true) const;
+
+	/// @brief Bottleneck function to report an error in validation
+	void report_error(validation_error err, std::string_view category,
+		std::string_view item, bool fatal = true) const
+	{
+		report_error(make_error_code(err), category, item, fatal);
+	}
+
+	/// @brief Bottleneck function to report an error in validation
+	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

rsrc/ccd-subset.cif

@@ -2712,4 +2712,96 @@ _pdbx_chem_comp_audit.processing_site
 HIS "Create component"  1999-07-08 EBI  
 HIS "Modify descriptor" 2011-06-04 RCSB 
 # 
+data_HOH
+#
 
+_chem_comp.id                                   HOH
+_chem_comp.name                                 WATER
+_chem_comp.type                                 NON-POLYMER
+_chem_comp.pdbx_type                            HETAS
+_chem_comp.formula                              "H2 O"
+_chem_comp.mon_nstd_parent_comp_id              ?
+_chem_comp.pdbx_synonyms                        ?
+_chem_comp.pdbx_formal_charge                   0
+_chem_comp.pdbx_initial_date                    1999-07-08
+_chem_comp.pdbx_modified_date                   2011-06-04
+_chem_comp.pdbx_ambiguous_flag                  N
+_chem_comp.pdbx_release_status                  REL
+_chem_comp.pdbx_replaced_by                     ?
+_chem_comp.pdbx_replaces                        MTO
+_chem_comp.formula_weight                       18.015
+_chem_comp.one_letter_code                      ?
+_chem_comp.three_letter_code                    HOH
+_chem_comp.pdbx_model_coordinates_details       ?
+_chem_comp.pdbx_model_coordinates_missing_flag  N
+_chem_comp.pdbx_ideal_coordinates_details       ?
+_chem_comp.pdbx_ideal_coordinates_missing_flag  N
+_chem_comp.pdbx_model_coordinates_db_code       1NHE
+_chem_comp.pdbx_subcomponent_list               ?
+_chem_comp.pdbx_processing_site                 RCSB
+#   #
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.alt_atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.charge
+_chem_comp_atom.pdbx_align
+_chem_comp_atom.pdbx_aromatic_flag
+_chem_comp_atom.pdbx_leaving_atom_flag
+_chem_comp_atom.pdbx_stereo_config
+_chem_comp_atom.model_Cartn_x
+_chem_comp_atom.model_Cartn_y
+_chem_comp_atom.model_Cartn_z
+_chem_comp_atom.pdbx_model_Cartn_x_ideal
+_chem_comp_atom.pdbx_model_Cartn_y_ideal
+_chem_comp_atom.pdbx_model_Cartn_z_ideal
+_chem_comp_atom.pdbx_component_atom_id
+_chem_comp_atom.pdbx_component_comp_id
+_chem_comp_atom.pdbx_ordinal
+HOH  O   O   O  0  1  N  N  N  -23.107  18.401  -21.626  -0.064  0.000   0.000  O   HOH  1  
+HOH  H1  1H  H  0  1  N  N  N  -22.157  18.401  -21.626   0.512  0.000  -0.776  H1  HOH  2  
+HOH  H2  2H  H  0  1  N  N  N  -23.424  18.401  -20.730   0.512  0.000   0.776  H2  HOH  3  
+#   #
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.value_order
+_chem_comp_bond.pdbx_aromatic_flag
+_chem_comp_bond.pdbx_stereo_config
+_chem_comp_bond.pdbx_ordinal
+HOH  O  H1  SING  N  N  1  
+HOH  O  H2  SING  N  N  2  
+#   #
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+HOH  SMILES            ACDLabs               10.04  O                            
+HOH  SMILES_CANONICAL  CACTVS                3.341  O                            
+HOH  SMILES            CACTVS                3.341  O                            
+HOH  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  O                            
+HOH  SMILES            "OpenEye OEToolkits"  1.5.0  O                            
+HOH  InChI             InChI                 1.03   InChI=1S/H2O/h1H2            
+HOH  InChIKey          InChI                 1.03   XLYOFNOQVPJJNP-UHFFFAOYSA-N  
+#   #
+loop_
+_pdbx_chem_comp_identifier.comp_id
+_pdbx_chem_comp_identifier.type
+_pdbx_chem_comp_identifier.program
+_pdbx_chem_comp_identifier.program_version
+_pdbx_chem_comp_identifier.identifier
+HOH  "SYSTEMATIC NAME"  ACDLabs               10.04  water    
+HOH  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  oxidane  
+#   #
+loop_
+_pdbx_chem_comp_audit.comp_id
+_pdbx_chem_comp_audit.action_type
+_pdbx_chem_comp_audit.date
+_pdbx_chem_comp_audit.processing_site
+HOH  "Create component"   1999-07-08  RCSB  
+HOH  "Modify descriptor"  2011-06-04  RCSB  
+##

src/compound.cpp

@@ -136,14 +136,17 @@ compound::compound(cif::datablock &db)
 	if (chemComp.size() != 1)
 		throw std::runtime_error("Invalid compound file, chem_comp should contain a single row");
 
-	cif::tie(m_id, m_name, m_type, m_formula, m_formula_weight, m_formal_charge) =
-		chemComp.front().get("id", "name", "type", "formula", "formula_weight", "pdbx_formal_charge");
+	std::string one_letter_code;
+
+	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();
 
 	// The name should not contain newline characters since that triggers validation errors later on
 	cif::replace_all(m_name, "\n", "");
 
-	m_group = "non-polymer";
-
 	auto &chemCompAtom = db["chem_comp_atom"];
 	for (auto row : chemCompAtom)
 	{
@@ -153,6 +156,9 @@ compound::compound(cif::datablock &db)
 			row.get("atom_id", "type_symbol", "charge", "pdbx_aromatic_flag", "pdbx_leaving_atom_flag", "pdbx_stereo_config",
 				"model_Cartn_x", "model_Cartn_y", "model_Cartn_z");
 		atom.type_symbol = atom_type_traits(type_symbol).type();
+		if (stereo_config.empty())
+			atom.stereo_config = stereo_config_type::N;
+		else
 		atom.stereo_config = parse_stereo_config_from_string(stereo_config);
 		m_atoms.push_back(std::move(atom));
 	}
@@ -163,17 +169,28 @@ compound::compound(cif::datablock &db)
 		compound_bond bond;
 		std::string valueOrder;
 		cif::tie(bond.atom_id[0], bond.atom_id[1], valueOrder, bond.aromatic, bond.stereo_config) = row.get("atom_id_1", "atom_id_2", "value_order", "pdbx_aromatic_flag", "pdbx_stereo_config");
+		if (valueOrder.empty())
+			bond.type = bond_type::sing;
+		else
 		bond.type = parse_bond_type_from_string(valueOrder);
 		m_bonds.push_back(std::move(bond));
 	}
 }
 
-compound::compound(cif::datablock &db, const std::string &id, const std::string &name, const std::string &type, const std::string &group)
-	: m_id(id)
-	, m_name(name)
-	, m_type(type)
-	, m_group(group)
+compound::compound(cif::datablock &db, int)
 {
+	auto &chemComp = db["chem_comp"];
+
+	if (chemComp.size() != 1)
+		throw std::runtime_error("Invalid compound file, chem_comp should contain a single row");
+
+	cif::tie(m_id, m_name) =
+		chemComp.front().get("id", "name");
+	
+	cif::trim(m_name);
+
+	m_type = "NON-POLYMER";
+
 	auto &chemCompAtom = db["chem_comp_atom"];
 	for (auto row : chemCompAtom)
 	{
@@ -184,7 +201,6 @@ compound::compound(cif::datablock &db, const std::string &id, const std::string
 		atom.type_symbol = atom_type_traits(type_symbol).type();
 
 		m_formal_charge += atom.charge;
-		m_formula_weight += atom_type_traits(atom.type_symbol).weight();
 
 		m_atoms.push_back(std::move(atom));
 	}
@@ -209,11 +225,39 @@ compound::compound(cif::datablock &db, const std::string &id, const std::string
 		else
 		{
 			if (cif::VERBOSE > 0)
-				std::cerr << "Unimplemented chem_comp_bond.type " << btype << " in " << id << '\n';
+				std::cerr << "Unimplemented chem_comp_bond.type " << btype << " in " << db.name() << '\n';
 			bond.type = bond_type::sing;
 		}
 		m_bonds.push_back(std::move(bond));
 	}
+
+	// reconstruct a formula and weight
+
+	m_formula_weight = 0;
+
+	std::map<atom_type, int> f;
+	for (auto &atom : m_atoms)
+		f[atom.type_symbol] += 1;
+	
+	if (f.count(atom_type::C))
+	{
+		atom_type_traits att(atom_type::C);
+		m_formula += att.symbol() + std::to_string(f[atom_type::C]) + ' ';
+		m_formula_weight += att.weight() * f[atom_type::C];
+	}
+
+	for (const auto &[type, count] : f)
+	{
+		if (type == atom_type::C)
+			continue;
+
+		atom_type_traits att(type);
+		m_formula += att.symbol() + std::to_string(count) + ' ';
+		m_formula_weight += att.weight() * count;
+	}
+	
+	if (not m_formula.empty())
+		m_formula.pop_back();
 }
 
 compound_atom compound::get_atom_by_atom_id(const std::string &atom_id) const
@@ -260,12 +304,23 @@ float compound::bond_length(const std::string &atomId_1, const std::string &atom
 		auto a = get_atom_by_atom_id(atomId_1);
 		auto b = get_atom_by_atom_id(atomId_2);
 
-		result = distance(point{a.x, a.y, a.z}, point{b.x, b.y, b.z});
+		result = distance(point{ a.x, a.y, a.z }, point{ b.x, b.y, b.z });
 	}
 
 	return result;
 }
 
+// --------------------------------------------------------------------
+
+bool compound::is_peptide() const
+{
+	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");
+}
 
 // --------------------------------------------------------------------
 // known amino acids and bases
@@ -316,7 +371,7 @@ class compound_factory_impl : public std::enable_shared_from_this<compound_facto
 	compound_factory_impl();
 	compound_factory_impl(const fs::path &file, std::shared_ptr<compound_factory_impl> next);
 
-	~compound_factory_impl()
+	virtual ~compound_factory_impl()
 	{
 		for (auto c : m_compounds)
 			delete c;
@@ -373,13 +428,15 @@ class compound_factory_impl : public std::enable_shared_from_this<compound_facto
 			os << "CCD components.cif resource\n";
 		else
 			os << "CCD components file: " << std::quoted(m_file.string()) << '\n';
-		
+
 		if (m_next)
 			m_next->describe(os);
 	}
 
-  private:
-	compound *create(const std::string &id);
+  protected:
+	compound_factory_impl(std::shared_ptr<compound_factory_impl> next);
+
+	virtual compound *create(const std::string &id);
 
 	std::shared_timed_mutex mMutex;
 
@@ -395,12 +452,17 @@ compound_factory_impl::compound_factory_impl()
 {
 }
 
-compound_factory_impl::compound_factory_impl(const fs::path &file, std::shared_ptr<compound_factory_impl> next)
-	: m_file(file)
-	, m_next(next)
+compound_factory_impl::compound_factory_impl(std::shared_ptr<compound_factory_impl> next)
+	: m_next(next)
 {
 }
 
+compound_factory_impl::compound_factory_impl(const fs::path &file, std::shared_ptr<compound_factory_impl> next)
+	: compound_factory_impl(next)
+{
+	m_file = file;
+}
+
 compound *compound_factory_impl::create(const std::string &id)
 {
 	compound *result = nullptr;
@@ -476,6 +538,45 @@ compound *compound_factory_impl::create(const std::string &id)
 
 // --------------------------------------------------------------------
 
+class local_compound_factory_impl : public compound_factory_impl
+{
+  public:
+	local_compound_factory_impl(const cif::file &file, std::shared_ptr<compound_factory_impl> next)
+		: compound_factory_impl(next)
+		, m_local_file(file)
+	{
+	}
+
+	compound *create(const std::string &id) override;
+
+  private:
+	const cif::file &m_local_file;
+};
+
+compound *local_compound_factory_impl::create(const std::string &id)
+{
+	compound *result = nullptr;
+
+	for (auto &db : m_local_file)
+	{
+		if (db.name() == "comp_" + id)
+		{
+			cif::datablock db_copy(db);
+
+			result = new compound(db_copy, 1);
+
+			std::shared_lock lock(mMutex);
+			m_compounds.push_back(result);
+
+			break;
+		}
+	}
+
+	return result;
+}
+
+// --------------------------------------------------------------------
+
 std::unique_ptr<compound_factory> compound_factory::s_instance;
 thread_local std::unique_ptr<compound_factory> compound_factory::tl_instance;
 bool compound_factory::s_use_thread_local_instance;
@@ -553,56 +654,111 @@ void compound_factory::push_dictionary(const fs::path &inDictFile)
 	}
 }
 
+void compound_factory::push_dictionary(const cif::file &inDictFile)
+{
+	try
+	{
+		m_impl.reset(new local_compound_factory_impl(inDictFile, m_impl));
+	}
+	catch (const std::exception &)
+	{
+		std::throw_with_nested(std::runtime_error("Error loading dictionary from local mmCIF file"));
+	}
+}
+
 void compound_factory::pop_dictionary()
 {
 	if (m_impl)
 		m_impl = m_impl->next();
 }
 
-const compound *compound_factory::create(std::string id)
+const compound *compound_factory::create(std::string_view id)
 {
-	auto result = m_impl ? m_impl->get(id) : nullptr;
+	auto result = m_impl ? m_impl->get(std::string{ id }) : nullptr;
 	if (not result)
 		report_missing_compound(id);
 	return result;
 }
 
-bool compound_factory::is_known_peptide(const std::string &resName) const
+bool compound_factory::is_known_peptide(const std::string &res_name) const
 {
-	return kAAMap.count(resName) > 0;
+	return kAAMap.count(res_name) > 0;
 }
 
-bool compound_factory::is_known_base(const std::string &resName) const
+bool compound_factory::is_known_base(const std::string &res_name) const
 {
-	return kBaseMap.count(resName) > 0;
+	return kBaseMap.count(res_name) > 0;
 }
 
-void compound_factory::report_missing_compound(const std::string &compound_id)
+/// Return whether @a res_name is a peptide
+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);
+		result = compound != nullptr and compound->is_peptide();
+	}
+	return result;
+}
+
+/// Return whether @a res_name is a base
+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);
+		result = compound != nullptr and compound->is_base();
+	}
+	return result;
+}
+
+/// Return whether @a res_name is one of the standard peptides
+bool compound_factory::is_std_peptide(std::string_view res_name) const
+{
+	return kAAMap.count(std::string{ res_name }) > 0;
+}
+
+/// Return whether @a res_name is one of the standard bases
+bool compound_factory::is_std_base(std::string_view res_name) const
+{
+	return kBaseMap.count(std::string{ res_name }) > 0;
+}
+
+/// Return whether @a res_name is a monomer (either base or peptide)
+bool compound_factory::is_monomer(std::string_view res_name) const
+{
+	return is_peptide(res_name) or is_base(res_name);
+}
+
+void compound_factory::report_missing_compound(std::string_view compound_id)
 {
 	static bool s_reported = false;
 	if (std::exchange(s_reported, true) == false)
 	{
 		using namespace cif::colour;
 
-		std::clog << "\n" << cif::coloured("Configuration error:", white, red) << "\n\n"
+		std::clog << "\n"
+				  << cif::coloured("Configuration error:", white, red) << "\n\n"
 				  << "The attempt to retrieve compound information for " << std::quoted(compound_id) << " failed.\n\n"
 				  << "This information is searched for in a CCD file called components.cif or\n"
 				  << "components.cif.gz which should be located in one of the following directories:\n\n";
-		
+
 		cif::list_data_directories(std::clog);
 
 		std::clog << "\n(Note that you can add a directory to the search paths by setting the \n"
 				  << "LIBCIFPP_DATA_DIR environmental variable)\n\n";
 
-#if defined(CACHE_DIR)		
+#if defined(CACHE_DIR)
 		std::clog << "On Linux an optional cron script might have been installed that automatically updates\n"
 				  << "components.cif and mmCIF dictionary files. This script only works when the file\n"
 				  << "libcifpp.conf contains an uncommented line with the text:\n\n"
 				  << "update=true\n\n"
 				  << "If you do not have a working cron script, you can manually update the files\n"
 				  << "in /var/cache/libcifpp using the following commands:\n\n"
-				  << "curl -o " << CACHE_DIR << "/components.cif https://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz\n" 
-				  << "curl -o " << CACHE_DIR << "/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz\n" 
+				  << "curl -o " << CACHE_DIR << "/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz\n"
+				  << "curl -o " << CACHE_DIR << "/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz\n"
 				  << "curl -o " << CACHE_DIR << "/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic\n\n";
 #endif
 
@@ -613,9 +769,9 @@ void compound_factory::report_missing_compound(const std::string &compound_id)
 		}
 		else
 			std::clog << "No compound factory objects are created since none of the data sources is found.\n";
-		
+
 		cif::list_file_resources(std::clog);
-		
+
 		std::clog.flush();
 	}
 }

src/condition.cpp

@@ -30,17 +30,17 @@
 namespace cif
 {
 
-iset get_category_fields(const category &cat)
+iset get_category_items(const category &cat)
 {
-	return cat.key_fields();
+	return cat.key_items();
 }
 
-uint16_t get_column_ix(const category &cat, std::string_view col)
+uint16_t get_item_ix(const category &cat, std::string_view col)
 {
-	return cat.get_column_ix(col);
+	return cat.get_item_ix(col);
 }
 
-bool is_column_type_uchar(const category &cat, std::string_view col)
+bool is_item_type_uchar(const category &cat, std::string_view col)
 {
 	bool result = false;
 
@@ -63,14 +63,14 @@ namespace detail
 
 	condition_impl *key_equals_condition_impl::prepare(const category &c)
 	{
-		m_item_ix = c.get_column_ix(m_item_tag);
-		m_icase = is_column_type_uchar(c, m_item_tag);
+		m_item_ix = c.get_item_ix(m_item_name);
+		m_icase = is_item_type_uchar(c, m_item_name);
 
 		if (c.get_cat_validator() != nullptr and
-			c.key_field_indices().contains(m_item_ix) and
-			c.key_field_indices().size() == 1)
+			c.key_item_indices().contains(m_item_ix) and
+			c.key_item_indices().size() == 1)
 		{
-			m_single_hit = c[{ { m_item_tag, m_value } }];
+			m_single_hit = c[{ { m_item_name, m_value } }];
 		}
 
 		return this;

src/datablock.cpp

@@ -85,13 +85,47 @@ 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)
 		result = cat.validate_links() and result;
-	
+
 	return result;
 }
 
@@ -143,13 +177,6 @@ std::tuple<datablock::iterator, bool> datablock::emplace(std::string_view name)
 		if (iequals(name, i->name()))
 		{
 			is_new = false;
-
-			if (i != begin())
-			{
-				auto n = std::next(i);
-				splice(begin(), *this, i, n);
-			}
-
 			break;
 		}
 
@@ -158,30 +185,32 @@ std::tuple<datablock::iterator, bool> datablock::emplace(std::string_view name)
 
 	if (is_new)
 	{
-		auto &c = emplace_front(name);
-		c.set_validator(m_validator, *this);
+		i = insert(end(), {name});
+		i->set_validator(m_validator, *this);
 	}
 
-	return std::make_tuple(begin(), is_new);
+	assert(i != end());
+	return std::make_tuple(i, is_new);
 }
 
-std::vector<std::string> datablock::get_tag_order() const
+std::vector<std::string> datablock::get_item_order() const
 {
 	std::vector<std::string> result;
 
 	// for entry and audit_conform on top
-
-	auto ci = find_if(begin(), end(), [](const category &cat) { return cat.name() == "entry"; });
+	auto ci = find_if(begin(), end(), [](const category &cat)
+		{ return cat.name() == "entry"; });
 	if (ci != end())
 	{
-		auto cto = ci->get_tag_order();
+		auto cto = ci->get_item_order();
 		result.insert(result.end(), cto.begin(), cto.end());
 	}
 
-	ci = find_if(begin(), end(), [](const category &cat) { return cat.name() == "audit_conform"; });
+	ci = find_if(begin(), end(), [](const category &cat)
+		{ return cat.name() == "audit_conform"; });
 	if (ci != end())
 	{
-		auto cto = ci->get_tag_order();
+		auto cto = ci->get_item_order();
 		result.insert(result.end(), cto.begin(), cto.end());
 	}
 
@@ -189,62 +218,141 @@ std::vector<std::string> datablock::get_tag_order() const
 	{
 		if (cat.name() == "entry" or cat.name() == "audit_conform")
 			continue;
-		auto cto = cat.get_tag_order();
+		auto cto = cat.get_item_order();
 		result.insert(result.end(), cto.begin(), cto.end());
 	}
 
 	return result;
 }
 
+namespace
+{
+	using elem_t = std::tuple<std::string, int, bool>;
+	using cat_order_t = std::vector<elem_t>;
+	using iter_t = cat_order_t::iterator;
+
+	inline int get_count(iter_t i)
+	{
+		return std::get<1>(*i);
+	}
+
+	inline bool is_on_stack(iter_t i)
+	{
+		return std::get<2>(*i);
+	}
+
+	void calculate_cat_order(cat_order_t &cat_order, iter_t i, const validator &validator)
+	{
+		if (i == cat_order.end() or get_count(i) >= 0)
+			return;
+
+		auto &&[cat, count, on_stack] = *i;
+
+		on_stack = true;
+
+		int parent_count = 0;
+
+		for (auto link : validator.get_links_for_child(cat))
+		{
+			auto ei = std::find_if(cat_order.begin(), cat_order.end(), [parent = link->m_parent_category](elem_t &a)
+				{ return std::get<0>(a) == parent; });
+
+			if (ei == cat_order.end())
+				continue;
+
+			if (not is_on_stack(ei))
+				calculate_cat_order(cat_order, ei, validator);
+
+			parent_count += get_count(ei);
+		}
+
+		count = parent_count + 1;
+	}
+} // namespace
+
 void datablock::write(std::ostream &os) const
 {
 	os << "data_" << m_name << '\n'
 	   << "# \n";
 
-	// mmcif support, sort of. First write the 'entry' Category
-	// and if it exists, _AND_ we have a Validator, write out the
-	// audit_conform record.
-
-	for (auto &cat : *this)
+	if (m_validator and size() > 0)
 	{
-		if (cat.name() != "entry")
-			continue;
+		// base order on parent child relationships, parents first
 
-		cat.write(os);
+		cat_order_t cat_order;
 
-		break;
+		for (auto &cat : *this)
+			cat_order.emplace_back(cat.name(), -1, false);
+
+		for (auto i = cat_order.begin(); i != cat_order.end(); ++i)
+			calculate_cat_order(cat_order, i, *m_validator);
+
+		std::sort(cat_order.begin(), cat_order.end(), [](const elem_t &a, const elem_t &b)
+			{
+			const auto &[cat_a, count_a, on_stack_a] = a;
+			const auto &[cat_b, count_b, on_stack_b] = b;
+
+			int d = 0;
+
+			if (cat_a == "audit_conform")
+				d = -1;
+			else if (cat_b == "audit_conform")
+				d = 1;
+			else if (cat_a == "entry")
+				d = -1;
+			else if (cat_b == "entry")
+				d = 1;
+			else
+			{
+				d = std::get<1>(a) - std::get<1>(b);
+				if (d == 0)
+					d = cat_b.compare(cat_a);
+			}
+
+			return d < 0; });
+
+		for (auto &&[cat, count, on_stack] : cat_order)
+			get(cat)->write(os);
 	}
-
-	// If the dictionary declares an audit_conform category, put it in,
-	// but only if it does not exist already!
-	if (get("audit_conform"))
-		get("audit_conform")->write(os);
-	else if (m_validator != nullptr and m_validator->get_validator_for_category("audit_conform") != nullptr)
+	else
 	{
-		category auditConform("audit_conform");
-		auditConform.emplace({
-			{"dict_name", m_validator->name()},
-			{"dict_version", m_validator->version()}});
-		auditConform.write(os);
-	}
+		// mmcif support, sort of. First write the 'entry' Category
+		// and if it exists, _AND_ we have a Validator, write out the
+		// audit_conform record.
+
+		for (auto &cat : *this)
+		{
+			if (cat.name() != "entry")
+				continue;
 
-	for (auto &cat : *this)
-	{
-		if (cat.name() != "entry" and cat.name() != "audit_conform")
 			cat.write(os);
+
+			break;
+		}
+
+		// If the dictionary declares an audit_conform category, put it in,
+		// but only if it does not exist already!
+		if (get("audit_conform"))
+			get("audit_conform")->write(os);
+
+		for (auto &cat : *this)
+		{
+			if (cat.name() != "entry" and cat.name() != "audit_conform")
+				cat.write(os);
+		}
 	}
 }
 
-void datablock::write(std::ostream &os, const std::vector<std::string> &tag_order)
+void datablock::write(std::ostream &os, const std::vector<std::string> &item_name_order)
 {
 	os << "data_" << m_name << '\n'
 	   << "# \n";
 
 	std::vector<std::string> cat_order;
-	for (auto &o : tag_order)
+	for (auto &o : item_name_order)
 	{
 		std::string cat_name, item_name;
-		std::tie(cat_name, item_name) = split_tag_name(o);
+		std::tie(cat_name, item_name) = split_item_name(o);
 		if (find_if(cat_order.rbegin(), cat_order.rend(), [cat_name](const std::string &s) -> bool
 				{ return iequals(cat_name, s); }) == cat_order.rend())
 			cat_order.push_back(cat_name);
@@ -257,10 +365,10 @@ void datablock::write(std::ostream &os, const std::vector<std::string> &tag_orde
 			continue;
 
 		std::vector<std::string> items;
-		for (auto &o : tag_order)
+		for (auto &o : item_name_order)
 		{
 			std::string cat_name, item_name;
-			std::tie(cat_name, item_name) = split_tag_name(o);
+			std::tie(cat_name, item_name) = split_item_name(o);
 
 			if (cat_name == c)
 				items.push_back(item_name);
@@ -282,6 +390,10 @@ void datablock::write(std::ostream &os, const std::vector<std::string> &tag_orde
 
 bool datablock::operator==(const datablock &rhs) const
 {
+	// shortcut
+	if (this == &rhs)
+		return true;
+
 	auto &dbA = *this;
 	auto &dbB = rhs;
 
@@ -337,7 +449,7 @@ bool datablock::operator==(const datablock &rhs) const
 			++catA_i;
 		else
 		{
-			if (not (*dbA.get(*catA_i) == *dbB.get(*catB_i)))
+			if (not(*dbA.get(*catA_i) == *dbB.get(*catB_i)))
 				return false;
 			++catA_i;
 			++catB_i;
@@ -347,4 +459,4 @@ bool datablock::operator==(const datablock &rhs) const
 	return true;
 }
 
-} // namespace cif::cif
+} // namespace cif

src/dictionary_parser.cpp

@@ -50,7 +50,7 @@ class dictionary_parser : public parser
 
 		try
 		{
-			while (m_lookahead != CIFToken::Eof)
+			while (m_lookahead != CIFToken::END_OF_FILE)
 			{
 				switch (m_lookahead)
 				{
@@ -87,7 +87,7 @@ class dictionary_parser : public parser
 				error("Undefined category '" + iv.first);
 
 			for (auto &v : iv.second)
-				const_cast<category_validator *>(cv)->addItemValidator(std::move(v));
+				const_cast<category_validator *>(cv)->add_item_validator(std::move(v));
 		}
 
 		// check all item validators for having a typeValidator
@@ -128,7 +128,7 @@ class dictionary_parser : public parser
 		datablock::iterator cat = dict.end();
 
 		match(CIFToken::SAVE_NAME);
-		while (m_lookahead == CIFToken::LOOP or m_lookahead == CIFToken::Tag)
+		while (m_lookahead == CIFToken::LOOP or m_lookahead == CIFToken::ITEM_NAME)
 		{
 			if (m_lookahead == CIFToken::LOOP)
 			{
@@ -136,30 +136,30 @@ class dictionary_parser : public parser
 
 				match(CIFToken::LOOP);
 
-				std::vector<std::string> tags;
-				while (m_lookahead == CIFToken::Tag)
+				std::vector<std::string> item_names;
+				while (m_lookahead == CIFToken::ITEM_NAME)
 				{
 					std::string catName, item_name;
-					std::tie(catName, item_name) = split_tag_name(m_token_value);
+					std::tie(catName, item_name) = split_item_name(m_token_value);
 
 					if (cat == dict.end())
 						std::tie(cat, std::ignore) = dict.emplace(catName);
 					else if (not iequals(cat->name(), catName))
 						error("inconsistent categories in loop_");
 
-					tags.push_back(item_name);
-					match(CIFToken::Tag);
+					item_names.push_back(item_name);
+					match(CIFToken::ITEM_NAME);
 				}
 
-				while (m_lookahead == CIFToken::Value)
+				while (m_lookahead == CIFToken::VALUE)
 				{
 					cat->emplace({});
 					auto row = cat->back();
 
-					for (auto tag : tags)
+					for (auto item_name : item_names)
 					{
-						row[tag] = m_token_value;
-						match(CIFToken::Value);
+						row[item_name] = m_token_value;
+						match(CIFToken::VALUE);
 					}
 				}
 
@@ -168,18 +168,18 @@ class dictionary_parser : public parser
 			else
 			{
 				std::string catName, item_name;
-				std::tie(catName, item_name) = split_tag_name(m_token_value);
+				std::tie(catName, item_name) = split_item_name(m_token_value);
 
 				if (cat == dict.end() or not iequals(cat->name(), catName))
 					std::tie(cat, std::ignore) = dict.emplace(catName);
 
-				match(CIFToken::Tag);
+				match(CIFToken::ITEM_NAME);
 
 				if (cat->empty())
 					cat->emplace({});
 				cat->back()[item_name] = m_token_value;
 
-				match(CIFToken::Value);
+				match(CIFToken::VALUE);
 			}
 		}
 
@@ -191,7 +191,7 @@ class dictionary_parser : public parser
 
 			std::vector<std::string> keys;
 			for (auto k : dict["category_key"])
-				keys.push_back(std::get<1>(split_tag_name(k["name"].as<std::string>())));
+				keys.push_back(std::get<1>(split_item_name(k["name"].as<std::string>())));
 
 			iset groups;
 			for (auto g : dict["category_group"])
@@ -224,20 +224,27 @@ class dictionary_parser : public parser
 			// 	}
 			// }
 
+			std::vector<item_alias> aliases;
+			for (const auto &[alias_name, dictionary, version] :
+				dict["item_aliases"].rows<std::string,std::string,std::string>("alias_name", "dictionary", "version"))
+			{
+				aliases.emplace_back(alias_name, dictionary, version);
+			}
+
 			// collect the dict from our dataBlock and construct validators
 			for (auto i : dict["item"])
 			{
-				std::string tagName, category, mandatory;
-				cif::tie(tagName, category, mandatory) = i.get("name", "category_id", "mandatory_code");
+				std::string item, category, mandatory;
+				cif::tie(item, category, mandatory) = i.get("name", "category_id", "mandatory_code");
 
 				std::string cat_name, item_name;
-				std::tie(cat_name, item_name) = split_tag_name(tagName);
+				std::tie(cat_name, item_name) = split_item_name(item);
 
 				if (cat_name.empty() or item_name.empty())
-					error("Invalid tag name in _item.name " + tagName);
+					error("Invalid item name in _item.name " + item);
 
 				if (not iequals(category, cat_name) and not(category.empty() or category == "?"))
-					error("specified category id does match the implicit category name for tag '" + tagName + '\'');
+					error("specified category id does match the implicit category name for item '" + item + '\'');
 				else
 					category = cat_name;
 
@@ -245,7 +252,7 @@ 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 /*, defaultIsNull*/ });
+					ivs.push_back(item_validator{ item_name, iequals(mandatory, "yes"), tv, ess, defaultValue, nullptr, std::move(aliases) });
 				else
 				{
 					// need to update the itemValidator?
@@ -253,22 +260,22 @@ class dictionary_parser : public parser
 					{
 						if (VERBOSE > 2)
 						{
-							std::cerr << "inconsistent mandatory value for " << tagName << " in dictionary\n";
+							std::cerr << "inconsistent mandatory value for " << item << " in dictionary\n";
 
-							if (iequals(tagName, saveFrameName))
+							if (iequals(item, saveFrameName))
 								std::cerr << "choosing " << mandatory << '\n';
 							else
 								std::cerr << "choosing " << (vi->m_mandatory ? "Y" : "N") << '\n';
 						}
 
-						if (iequals(tagName, saveFrameName))
+						if (iequals(item, saveFrameName))
 							vi->m_mandatory = (iequals(mandatory, "yes"));
 					}
 
 					if (vi->m_type != nullptr and tv != nullptr and vi->m_type != tv)
 					{
 						if (VERBOSE > 1)
-							std::cerr << "inconsistent type for " << tagName << " in dictionary\n";
+							std::cerr << "inconsistent type for " << item << " in dictionary\n";
 					}
 
 					//				vi->mMandatory = (iequals(mandatory, "yes"));
@@ -351,7 +358,7 @@ class dictionary_parser : public parser
 			}
 
 			size_t ix = linkIndex.at(key);
-			addLink(ix, piv->m_tag, civ->m_tag);
+			addLink(ix, piv->m_item_name, civ->m_item_name);
 		}
 
 		// Only process inline linked items if the linked group list is absent
@@ -379,7 +386,7 @@ class dictionary_parser : public parser
 				}
 
 				size_t ix = linkIndex.at(key);
-				addLink(ix, piv->m_tag, civ->m_tag);
+				addLink(ix, piv->m_item_name, civ->m_item_name);
 			}
 		}
 
@@ -410,7 +417,7 @@ class dictionary_parser : public parser
 			for (auto &iv : cv.m_item_validators)
 			{
 				if (iv.m_type == nullptr and cif::VERBOSE >= 0)
-					std::cerr << "Missing item_type for " << iv.m_tag << '\n';
+					std::cerr << "Missing item_type for " << iv.m_item_name << '\n';
 			}
 		}
 	}

src/file.cpp

@@ -158,13 +158,6 @@ std::tuple<file::iterator, bool> file::emplace(std::string_view name)
 		if (iequals(name, i->name()))
 		{
 			is_new = false;
-
-			if (i != begin())
-			{
-				auto n = std::next(i);
-				splice(begin(), *this, i, n);
-			}
-
 			break;
 		}
 
@@ -173,11 +166,12 @@ std::tuple<file::iterator, bool> file::emplace(std::string_view name)
 
 	if (is_new)
 	{
-		auto &db = emplace_front(name);
-		db.set_validator(m_validator);
+		i = insert(end(), { name });
+		i->set_validator(m_validator);
 	}
 
-	return std::make_tuple(begin(), is_new);
+	assert(i != end());
+	return std::make_tuple(i, is_new);
 }
 
 void file::load(const std::filesystem::path &p)

src/item.cpp

@@ -35,7 +35,7 @@ const item_handle item_handle::s_null_item;
 row_handle s_null_row_handle;
 
 item_handle::item_handle()
-	: m_column(std::numeric_limits<uint16_t>::max())
+	: m_item_ix(std::numeric_limits<uint16_t>::max())
 	, m_row_handle(s_null_row_handle)
 {
 }
@@ -44,7 +44,7 @@ std::string_view item_handle::text() const
 {
 	if (not m_row_handle.empty())
 	{
-		auto iv = m_row_handle.m_row->get(m_column);
+		auto iv = m_row_handle.m_row->get(m_item_ix);
 		if (iv != nullptr)
 			return iv->text();
 	}
@@ -55,14 +55,14 @@ std::string_view item_handle::text() const
 void item_handle::assign_value(const item &v)
 {
 	assert(not m_row_handle.empty());
-	m_row_handle.assign(m_column, v.value(), true);
+	m_row_handle.assign(m_item_ix, v.value(), true);
 }
 
 void item_handle::swap(item_handle &b)
 {
-	assert(m_column == b.m_column);
+	assert(m_item_ix == b.m_item_ix);
 	// assert(&m_row_handle.m_category == &b.m_row_handle.m_category);
-	m_row_handle.swap(m_column, b.m_row_handle);
+	m_row_handle.swap(m_item_ix, b.m_row_handle);
 }
 
 }

src/model.cpp

@@ -163,9 +163,9 @@ int atom::atom_impl::get_charge() const
 
 // const std::string atom::atom_impl::get_property(const std::string_view name) const
 // {
-// 	for (auto &&[tag, ref] : mCachedRefs)
+// 	for (auto &&[item_name, ref] : mCachedRefs)
 // 	{
-// 		if (tag == name)
+// 		if (item_name == name)
 // 			return ref.as<std::string>();
 // 	}
 
@@ -175,9 +175,9 @@ int atom::atom_impl::get_charge() const
 
 // void atom::atom_impl::set_property(const std::string_view name, const std::string &value)
 // {
-// 	for (auto &&[tag, ref] : mCachedRefs)
+// 	for (auto &&[item_name, ref] : mCachedRefs)
 // 	{
-// 		if (tag != name)
+// 		if (item_name != name)
 // 			continue;
 
 // 		ref = value;
@@ -1783,7 +1783,7 @@ atom &structure::emplace_atom(atom &&atom)
 	std::string symbol = atom.get_property("type_symbol");
 
 	using namespace cif::literals;
-	if (not atom_type.exists("symbol"_key == symbol))
+	if (not atom_type.contains("symbol"_key == symbol))
 		atom_type.emplace({ { "symbol", symbol } });
 
 	return m_atoms.emplace_back(std::move(atom));
@@ -1969,7 +1969,7 @@ void structure::change_residue(residue &res, const std::string &newCompound,
 
 		// create rest
 		auto &chemComp = m_db["chem_comp"];
-		if (not chemComp.exists(key("id") == newCompound))
+		if (not chemComp.contains(key("id") == newCompound))
 		{
 			chemComp.emplace({{"id", newCompound},
 				{"name", compound->name()},
@@ -2006,7 +2006,10 @@ void structure::change_residue(residue &res, const std::string &newCompound,
 			continue;
 
 		if (a2.empty() or a2 == ".")
+		{
+			i->set_property("label_comp_id", newCompound);
 			remove_atom(*i);
+		}
 		else if (a1 != a2)
 		{
 			auto ra = r.front();
@@ -2699,7 +2702,7 @@ void structure::cleanup_empty_categories()
 	for (auto chemComp : chem_comp)
 	{
 		std::string compID = chemComp["id"].as<std::string>();
-		if (atomSite.exists("label_comp_id"_key == compID or "auth_comp_id"_key == compID))
+		if (atomSite.contains("label_comp_id"_key == compID or "auth_comp_id"_key == compID))
 			continue;
 
 		obsoleteChemComps.push_back(chemComp);
@@ -2716,7 +2719,7 @@ void structure::cleanup_empty_categories()
 	for (auto entity : entities)
 	{
 		std::string entityID = entity["id"].as<std::string>();
-		if (atomSite.exists("label_entity_id"_key == entityID))
+		if (atomSite.contains("label_entity_id"_key == entityID))
 			continue;
 
 		obsoleteEntities.push_back(entity);
@@ -2833,15 +2836,4 @@ void structure::validate_atoms() const
 	assert(atoms.empty());
 }
 
-// --------------------------------------------------------------------
-
-void reconstruct_pdbx(datablock &db)
-{
-	if (db.get("atom_site") == nullptr)
-		throw std::runtime_error("Cannot reconstruct PDBx file, atom data missing");
-	
-	assert(false);
-	throw std::runtime_error("not implemented yet");
-}
-
 } // namespace pdbx

src/parser.cpp

@@ -269,7 +269,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
 {
 	const auto kEOF = std::char_traits<char>::eof();
 
-	CIFToken result = CIFToken::Unknown;
+	CIFToken result = CIFToken::UNKNOWN;
 	int quoteChar = 0;
 	State state = State::Start;
 	m_bol = false;
@@ -279,7 +279,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
 
 	reserved_words_automaton dag;
 
-	while (result == CIFToken::Unknown)
+	while (result == CIFToken::UNKNOWN)
 	{
 		auto ch = get_next_char();
 
@@ -287,7 +287,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
 		{
 			case State::Start:
 				if (ch == kEOF)
-					result = CIFToken::Eof;
+					result = CIFToken::END_OF_FILE;
 				else if (ch == '\n')
 				{
 					m_bol = true;
@@ -298,9 +298,9 @@ sac_parser::CIFToken sac_parser::get_next_token()
 				else if (ch == '#')
 					state = State::Comment;
 				else if (ch == '_')
-					state = State::Tag;
+					state = State::ItemName;
 				else if (ch == ';' and m_bol)
-					state = State::TextField;
+					state = State::TextItem;
 				else if (ch == '?')
 					state = State::QuestionMark;
 				else if (ch == '\'' or ch == '"')
@@ -316,7 +316,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
 
 			case State::White:
 				if (ch == kEOF)
-					result = CIFToken::Eof;
+					result = CIFToken::END_OF_FILE;
 				else if (not is_space(ch))
 				{
 					state = State::Start;
@@ -335,7 +335,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
 					m_token_buffer.clear();
 				}
 				else if (ch == kEOF)
-					result = CIFToken::Eof;
+					result = CIFToken::END_OF_FILE;
 				else if (not is_any_print(ch))
 					error("invalid character in comment");
 				break;
@@ -344,29 +344,29 @@ sac_parser::CIFToken sac_parser::get_next_token()
 				if (not is_non_blank(ch))
 				{
 					retract();
-					result = CIFToken::Value;
+					result = CIFToken::VALUE;
 				}
 				else
 					state = State::Value;
 				break;
 
-			case State::TextField:
+			case State::TextItem:
 				if (ch == '\n')
-					state = State::TextFieldNL;
+					state = State::TextItemNL;
 				else if (ch == kEOF)
 					error("unterminated textfield");
 				else if (not is_any_print(ch) and cif::VERBOSE > 2)
 					warning("invalid character in text field '" + std::string({static_cast<char>(ch)}) + "' (" + std::to_string((int)ch) + ")");
 				break;
 
-			case State::TextFieldNL:
+			case State::TextItemNL:
 				if (is_text_lead(ch) or ch == ' ' or ch == '\t')
-					state = State::TextField;
+					state = State::TextItem;
 				else if (ch == ';')
 				{
 					assert(m_token_buffer.size() >= 2);
 					m_token_value = std::string_view(m_token_buffer.data() + 1, m_token_buffer.size() - 3);
-					result = CIFToken::Value;
+					result = CIFToken::VALUE;
 				}
 				else if (ch == kEOF)
 					error("unterminated textfield");
@@ -387,7 +387,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
 				if (is_white(ch))
 				{
 					retract();
-					result = CIFToken::Value;
+					result = CIFToken::VALUE;
 					if (m_token_buffer.size() < 2)
 						error("Invalid quoted string token");
 
@@ -403,11 +403,11 @@ sac_parser::CIFToken sac_parser::get_next_token()
 					error("invalid character in quoted string");
 				break;
 
-			case State::Tag:
+			case State::ItemName:
 				if (not is_non_blank(ch))
 				{
 					retract();
-					result = CIFToken::Tag;
+					result = CIFToken::ITEM_NAME;
 					m_token_value = std::string_view(m_token_buffer.data(), m_token_buffer.size());
 				}
 				break;
@@ -422,7 +422,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
 						if (not is_non_blank(ch))
 						{
 							retract();
-							result = CIFToken::Value;
+							result = CIFToken::VALUE;
 							m_token_value = std::string_view(m_token_buffer.data(), m_token_buffer.size());
 						}
 						else
@@ -467,7 +467,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
 				if (not is_non_blank(ch))
 				{
 					retract();
-					result = CIFToken::Value;
+					result = CIFToken::VALUE;
 					m_token_value = std::string_view(m_token_buffer.data(), m_token_buffer.size());
 					break;
 				}
@@ -483,7 +483,7 @@ sac_parser::CIFToken sac_parser::get_next_token()
 	if (VERBOSE >= 5)
 	{
 		std::cerr << get_token_name(result);
-		if (result != CIFToken::Eof)
+		if (result != CIFToken::END_OF_FILE)
 			std::cerr << " " << std::quoted(m_token_value);
 		std::cerr << '\n';
 	}
@@ -710,7 +710,7 @@ bool sac_parser::parse_single_datablock(const std::string &datablock, const data
 
 void sac_parser::parse_file()
 {
-	while (m_lookahead != CIFToken::Eof)
+	while (m_lookahead != CIFToken::END_OF_FILE)
 	{
 		switch (m_lookahead)
 		{
@@ -735,10 +735,10 @@ void sac_parser::parse_file()
 void sac_parser::parse_global()
 {
 	match(CIFToken::GLOBAL);
-	while (m_lookahead == CIFToken::Tag)
+	while (m_lookahead == CIFToken::ITEM_NAME)
 	{
-		match(CIFToken::Tag);
-		match(CIFToken::Value);
+		match(CIFToken::ITEM_NAME);
+		match(CIFToken::VALUE);
 	}
 }
 
@@ -747,7 +747,7 @@ void sac_parser::parse_datablock()
 	static const std::string kUnitializedCategory("<invalid>");
 	std::string cat = kUnitializedCategory;	// intial value acts as a guard for empty category names
 
-	while (m_lookahead == CIFToken::LOOP or m_lookahead == CIFToken::Tag or m_lookahead == CIFToken::SAVE_NAME)
+	while (m_lookahead == CIFToken::LOOP or m_lookahead == CIFToken::ITEM_NAME or m_lookahead == CIFToken::SAVE_NAME)
 	{
 		switch (m_lookahead)
 		{
@@ -757,12 +757,12 @@ void sac_parser::parse_datablock()
 
 				match(CIFToken::LOOP);
 
-				std::vector<std::string> tags;
+				std::vector<std::string> item_names;
 
-				while (m_lookahead == CIFToken::Tag)
+				while (m_lookahead == CIFToken::ITEM_NAME)
 				{
 					std::string catName, itemName;
-					std::tie(catName, itemName) = split_tag_name(m_token_value);
+					std::tie(catName, itemName) = split_item_name(m_token_value);
 
 					if (cat == kUnitializedCategory)
 					{
@@ -772,19 +772,19 @@ void sac_parser::parse_datablock()
 					else if (not iequals(cat, catName))
 						error("inconsistent categories in loop_");
 
-					tags.push_back(itemName);
+					item_names.push_back(itemName);
 
-					match(CIFToken::Tag);
+					match(CIFToken::ITEM_NAME);
 				}
 
-				while (m_lookahead == CIFToken::Value)
+				while (m_lookahead == CIFToken::VALUE)
 				{
 					produce_row();
 
-					for (auto tag : tags)
+					for (auto item_name : item_names)
 					{
-						produce_item(cat, tag, m_token_value);
-						match(CIFToken::Value);
+						produce_item(cat, item_name, m_token_value);
+						match(CIFToken::VALUE);
 					}
 				}
 
@@ -792,10 +792,10 @@ void sac_parser::parse_datablock()
 				break;
 			}
 
-			case CIFToken::Tag:
+			case CIFToken::ITEM_NAME:
 			{
 				std::string catName, itemName;
-				std::tie(catName, itemName) = split_tag_name(m_token_value);
+				std::tie(catName, itemName) = split_item_name(m_token_value);
 
 				if (not iequals(cat, catName))
 				{
@@ -804,11 +804,11 @@ void sac_parser::parse_datablock()
 					produce_row();
 				}
 
-				match(CIFToken::Tag);
+				match(CIFToken::ITEM_NAME);
 
 				produce_item(cat, itemName, m_token_value);
 
-				match(CIFToken::Value);
+				match(CIFToken::VALUE);
 				break;
 			}
 

src/pdb/pdb2cif_remark_3.cpp

@@ -1493,8 +1493,8 @@ bool Remark3Parser::parse(const std::string &expMethod, PDBRecord *r, cif::datab
 					auto r1 = cat1.front();
 					auto r2 = cat2.front();
 
-					for (auto column : cat1.key_fields())
-						r2[column] = r1[column].text();
+					for (auto item : cat1.key_items())
+						r2[item] = r1[item].text();
 				}
 			}
 			else

src/pdb/validate-pdbx.cpp

@@ -0,0 +1,336 @@
+/*-
+ * 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
+ * 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++.hpp"
+
+namespace cif::pdb
+{
+
+condition get_parents_condition(const validator &validator, row_handle rh, const category &parentCat)
+{
+	condition result;
+
+	auto &childCat = rh.get_category();
+	auto childName = childCat.name();
+	auto parentName = parentCat.name();
+
+	auto links = validator.get_links_for_child(childName);
+	links.erase(remove_if(links.begin(), links.end(), [n = parentName](auto &l)
+					{ return l->m_parent_category != n; }),
+		links.end());
+
+	if (not links.empty())
+	{
+		for (auto &link : links)
+		{
+			condition cond;
+
+			for (size_t ix = 0; ix < link->m_child_keys.size(); ++ix)
+			{
+				auto childValue = rh[link->m_child_keys[ix]];
+
+				if (childValue.empty())
+					continue;
+
+				cond = std::move(cond) and key(link->m_parent_keys[ix]) == childValue.text();
+			}
+
+			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)
+{
+	std::error_code ec;
+	bool result = is_valid_pdbx_file(file, dictionary, ec);
+	return result and ec == std::errc();
+}
+
+bool is_valid_pdbx_file(const file &file, std::error_code &ec)
+{
+	bool result = false;
+
+	if (file.empty())
+		ec = make_error_code(validation_error::empty_file);
+	else
+	{
+		std::string dictionary = "mmcif_pdbx";
+
+		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)
+{
+	using namespace cif::literals;
+
+	bool result = true;
+
+	try
+	{
+		auto &cf = cif::compound_factory::instance();
+		auto &validator = cif::validator_factory::instance().operator[](dictionary);
+
+		if (file.empty())
+			throw std::runtime_error("Empty file");
+
+		auto &db = file.front();
+
+		if (db.empty())
+			throw std::runtime_error("Empty datablock");
+
+		auto &atom_site = db["atom_site"];
+		if (atom_site.empty())
+			throw std::runtime_error("Empty or missing atom_site category");
+
+		auto &pdbx_poly_seq_scheme = db["pdbx_poly_seq_scheme"];
+
+		std::string last_asym_id;
+		int last_seq_id = -1;
+		for (auto r : atom_site)
+		{
+			auto seq_id = r.get<std::optional<int>>("label_seq_id");
+			if (not seq_id.has_value()) // not a residue in a polymer
+				continue;
+
+			if (*seq_id == last_seq_id)
+				continue;
+
+			last_seq_id = *seq_id;
+
+			auto comp_id = r.get<std::string>("label_comp_id");
+			if (not cf.is_monomer(comp_id))
+				continue;
+
+			auto p = pdbx_poly_seq_scheme.find(get_parents_condition(validator, r, pdbx_poly_seq_scheme));
+			if (p.size() != 1)
+			{
+				if (cif::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");
+			}
+		}
+
+		auto &entity = db["entity"];
+		if (entity.empty())
+			throw std::runtime_error("Entity category is missing or empty");
+
+		auto &entity_poly = db["entity_poly"];
+		if (entity_poly.empty())
+			throw std::runtime_error("Entity_poly category is missing or empty");
+
+		auto &entity_poly_seq = db["entity_poly_seq"];
+		if (entity_poly_seq.empty())
+			throw std::runtime_error("Entity_poly_seq category is missing or empty");
+
+		auto &struct_asym = db["struct_asym"];
+		if (struct_asym.empty())
+			throw std::runtime_error("struct_asym category is missing or empty");
+
+		for (auto entity_id : entity.find<std::string>("type"_key == "polymer", "id"))
+		{
+			if (entity_poly.count("entity_id"_key == entity_id) != 1)
+				throw std::runtime_error("There should be exactly one entity_poly record per polymer entity");
+
+			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;
+
+			for (const auto &[num, mon_id, hetero] : entity_poly_seq.find<int, std::string, bool>("entity_id"_key == entity_id, "num", "mon_id", "hetero"))
+			{
+				mon_per_seq_id[num].emplace(mon_id);
+
+				for (auto asym_id : struct_asym.find<std::string>("entity_id"_key == entity_id, "id"))
+				{
+					if (pdbx_poly_seq_scheme.count(
+							"asym_id"_key == asym_id and
+							"mon_id"_key == mon_id and
+							"seq_id"_key == num and
+							"hetero"_key == hetero) != 1)
+					{
+						throw std::runtime_error("For each entity_poly_seq record there should be exactly one pdbx_poly_seq record");
+					}
+				}
+			}
+
+			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(
+						"mon_id"_key == mon_id and
+						"num"_key == seq_id and
+						"hetero"_key == hetero) != 1)
+				{
+					throw std::runtime_error("For each pdbx_poly_seq/struct_asym record there should be exactly one entity_poly_seq record");
+				}
+
+				if ((mon_per_seq_id[seq_id].size() > 1) != hetero)
+					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;
+
+					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");
+				}
+			}
+
+			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)
+			{
+				for (const auto &[seq_id, comp_ids] : mon_per_seq_id)
+				{
+					if (si == se)
+						return false;
+
+					bool match = false;
+
+					for (auto comp_id : comp_ids)
+					{
+						std::string letter;
+
+						if (can)
+						{
+							if (compound_factory::kBaseMap.contains(comp_id))
+								letter = compound_factory::kBaseMap.at(comp_id);
+							else
+							{
+								auto c = cf.create(comp_id);
+								if (c and c->one_letter_code())
+									letter = c->one_letter_code();
+								else
+									letter = "X";
+							}
+						}
+						else
+						{
+							if (compound_factory::kAAMap.contains(comp_id))
+								letter = compound_factory::kAAMap.at(comp_id);
+							else if (comp_id.length() == 1 and compound_factory::kBaseMap.contains(comp_id))
+								letter = compound_factory::kBaseMap.at(comp_id);
+							else
+								letter = '(' + comp_id + ')';
+						}
+						
+						if (iequals(std::string{si, si + letter.length()}, letter))
+						{
+							match = true;
+							si += letter.length();
+							break;
+						}
+						else
+							return false;
+					}
+
+					if (not match)
+						break;
+				}
+
+				return si == se;
+			};
+
+			if (not seq.has_value())
+			{
+				if (cif::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());
+
+				if (not seq_match(false, seq->begin(), seq->end()))
+					throw std::runtime_error("Sequences do not match for entity " + entity_id);
+			}
+
+			if (not seq_can.has_value())
+			{
+				if (cif::VERBOSE > 0)
+					std::clog << "Warning: entity_poly has no 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());
+
+				if (not seq_match(true, seq_can->begin(), seq_can->end()))
+					throw std::runtime_error("Canonical sequences do not match for entity " + entity_id);
+			}
+		}
+
+		result = true;
+	}
+	catch (const std::exception &ex)
+	{
+		result = false;
+		if (cif::VERBOSE > 0)
+			std::clog << ex.what() << '\n';
+		ec = make_error_code(validation_error::not_valid_pdbx);
+	}
+
+	if (not result and ec == std::errc())
+		ec = make_error_code(validation_error::not_valid_pdbx);
+
+	return result;
+}
+
+} // namespace cif::pdb
+  

src/row.cpp

@@ -29,44 +29,44 @@
 namespace cif
 {
 
-void row_handle::assign(uint16_t column, std::string_view value, bool updateLinked, bool validate)
+void row_handle::assign(uint16_t item, std::string_view value, bool updateLinked, bool validate)
 {
 	if (not m_category)
 		throw std::runtime_error("uninitialized row");
 
-	m_category->update_value(m_row, column, value, updateLinked, validate);
+	m_category->update_value(m_row, item, value, updateLinked, validate);
 }
 
-uint16_t row_handle::get_column_ix(std::string_view name) const
+uint16_t row_handle::get_item_ix(std::string_view name) const
 {
 	if (not m_category)
 		throw std::runtime_error("uninitialized row");
 
-	return m_category->get_column_ix(name);
+	return m_category->get_item_ix(name);
 }
 
-std::string_view row_handle::get_column_name(uint16_t ix) const
+std::string_view row_handle::get_item_name(uint16_t ix) const
 {
 	if (not m_category)
 		throw std::runtime_error("uninitialized row");
 
-	return m_category->get_column_name(ix);
+	return m_category->get_item_name(ix);
 }
 
-uint16_t row_handle::add_column(std::string_view name)
+uint16_t row_handle::add_item(std::string_view name)
 {
 	if (not m_category)
 		throw std::runtime_error("uninitialized row");
 
-	return m_category->add_column(name);
+	return m_category->add_item(name);
 }
 
-void row_handle::swap(uint16_t column, row_handle &b)
+void row_handle::swap(uint16_t item, row_handle &b)
 {
 	if (not m_category)
 		throw std::runtime_error("uninitialized row");
 
-	m_category->swap_item(column, *this, b);
+	m_category->swap_item(item, *this, b);
 }
 
 // --------------------------------------------------------------------
@@ -86,7 +86,7 @@ row_initializer::row_initializer(row_handle rh)
 		auto &i = r->operator[](ix);
 		if (not i)
 			continue;
-		emplace_back(cat.get_column_name(ix), i.text());
+		emplace_back(cat.get_item_name(ix), i.text());
 	}
 }
 

src/text.cpp

@@ -215,19 +215,19 @@ std::string trim_copy(std::string_view s)
 
 // --------------------------------------------------------------------
 
-std::tuple<std::string, std::string> split_tag_name(std::string_view tag)
+std::tuple<std::string, std::string> split_item_name(std::string_view item_name)
 {
-	if (tag.empty())
-		throw std::runtime_error("empty tag");
-	if (tag[0] != '_')
-		throw std::runtime_error("tag '" + std::string { tag } + "' does not start with underscore");
+	if (item_name.empty())
+		throw std::runtime_error("empty item_name");
+	if (item_name[0] != '_')
+		throw std::runtime_error("item_name '" + std::string { item_name } + "' does not start with underscore");
 
-	auto s = tag.find('.');
+	auto s = item_name.find('.');
 	if (s == std::string::npos)
-		// throw std::runtime_error("tag does not contain dot (" + std::string{ tag } + ')');
-		return std::tuple<std::string, std::string>{ "", tag.substr(1) };
+		// throw std::runtime_error("item_name does not contain dot (" + std::string{ item_name } + ')');
+		return std::tuple<std::string, std::string>{ "", item_name.substr(1) };
 	else
-		return std::tuple<std::string, std::string>{tag.substr(1, s - 1), tag.substr(s + 1)};
+		return std::tuple<std::string, std::string>{item_name.substr(1, s - 1), item_name.substr(s + 1)};
 }
 
 // --------------------------------------------------------------------

src/validate.cpp

@@ -39,16 +39,35 @@
 // the code will use boost::regex instead.
 
 #if USE_BOOST_REGEX
-#include <boost/regex.hpp>
+# include <boost/regex.hpp>
 using boost::regex;
 #else
-#include <regex>
+# include <regex>
 using std::regex;
 #endif
 
 namespace cif
 {
 
+validation_exception::validation_exception(std::error_code ec)
+	: runtime_error(ec.message())
+{
+}
+
+validation_exception::validation_exception(std::error_code ec, std::string_view category)
+	: runtime_error(
+		  (std::ostringstream{} << ec.message() << "; category: " << std::quoted(category)).str())
+{
+}
+
+validation_exception::validation_exception(std::error_code ec, std::string_view category, std::string_view item)
+	: runtime_error(
+		  (std::ostringstream{} << ec.message() << "; category: " << std::quoted(category) << "; item: " << std::quoted(item)).str())
+{
+}
+
+// --------------------------------------------------------------------
+
 struct regex_impl : public regex
 {
 	regex_impl(std::string_view rx)
@@ -57,20 +76,11 @@ struct regex_impl : public regex
 	}
 };
 
-validation_error::validation_error(const std::string &msg)
-	: m_msg(msg)
-{
-}
-
-validation_error::validation_error(const std::string &cat, const std::string &item, const std::string &msg)
-	: m_msg("When validating _" + cat + '.' + item + ": " + msg)
-{
-}
-
 // --------------------------------------------------------------------
 
-DDL_PrimitiveType map_to_primitive_type(std::string_view s)
+DDL_PrimitiveType map_to_primitive_type(std::string_view s, std::error_code &ec) noexcept
 {
+	ec = {};
 	DDL_PrimitiveType result;
 	if (iequals(s, "char"))
 		result = DDL_PrimitiveType::Char;
@@ -79,7 +89,16 @@ DDL_PrimitiveType map_to_primitive_type(std::string_view s)
 	else if (iequals(s, "numb"))
 		result = DDL_PrimitiveType::Numb;
 	else
-		throw validation_error("Not a known primitive type");
+		ec = make_error_code(validation_error::not_a_known_primitive_type);
+	return result;
+}
+
+DDL_PrimitiveType map_to_primitive_type(std::string_view s)
+{
+	std::error_code ec;
+	auto result = map_to_primitive_type(s, ec);
+	if (ec)
+		throw std::system_error(ec, std::string{ s });
 	return result;
 }
 
@@ -196,63 +215,72 @@ int type_validator::compare(std::string_view a, std::string_view b) const
 
 // --------------------------------------------------------------------
 
-// void ValidateItem::addLinked(ValidateItem* parent, const std::string& parentItem, const std::string& childItem)
-//{
-////	if (mParent != nullptr and VERBOSE)
-////		cerr << "replacing parent in " << mCategory->m_name << " from " << mParent->mCategory->m_name << " to " << parent->mCategory->m_name << endl;
-////	mParent = parent;
-//
-//	if (m_type == nullptr and parent != nullptr)
-//		m_type = parent->m_type;
-//
-//	if (parent != nullptr)
-//	{
-//		mLinked.push_back({parent, parentItem, childItem});
-//
-//		parent->mChildren.insert(this);
-////
-////		if (mCategory->mKeys == std::vector<std::string>{mTag})
-////			parent->mForeignKeys.insert(this);
-//	}
-//}
-
 void item_validator::operator()(std::string_view value) const
 {
+	std::error_code ec;
+	if (not validate_value(value, ec))
+		throw std::system_error(ec, std::string{ value } + " does not match rx for " + m_item_name);
+}
+
+bool item_validator::validate_value(std::string_view value, std::error_code &ec) const noexcept
+{
+	ec = {};
+
 	if (not value.empty() and value != "?" and value != ".")
 	{
 		if (m_type != nullptr and not regex_match(value.begin(), value.end(), *m_type->m_rx))
-			throw validation_error(m_category->m_name, m_tag, "Value '" + std::string{ value } + "' does not match type expression for type " + m_type->m_name);
-
-		if (not m_enums.empty())
-		{
-			if (m_enums.count(std::string{ value }) == 0)
-				throw validation_error(m_category->m_name, m_tag, "Value '" + std::string{ value } + "' is not in the list of allowed values");
-		}
+			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();
 }
 
 // --------------------------------------------------------------------
 
-void category_validator::addItemValidator(item_validator &&v)
+void category_validator::add_item_validator(item_validator &&v)
 {
 	if (v.m_mandatory)
-		m_mandatory_fields.insert(v.m_tag);
+		m_mandatory_items.insert(v.m_item_name);
 
 	v.m_category = this;
 
 	auto r = m_item_validators.insert(std::move(v));
 	if (not r.second and VERBOSE >= 4)
-		std::cout << "Could not add validator for item " << v.m_tag << " to category " << m_name << '\n';
+		std::cout << "Could not add validator for item " << v.m_item_name << " to category " << m_name << '\n';
 }
 
-const item_validator *category_validator::get_validator_for_item(std::string_view tag) const
+const item_validator *category_validator::get_validator_for_item(std::string_view item_name) const
 {
 	const item_validator *result = nullptr;
-	auto i = m_item_validators.find(item_validator{ std::string(tag) });
+	auto i = m_item_validators.find(item_validator{ std::string(item_name) });
 	if (i != m_item_validators.end())
 		result = &*i;
 	else if (VERBOSE > 4)
-		std::cout << "No validator for tag " << tag << '\n';
+		std::cout << "No validator for item " << item_name << '\n';
+	return result;
+}
+
+const item_validator *category_validator::get_validator_for_aliased_item(std::string_view item_name) const
+{
+	const item_validator *result = nullptr;
+
+	for (auto &iv : m_item_validators)
+	{
+		for (auto &ai : iv.m_aliases)
+		{
+			const auto &[cat, name] = split_item_name(ai.m_name);
+			if (iequals(name, item_name) and iequals(cat, m_name))
+			{
+				result = &iv;
+				break;
+			}
+		}
+		if (result)
+			break;
+	}
+
 	return result;
 }
 
@@ -295,19 +323,19 @@ const category_validator *validator::get_validator_for_category(std::string_view
 	return result;
 }
 
-item_validator *validator::get_validator_for_item(std::string_view tag) const
+item_validator *validator::get_validator_for_item(std::string_view item_name) const
 {
 	item_validator *result = nullptr;
 
 	std::string cat, item;
-	std::tie(cat, item) = split_tag_name(tag);
+	std::tie(cat, item) = split_item_name(item_name);
 
 	auto *cv = get_validator_for_category(cat);
 	if (cv != nullptr)
 		result = const_cast<item_validator *>(cv->get_validator_for_item(item));
 
 	if (result == nullptr and VERBOSE > 4)
-		std::cout << "No validator for item " << tag << '\n';
+		std::cout << "No validator for item " << item_name << '\n';
 
 	return result;
 }
@@ -332,11 +360,11 @@ void validator::add_link_validator(link_validator &&v)
 		auto piv = pcv->get_validator_for_item(v.m_parent_keys[i]);
 
 		if (piv == nullptr)
-			throw std::runtime_error("unknown parent tag _" + v.m_parent_category + '.' + v.m_parent_keys[i]);
+			throw std::runtime_error("unknown parent item _" + v.m_parent_category + '.' + v.m_parent_keys[i]);
 
 		auto civ = ccv->get_validator_for_item(v.m_child_keys[i]);
 		if (civ == nullptr)
-			throw std::runtime_error("unknown child tag _" + v.m_child_category + '.' + v.m_child_keys[i]);
+			throw std::runtime_error("unknown child item _" + v.m_child_category + '.' + v.m_child_keys[i]);
 
 		if (civ->m_type == nullptr and piv->m_type != nullptr)
 			const_cast<item_validator *>(civ)->m_type = piv->m_type;
@@ -351,7 +379,7 @@ std::vector<const link_validator *> validator::get_links_for_parent(std::string_
 
 	for (auto &l : m_link_validators)
 	{
-		if (l.m_parent_category == category)
+		if (iequals(l.m_parent_category, category))
 			result.push_back(&l);
 	}
 
@@ -364,19 +392,32 @@ std::vector<const link_validator *> validator::get_links_for_child(std::string_v
 
 	for (auto &l : m_link_validators)
 	{
-		if (l.m_child_category == category)
+		if (iequals(l.m_child_category, category))
 			result.push_back(&l);
 	}
 
 	return result;
 }
 
-void validator::report_error(const std::string &msg, bool fatal) const
+void validator::report_error(std::error_code ec, bool fatal) const
 {
 	if (m_strict or fatal)
-		throw validation_error(msg);
-	else if (VERBOSE > 0)
-		std::cerr << msg << '\n';
+		throw validation_exception(ec);
+	else
+		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);
+
+	if (m_strict or fatal)
+		throw ex;
+	else
+		std::cerr << ex.what() << '\n';
 }
 
 // --------------------------------------------------------------------
@@ -438,12 +479,12 @@ const validator &validator_factory::operator[](std::string_view dictionary_name)
 			if (not std::filesystem::exists(p, ec) or ec)
 			{
 				for (const char *dir : {
-#if defined(CACHE_DIR)
+# if defined(CACHE_DIR)
 						 CACHE_DIR,
-#endif
-#if defined(DATA_DIR)
+# endif
+# if defined(DATA_DIR)
 							 DATA_DIR
-#endif
+# endif
 					 })
 				{
 					auto p2 = std::filesystem::path(dir) / p;

test/reconstruction-test.cpp

@@ -0,0 +1,64 @@
+/*-
+ * 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
+ * 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 "test-main.hpp"
+
+#include <cif++.hpp>
+
+#include <catch2/catch.hpp>
+
+#include <iostream>
+#include <fstream>
+
+TEST_CASE("reconstruct")
+{
+	cif::compound_factory::instance().push_dictionary(gTestDir / "REA.cif");
+
+	for (std::filesystem::directory_iterator i(gTestDir / "reconstruct"); i != std::filesystem::directory_iterator{}; ++i)
+	{
+		std::cout << i->path() << '\n';
+
+		if (i->path().extension() == ".pdb")
+		{
+			cif::file f = cif::pdb::read(i->path());
+
+			std::error_code ec;
+
+			if (not cif::pdb::is_valid_pdbx_file(f, ec))
+				CHECK(cif::pdb::reconstruct_pdbx(f));
+		}
+		else
+		{
+			cif::file f(i->path());
+
+			std::error_code ec;
+			CHECK_FALSE(cif::pdb::is_valid_pdbx_file(f, ec));
+			CHECK(ec != std::errc{});
+
+			CHECK(cif::pdb::reconstruct_pdbx(f));
+		}
+	}
+}

test/rename-compound-test.cpp

@@ -37,8 +37,8 @@ TEST_CASE("rename")
 {
 	cif::VERBOSE = 3;
 
-	if (std::filesystem::exists(gTestDir / ".." / "data" / "ccd-subset.cif"))
-		cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
+	if (std::filesystem::exists(gTestDir / ".." / "rsrc" / "ccd-subset.cif"))
+		cif::add_file_resource("components.cif", gTestDir / ".." / "rsrc" / "ccd-subset.cif");
 
 	if (std::filesystem::exists(gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic"))
 		cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");

test/test-main.cpp

@@ -13,10 +13,11 @@ int main(int argc, char *argv[])
 
 	// Build a new parser on top of Catch2's
 	using namespace Catch::clara;
-	auto cli = session.cli()                                // Get Catch2's command line parser
-	           | Opt(gTestDir, "data-dir")                // bind variable to a new option, with a hint string
-	                 ["-D"]["--data-dir"]                   // the option names it will respond to
-	           ("The directory containing the data files"); // description string for the help output
+	auto cli = session.cli()                               // Get Catch2's command line parser
+	           | Opt(gTestDir, "data-dir")                 // bind variable to a new option, with a hint string
+	                 ["-D"]["--data-dir"]                  // the option names it will respond to
+	           ("The directory containing the data files") // description string for the help output
+	           | Opt(cif::VERBOSE, "verbose")["-v"]["--cif-verbose"]("Flag for cif::VERBOSE");
 
 	// Now pass the new composite back to Catch2 so it uses that
 	session.cli(cli);
@@ -30,10 +31,9 @@ int main(int argc, char *argv[])
 	cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
 
 	// initialize CCD location
-	cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
+	cif::add_file_resource("components.cif", gTestDir / ".." / "rsrc" / "ccd-subset.cif");
 
 	cif::compound_factory::instance().push_dictionary(gTestDir / "HEM.cif");
 
-
 	return session.run();
 }

test/unit-v2-test.cpp

@@ -568,7 +568,7 @@ _test.value
 	auto &test = db["test"];
 	REQUIRE(test.size() == 5);
 
-	REQUIRE(test.exists("value"_key == cif::null));
+	REQUIRE(test.contains("value"_key == cif::null));
 	REQUIRE(test.find("value"_key == cif::null).size() == 2);
 }
 
@@ -3468,3 +3468,22 @@ TEST_CASE("compound_not_found_test_1")
 	auto cmp = cif::compound_factory::instance().create("&&&");
 	REQUIRE(cmp == nullptr);
 }
+
+// --------------------------------------------------------------------
+// PDB2CIF tests
+
+TEST_CASE("pdb2cif_formula_weight")
+{
+	cif::compound_factory::instance().push_dictionary(gTestDir / "REA.cif");
+
+	cif::file a = cif::pdb::read(gTestDir / "pdb1cbs.ent.gz");
+	
+	auto fw = a.front()["entity"].find1<float>(cif::key("id") == 1, "formula_weight");
+	CHECK(std::abs(fw - 15581.802f) < 0.1f);
+
+	fw = a.front()["entity"].find1<float>(cif::key("id") == 2, "formula_weight");
+	CHECK(fw == 300.435f);
+
+	fw = a.front()["entity"].find1<float>(cif::key("id") == 3, "formula_weight");
+	CHECK(fw == 18.015f);
+}

test/validate-pdbx-test.cpp

@@ -0,0 +1,286 @@
+/*-
+ * SPDX-License-Identifier: BSD-2-Clause
+ *
+ * Copyright (c) 2020 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 "test-main.hpp"
+
+#include <catch2/catch.hpp>
+
+#include <cif++.hpp>
+
+#include <stdexcept>
+
+// --------------------------------------------------------------------
+
+cif::file operator""_cf(const char *text, size_t length)
+{
+	struct membuf : public std::streambuf
+	{
+		membuf(char *text, size_t length)
+		{
+			this->setg(text, text, text + length);
+		}
+	} buffer(const_cast<char *>(text), length);
+
+	std::istream is(&buffer);
+	return cif::file(is);
+}
+
+// --------------------------------------------------------------------
+
+TEST_CASE("test-1")
+{
+	auto f = R"(data_1CBS
+# 
+_entry.id   1CBS 
+# 
+_entity.id                     1
+_entity.type                   polymer
+# 
+_entity_poly.entity_id                      1 
+_entity_poly.type                           'polypeptide(L)' 
+_entity_poly.nstd_linkage                   no 
+_entity_poly.nstd_monomer                   no 
+_entity_poly.pdbx_seq_one_letter_code       
+;PNFSG
+;
+_entity_poly.pdbx_seq_one_letter_code_can   
+;PNFSG
+;
+_entity_poly.pdbx_strand_id                 A 
+_entity_poly.pdbx_target_identifier         ? 
+# 
+loop_
+_entity_poly_seq.entity_id 
+_entity_poly_seq.num 
+_entity_poly_seq.mon_id 
+_entity_poly_seq.hetero 
+1 1   PRO n 
+1 2   ASN n 
+1 3   PHE n 
+1 4   SER n 
+1 5   GLY n 
+#
+loop_
+_struct_asym.id 
+_struct_asym.pdbx_blank_PDB_chainid_flag 
+_struct_asym.pdbx_modified 
+_struct_asym.entity_id 
+_struct_asym.details 
+A N N 1 ? 
+# 
+loop_
+_atom_type.symbol 
+C 
+N 
+O 
+S 
+# 
+loop_
+_atom_site.group_PDB 
+_atom_site.id 
+_atom_site.type_symbol 
+_atom_site.label_atom_id 
+_atom_site.label_alt_id 
+_atom_site.label_comp_id 
+_atom_site.label_asym_id 
+_atom_site.label_entity_id 
+_atom_site.label_seq_id 
+_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_asym_id 
+_atom_site.auth_atom_id 
+_atom_site.pdbx_PDB_model_num 
+ATOM   2    C CA  . PRO A 1 1   ? 18.150 13.525 43.680 1.00 28.82 ? 1   PRO A CA  1 
+ATOM   9    C CA  . ASN A 1 2   ? 20.576 16.457 43.578 1.00 20.79 ? 2   ASN A CA  1 
+ATOM   17   C CA  . PHE A 1 3   ? 21.144 17.838 40.087 1.00 12.62 ? 3   PHE A CA  1 
+ATOM   28   C CA  . SER A 1 4   ? 23.170 20.780 41.464 1.00 11.30 ? 4   SER A CA  1 
+ATOM   34   C CA  . GLY A 1 5   ? 26.628 21.486 40.103 1.00 10.86 ? 5   GLY A CA  1 
+# 
+loop_
+_pdbx_poly_seq_scheme.asym_id 
+_pdbx_poly_seq_scheme.entity_id 
+_pdbx_poly_seq_scheme.seq_id 
+_pdbx_poly_seq_scheme.mon_id 
+_pdbx_poly_seq_scheme.ndb_seq_num 
+_pdbx_poly_seq_scheme.pdb_seq_num 
+_pdbx_poly_seq_scheme.auth_seq_num 
+_pdbx_poly_seq_scheme.pdb_mon_id 
+_pdbx_poly_seq_scheme.auth_mon_id 
+_pdbx_poly_seq_scheme.pdb_strand_id 
+_pdbx_poly_seq_scheme.pdb_ins_code 
+_pdbx_poly_seq_scheme.hetero 
+A 1 1   PRO 1   1   1   PRO PRO A . n 
+A 1 2   ASN 2   2   2   ASN ASN A . n 
+A 1 3   PHE 3   3   3   PHE PHE A . n 
+A 1 4   SER 4   4   4   SER SER A . n 
+A 1 5   GLY 5   5   5   GLY GLY A . n 
+# 
+)"_cf;
+
+	SECTION("Plain file")
+	{
+		REQUIRE(cif::pdb::is_valid_pdbx_file(f));
+	}
+
+	SECTION("Delete one atom_site")
+	{
+		auto &db = f.front();
+		auto n = db["atom_site"].erase(cif::key("id") == 2);
+
+		REQUIRE(n == 1);
+
+		REQUIRE(cif::pdb::is_valid_pdbx_file(f));
+	}
+
+	SECTION("Delete a pdbx_poly_seq_scheme record")
+	{
+		auto &db = f.front();
+		auto n = db["pdbx_poly_seq_scheme"].erase(cif::key("seq_id") == 2);
+
+		REQUIRE(n == 1);
+
+		REQUIRE_FALSE(cif::pdb::is_valid_pdbx_file(f));
+	}
+
+	SECTION("Delete an entity_poly_seq record")
+	{
+		auto &db = f.front();
+		auto n = db["entity_poly_seq"].erase(cif::key("num") == 2);
+
+		REQUIRE(n == 1);
+
+		REQUIRE_FALSE(cif::pdb::is_valid_pdbx_file(f));
+	}
+
+	SECTION("Delete an entity_poly record")
+	{
+		auto &db = f.front();
+		auto n = db["entity_poly"].erase(cif::key("entity_id") == 1);
+
+		REQUIRE(n == 1);
+
+		REQUIRE_FALSE(cif::pdb::is_valid_pdbx_file(f));
+	}
+
+	SECTION("Mutate an atom_site record")
+	{
+		auto &db = f.front();
+		auto r = db["atom_site"].find1(cif::key("id") == 9);
+		r.assign({
+			{ "label_comp_id", "ALA" },
+			{ "auth_comp_id", "ALA" }
+		});
+
+		REQUIRE_FALSE(cif::pdb::is_valid_pdbx_file(f));
+	}
+
+	SECTION("Hetero consistency")
+	{
+		auto &db = f.front();
+		db["entity_poly_seq"].emplace({ //
+			{ "entity_id", 1 },
+			{ "num", 1 },
+			{ "mon_id", "ALA" },
+			{ "hetero", "n" }
+		});
+
+		db["pdbx_poly_seq_scheme"].emplace({ //
+			{ "asym_id", "A" },
+			{ "entity_id", "1" },
+			{ "seq_id", "1" },
+			{ "mon_id", "ALA" },
+			{ "ndb_seq_num", "1" },
+			{ "pdb_seq_num", "1" },
+			{ "auth_seq_num", "1" },
+			{ "pdb_mon_id", "ALA" },
+			{ "auth_mon_id", "ALA" },
+			{ "pdb_strand_id", "A" },
+			{ "pdb_ins_code", "." },
+			{ "hetero", "n" }
+		});
+
+		REQUIRE_FALSE(cif::pdb::is_valid_pdbx_file(f));
+	}
+
+	SECTION("Missing hetero for record in atom_site")
+	{
+		auto &db = f.front();
+		
+		auto r1 = db["atom_site"].front();
+		cif::row_initializer cr(r1);
+		cr.set_value("id", "3");
+		cr.set_value("label_comp_id", "ALA");
+
+		db["atom_site"].emplace(std::move(cr));
+
+		REQUIRE_FALSE(cif::pdb::is_valid_pdbx_file(f));
+	}
+
+	SECTION("Missing letter in entity_poly.pdbx_seq_one_letter_code")
+	{
+		auto &db = f.front();
+		auto &entity_poly = db["entity_poly"];
+
+		entity_poly.front().assign({
+			{ "pdbx_seq_one_letter_code", "PNSG" }
+		});
+
+		REQUIRE_FALSE(cif::pdb::is_valid_pdbx_file(f));
+	}
+
+	SECTION("Too many letters in entity_poly.pdbx_seq_one_letter_code")
+	{
+		auto &db = f.front();
+		auto &entity_poly = db["entity_poly"];
+
+		entity_poly.front().assign({
+			{ "pdbx_seq_one_letter_code", "PNFSGX" }
+		});
+
+		REQUIRE_FALSE(cif::pdb::is_valid_pdbx_file(f));
+	}
+
+	SECTION("Mismatch in entity_poly.pdbx_seq_one_letter_code")
+	{
+		auto &db = f.front();
+		auto &entity_poly = db["entity_poly"];
+
+		entity_poly.front().assign({
+			{ "pdbx_seq_one_letter_code", "PNASG" }
+		});
+
+		REQUIRE_FALSE(cif::pdb::is_valid_pdbx_file(f));
+	}
+
+
+}

tools/update-libcifpp-data.in

@@ -10,7 +10,7 @@ euid=${EUID:-$(id -u)}
 
 if [ "${euid}" -ne 0 ]; then
 	echo "Please run as root"
-	exit
+	exit 1
 fi
 
 if [ -f "@CIFPP_ETC_DIR@/libcifpp.conf" ]; then
@@ -19,12 +19,13 @@ fi
 
 # check to see if we're supposed to run at all
 if [ "$update" != "true" ]; then
-	exit
+	exit 0
 fi
 
 # if cache directory doesn't exist, exit.
 if ! [ -d "@CIFPP_CACHE_DIR@" ]; then
-	exit
+	echo "Cache directory '@CIFPP_CACHE_DIR@' does not exist"
+	exit 1
 fi
 
 # Create a temp file in the right directory and
@@ -60,12 +61,16 @@ update_dictionary() {
 
 # Update the dictionaries
 
-update_dictionary "@CIFPP_CACHE_DIR@/components.cif" "https://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz"
+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"
 
-# notify subscribers, will fail on FreeBSD
+# notify subscribers, using find instead of run-parts to make it work on FreeBSD as well
 
-if [ -d "@CIFPP_ETC_DIR@/libcifpp/cache-update.d" ] && [ -x /bin/run-parts ]; then
-	run-parts --arg "@CIFPP_CACHE_DIR@" -- "@CIFPP_ETC_DIR@/libcifpp/cache-update.d"
+if [ -d "@CIFPP_ETC_DIR@/libcifpp/cache-update.d" ]; then
+	find "@CIFPP_ETC_DIR@/libcifpp/cache-update.d" \
+		-exec test -x {} \; -and -not -exec test -d {} \; \
+		-exec {} "@CIFPP_CACHE_DIR@" \;
 fi
+
+exit 0