Merge branch 'trunk' into dict-for-data

.clang-format

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

.github/workflows/build-documentation.yml

@@ -19,7 +19,7 @@ jobs:
   docs:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - 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.
@@ -47,7 +47,7 @@ jobs:
         ls -l ${{ steps.strings.outputs.build-output-dir }}/docs/sphinx
 
     - name: Upload artifact
-      uses: actions/upload-pages-artifact@v3
+      uses: actions/upload-pages-artifact@v2
       with:
         path: ${{ steps.strings.outputs.build-output-dir }}/docs/sphinx
 
@@ -62,4 +62,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v4
+        uses: actions/deploy-pages@v2

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

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

.gitignore

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

CMakeLists.txt

@@ -24,25 +24,29 @@
 
 cmake_minimum_required(VERSION 3.23)
 
-if(CMAKE_SOURCE_DIR STREQUAL CMAKE_CURRENT_SOURCE_DIR AND NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
-	set(CMAKE_BUILD_TYPE Release CACHE STRING "Build type" FORCE)
-	set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
-endif()
-
 # set the project name
 project(
 	libcifpp
-	VERSION 9.0.4
-	LANGUAGES CXX C)
+	VERSION 8.0.0
+	LANGUAGES CXX)
 
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 
 include(FindAtomic)
+include(CheckFunctionExists)
+include(CheckIncludeFiles)
+include(CheckLibraryExists)
 include(CMakePackageConfigHelpers)
+include(CheckCXXSourceCompiles)
 include(GenerateExportHeader)
 include(CTest)
-include(ExternalProject)
 include(FetchContent)
+include(ExternalProject)
+
+# FindBoost, take care of it now.
+if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.30)
+	cmake_policy(SET CMP0167 NEW)
+endif()
 
 # When building with ninja-multiconfig, build both debug and release by default
 if(CMAKE_GENERATOR STREQUAL "Ninja Multi-Config")
@@ -59,23 +63,25 @@ elseif(MSVC)
 endif()
 
 # Build documentation?
-set(BUILD_DOCUMENTATION OFF CACHE BOOL "Build the documentation")
+option(BUILD_DOCUMENTATION "Build the documentation" OFF)
 
 # Optionally build a version to be installed inside CCP4
-set(BUILD_FOR_CCP4 OFF CACHE BOOL "Build a version to be installed in CCP4")
+option(BUILD_FOR_CCP4 "Build a version to be installed in CCP4")
 
 # Building shared libraries?
 if(NOT(BUILD_FOR_CCP4 AND WIN32))
-	set(BUILD_SHARED_LIBS OFF CACHE BOOL "Build a shared library instead of a static one")
+	option(BUILD_SHARED_LIBS "Build a shared library instead of a static one" OFF)
 endif()
 
 if(PROJECT_IS_TOP_LEVEL AND NOT BUILD_FOR_CCP4)
 	# Lots of code depend on the availability of the components.cif file
-	set(CIFPP_DOWNLOAD_CCD ON CACHE BOOL "Download the CCD file components.cif during installation")
+	option(CIFPP_DOWNLOAD_CCD
+		"Download the CCD file components.cif during installation" ON)
 
 	# An optional cron script can be installed to keep the data files up-to-date
 	if(UNIX AND NOT APPLE)
-		set(CIFPP_INSTALL_UPDATE_SCRIPT ON CACHE BOOL "Install the script to update CCD and dictionary files")
+		option(CIFPP_INSTALL_UPDATE_SCRIPT
+			"Install the script to update CCD and dictionary files" ON)
 	endif()
 else()
 	unset(CIFPP_DOWNLOAD_CCD)
@@ -85,13 +91,14 @@ endif()
 # When CCP4 is sourced in the environment, we can recreate the symmetry
 # operations table
 if(EXISTS "$ENV{CCP4}/lib/data/syminfo.lib")
-	set(CIFPP_RECREATE_SYMOP_DATA ON CACHE BOOL "Recreate SymOp data table in case it is out of date")
+	option(CIFPP_RECREATE_SYMOP_DATA
+		"Recreate SymOp data table in case it is out of date" ON)
 endif()
 
 # CCP4 build
 if(BUILD_FOR_CCP4)
 	if("$ENV{CCP4}" STREQUAL "" OR NOT EXISTS $ENV{CCP4})
-		message(FATAL_ERROR "cifpp: A CCP4 built was requested but CCP4 was not sourced")
+		message(FATAL_ERROR "A CCP4 built was requested but CCP4 was not sourced")
 	else()
 		list(PREPEND CMAKE_MODULE_PATH "$ENV{CCP4}")
 		list(PREPEND CMAKE_PREFIX_PATH "$ENV{CCP4}")
@@ -121,6 +128,9 @@ if(WIN32)
 		add_definitions(-D _WIN32_WINNT=0x0501)
 	endif()
 
+	# Man, this is 2024 we're living in...
+	add_definitions(-DNOMINMAX)
+
 	# We do not want to write an export file for all our symbols...
 	set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
 endif()
@@ -140,8 +150,51 @@ endif()
 
 # Libraries
 
+# Start by finding out if std:regex is usable. Note that the current
+# implementation in GCC is not acceptable, it crashes on long lines. The
+# implementation in libc++ (clang) and MSVC seem to be OK.
+check_cxx_source_compiles(
+	"
+#include <iostream>
+#ifndef __GLIBCXX__
+#error
+#endif
+int main(int argc, char *argv[]) { return 0; }"
+	GXX_LIBSTDCPP)
+
+if(GXX_LIBSTDCPP)
+	message(
+		STATUS "Testing for known regex bug, since you're using GNU libstdc++")
+
+	try_run(STD_REGEX_RUNNING STD_REGEX_COMPILING
+		${CMAKE_CURRENT_BINARY_DIR}/test
+		${CMAKE_CURRENT_SOURCE_DIR}/cmake/test-rx.cpp)
+
+	if(STD_REGEX_RUNNING STREQUAL FAILED_TO_RUN)
+		message(
+			STATUS
+			"You are probably trying to compile using the g++ standard library which contains a crashing std::regex implementation. Will use boost::regex instead"
+		)
+
+		find_package(Boost 1.80 QUIET COMPONENTS regex)
+
+		if(NOT Boost_FOUND)
+			set(BOOST_REGEX_STANDALONE ON)
+
+			FetchContent_Declare(
+				boost-rx
+				GIT_REPOSITORY https://github.com/boostorg/regex
+				GIT_TAG boost-1.83.0)
+
+			FetchContent_MakeAvailable(boost-rx)
+		endif()
+
+		set(BOOST_REGEX ON)
+	endif()
+endif()
+
 if(MSVC)
-	# Avoid linking the shared library of zlib. Search ZLIB_ROOT first if it is
+	# Avoid linking the shared library of zlib Search ZLIB_ROOT first if it is
 	# set.
 	if(ZLIB_ROOT)
 		set(_ZLIB_SEARCH_ROOT PATHS ${ZLIB_ROOT} NO_DEFAULT_PATH)
@@ -168,43 +221,11 @@ if(MSVC)
 	endforeach()
 endif()
 
-# First check if <format> is available
-find_file(FMT NAME format)
-
-if(FMT EQUAL "FMT-NOTFOUND")
-	if(NOT (fmt_FOUND OR TARGET fmt))
-		find_package(fmt REQUIRED)
-		message(FATAL_ERROR "cifpp: <format> not found and neither was libfmt, compiler too old, you're out of luck")
-	endif()
-endif()
-
-# Using fast_float for float parsing, but only if needed
-# try_compile(STD_CHARCONV_COMPILING
-# 	SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/cmake/test-charconv.cpp)
-
-if(NOT STD_CHARCONV_COMPILING)
-	message(NOTICE "libcifpp: Using fast_float for std::from_chars")
-	FetchContent_Declare(fastfloat
-		GIT_REPOSITORY "https://github.com/fastfloat/fast_float"
-		GIT_TAG v8.0.2)
-	FetchContent_MakeAvailable(fastfloat)
-endif()
-
-find_package(Threads)
 find_package(ZLIB QUIET)
+find_package(Threads)
 
 if(NOT ZLIB_FOUND)
-	message(FATAL_ERROR "cifpp: The zlib development files were not found you this system, please install them and try again (hint: on debian/ubuntu use apt-get install zlib1g-dev)")
-endif()
-
-include(FindPkgConfig)
-
-if(PKG_CONFIG_FOUND)
-	pkg_check_modules(PCRE2 IMPORTED_TARGET libpcre2-8)
-endif()
-
-if(NOT PCRE2_FOUND)
-	add_subdirectory(pcre2-simple)
+	message(FATAL_ERROR "The zlib development files were not found you this system, please install them and try again (hint: on debian/ubuntu use apt-get install zlib1g-dev)")
 endif()
 
 # Using Eigen3 is a bit of a thing. We don't want to build it completely since
@@ -218,16 +239,16 @@ if(Eigen3_FOUND AND TARGET Eigen3::Eigen)
 else()
 	# Use ExternalProject since FetchContent always tries to install the result...
 	ExternalProject_Add(my-eigen3
-		URL https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.zip
-		DOWNLOAD_EXTRACT_TIMESTAMP TRUE
-		CONFIGURE_COMMAND ""
-		BUILD_COMMAND ""
+		GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
+		GIT_TAG 3.4.0
 		INSTALL_COMMAND "")
-
+	
 	ExternalProject_Get_Property(my-eigen3 SOURCE_DIR)
 	set(EIGEN_INCLUDE_DIR ${SOURCE_DIR})
 endif()
 
+message(STATUS "Eigen include dir is ${EIGEN_INCLUDE_DIR}")
+
 # Create a revision file, containing the current git version info
 include(VersionString)
 write_version_header(${CMAKE_CURRENT_SOURCE_DIR}/src/ LIB_NAME "LibCIFPP")
@@ -330,9 +351,19 @@ target_sources(cifpp
 # The code now really requires C++20
 target_compile_features(cifpp PUBLIC cxx_std_20)
 
+set(CMAKE_DEBUG_POSTFIX d)
+set_target_properties(cifpp PROPERTIES DEBUG_POSTFIX "d")
+
 generate_export_header(cifpp EXPORT_FILE_NAME
 	${CMAKE_CURRENT_SOURCE_DIR}/include/cif++/exports.hpp)
 
+if(BOOST_REGEX)
+	target_compile_definitions(cifpp PRIVATE USE_BOOST_REGEX=1
+		BOOST_REGEX_STANDALONE=1)
+	get_target_property(BOOST_REGEX_INCLUDE_DIR Boost::regex
+		INTERFACE_INCLUDE_DIRECTORIES)
+endif()
+
 if(MSVC)
 	target_compile_definitions(cifpp PUBLIC NOMINMAX=1)
 endif()
@@ -343,25 +374,9 @@ target_include_directories(
 	cifpp
 	PUBLIC "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
 	"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
-	PRIVATE "${EIGEN_INCLUDE_DIR}")
+	PRIVATE "${BOOST_REGEX_INCLUDE_DIR}" "${EIGEN_INCLUDE_DIR}")
 
-target_link_libraries(cifpp
-	PUBLIC Threads::Threads ZLIB::ZLIB $<$<TARGET_EXISTS:std::atomic>:std::atomic>)
-
-if(PCRE2_FOUND)
-	target_include_directories(cifpp PRIVATE ${PCRE2_INCLUDE_DIRS})
-	target_link_libraries(cifpp PRIVATE ${PCRE2_LINK_LIBRARIES})
-else()
-	target_link_libraries(cifpp PRIVATE $<BUILD_INTERFACE:pcre2s>)
-endif()
-
-if(NOT STD_CHARCONV_COMPILING)
-	target_link_libraries(cifpp PUBLIC FastFloat::fast_float)
-endif()
-
-if(fmt_FOUND)
-	target_link_libraries(cifpp PUBLIC fmt)
-endif()
+target_link_libraries(cifpp PUBLIC Threads::Threads ZLIB::ZLIB $<$<TARGET_EXISTS:std::atomic>:std::atomic>)
 
 if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
 	target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
@@ -375,7 +390,7 @@ if(CIFPP_DOWNLOAD_CCD)
 		file(SIZE ${COMPONENTS_CIF} CCD_FILE_SIZE)
 
 		if(CCD_FILE_SIZE EQUAL 0)
-			message(STATUS "cifpp: Removing empty ${COMPONENTS_CIF} file")
+			message(STATUS "Removing empty ${COMPONENTS_CIF} file")
 			file(REMOVE "${COMPONENTS_CIF}")
 		endif()
 	endif()
@@ -414,7 +429,7 @@ if(CIFPP_DOWNLOAD_CCD)
 
 		if(CCD_FETCH_STATUS_CODE)
 			message(
-				FATAL_ERROR "cifpp: Error trying to download CCD file: ${CCD_FETCH_STATUS}")
+				FATAL_ERROR "Error trying to download CCD file: ${CCD_FETCH_STATUS}")
 		endif()
 	endif()
 endif()
@@ -478,7 +493,7 @@ file(GLOB OLD_CONFIG_FILES
 
 if(OLD_CONFIG_FILES)
 	message(
-		STATUS "cifpp: Installation will remove old config files: ${OLD_CONFIG_FILES}")
+		STATUS "Installation will remove old config files: ${OLD_CONFIG_FILES}")
 	install(CODE "file(REMOVE ${OLD_CONFIG_FILES})")
 endif()
 
@@ -499,7 +514,6 @@ if(CIFPP_DATA_DIR AND CIFPP_DOWNLOAD_CCD)
 endif()
 
 set(CONFIG_TEMPLATE_FILE ${CMAKE_CURRENT_SOURCE_DIR}/cmake/cifpp-config.cmake.in)
-set(REQUIRE_FMT ${fmt_FOUND})
 
 configure_package_config_file(
 	${CONFIG_TEMPLATE_FILE} ${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifpp-config.cmake
@@ -545,7 +559,7 @@ if(CIFPP_INSTALL_UPDATE_SCRIPT)
 			PERMISSIONS OWNER_EXECUTE OWNER_READ GROUP_EXECUTE GROUP_READ WORLD_EXECUTE
 			WORLD_READ)
 	else()
-		message(FATAL_ERROR "cifpp: Don't know where to install the update script")
+		message(FATAL_ERROR "Don't know where to install the update script")
 	endif()
 
 	# a config file, to make it complete
@@ -559,7 +573,7 @@ if(CIFPP_INSTALL_UPDATE_SCRIPT)
 		install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf
 			DESTINATION ${CMAKE_INSTALL_SYSCONFDIR})
 		install(
-			CODE "message(\"cifpp: A configuration file has been written to ${CIFPP_ETC_DIR}/libcifpp.conf, please edit this file to enable automatic updates\")"
+			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 ${CMAKE_INSTALL_SYSCONFDIR}/libcifpp/cache-update.d)

README.md

@@ -117,8 +117,12 @@ Other libraries you might want to install beforehand are:
   `libeigen3-dev`
 - [zlib](https://github.com/madler/zlib), the development version of this
   library. On Debian/Ubuntu this is the package `zlib1g-dev`.
-- [pcre2](https://www.pcre.org/), the Perl Compatible Regular Expression
-  library. On Debian/Ubuntu this is the package `libpcre2-dev`.
+- [boost](https://www.boost.org), in Debian/Ubuntu this is `libboost-dev`.
+  
+  The Boost libraries are only needed in case you are using GCC due to a long
+  standing bug in GNU's implementation of std::regex. It simply crashes
+  on the regular expressions used in the mmcif_pdbx dictionary and so
+  we use the boost regex implementation instead.
 
 ### Building
 

changelog

@@ -1,33 +1,3 @@
-Version 9.0.4
-- Fix various stopping and reconstruction errors
-
-Version 9.0.3
-- Reconstruction fixed when some entity ids are missing
-
-Version 9.0.2
-- Fix code that reconstructs sequences, could throw a map::at
-- Many optimisations in validation and reconstruction code.
-
-Version 9.0.1
-- Use pcre2 from pkg-config if available, if not
-  build a version from the original code.
-
-Version 9.0.0
-- Rename fields of cif::mm::polymer to match the naming
-  in mmcif_pdbx.dic. Also, related, fix building mm::structure
-  using the correct mapping between atom_site and residues.
-- _atom_site.auth_alt_id does not exist, it should be
-  _atom_site.pdbx_auth_alt_id of course.
-- Added a more lightweight fixup for mmcif_pdbx files
-  that lack certain categories.
-
-Version 8.0.1
-- Fix cif::mm::structure::cleanup_empty_categories, removed too much
-- Add default value for B_iso_or_equiv in residue::create_new_atom
-- Reconstruct some branch records in bare pdbx files
-- Fix parsing PDB files (bug due to missing validator in dest. cat.)
-- Do not fail conversion of PDB files when compound info is missing
-
 Version 8.0.0
 - A dictionary is for a datablock and a file can have
   datablocks with differing dictionaries.

cmake/FindPCRE2.cmake

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

cmake/cifpp-config.cmake.in

@@ -8,8 +8,5 @@ include(CMakeFindDependencyMacro)
 
 find_dependency(Threads)
 find_dependency(ZLIB REQUIRED)
-if(@REQUIRE_FMT@)
-    find_dependency(fmt REQUIRED)
-endif()
 
 check_required_components(cifpp)

cmake/test-charconv.cpp

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

cmake/test-rx.cpp

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

docs/basics.rst

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

include/cif++/category.hpp

@@ -32,6 +32,7 @@
 #include "cif++/iterator.hpp"
 #include "cif++/row.hpp"
 #include "cif++/text.hpp"
+#include "cif++/validate.hpp"
 
 #include <array>
 
@@ -50,11 +51,6 @@
 namespace cif
 {
 
-class validator;
-struct category_validator;
-struct item_validator;
-struct link_validator;
-
 // --------------------------------------------------------------------
 // special exceptions
 
@@ -147,17 +143,7 @@ class category
 
 	category() = default;            ///< Default constructor
 	category(std::string_view name); ///< Constructor taking a \a name
-
-	/// @brief Constructor creating a category named @a name and filled with @a rows
-	/// @param name Name for the new category
-	/// @param rows The data stored in the category
-	category(std::string_view name, row_initializer &&rows)
-		: category(name)
-	{
-		emplace(std::forward<row_initializer>(rows));
-	}
-
-	category(const category &rhs); ///< Copy constructor
+	category(const category &rhs);   ///< Copy constructor
 
 	category(category &&rhs) noexcept ///< Move constructor
 	{
@@ -223,11 +209,6 @@ class category
 	/// @return Returns true is all validations pass
 	bool validate_links() const;
 
-	/**
-	 * @brief Strip removes items from this category that are invalid according to the assigned validator
-	 */
-	void strip();
-
 	/// @brief Equality operator, returns true if @a rhs is equal to this
 	/// @param rhs The object to compare with
 	/// @return True if the data contained is equal
@@ -332,16 +313,8 @@ class category
 	// --------------------------------------------------------------------
 	// A category can have a key, as defined by the validator/dictionary
 
-	/// @brief The type of an element of the key_type
-	struct key_element_type
-	{
-		std::string name;         ///< Name of the item
-		std::string value;        ///< Value to be found
-		bool may_be_null = false; ///< If true, value should be same or empty
-	};
-
 	/// @brief The key type
-	using key_type = std::vector<key_element_type>;
+	using key_type = row_initializer;
 
 	/// @brief Return a row_handle for the row specified by \a key
 	/// @param key The value for the key, items specified in the dictionary should have a value
@@ -974,12 +947,6 @@ class category
 		return insert_impl(cend(), r);
 	}
 
-	void emplace(const_iterator b, const_iterator e)
-	{
-		while (b != e)
-			emplace(*b++);
-	}
-
 	/// @brief Completely erase all rows contained in this category
 	void clear();
 
@@ -1112,7 +1079,25 @@ class category
 	// --------------------------------------------------------------------
 	/// \brief Return the index number for \a item_name
 
-	uint16_t get_item_ix(std::string_view item_name) const;
+	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
@@ -1128,7 +1113,28 @@ class category
 	/// @brief Make sure a item with name @a item_name is known and return its index number
 	/// @param item_name The name of the item
 	/// @return The index number of the item
-	uint16_t add_item(std::string_view item_name);
+	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
@@ -1257,7 +1263,7 @@ class category
 		{
 		}
 
-		// TODO: NEED TO FIX THIS!
+// TODO: NEED TO FIX THIS!
 		category *linked;
 		const link_validator *v;
 	};

include/cif++/compound.hpp

@@ -180,7 +180,7 @@ class compound
 	friend class local_compound_factory_impl;
 
 	compound(cif::datablock &db);
-
+	
 	std::string m_id;
 	std::string m_name;
 	std::string m_type;
@@ -290,13 +290,6 @@ class compound_factory
 
 	void report_missing_compound(std::string_view compound_id);
 
-	bool get_report_missing() const { return m_report_missing; }
-
-	void set_report_missing(bool report)
-	{
-		m_report_missing = report;
-	}
-
   private:
 	compound_factory();
 
@@ -308,7 +301,6 @@ class compound_factory
 	static bool s_use_thread_local_instance;
 
 	std::shared_ptr<compound_factory_impl> m_impl;
-	bool m_report_missing = true;
 };
 
 // --------------------------------------------------------------------

include/cif++/condition.hpp

@@ -27,7 +27,6 @@
 #pragma once
 
 #include "cif++/row.hpp"
-#include "cif++/format.hpp"
 
 #include <cassert>
 #include <concepts>
@@ -50,49 +49,49 @@
  * @code {.cpp}
  * cif::condition c = cif::key("id") == 1;
  * @endcode
- *
+ * 
  * That will find rows where the ID item contains the number 1. If
  * using cif::key is a bit too much typing, you can also write:
- *
+ * 
  * @code{.cpp}
  * using namespace cif::literals;
- *
+ * 
  * cif::condition c2 = "id"_key == 1;
  * @endcode
- *
+ * 
  * Now if you want both ID = 1 and ID = 2 in the result:
- *
+ * 
  * @code{.cpp}
  * auto c3 = "id"_key == 1 or "id"_key == 2;
  * @endcode
- *
+ * 
  * There are some special values you can use. To find rows with item that
  * do not have a value:
- *
+ * 
  * @code{.cpp}
  * auto c4 = "type"_key == cif::null;
- * @endcode
- *
+ * @endcode 
+ * 
  * Of if it should not be NULL:
- *
+ * 
  * @code{.cpp}
  * auto c5 = "type"_key != cif::null;
- * @endcode
- *
+ * @endcode 
+ * 
  * There's even a way to find all records:
- *
+ * 
  * @code{.cpp}
  * auto c6 = cif::all;
  * @endcode
- *
+ * 
  * And when you want to search for any item containing the value 'foo':
- *
+ * 
  * @code{.cpp}
  * auto c7 = cif::any == "foo";
- * @endcode
- *
+ * @endcode 
+ * 
  * All these conditions can be chained together again:
- *
+ * 
  * @code{.cpp}
  * auto c8 = std::move(c3) and std::move(c5);
  * @endcode
@@ -107,7 +106,7 @@ namespace cif
 
 /**
  * @brief Get the items that can be used as key in conditions for a category
- *
+ * 
  * @param cat The category whose items to return
  * @return iset The set of key item names
  */
@@ -116,7 +115,7 @@ iset get_category_fields(const category &cat);
 
 /**
  * @brief Get the items that can be used as key in conditions for a category
- *
+ * 
  * @param cat The category whose items to return
  * @return iset The set of key field names
  */
@@ -124,7 +123,7 @@ iset get_category_items(const category &cat);
 
 /**
  * @brief Get the item index for item @a col in category @a cat
- *
+ * 
  * @param cat The category
  * @param col The name of the item
  * @return uint16_t The index
@@ -133,7 +132,7 @@ uint16_t get_item_ix(const category &cat, std::string_view col);
 
 /**
  * @brief Return whether the item @a col in category @a cat has a primitive type of *uchar*
- *
+ * 
  * @param cat The category
  * @param col The item name
  * @return true If the primitive type is of type *uchar*
@@ -176,13 +175,14 @@ namespace detail
 class condition
 {
   public:
+
 	/** @cond */
 	using condition_impl = detail::condition_impl;
 	/** @endcond */
 
 	/**
 	 * @brief Construct a new, empty condition object
-	 *
+	 * 
 	 */
 	condition()
 		: m_impl(nullptr)
@@ -191,7 +191,7 @@ class condition
 
 	/**
 	 * @brief Construct a new condition object with implementation @a impl
-	 *
+	 * 
 	 * @param impl The implementation to use
 	 */
 	explicit condition(condition_impl *impl)
@@ -230,15 +230,15 @@ class condition
 	/**
 	 * @brief Prepare the condition to be used on category @a c. This will
 	 * take care of setting the correct indices for items e.g.
-	 *
+	 * 
 	 * @param c The category this query should act upon
 	 */
 	void prepare(const category &c);
 
 	/**
-	 * @brief This operator returns true if the row referenced by @a r is
+	 * @brief This operator returns true if the row referenced by @a r is 
 	 * a match for this condition.
-	 *
+	 * 
 	 * @param r The reference to a row.
 	 * @return true If there is a match
 	 * @return false If there is no match
@@ -263,7 +263,7 @@ class condition
 	/**
 	 * @brief If the prepare step found out there is only one hit
 	 * this single hit can be returned by this method.
-	 *
+	 * 
 	 * @return std::optional<row_handle> The result will contain
 	 * a row reference if there is a single hit, it will be empty otherwise
 	 */
@@ -292,7 +292,7 @@ class condition
 
 	/**
 	 * @brief Operator to use to write out a condition to @a os, for debugging purposes
-	 *
+	 * 
 	 * @param os The std::ostream to write to
 	 * @param cond The condition to write
 	 * @return std::ostream& The same as @a os
@@ -752,9 +752,28 @@ namespace detail
 				delete sub;
 		}
 
-		condition_impl *prepare(const category &c) override;
+		condition_impl *prepare(const category &c) override
+		{
+			for (auto &sub : m_sub)
+				sub = sub->prepare(c);
+			return this;
+		}
 
-		bool test(row_handle r) const override;
+		bool test(row_handle r) const override
+		{
+			bool result = true;
+
+			for (auto sub : m_sub)
+			{
+				if (sub->test(r))
+					continue;
+
+				result = false;
+				break;
+			}
+
+			return result;
+		}
 
 		void str(std::ostream &os) const override
 		{
@@ -801,7 +820,6 @@ namespace detail
 		static condition_impl *combine_equal(std::vector<and_condition_impl *> &subs, or_condition_impl *oc);
 
 		std::vector<condition_impl *> m_sub;
-		std::optional<row_handle> m_single; // Potential result of index lookup
 	};
 
 	struct or_condition_impl : public condition_impl
@@ -959,9 +977,9 @@ inline condition operator or(condition &&a, condition &&b)
 			if (ci->m_item_name == ce->m_item_name)
 				return condition(new detail::key_equals_or_empty_condition_impl(ci));
 		}
-
+		
 		if (typeid(*b.m_impl) == typeid(detail::key_equals_condition_impl) and
-			typeid(*a.m_impl) == typeid(detail::key_is_empty_condition_impl))
+				 typeid(*a.m_impl) == typeid(detail::key_is_empty_condition_impl))
 		{
 			auto ci = static_cast<detail::key_equals_condition_impl *>(b.m_impl);
 			auto ce = static_cast<detail::key_is_empty_condition_impl *>(a.m_impl);
@@ -979,9 +997,9 @@ inline condition operator or(condition &&a, condition &&b)
 			if (ci->m_item_name == ce->m_item_name)
 				return condition(new detail::key_equals_number_or_empty_condition_impl(ci));
 		}
-
+		
 		if (typeid(*b.m_impl) == typeid(detail::key_equals_number_condition_impl) and
-			typeid(*a.m_impl) == typeid(detail::key_is_empty_condition_impl))
+				 typeid(*a.m_impl) == typeid(detail::key_is_empty_condition_impl))
 		{
 			auto ci = static_cast<detail::key_equals_number_condition_impl *>(b.m_impl);
 			auto ce = static_cast<detail::key_is_empty_condition_impl *>(a.m_impl);
@@ -1001,7 +1019,7 @@ inline condition operator or(condition &&a, condition &&b)
 
 /**
  * @brief A helper class to make it possible to search for empty items (NULL)
- *
+ * 
  * @code{.cpp}
  * "id"_key == cif::empty_type();
  * @endcode
@@ -1013,7 +1031,7 @@ struct empty_type
 
 /**
  * @brief A helper to make it possible to have conditions like
- *
+ * 
  * @code{.cpp}
  * "id"_key == cif::null;
  * @endcode
@@ -1023,14 +1041,14 @@ inline constexpr empty_type null = empty_type();
 
 /**
  * @brief Class to use in creating conditions, creates a reference to a item or item
- *
+ * 
  */
 struct key
 {
 	/**
 	 * @brief Construct a new key object using @a item_name as name
-	 *
-	 * @param item_name
+	 * 
+	 * @param item_name 
 	 */
 	explicit key(const std::string &item_name)
 		: m_item_name(item_name)
@@ -1039,8 +1057,8 @@ struct key
 
 	/**
 	 * @brief Construct a new key object using @a item_name as name
-	 *
-	 * @param item_name
+	 * 
+	 * @param item_name 
 	 */
 	explicit key(const char *item_name)
 		: m_item_name(item_name)
@@ -1049,8 +1067,8 @@ struct key
 
 	/**
 	 * @brief Construct a new key object using @a item_name as name
-	 *
-	 * @param item_name
+	 * 
+	 * @param item_name 
 	 */
 	explicit key(std::string_view item_name)
 		: m_item_name(item_name)
@@ -1072,8 +1090,7 @@ concept Numeric = ((std::is_floating_point_v<T> or std::is_integral_v<T>) and no
 template <Numeric T>
 condition operator==(const key &key, const T &v)
 {
-	// TODO: change key_equals_etc... to use std::variant<double,int64_t> or something
-	return condition(new detail::key_equals_number_condition_impl(key.m_item_name, static_cast<double>(v)));
+	return condition(new detail::key_equals_number_condition_impl(key.m_item_name, v));
 }
 
 /**
@@ -1120,10 +1137,13 @@ inline condition operator!=(const key &key, std::string_view value)
 template <Numeric T>
 condition operator>(const key &key, const T &v)
 {
+	std::ostringstream s;
+	s << " > " << v;
+
 	return condition(new detail::key_compare_condition_impl(
 		key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
 		{ return r[item_name].compare(v) > 0; },
-		cif::format(" > {}", v)));
+		s.str()));
 }
 
 /**
@@ -1132,10 +1152,13 @@ condition operator>(const key &key, const T &v)
 template <Numeric T>
 condition operator>=(const key &key, const T &v)
 {
+	std::ostringstream s;
+	s << " >= " << v;
+
 	return condition(new detail::key_compare_condition_impl(
 		key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
 		{ return r[item_name].compare(v) >= 0; },
-		cif::format(" >= {}", v)));
+		s.str()));
 }
 
 /**
@@ -1144,10 +1167,13 @@ condition operator>=(const key &key, const T &v)
 template <Numeric T>
 condition operator<(const key &key, const T &v)
 {
+	std::ostringstream s;
+	s << " < " << v;
+
 	return condition(new detail::key_compare_condition_impl(
 		key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
 		{ return r[item_name].compare(v) < 0; },
-		cif::format(" < {}", v)));
+		s.str()));
 }
 
 /**
@@ -1156,10 +1182,13 @@ condition operator<(const key &key, const T &v)
 template <Numeric T>
 condition operator<=(const key &key, const T &v)
 {
+	std::ostringstream s;
+	s << " <= " << v;
+
 	return condition(new detail::key_compare_condition_impl(
 		key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
 		{ return r[item_name].compare(v) <= 0; },
-		cif::format(" <= {}", v)));
+		s.str()));
 }
 
 /**
@@ -1167,10 +1196,13 @@ condition operator<=(const key &key, const T &v)
  */
 inline condition operator>(const key &key, std::string_view v)
 {
+	std::ostringstream s;
+	s << " > " << v;
+
 	return condition(new detail::key_compare_condition_impl(
 		key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
 		{ return r[item_name].compare(v, icase) > 0; },
-		cif::format(" > {}", v)));
+		s.str()));
 }
 
 /**
@@ -1178,10 +1210,13 @@ inline condition operator>(const key &key, std::string_view v)
  */
 inline condition operator>=(const key &key, std::string_view v)
 {
+	std::ostringstream s;
+	s << " >= " << v;
+
 	return condition(new detail::key_compare_condition_impl(
 		key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
 		{ return r[item_name].compare(v, icase) >= 0; },
-		cif::format(" >= {}", v)));
+		s.str()));
 }
 
 /**
@@ -1189,10 +1224,13 @@ inline condition operator>=(const key &key, std::string_view v)
  */
 inline condition operator<(const key &key, std::string_view v)
 {
+	std::ostringstream s;
+	s << " < " << v;
+
 	return condition(new detail::key_compare_condition_impl(
 		key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
 		{ return r[item_name].compare(v, icase) < 0; },
-		cif::format(" < {}", v)));
+		s.str()));
 }
 
 /**
@@ -1200,10 +1238,13 @@ inline condition operator<(const key &key, std::string_view v)
  */
 inline condition operator<=(const key &key, std::string_view v)
 {
+	std::ostringstream s;
+	s << " <= " << v;
+
 	return condition(new detail::key_compare_condition_impl(
 		key.m_item_name, [item_name = key.m_item_name, v](row_handle r, bool icase)
 		{ return r[item_name].compare(v, icase) <= 0; },
-		cif::format(" <= {}", v)));
+		s.str()));
 }
 
 /**
@@ -1304,7 +1345,7 @@ namespace literals
 {
 	/**
 	 * @brief Return a cif::key for the item name @a text
-	 *
+	 * 
 	 * @param text The name of the item
 	 * @param length The length of @a text
 	 * @return key The cif::key created

include/cif++/datablock.hpp

@@ -29,8 +29,6 @@
 #include "cif++/category.hpp"
 #include "cif++/forward_decl.hpp"
 
-#include <list>
-
 /** \file datablock.hpp
  * Each valid mmCIF file contains at least one @ref cif::datablock.
  * A datablock has a name and can contain one or more @ref cif::category "categories"
@@ -106,6 +104,13 @@ class datablock : public std::list<category>
 	 */
 	void load_dictionary();
 
+	/**
+	 * @brief Load the dictionary named @a dict_name
+	 * 
+	 * @param dict_name 
+	 */
+	void load_dictionary(std::string_view dict_name);
+
 	/**
 	 * @brief Set the validator object to @a v
 	 * 
@@ -128,6 +133,15 @@ 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
@@ -137,14 +151,6 @@ class datablock : public std::list<category>
 	 */
 	bool validate_links() const;
 
-	/**
-	 * @brief Strip removes all categories and items that are invalid according
-	 * to the assigned validator. Will also add a valid audit_conform block.
-	 * 
-	 * @return true if the remaining datablock is valid
-	 */
-	bool strip();
-
 	// --------------------------------------------------------------------
 
 	/**
@@ -183,15 +189,6 @@ class datablock : public std::list<category>
 	 */
 	const category *get(std::string_view name) const;
 
-
-	/**
-	 * @brief Return true if this datablock contains a non-empty category
-	 */
-	bool contains(std::string_view name) const
-	{
-		return get(name) != nullptr;
-	}
-
 	/**
 	 * @brief Tries to find a category with name @a name and will create a
 	 * new one if it is not found. The result is a tuple of an iterator
@@ -250,4 +247,4 @@ class datablock : public std::list<category>
 	const validator *m_validator = nullptr;
 };
 
-} // namespace cif
+} // namespace cif

include/cif++/dictionary_parser.hpp

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

include/cif++/file.hpp

@@ -210,6 +210,12 @@ class file : public std::list<datablock>
 	/** Load the data from @a is using validator @a v */
 	void load(std::istream &is, const validator &v);
 
+	/** Load the data from the file specified by @a p using a validator constructed from dictionary @a dict */
+	void load(const std::filesystem::path &p, std::string_view dict);
+
+	/** Load the data from @a is using a validator constructed from dictionary @a dict */
+	void load(std::istream &is, std::string_view dict);
+
 	/** Save the data to the file specified by @a p */
 	void save(const std::filesystem::path &p) const;
 
@@ -226,4 +232,4 @@ class file : public std::list<datablock>
 	}
 };
 
-} // namespace cif
+} // namespace cif

include/cif++/format.hpp

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

include/cif++/gzio.hpp

@@ -1,33 +1,7 @@
-/*-
- * SPDX-License-Identifier: BSD-2-Clause
- * 
- * Copyright (c) 2025 NKI/AVL, Netherlands Cancer Institute
- * 
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- * 
- * 1. Redistributions of source code must retain the above copyright notice, this
- *    list of conditions and the following disclaimer
- * 2. Redistributions in binary form must reproduce the above copyright notice,
- *    this list of conditions and the following disclaimer in the documentation
- *    and/or other materials provided with the distribution.
- * 
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
- * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
-/*
-	Original code comes from libgxrio at https://github.com/mhekkel/gxrio
-	This is a stripped down version.
-*/
+//          Copyright Maarten L. Hekkelman, 2022
+// Distributed under the Boost Software License, Version 1.0.
+//    (See accompanying file LICENSE_1_0.txt or copy at
+//          http://www.boost.org/LICENSE_1_0.txt)
 
 #pragma once
 

include/cif++/item.hpp

@@ -53,12 +53,12 @@ namespace cif
 // --------------------------------------------------------------------
 /** @brief item is a transient class that is used to pass data into rows
  * but it also takes care of formatting data.
- *
- *
- *
+ * 
+ * 
+ * 
  * The class cif::item is often used implicitly when creating a row in a category
  * using the emplace function.
- *
+ * 
  * @code{.cpp}
  * cif::category cat("my-cat");
  * cat.emplace({
@@ -68,12 +68,12 @@ namespace cif
  *   { "item-4", std::make_optional<int>(42) },   // <- stores an item with value 42
  *   { "item-5" }                                 // <- stores an item with value .
  * });
- *
+ * 
  * std::cout << cat << '\n';
  * @endcode
- *
+ * 
  * Will result in:
- *
+ * 
  * @code{.txt}
  * _my-cat.item-1 1
  * _my-cat.item-2 1.00
@@ -176,7 +176,7 @@ class item
 
 	/// \brief constructor for an item with name \a name and as
 	/// content value \a value
-	template <typename T, std::enable_if_t<std::is_same_v<T, std::string>, int> = 0>
+	template<typename T, std::enable_if_t<std::is_same_v<T, std::string>, int> = 0>
 	item(const std::string_view name, T &&value)
 		: m_name(name)
 		, m_value(std::move(value))
@@ -221,8 +221,8 @@ class item
 	item &operator=(item &&rhs) noexcept = default;
 	/** @endcond */
 
-	std::string_view name() const { return m_name; }            ///< Return the name of the item
-	std::string_view value() const & { return m_value; }        ///< Return the value of the item
+	std::string_view name() const { return m_name; }   ///< Return the name of the item
+	std::string_view value() const & { return m_value; } ///< Return the value of the item
 	std::string value() const && { return std::move(m_value); } ///< Return the value of the item
 
 	/// \brief replace the content of the stored value with \a v
@@ -250,8 +250,6 @@ class item
 			return value();
 	}
 
-	auto operator<=>(const item &rhs) const = default;
-
   private:
 	std::string_view m_name;
 	std::string m_value;
@@ -560,9 +558,7 @@ struct item_handle::item_value_as<T, std::enable_if_t<std::is_arithmetic_v<T> an
 			auto b = txt.data();
 			auto e = txt.data() + txt.size();
 
-			std::from_chars_result r = (b + 1 < e and *b == '+' and std::isdigit(b[1])) //
-			                               ? from_chars(b + 1, e, result)
-			                               : from_chars(b, e, result);
+			std::from_chars_result r = (b + 1 < e and *b == '+' and std::isdigit(b[1])) ? selected_charconv<value_type>::from_chars(b + 1, e, result) : selected_charconv<value_type>::from_chars(b, e, result);
 
 			if ((bool)r.ec or r.ptr != e)
 			{
@@ -597,9 +593,7 @@ struct item_handle::item_value_as<T, std::enable_if_t<std::is_arithmetic_v<T> an
 			auto b = txt.data();
 			auto e = txt.data() + txt.size();
 
-			std::from_chars_result r = (b + 1 < e and *b == '+' and std::isdigit(b[1]))
-			                               ? from_chars(b + 1, e, v)
-			                               : from_chars(b, e, v);
+			std::from_chars_result r = (b + 1 < e and *b == '+' and std::isdigit(b[1])) ? selected_charconv<value_type>::from_chars(b + 1, e, v) : selected_charconv<value_type>::from_chars(b, e, v);
 
 			if ((bool)r.ec or r.ptr != e)
 			{

include/cif++/model.hpp

@@ -34,7 +34,7 @@
 #include <numeric>
 
 #if __cpp_lib_format
-# include <format>
+#include <format>
 #endif
 
 /** @file model.hpp
@@ -106,6 +106,8 @@ class atom
 
 		atom_impl(const atom_impl &i) = default;
 
+		void prefetch();
+
 		int compare(const atom_impl &b) const;
 
 		// bool getAnisoU(float anisou[6]) const;
@@ -343,7 +345,7 @@ class atom
 	std::string get_auth_asym_id() const { return get_property("auth_asym_id"); }      ///< Return the auth_asym_id property
 	std::string get_auth_seq_id() const { return get_property("auth_seq_id"); }        ///< Return the auth_seq_id property
 	std::string get_auth_atom_id() const { return get_property("auth_atom_id"); }      ///< Return the auth_atom_id property
-	std::string get_auth_alt_id() const { return get_property("pdbx_auth_alt_id"); }   ///< Return the auth_alt_id property
+	std::string get_auth_alt_id() const { return get_property("auth_alt_id"); }        ///< Return the auth_alt_id property
 	std::string get_auth_comp_id() const { return get_property("auth_comp_id"); }      ///< Return the auth_comp_id property
 	std::string get_pdb_ins_code() const { return get_property("pdbx_PDB_ins_code"); } ///< Return the pdb_ins_code property
 
@@ -479,8 +481,8 @@ class residue
 		, m_compound_id(compoundID)
 		, m_asym_id(asymID)
 		, m_seq_id(seqID)
-		, m_pdb_strand_id(authAsymID)
-		, m_pdb_seq_num(authSeqID)
+		, m_auth_asym_id(authAsymID)
+		, m_auth_seq_id(authSeqID)
 		, m_pdb_ins_code(pdbInsCode)
 	{
 	}
@@ -507,9 +509,9 @@ class residue
 	const std::string &get_asym_id() const { return m_asym_id; } ///< Return the asym_id
 	int get_seq_id() const { return m_seq_id; }                  ///< Return the seq_id
 
-	const std::string get_pdb_strand_id() const { return m_pdb_strand_id; } ///< Return the pdb_strand_id
-	const std::string get_pdb_seq_num() const { return m_pdb_seq_num; }     ///< Return the pdb_seq_num
-	std::string get_pdb_ins_code() const { return m_pdb_ins_code; }         ///< Return the pdb_ins_code
+	const std::string get_auth_asym_id() const { return m_auth_asym_id; } ///< Return the auth_asym_id
+	const std::string get_auth_seq_id() const { return m_auth_seq_id; }   ///< Return the auth_seq_id
+	std::string get_pdb_ins_code() const { return m_pdb_ins_code; }       ///< Return the pdb_ins_code
 
 	const std::string &get_compound_id() const { return m_compound_id; } ///< Return the compound_id
 	void set_compound_id(const std::string &id) { m_compound_id = id; }  ///< Set the compound_id to @a id
@@ -538,9 +540,6 @@ class residue
 	/// \brief Return the atom with atom_id @a atomID
 	atom get_atom_by_atom_id(const std::string &atomID) const;
 
-	/// \brief Return the atom with atom_id @a atomID and alternate_id @a altID
-	atom get_atom_by_atom_id(const std::string &atomID, const std::string &altID) const;
-
 	/// \brief Return the list of atoms having ID \a atomID
 	///
 	/// This includes all alternate atoms with this ID
@@ -578,7 +577,7 @@ class residue
 								   m_seq_id == rhs.m_seq_id and
 								   m_asym_id == rhs.m_asym_id and
 								   m_compound_id == rhs.m_compound_id and
-								   m_pdb_seq_num == rhs.m_pdb_seq_num);
+								   m_auth_seq_id == rhs.m_auth_seq_id);
 	}
 
 	/// @brief Create a new atom and add it to the list
@@ -592,7 +591,7 @@ class residue
 	structure *m_structure = nullptr;
 	std::string m_compound_id, m_asym_id;
 	int m_seq_id = 0;
-	std::string m_pdb_strand_id, m_pdb_seq_num, m_pdb_ins_code;
+	std::string m_auth_asym_id, m_auth_seq_id, m_pdb_ins_code;
 	std::vector<atom> m_atoms;
 	/** @endcond */
 };
@@ -623,9 +622,6 @@ class monomer : public residue
 	bool is_first_in_chain() const; ///< Return if this residue is the first residue in the chain
 	bool is_last_in_chain() const;  ///< Return if this residue is the last residue in the chain
 
-	const monomer &prev() const; // Return previous monomer in polymer
-	const monomer &next() const; // Return next monomer in polymer
-
 	// convenience
 	bool has_alpha() const; ///< Return if a alpha value can be calculated (depends on location in chain)
 	bool has_kappa() const; ///< Return if a kappa value can be calculated (depends on location in chain)
@@ -712,15 +708,15 @@ class polymer : public std::vector<monomer>
 
 	structure *get_structure() const { return m_structure; } ///< Return the structure
 
-	std::string get_asym_id() const { return m_asym_id; }             ///< Return the asym_id
-	std::string get_pdb_strand_id() const { return m_pdb_strand_id; } ///< Return the PDB chain ID, actually
-	std::string get_entity_id() const { return m_entity_id; }         ///< Return the entity_id
+	std::string get_asym_id() const { return m_asym_id; }           ///< Return the asym_id
+	std::string get_auth_asym_id() const { return m_auth_asym_id; } ///< Return the PDB chain ID, actually
+	std::string get_entity_id() const { return m_entity_id; }       ///< Return the entity_id
 
   private:
 	structure *m_structure;
 	std::string m_entity_id;
 	std::string m_asym_id;
-	std::string m_pdb_strand_id;
+	std::string m_auth_asym_id;
 };
 
 // --------------------------------------------------------------------
@@ -758,7 +754,7 @@ class sugar : public residue
 	int num() const
 	{
 		int result;
-		auto r = std::from_chars(m_pdb_seq_num.data(), m_pdb_seq_num.data() + m_pdb_seq_num.length(), result);
+		auto r = std::from_chars(m_auth_seq_id.data(), m_auth_seq_id.data() + m_auth_seq_id.length(), result);
 		if ((bool)r.ec)
 			throw std::runtime_error("The auth_seq_id should be a number for a sugar");
 		return result;
@@ -857,38 +853,19 @@ class branch : public std::vector<sugar>
 	std::string m_asym_id, m_entity_id;
 };
 
-/** @brief Enumeration for controlling atom selection based on occupancy. */
-enum class occupancy_policy
+// --------------------------------------------------------------------
+
+/// \brief A still very limited set of options for reading structures
+enum class StructureOpenOptions
 {
-	/** @brief Include all atoms regardless of their occupancy factor. */
-	ALL = 0,
-
-	/** @brief Select only alternate atoms with the maximum occupancy factor.
-	 * If multiple atoms have the same maximum occupancy, choose the one with the minimum B-factor.
-	 * If multiple atoms share both the maximum occupancy and the minimum B-factor, select the first encountered atom.
-	 */
-	MAX = 1,
-
-	/** @brief Select only alternate atoms with the minimum occupancy factor.
-	 * Similar to MAX, if multiple atoms have the same minimum occupancy, choose the one with the minimum B-factor.
-	 * If multiple atoms share both the minimum occupancy and the minimum B-factor, select the first encountered atom.
-	 */
-	MIN = 2,
-
-	/** @brief Exclude all atoms with an occupancy factor greater than zero. */
-	UNOCCUPIED = 3
+	SkipHydrogen = 1 << 0 ///< Do not include hydrogen atoms in the structure object
 };
 
-struct structure_open_options
+/// \brief A way to combine two options. Not very useful as there is only one...
+constexpr inline bool operator&(StructureOpenOptions a, StructureOpenOptions b)
 {
-	bool skip_hydrogen = false;                              ///< Do not include hydrogen atoms in the structure object
-	bool skip_hetatom = false;                               ///< Do not include HET atoms in the structure object
-	bool skip_water = false;                                 ///< Do not include water atoms in the structure object
-	occupancy_policy occupancy_mode = occupancy_policy::ALL; ///< By default, the occupancy policy is set to occupancy_policy::ALL
-	std::vector<std::string> asyms;                          ///< The asyms to load, if empty load all
-	std::optional<float> min_b_factor;                       ///< Only load atoms with at least this b_factor
-	std::optional<float> max_b_factor;                       ///< Only load atoms with at most this b_factor
-};
+	return static_cast<int>(a) bitand static_cast<int>(b);
+}
 
 // --------------------------------------------------------------------
 
@@ -902,10 +879,10 @@ class structure
 {
   public:
 	/// \brief Read the structure from cif::file @a p
-	structure(file &p, std::size_t modelNr = 1, structure_open_options options = {});
+	structure(file &p, std::size_t modelNr = 1, StructureOpenOptions options = {});
 
 	/// \brief Load the structure from already parsed mmCIF data in @a db
-	structure(datablock &db, std::size_t modelNr = 1, structure_open_options options = {});
+	structure(datablock &db, std::size_t modelNr = 1, StructureOpenOptions options = {});
 
 	/** @cond */
 	structure(structure &&s) = default;
@@ -1015,18 +992,18 @@ class structure
 	/**
 	 * @brief Change residue @a res to a new compound ID optionally
 	 * remapping atoms.
-	 *
+	 * 
 	 * A new chem_comp entry as well as an entity is created if needed and
 	 * if the list of @a remappedAtoms is not empty it is used to remap.
-	 *
+	 * 
 	 * The array in @a remappedAtoms contains tuples of strings, both
 	 * strings contain an atom_id. The first is the one in the current
 	 * residue and the second is the atom_id that should be used instead.
 	 * If the second string is empty, the atom is removed from the residue.
-	 *
-	 * @param res
-	 * @param newcompound
-	 * @param remappedAtoms
+	 * 
+	 * @param res 
+	 * @param newcompound 
+	 * @param remappedAtoms 
 	 */
 	void change_residue(residue &res, const std::string &newcompound,
 		const std::vector<std::tuple<std::string, std::string>> &remappedAtoms);
@@ -1065,16 +1042,6 @@ class structure
 	/// \param atom			The set of item data containing the data for the atoms.
 	void create_water(row_initializer atom);
 
-	/// \brief Create a link, a struct_conn record for two atoms.
-	///
-	/// \param a1			Atom 1
-	/// \param a2			Atom 2
-	/// \param link_type	The struct_conn_type ID for the link
-	/// \param role			The pdbx_role field value
-	/// \return 			The ID of the struct_conn record created
-
-	std::string create_link(atom a1, atom a2, const std::string &link_type, const std::string &role);
-
 	/// \brief Create a new and empty (sugar) branch
 	branch &create_branch();
 
@@ -1145,7 +1112,7 @@ class structure
 	friend polymer;
 	friend residue;
 
-	void load_atoms_for_model(structure_open_options options);
+	void load_atoms_for_model(StructureOpenOptions options);
 
 	std::string insert_compound(const std::string &compoundID, bool is_entity);
 

include/cif++/pdb.hpp

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

include/cif++/text.hpp

@@ -355,35 +355,279 @@ std::string cif_id_for_number(int number);
 std::vector<std::string> word_wrap(const std::string &text, std::size_t width);
 
 // --------------------------------------------------------------------
+/// \brief std::from_chars for floating point types.
+///
+/// These are optional, there's a selected_charconv class below that selects
+/// the best option to use based on support by the stl library.
+///
+/// I.e. that in case of GNU < 12 (or something) the cif implementation will
+/// be used, all other cases will use the stl version.
 
+template <typename FloatType, std::enable_if_t<std::is_floating_point_v<FloatType>, int> = 0>
+std::from_chars_result from_chars(const char *first, const char *last, FloatType &value)
+{
+	std::from_chars_result result{ first, {} };
+
+	enum State
+	{
+		IntegerSign,
+		Integer,
+		Fraction,
+		ExponentSign,
+		Exponent
+	} state = IntegerSign;
+	int sign = 1;
+	unsigned long long vi = 0;
+	int fl = 0, tz = 0;
+	int exponent_sign = 1;
+	int exponent = 0;
+	bool done = false;
+
+	while (not done and not (bool)result.ec)
+	{
+		char ch = result.ptr != last ? *result.ptr : 0;
+		++result.ptr;
+
+		switch (state)
+		{
+			case IntegerSign:
+				if (ch == '-')
+				{
+					sign = -1;
+					state = Integer;
+				}
+				else if (ch == '+')
+					state = Integer;
+				else if (ch >= '0' and ch <= '9')
+				{
+					vi = ch - '0';
+					state = Integer;
+				}
+				else if (ch == '.')
+					state = Fraction;
+				else
+					result.ec = std::errc::invalid_argument;
+				break;
+
+			case Integer:
+				if (ch >= '0' and ch <= '9')
+					vi = 10 * vi + (ch - '0');
+				else if (ch == 'e' or ch == 'E')
+					state = ExponentSign;
+				else if (ch == '.')
+					state = Fraction;
+				else
+				{
+					done = true;
+					--result.ptr;
+				}
+				break;
+
+			case Fraction:
+				if (ch >= '0' and ch <= '9')
+				{
+					vi = 10 * vi + (ch - '0');
+
+					if (ch == '0')
+						tz += 1;
+					else
+					{
+						fl += tz + 1;
+						tz = 0;
+					}
+				}
+				else if (ch == 'e' or ch == 'E')
+					state = ExponentSign;
+				else
+				{
+					done = true;
+					--result.ptr;
+				}
+				break;
+
+			case ExponentSign:
+				if (ch == '-')
+				{
+					exponent_sign = -1;
+					state = Exponent;
+				}
+				else if (ch == '+')
+					state = Exponent;
+				else if (ch >= '0' and ch <= '9')
+				{
+					exponent = ch - '0';
+					state = Exponent;
+				}
+				else
+					result.ec = std::errc::invalid_argument;
+				break;
+
+			case Exponent:
+				if (ch >= '0' and ch <= '9')
+					exponent = 10 * exponent + (ch - '0');
+				else
+				{
+					done = true;
+					--result.ptr;
+				}
+				break;
+		}
+	}
+
+	if (not (bool)result.ec)
+	{
+		while (tz-- > 0)
+			vi /= 10;
+
+		long double v = std::pow(10, -fl) * vi * sign;
+		if (exponent != 0)
+			v *= std::pow(10, exponent * exponent_sign);
+
+		if (std::isnan(v))
+			result.ec = std::errc::invalid_argument;
+		else if (std::abs(v) > std::numeric_limits<FloatType>::max())
+			result.ec = std::errc::result_out_of_range;
+
+		value = static_cast<FloatType>(v);
+	}
+
+	return result;
+}
+
+/// \brief duplication of std::chars_format for deficient STL implementations
+enum class chars_format
+{
+	scientific = 1,
+	fixed = 2,
+	// hex,
+	general = fixed | scientific
+};
+
+/// \brief a simplistic implementation of std::to_chars for old STL implementations
+template <typename FloatType, std::enable_if_t<std::is_floating_point_v<FloatType>, int> = 0>
+std::to_chars_result to_chars(char *first, char *last, FloatType &value, chars_format fmt)
+{
+	int size = static_cast<int>(last - first);
+	int r = 0;
+
+	switch (fmt)
+	{
+		case chars_format::scientific:
+			if constexpr (std::is_same_v<FloatType, long double>)
+				r = snprintf(first, last - first, "%le", value);
+			else
+				r = snprintf(first, last - first, "%e", value);
+			break;
+
+		case chars_format::fixed:
+			if constexpr (std::is_same_v<FloatType, long double>)
+				r = snprintf(first, last - first, "%lf", value);
+			else
+				r = snprintf(first, last - first, "%f", value);
+			break;
+
+		case chars_format::general:
+			if constexpr (std::is_same_v<FloatType, long double>)
+				r = snprintf(first, last - first, "%lg", value);
+			else
+				r = snprintf(first, last - first, "%g", value);
+			break;
+	}
+
+	std::to_chars_result result;
+	if (r < 0 or r >= size)
+		result = { first, std::errc::value_too_large };
+	else
+		result = { first + r, std::errc() };
+
+	return result;
+}
+
+/// \brief a simplistic implementation of std::to_chars for old STL implementations
+template <typename FloatType, std::enable_if_t<std::is_floating_point_v<FloatType>, int> = 0>
+std::to_chars_result to_chars(char *first, char *last, FloatType &value, chars_format fmt, int precision)
+{
+	int size = static_cast<int>(last - first);
+	int r = 0;
+
+	switch (fmt)
+	{
+		case chars_format::scientific:
+			if constexpr (std::is_same_v<FloatType, long double>)
+				r = snprintf(first, last - first, "%.*le", precision, value);
+			else
+				r = snprintf(first, last - first, "%.*e", precision, value);
+			break;
+
+		case chars_format::fixed:
+			if constexpr (std::is_same_v<FloatType, long double>)
+				r = snprintf(first, last - first, "%.*lf", precision, value);
+			else
+				r = snprintf(first, last - first, "%.*f", precision, value);
+			break;
+
+		case chars_format::general:
+			if constexpr (std::is_same_v<FloatType, long double>)
+				r = snprintf(first, last - first, "%.*lg", precision, value);
+			else
+				r = snprintf(first, last - first, "%.*g", precision, value);
+			break;
+	}
+
+	std::to_chars_result result;
+	if (r < 0 or r >= size)
+		result = { first, std::errc::value_too_large };
+	else
+		result = { first + r, std::errc() };
+
+	return result;
+}
+
+/// \brief class that uses our implementation of std::from_chars and std::to_chars
 template <typename T>
-using from_chars_function = decltype(std::from_chars(std::declval<const char *>(), std::declval<const char *>(), std::declval<T &>()));
+struct my_charconv
+{
+	/// @brief Simply call our version of std::from_chars
+	static std::from_chars_result from_chars(const char *a, const char *b, T &d)
+	{
+		return cif::from_chars(a, b, d);
+	}
 
+	/// @brief Simply call our version of std::to_chars
+	static std::to_chars_result to_chars(char *first, char *last, T &value, chars_format fmt)
+	{
+		return cif::to_chars(first, last, value, fmt);
+	}
+};
+
+/// \brief class that uses the STL implementation of std::from_chars and std::to_chars
 template <typename T>
 struct std_charconv
 {
+	/// @brief Simply call std::from_chars
 	static std::from_chars_result from_chars(const char *a, const char *b, T &d)
 	{
 		return std::from_chars(a, b, d);
 	}
+
+	/// @brief Simply call std::to_chars
+	static std::to_chars_result to_chars(char *first, char *last, T &value, chars_format fmt)
+	{
+		return std::to_chars(first, last, value, fmt);
+	}
 };
 
-template <typename T, typename = void>
-struct ff_charconv;
-
+/// \brief helper to find a from_chars function
 template <typename T>
-struct ff_charconv<T, typename std::enable_if_t<std::is_floating_point_v<T>>>
-{
-	static std::from_chars_result from_chars(const char *a, const char *b, T &v);
-};
+using from_chars_function = decltype(std::from_chars(std::declval<const char *>(), std::declval<const char *>(), std::declval<T &>()));
 
+/**
+ * @brief Helper to select the best implementation of charconv based on availability of the
+ * function in the std:: namespace
+ *
+ * @tparam T The type for which we want to find a from_chars/to_chars function
+ */
 template <typename T>
-using charconv = typename std::conditional_t<std_experimental::is_detected_v<from_chars_function, T>, std_charconv<T>, ff_charconv<T>>;
-
-template <typename T>
-constexpr auto from_chars(const char *s, const char *e, T &v)
-{
-	return charconv<T>::from_chars(s, e, v);
-}
+using selected_charconv = typename std::conditional_t<std_experimental::is_detected_v<from_chars_function, T>, std_charconv<T>, my_charconv<T>>;
 
 } // namespace cif

include/cif++/utilities.hpp

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

include/cif++/validate.hpp

@@ -26,14 +26,12 @@
 
 #pragma once
 
-#include "cif++/category.hpp"
 #include "cif++/text.hpp"
 
 #include <cassert>
 #include <filesystem>
 #include <list>
 #include <mutex>
-#include <optional>
 #include <system_error>
 #include <utility>
 
@@ -50,7 +48,6 @@
 namespace cif
 {
 
-class category;
 struct category_validator;
 
 // --------------------------------------------------------------------
@@ -230,39 +227,38 @@ struct type_validator
 {
 	std::string m_name;                 ///< The name of the type
 	DDL_PrimitiveType m_primitive_type; ///< The primitive_type of the type
-	std::shared_ptr<regex_impl> m_rx;   ///< The regular expression for the type
+	regex_impl *m_rx;                   ///< The regular expression for the type
 
 	type_validator() = delete;
 
 	/// @brief Constructor
 	type_validator(std::string_view name, DDL_PrimitiveType type, std::string_view rx);
 
-	/// @brief Copy constructor
-	type_validator(const type_validator &tv);
+	type_validator(const type_validator &) = delete;
 
-	/// @brief Move constructor
+	/// @brief Copy constructor
 	type_validator(type_validator &&rhs)
+		: m_name(std::move(rhs.m_name))
+		, m_primitive_type(rhs.m_primitive_type)
 	{
-		swap(*this, rhs);
+		m_rx = std::exchange(rhs.m_rx, nullptr);
 	}
 
+	type_validator &operator=(const type_validator &) = delete;
+
 	/// @brief Move constructor
-	type_validator &operator=(type_validator rhs)
+	type_validator &operator=(type_validator &&rhs)
 	{
-		swap(*this, rhs);
+		m_name = std::move(rhs.m_name);
+		m_primitive_type = rhs.m_primitive_type;
+		m_rx = std::exchange(rhs.m_rx, nullptr);
+
 		return *this;
 	}
 
 	/// @brief Destructor
 	~type_validator();
 
-	friend void swap(type_validator &a, type_validator &b)
-	{
-		std::swap(a.m_name, b.m_name);
-		std::swap(a.m_primitive_type, b.m_primitive_type);
-		std::swap(a.m_rx, b.m_rx);
-	}
-
 	/// @brief Return the sorting order
 	bool operator<(const type_validator &rhs) const
 	{
@@ -307,13 +303,13 @@ struct item_alias
  */
 struct item_validator
 {
-	std::string m_item_name;           ///< The item name
-	bool m_mandatory;                  ///< Flag indicating this item is mandatory
-	const type_validator *m_type;      ///< The type for this item
-	cif::iset m_enums;                 ///< If filled, the set of allowed values
-	std::string m_default;             ///< If filled, a default value for this item
-	std::string m_category;            ///< The category this item_validator belongs to
-	std::vector<item_alias> m_aliases; ///< The aliases for this item
+	std::string m_item_name;                  ///< The item name
+	bool m_mandatory;                         ///< Flag indicating this item is mandatory
+	const type_validator *m_type;             ///< The type for this item
+	cif::iset m_enums;                        ///< If filled, the set of allowed values
+	std::string m_default;                    ///< If filled, a default value for this item
+	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
@@ -400,48 +396,24 @@ class validator
 	 *
 	 * @param name The name of the underlying dictionary
 	 */
-	validator()
-		: m_audit_conform("audit_conform")
+	validator(std::string_view name)
+		: m_name(name)
 	{
 	}
 
-	/**
-	 * @brief Construct a new validator object
-	 *
-	 * @param name The name of the underlying dictionary
-	 * @param is The data to parse
-	 */
-	validator(std::istream &is)
-		: m_audit_conform("audit_conform")
-	{
-		parse(is);
-	}
-
 	/// @brief destructor
 	~validator() = default;
 
-	validator(const validator &rhs);
+	validator(const validator &rhs) = delete;
+	validator &operator=(const validator &rhs) = delete;
 
 	/// @brief move constructor
-	validator(validator &&rhs)
-	{
-		swap(*this, rhs);
-	}
+	validator(validator &&rhs) = default;
 
-	validator &operator=(validator rhs)
-	{
-		swap(*this, rhs);
-		return *this;
-	}
-
-	friend void swap(validator &a, validator &b) noexcept;
+	/// @brief move assignment operator
+	validator &operator=(validator &&rhs) = default;
 
 	friend class dictionary_parser;
-	friend class validator_factory;
-
-	/// @brief Parse dictionary in @a is and put content in this validator, optionally extending it
-	/// @param is The stream containing a valid cif dictionary
-	void parse(std::istream &is);
 
 	/// @brief Add type_validator @a v to the list of type validators
 	void add_type_validator(type_validator &&v);
@@ -484,22 +456,18 @@ class validator
 	void report_error(std::error_code ec, std::string_view category,
 		std::string_view item, bool fatal = true) const;
 
-	/// @brief Write out the audit_conform data for this validator
-	/// @param audit_conform
-	void fill_audit_conform(category &audit_conform) const;
+	const std::string &name() const { return m_name; }        ///< Get the name of this validator
+	void set_name(const std::string &name) { m_name = name; } ///< Set the name of this validator
 
-	/// @brief Return true if this validator matches @a audit_conform
-	bool matches_audit_conform(const category &audit_conform) const;
-
-	/// @brief Add info
-	void append_audit_conform(const std::string &name, const std::optional<std::string> &version);
+	const std::string &version() const { return m_version; }              ///< Get the version of this validator
+	void set_version(const std::string &version) { m_version = version; } ///< Set the version of this validator
 
   private:
 	// name is fully qualified here:
 	item_validator *get_validator_for_item(std::string_view name) const;
 
-	category m_audit_conform;
-
+	std::string m_name;
+	std::string m_version;
 	bool m_strict = false;
 	std::set<type_validator> m_type_validators;
 	std::set<category_validator> m_category_validators;
@@ -519,27 +487,16 @@ class validator_factory
 	/// @brief Return the singleton instance
 	static validator_factory &instance();
 
-	/// @brief Return validator with info recorded in @a audit_conform
-	const validator &get(const category &audit_conform);
+	/// @brief Return the validator with name @a dictionary_name
+	const validator &operator[](std::string_view dictionary_name);
 
-	/// @brief Return the single-file validator with name @a dictionary_name
-	const validator &get(std::string_view dictionary_name);
-
-	/// @brief Return true if the version @a found is equal or higher than @a expected for dictionary @a name
-	static bool check_version(std::string_view name, std::string_view expected, std::string_view found);
-
-	/// @brief Add validator @a v to the list of known validators
-	const validator &add(validator &&v)
-	{
-		std::unique_lock lock(m_mutex);
-		return m_validators.emplace_back(std::move(v));
-	}
+	/// @brief Construct a new validator with name @a name from the data in @a is
+	const validator &construct_validator(std::string_view name, std::istream &is);
 
   private:
-	validator_factory() = default;
+	// --------------------------------------------------------------------
 
-	/// @brief Construct a new validator with name @a name from the data in @a is with at least version @a version if specified
-	validator construct_validator(std::string_view name, std::optional<std::string> version);
+	validator_factory() = default;
 
 	std::mutex m_mutex;
 	std::list<validator> m_validators;

pcre2-simple/CMakeLists.txt

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

src/category.cpp

@@ -28,7 +28,6 @@
 #include "cif++/datablock.hpp"
 #include "cif++/parser.hpp"
 #include "cif++/utilities.hpp"
-#include "cif++/validate.hpp"
 
 #include <numeric>
 #include <stack>
@@ -92,7 +91,7 @@ class row_comparator
 		return d;
 	}
 
-	int operator()(const category &cat, const category::key_type &a, const row *b) const
+	int operator()(const category &cat, const row_initializer &a, const row *b) const
 	{
 		assert(b);
 
@@ -105,11 +104,10 @@ class row_comparator
 		{
 			assert(ai != a.end());
 
-			std::string_view ka = ai->value;
+			std::string_view ka = ai->value();
 			std::string_view kb = rhb[k].text();
 
-			if (not (ai->may_be_null and rhb[k].empty()))
-				d = f(ka, kb);
+			d = f(ka, kb);
 
 			if (d != 0)
 				break;
@@ -143,7 +141,7 @@ class category_index
 	}
 
 	row *find(const category &cat, row *k) const;
-	row *find_by_value(const category &cat, const category::key_type &k) const;
+	row *find_by_value(const category &cat, row_initializer k) const;
 
 	void insert(category &cat, row *r);
 	void erase(category &cat, row *r);
@@ -353,19 +351,19 @@ row *category_index::find(const category &cat, row *k) const
 	return r ? r->m_row : nullptr;
 }
 
-row *category_index::find_by_value(const category &cat, const category::key_type &k) const
+row *category_index::find_by_value(const category &cat, row_initializer k) const
 {
 	// sort the values in k first
 
-	category::key_type k2;
+	row_initializer k2;
 	for (auto &f : cat.key_item_indices())
 	{
 		auto fld = cat.get_item_name(f);
 
 		auto ki = find_if(k.begin(), k.end(), [&fld](auto &i)
-			{ return i.name == fld; });
+			{ return i.name() == fld; });
 		if (ki == k.end())
-			k2.emplace_back(std::string{ fld }, "");
+			k2.emplace_back(fld, "");
 		else
 			k2.emplace_back(*ki);
 	}
@@ -544,49 +542,6 @@ category::~category()
 
 // --------------------------------------------------------------------
 
-uint16_t category::get_item_ix(std::string_view item_name) const
-{
-	uint16_t result;
-
-	for (result = 0; result < m_items.size(); ++result)
-	{
-		if (iequals(item_name, m_items[result].m_name))
-			break;
-	}
-
-	if (VERBOSE > 0 and result == m_items.size() and m_cat_validator != nullptr) // validate the name, if it is known at all (since it was not found)
-	{
-		auto iv = m_cat_validator->get_validator_for_item(item_name);
-		if (iv == nullptr)
-			std::cerr << "Invalid name used '" << item_name << "' is not a known item in " + m_name << '\n';
-	}
-
-	return result;
-}
-
-uint16_t category::add_item(std::string_view item_name)
-{
-	using namespace std::literals;
-
-	uint16_t result = get_item_ix(item_name);
-
-	if (result == m_items.size())
-	{
-		const item_validator *item_validator = nullptr;
-
-		if (m_cat_validator != nullptr)
-		{
-			item_validator = m_cat_validator->get_validator_for_item(item_name);
-			if (item_validator == nullptr)
-				m_validator->report_error(validation_error::item_not_allowed_in_category, m_name, item_name, false);
-		}
-
-		m_items.emplace_back(item_name, item_validator);
-	}
-
-	return result;
-}
-
 void category::remove_item(std::string_view item_name)
 {
 	for (std::size_t ix = 0; ix < m_items.size(); ++ix)
@@ -915,24 +870,6 @@ bool category::validate_links() const
 	return result;
 }
 
-void category::strip()
-{
-	std::vector<std::string> to_be_removed;
-
-	for (auto &item : m_items)
-	{
-		if (item.m_validator == nullptr)
-			to_be_removed.push_back(item.m_name);
-	}
-
-	for (auto item : to_be_removed)
-	{
-		if (cif::VERBOSE > 0)
-			std::clog << "Dropping item " << m_name << '.' << item << '\n';
-		remove_item(item);
-	}
-}
-
 // --------------------------------------------------------------------
 
 row_handle category::operator[](const key_type &key)
@@ -1339,7 +1276,8 @@ std::string category::get_unique_value(std::string_view item_name)
 		// brain-dead implementation
 		for (std::size_t ix = 0; ix < size(); ++ix)
 		{
-			result = cif_id_for_number(static_cast<int>(ix));
+			// result = m_name + "-" + std::to_string(ix);
+			result = cif_id_for_number(ix);
 			if (not contains(key(item_name) == result))
 				break;
 		}
@@ -2235,4 +2173,4 @@ bool category::operator==(const category &rhs) const
 	return true;
 }
 
-} // namespace cif
+} // namespace cif

src/compound.cpp

@@ -299,14 +299,37 @@ class compound_factory_impl : public std::enable_shared_from_this<compound_facto
 		std::shared_lock lock(mMutex);
 
 		compound *result = nullptr;
-		
+
+		// walk the list, see if any of the implementations has the compound already
 		for (auto impl = shared_from_this(); impl; impl = impl->m_next)
 		{
-			result = impl->create(id);
-			if (result != nullptr)
+			for (auto cmp : impl->m_compounds)
+			{
+				if (iequals(cmp->id(), id))
+				{
+					result = cmp;
+					break;
+				}
+			}
+
+			if (result)
 				break;
 		}
 
+		if (result == nullptr and
+			find_if(m_missing.begin(), m_missing.end(), [&id](const std::string &m_id) { return cif::iequals(id, m_id); }) == m_missing.end())
+		{
+			for (auto impl = shared_from_this(); impl; impl = impl->m_next)
+			{
+				result = impl->create(id);
+				if (result != nullptr)
+					break;
+			}
+
+			if (result == nullptr)
+				m_missing.emplace_back(id);
+		}
+
 		return result;
 	}
 
@@ -337,7 +360,7 @@ class compound_factory_impl : public std::enable_shared_from_this<compound_facto
 	cif::parser::datablock_index m_index;
 
 	std::vector<compound *> m_compounds;
-	cif::iset m_missing;
+	std::vector<std::string> m_missing;
 	std::shared_ptr<compound_factory_impl> m_next;
 };
 
@@ -358,14 +381,6 @@ compound_factory_impl::compound_factory_impl(const fs::path &file, std::shared_p
 
 compound *compound_factory_impl::create(const std::string &id)
 {
-	// shortcut
-
-	if (m_missing.contains(id))
-		return nullptr;
-
-	if (auto i = find_if(m_compounds.begin(), m_compounds.end(), [id](compound *c) { return c->id() == id; }); i != m_compounds.end())
-		return *i;
-
 	compound *result = nullptr;
 
 	std::unique_ptr<std::istream> ccd;
@@ -434,9 +449,6 @@ compound *compound_factory_impl::create(const std::string &id)
 		}
 	}
 
-	if (result == nullptr)
-		m_missing.insert(id);
-
 	return result;
 }
 
@@ -449,6 +461,20 @@ class local_compound_factory_impl : public compound_factory_impl
 		: compound_factory_impl(next)
 		, m_local_file(file)
 	{
+		// const std::regex peptideRx("(?:[lmp]-)?peptide", std::regex::icase);
+
+		// for (const auto &[id, name, threeLetterCode, group] :
+		// 	file["comp_list"]["chem_comp"].rows<std::string, std::string, std::string, std::string>("id", "name", "three_letter_code", "group"))
+		// {
+		// 	auto &rdb = m_local_file["comp_" + id];
+		// 	if (rdb.empty())
+		// 	{
+		// 		// std::cerr << "Missing data in restraint file for id " + id + '\n';
+		// 		continue;
+		// 	}
+
+		// 	construct_compound(rdb, id, name, threeLetterCode, group);
+		// }
 	}
 
 	compound *create(const std::string &id) override;
@@ -462,12 +488,6 @@ class local_compound_factory_impl : public compound_factory_impl
 
 compound *local_compound_factory_impl::create(const std::string &id)
 {
-	if (m_missing.contains(id))
-		return nullptr;
-
-	if (auto i = find_if(m_compounds.begin(), m_compounds.end(), [id](compound *c) { return c->id() == id; }); i != m_compounds.end())
-		return *i;
-
 	compound *result = nullptr;
 
 	for (auto &db : m_local_file)
@@ -480,13 +500,10 @@ compound *local_compound_factory_impl::create(const std::string &id)
 
 			try
 			{
-				const auto &[id2, name, threeLetterCode, group] =
+				const auto &[id, name, threeLetterCode, group] =
 					chem_comp->front().get<std::string, std::string, std::string, std::string>("id", "name", "three_letter_code", "group");
 
-				if (id == id2)
-					result = construct_compound(db, id, name, threeLetterCode, group);
-				else
-					throw std::runtime_error("Compound ID's don't match: id 1=" + id + ", id 2=" + id2);
+				result = construct_compound(db, id, name, threeLetterCode, group);
 			}
 			catch (const std::exception &ex)
 			{
@@ -497,9 +514,6 @@ compound *local_compound_factory_impl::create(const std::string &id)
 		}
 	}
 
-	if (result == nullptr)
-		m_missing.insert(id);
-
 	return result;
 }
 
@@ -512,13 +526,9 @@ compound *local_compound_factory_impl::construct_compound(const datablock &rdb,
 	int formal_charge = 0;
 	std::map<std::string,std::size_t> formula_data;
 
-	for (std::size_t ord = 1; const auto &[atom_id, type_symbol, type, charge, x, y, z, xi, yi, zi] :
-		rdb["chem_comp_atom"].rows<std::string, std::string, std::string, int,
-			std::optional<float>, std::optional<float>, std::optional<float>,
-			std::optional<float>, std::optional<float>, std::optional<float>>(
-			"atom_id", "type_symbol", "type", "charge",
-			"model_Cartn_x", "model_Cartn_y", "model_Cartn_z",
-			"pdbx_model_Cartn_x_ideal", "pdbx_model_Cartn_y_ideal", "pdbx_model_Cartn_z_ideal"))
+	for (std::size_t ord = 1; const auto &[atom_id, type_symbol, type, charge, x, y, z] :
+		rdb["chem_comp_atom"].rows<std::string, std::string, std::string, int, float, float, float>(
+			"atom_id", "type_symbol", "type", "charge", "x", "y", "z"))
 	{
 		auto atom = cif::atom_type_traits(type_symbol);
 		formula_weight += atom.weight();
@@ -530,9 +540,9 @@ compound *local_compound_factory_impl::construct_compound(const datablock &rdb,
 			{ "atom_id", atom_id },
 			{ "type_symbol", type_symbol },
 			{ "charge", charge },
-			{ "model_Cartn_x",  x.has_value() ? x : xi, 3 },
-			{ "model_Cartn_y",  y.has_value() ? y : yi, 3 },
-			{ "model_Cartn_z",  z.has_value() ? z : zi, 3 },
+			{ "model_Cartn_x",  x, 3 },
+			{ "model_Cartn_y",  y, 3 },
+			{ "model_Cartn_z",  z, 3 },
 			{ "pdbx_ordinal", ord++ }
 		});
 
@@ -760,7 +770,8 @@ bool compound_factory::is_monomer(std::string_view res_name) const
 
 void compound_factory::report_missing_compound(std::string_view compound_id)
 {
-	if (std::exchange(m_report_missing, false))
+	static bool s_reported = false;
+	if (std::exchange(s_reported, true) == false)
 	{
 		using namespace cif::colour;
 
@@ -784,7 +795,7 @@ void compound_factory::report_missing_compound(std::string_view compound_id)
 				  << "in /var/cache/libcifpp using the following commands:\n\n"
 				  << "curl -o " << CACHE_DIR << "/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif\n"
 				  << "curl -o " << CACHE_DIR << "/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic\n"
-				  << "curl -o " << CACHE_DIR << "/mmcif_ma.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_ma.dic\n\n";
+				  << "curl -o " << CACHE_DIR << "/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic\n\n";
 #endif
 
 		if (m_impl)

src/condition.cpp

@@ -24,9 +24,8 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-#include "cif++/condition.hpp"
 #include "cif++/category.hpp"
-#include "cif++/validate.hpp"
+#include "cif++/condition.hpp"
 
 namespace cif
 {
@@ -61,52 +60,6 @@ bool is_item_type_uchar(const category &cat, std::string_view col)
 
 namespace detail
 {
-	// 	// index lookup
-	// 	struct index_lookup_condition_impl : public condition_impl
-	// 	{
-	// 		index_lookup_condition_impl(row_initializer &&key_values)
-	// 			: m_key_values(std::move(key_values))
-	// 		{
-	// 		}
-	//
-	// 		condition_impl *prepare(const category &c) override
-	// 		{
-	// 			m_single_hit = c[m_key_values];
-	// 			return this;
-	// 		}
-	//
-	// 		bool test(row_handle r) const override
-	// 		{
-	// 			return m_single_hit == r;
-	// 		}
-	//
-	// 		void str(std::ostream &os) const override
-	// 		{
-	// 			os << "index scan";
-	// 		}
-	//
-	// 		virtual std::optional<row_handle> single() const override
-	// 		{
-	// 			return m_single_hit;
-	// 		}
-	//
-	// 		virtual bool equals(const condition_impl *rhs) const override
-	// 		{
-	// 			if (typeid(*rhs) == typeid(index_lookup_condition_impl))
-	// 			{
-	// 				auto ri = static_cast<const index_lookup_condition_impl *>(rhs);
-	// 				if (m_single_hit or ri->m_single_hit)
-	// 					return m_single_hit == ri->m_single_hit;
-	// 				else
-	// 					// watch out, both m_item_ix might be the same while item_names might be diffent (in case they both do not exist in the category)
-	// 					return m_key_values == ri->m_key_values;
-	// 			}
-	// 			return this == rhs;
-	// 		}
-	//
-	// 		row_initializer m_key_values;
-	// 		row_handle m_single_hit;
-	// 	};
 
 	condition_impl *key_equals_condition_impl::prepare(const category &c)
 	{
@@ -131,8 +84,7 @@ namespace detail
 			c.key_item_indices().contains(m_item_ix) and
 			c.key_item_indices().size() == 1)
 		{
-			item v(m_item_name, m_value);
-			m_single_hit = c[{ { m_item_name, std::string{ v.value() }, false } }];
+			m_single_hit = c[{ { m_item_name, m_value } }];
 		}
 
 		return this;
@@ -146,8 +98,7 @@ namespace detail
 		{
 			auto &cs = (*s)->m_sub;
 
-			if (find_if(cs.begin(), cs.end(), [c](const condition_impl *i)
-					{ return i->equals(c); }) == cs.end())
+			if (find_if(cs.begin(), cs.end(), [c](const condition_impl *i) { return i->equals(c); }) == cs.end())
 			{
 				result = false;
 				break;
@@ -167,8 +118,7 @@ namespace detail
 		for (size_t fc_i = 0; fc_i < fc.size();)
 		{
 			auto c = fc[fc_i];
-			if (not found_in_range(c, subs.begin() + 1, subs.end()))
-			{
+			if (not found_in_range(c, subs.begin() + 1, subs.end())) {
 				++fc_i;
 				continue;
 			}
@@ -186,12 +136,11 @@ namespace detail
 				for (size_t ssub_i = 0; ssub_i < ssub.size();)
 				{
 					auto sc = ssub[ssub_i];
-					if (not sc->equals(c))
-					{
+					if (not sc->equals(c)) {
 						++ssub_i;
 						continue;
 					}
-
+					
 					ssub.erase(ssub.begin() + ssub_i);
 					delete sc;
 					break;
@@ -208,99 +157,6 @@ namespace detail
 		return oc;
 	}
 
-	condition_impl *and_condition_impl::prepare(const category &c)
-	{
-		for (auto &sub : m_sub)
-			sub = sub->prepare(c);
-
-		if (auto cv = c.get_cat_validator(); cv != nullptr)
-		{
-			// See if we can collapse a search part of this and_condition into a single index lookup
-
-			cif::iset keys{ cv->m_keys.begin(), cv->m_keys.end() };
-			category::key_type lookup;
-			std::vector<condition_impl *> subs;
-			std::vector<std::string> may_be_empty;
-
-			for (auto &sub : m_sub)
-			{
-				if (auto s = dynamic_cast<const key_equals_condition_impl *>(sub); s != nullptr)
-				{
-					if (keys.contains(s->m_item_name))
-					{
-						lookup.emplace_back(s->m_item_name, s->m_value);
-						subs.emplace_back(sub);
-					}
-					continue;
-				}
-
-				if (auto s = dynamic_cast<const key_equals_number_condition_impl *>(sub); s != nullptr)
-				{
-					if (keys.contains(s->m_item_name))
-					{
-						item v{ s->m_item_name, s->m_value };
-						lookup.emplace_back(s->m_item_name, std::string{ v.value() } );
-						subs.emplace_back(sub);
-					}
-					continue;
-				}
-
-				if (auto s = dynamic_cast<const key_equals_or_empty_condition_impl *>(sub); s != nullptr)
-				{
-					if (keys.contains(s->m_item_name))
-					{
-						lookup.emplace_back(s->m_item_name, s->m_value, true);
-						subs.emplace_back(sub);
-						may_be_empty.emplace_back(s->m_item_name);
-					}
-					continue;
-				}
-
-				if (auto s = dynamic_cast<const key_equals_number_or_empty_condition_impl *>(sub); s != nullptr)
-				{
-					if (keys.contains(s->m_item_name))
-					{
-						item v{ s->m_item_name, s->m_value };
-						lookup.emplace_back(s->m_item_name, std::string{ v.value() }, true );
-						subs.emplace_back(sub);
-					}
-					continue;
-				}
-			}
-
-			if (lookup.size() == keys.size())
-			{
-				m_single = c[lookup];
-
-				for (auto s : subs)
-					m_sub.erase(std::remove(m_sub.begin(), m_sub.end(), s), m_sub.end());
-			}
-		}
-
-		return this;
-	}
-
-	bool and_condition_impl::test(row_handle r) const
-	{
-		bool result = true;
-
-		if (m_single.has_value() and *m_single != r)
-			result = false;
-		else
-		{
-			for (auto sub : m_sub)
-			{
-				if (sub->test(r))
-					continue;
-
-				result = false;
-				break;
-			}
-		}
-
-		return result;
-	}
-
 	condition_impl *or_condition_impl::prepare(const category &c)
 	{
 		std::vector<and_condition_impl *> and_conditions;
@@ -324,7 +180,7 @@ void condition::prepare(const category &c)
 {
 	if (m_impl)
 		m_impl = m_impl->prepare(c);
-
+	
 	m_prepared = true;
 }
 

src/datablock.cpp

@@ -26,10 +26,6 @@
 
 #include "cif++/datablock.hpp"
 
-#include "cif++/validate.hpp"
-
-#include <exception>
-
 namespace cif
 {
 
@@ -46,17 +42,31 @@ void datablock::load_dictionary()
 {
 	if (auto *audit_conform = get("audit_conform"); audit_conform and not audit_conform->empty())
 	{
-		try
+		std::string name = audit_conform->front().get<std::string>("dict_name");
+
+		if (name == "mmcif_pdbx_v50")
+			name = "mmcif_pdbx.dic"; // we had a bug here in libcifpp...
+
+		if (not name.empty())
 		{
-			set_validator(&validator_factory::instance().get(*audit_conform));
-		}
-		catch (const std::exception &ex)
-		{
-			std::clog << ex.what() << '\n';
+			try
+			{
+				load_dictionary(name);
+			}
+			catch (const std::exception &ex)
+			{
+				if (VERBOSE)
+					std::cerr << "Failed to load dictionary " << std::quoted(name) << ": " << ex.what() << '\n';
+			}
 		}
 	}
 }
 
+void datablock::load_dictionary(std::string_view name)
+{
+	set_validator(&validator_factory::instance()[name]);
+}
+
 void datablock::set_validator(const validator *v)
 {
 	m_validator = v;
@@ -90,6 +100,40 @@ bool datablock::is_valid() const
 	return result;
 }
 
+bool datablock::is_valid()
+{
+	if (m_validator == nullptr)
+		throw std::runtime_error("Validator not specified for datablock data_" + name());
+
+	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;
@@ -103,46 +147,6 @@ bool datablock::validate_links() const
 	return result;
 }
 
-bool datablock::strip()
-{
-	bool result = true;
-
-	// remove all categories that have no validator
-	erase(std::remove_if(begin(), end(), [](category &c)
-			  {
-		bool result = false;
-		if (c.get_cat_validator() == nullptr)
-		{
-			if (cif::VERBOSE > 0)
-				std::clog << "Dropping category " << c.name() << '\n';
-			result = true;
-		}
-		return result; }),
-		end());
-
-	// then strip the remaining categories
-	for (auto &cat : *this)
-		cat.strip();
-
-	// Add or remove the audit_conform block here.
-	if (is_valid())
-	{
-		// If the dictionary declares an audit_conform category, put it in,
-		// but only if it does not exist already!
-
-		if (auto audit_conform = get("audit_conform");
-			audit_conform != nullptr and m_validator->get_validator_for_category("audit_conform") != nullptr)
-		{
-			audit_conform->clear();
-			m_validator->fill_audit_conform(*audit_conform);
-		}
-	}
-	else
-		result = false;
-
-	return result;
-}
-
 // --------------------------------------------------------------------
 
 category &datablock::operator[](std::string_view name)
@@ -199,7 +203,7 @@ std::tuple<datablock::iterator, bool> datablock::emplace(std::string_view name)
 
 	if (is_new)
 	{
-		i = insert(end(), { name });
+		i = insert(end(), {name});
 		i->set_validator(m_validator, *this);
 	}
 
@@ -468,4 +472,4 @@ bool datablock::operator==(const datablock &rhs) const
 	return true;
 }
 
-} // namespace cif
+} // namespace cif

src/dictionary_parser.cpp

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

src/file.cpp

@@ -25,7 +25,6 @@
  */
 
 #include "cif++/file.hpp"
-#include "cif++/condition.hpp"
 #include "cif++/gzio.hpp"
 
 namespace cif
@@ -47,16 +46,8 @@ bool file::is_valid()
 {
 	bool result = not empty();
 
-	for (bool first = true; auto &d : *this)
-	{
-		if (first)
-		{
-			result = d.is_valid() and result;
-			first = false;
-		}
-		else if (d.get_validator() != nullptr)
-			result = d.is_valid() and result;
-	}
+	for (auto &d : *this)
+		result = d.is_valid() and result;
 
 	if (result)
 		result = validate_links();
@@ -74,6 +65,42 @@ bool file::validate_links() const
 	return result;
 }
 
+// void file::load_dictionary()
+// {
+// 	if (not empty())
+// 	{
+// 		auto *audit_conform = front().get("audit_conform");
+// 		if (audit_conform and not audit_conform->empty())
+// 		{
+// 			std::string name = audit_conform->front().get<std::string>("dict_name");
+
+// 			if (name == "mmcif_pdbx_v50")
+// 				name = "mmcif_pdbx.dic"; // we had a bug here in libcifpp...
+
+// 			if (not name.empty())
+// 			{
+// 				try
+// 				{
+// 					load_dictionary(name);
+// 				}
+// 				catch (const std::exception &ex)
+// 				{
+// 					if (VERBOSE)
+// 						std::cerr << "Failed to load dictionary " << std::quoted(name) << ": " << ex.what() << '\n';
+// 				}
+// 			}
+// 		}
+// 	}
+
+// 	// if (not m_validator)
+// 	// 	load_dictionary("mmcif_pdbx.dic");	// TODO: maybe incorrect? Perhaps improve?
+// }
+
+// void file::load_dictionary(std::string_view name)
+// {
+// 	set_validator(&validator_factory::instance()[name]);
+// }
+
 bool file::contains(std::string_view name) const
 {
 	return std::find_if(begin(), end(), [name](const datablock &db)
@@ -139,6 +166,16 @@ void file::load(const std::filesystem::path &p)
 	}
 }
 
+void file::load(const std::filesystem::path &p, std::string_view dict)
+{
+	load(p, validator_factory::instance().operator[](dict));
+}
+
+void file::load(std::istream &is, std::string_view dict)
+{
+	load(is, validator_factory::instance().operator[](dict));
+}
+
 void file::load(const std::filesystem::path &p, const validator &v)
 {
 	gzio::ifstream in(p);
@@ -184,4 +221,4 @@ void file::save(std::ostream &os) const
 		db.write(os);
 }
 
-} // namespace cif
+} // namespace cif

src/model.cpp

@@ -28,7 +28,6 @@
 
 #include <filesystem>
 #include <fstream>
-#include <initializer_list>
 #include <iomanip>
 #include <numeric>
 #include <stack>
@@ -48,10 +47,15 @@ void atom::atom_impl::moveTo(const point &p)
 
 	auto r = row();
 
-	r.assign("Cartn_x", cif::format("{:.3f}", p.m_x), false, false);
-	r.assign("Cartn_y", cif::format("{:.3f}", p.m_y), false, false);
-	r.assign("Cartn_z", cif::format("{:.3f}", p.m_z), false, false);
-
+#if __cpp_lib_format
+	r.assign("Cartn_x", std::format("{:.3f}", p.m_x), false, false);
+	r.assign("Cartn_y", std::format("{:.3f}", p.m_y), false, false);
+	r.assign("Cartn_z", std::format("{:.3f}", p.m_z), false, false);
+#else
+	r.assign("Cartn_x", cif::format("%.3f", p.m_x).str(), false, false);
+	r.assign("Cartn_y", cif::format("%.3f", p.m_y).str(), false, false);
+	r.assign("Cartn_z", cif::format("%.3f", p.m_z).str(), false, false);
+#endif
 	m_location = p;
 }
 
@@ -98,18 +102,18 @@ void atom::atom_impl::set_property(const std::string_view name, const std::strin
 	r.assign(name, value, true, true);
 }
 
-int atom::atom_impl::compare(const atom_impl &b) const
-{
-	int d = get_property("label_asym_id").compare(b.get_property("label_asym_id"));
-	if (d == 0)
-		d = get_property_int("label_seq_id") - b.get_property_int("label_seq_id");
-	if (d == 0)
-		d = get_property_int("auth_seq_id") - b.get_property_int("auth_seq_id");
-	if (d == 0)
-		d = get_property("label_atom_id").compare(b.get_property("label_atom_id"));
+// int atom::atom_impl::compare(const atom_impl &b) const
+// {
+// 	int d = m_asym_id.compare(b.m_asym_id);
+// 	if (d == 0)
+// 		d = m_seq_id - b.m_seq_id;
+// 	if (d == 0)
+// 		d = m_auth_seq_id.compare(b.m_auth_seq_id);
+// 	if (d == 0)
+// 		d = mAtom_id.compare(b.mAtom_id);
 
-	return d;
-}
+// 	return d;
+// }
 
 // bool atom::atom_impl::getAnisoU(float anisou[6]) const
 // {
@@ -145,6 +149,145 @@ int atom::atom_impl::get_charge() const
 	return formalCharge.value_or(0);
 }
 
+// const Compound *atom::atom_impl::compound() const
+// {
+// 	if (mCompound == nullptr)
+// 	{
+// 		std::string compID = get_property("label_comp_id");
+
+// 		mCompound = compound_factory::instance().create(compID);
+// 	}
+
+// 	return mCompound;
+// }
+
+// const std::string atom::atom_impl::get_property(const std::string_view name) const
+// {
+// 	for (auto &&[item_name, ref] : mCachedRefs)
+// 	{
+// 		if (item_name == name)
+// 			return ref.as<std::string>();
+// 	}
+
+// 	mCachedRefs.emplace_back(name, const_cast<Row &>(mRow)[name]);
+// 	return std::get<1>(mCachedRefs.back()).as<std::string>();
+// }
+
+// void atom::atom_impl::set_property(const std::string_view name, const std::string &value)
+// {
+// 	for (auto &&[item_name, ref] : mCachedRefs)
+// 	{
+// 		if (item_name != name)
+// 			continue;
+
+// 		ref = value;
+// 		return;
+// 	}
+
+// 	mCachedRefs.emplace_back(name, mRow[name]);
+// 	std::get<1>(mCachedRefs.back()) = value;
+// }
+
+// const Row atom::getRowAniso() const
+// {
+// 	auto &db = m_impl->m_db;
+// 	auto cat = db.get("atom_site_anisotrop");
+// 	if (not cat)
+// 		return {};
+// 	else
+// 		return cat->find1(key("id") == m_impl->m_id);
+// }
+
+// float atom::uIso() const
+// {
+// 	float result;
+
+// 	if (not get_property<std::string>("U_iso_or_equiv").empty())
+// 		result = get_property<float>("U_iso_or_equiv");
+// 	else if (not get_property<std::string>("B_iso_or_equiv").empty())
+// 		result = get_property<float>("B_iso_or_equiv") / static_cast<float>(8 * kPI * kPI);
+// 	else
+// 		throw std::runtime_error("Missing B_iso or U_iso");
+
+// 	return result;
+// }
+
+// const Compound &atom::compound() const
+// {
+// 	auto result = impl().compound();
+
+// 	if (result == nullptr)
+// 	{
+// 		if (VERBOSE > 0)
+// 			std::cerr << "Compound not found: '" << get_property<std::string>("label_comp_id") << '\'' << '\n';
+
+// 		throw std::runtime_error("no compound");
+// 	}
+
+// 	return *result;
+// }
+
+// std::string atom::labelEntityID() const
+// {
+// 	return get_property<std::string>("label_entity_id");
+// }
+
+// std::string atom::authAtom_id() const
+// {
+// 	return get_property<std::string>("auth_atom_id");
+// }
+
+// std::string atom::authCompID() const
+// {
+// 	return get_property<std::string>("auth_comp_id");
+// }
+
+// std::string atom::get_auth_asym_id() const
+// {
+// 	return get_property<std::string>("auth_asym_id");
+// }
+
+// std::string atom::get_pdb_ins_code() const
+// {
+// 	return get_property<std::string>("pdbx_PDB_ins_code");
+// }
+
+// std::string atom::pdbxAuthAltID() const
+// {
+// 	return get_property<std::string>("pdbx_auth_alt_id");
+// }
+
+// void atom::translate(point t)
+// {
+// 	auto loc = location();
+// 	loc += t;
+// 	location(loc);
+// }
+
+// void atom::rotate(quaternion q)
+// {
+// 	auto loc = location();
+// 	loc.rotate(q);
+// 	location(loc);
+// }
+
+// void atom::translate_and_rotate(point t, quaternion q)
+// {
+// 	auto loc = location();
+// 	loc += t;
+// 	loc.rotate(q);
+// 	location(loc);
+// }
+
+// void atom::translate_rotate_and_translate(point t1, quaternion q, point t2)
+// {
+// 	auto loc = location();
+// 	loc += t1;
+// 	loc.rotate(q);
+// 	loc += t2;
+// 	location(loc);
+// }
+
 std::ostream &operator<<(std::ostream &os, const atom &atom)
 {
 	if (atom.is_water())
@@ -176,8 +319,8 @@ residue::residue(structure &structure, const std::vector<atom> &atoms)
 	m_compound_id = a.get_label_comp_id();
 	m_asym_id = a.get_label_asym_id();
 	m_seq_id = a.get_label_seq_id();
-	m_pdb_strand_id = a.get_auth_asym_id();
-	m_pdb_seq_num = a.get_auth_seq_id();
+	m_auth_asym_id = a.get_auth_asym_id();
+	m_auth_seq_id = a.get_auth_seq_id();
 	m_pdb_ins_code = a.get_pdb_ins_code();
 
 	for (auto atom : atoms)
@@ -228,12 +371,11 @@ atom residue::create_new_atom(atom_type inType, const std::string &inAtomID, poi
 		{ "label_alt_id", "." },
 		{ "label_comp_id", m_compound_id },
 		{ "label_seq_id", m_seq_id },
-		{ "auth_asym_id", m_pdb_strand_id },
+		{ "auth_asym_id", m_auth_asym_id },
 		{ "auth_atom_id", inAtomID },
 		{ "auth_comp_id", m_compound_id },
-		{ "auth_seq_id", m_pdb_seq_num },
+		{ "auth_seq_id", m_auth_seq_id },
 		{ "occupancy", 1.0f, 2 },
-		{ "B_iso_or_equiv", 20.0f },
 		{ "pdbx_PDB_model_num", m_structure->get_model_nr() },
 	});
 
@@ -308,28 +450,6 @@ atom residue::get_atom_by_atom_id(const std::string &atom_id) const
 	return result;
 }
 
-atom residue::get_atom_by_atom_id(const std::string &atomID, const std::string &altID) const
-{
-	if (altID.empty())
-		return get_atom_by_atom_id(atomID);
-
-	atom result;
-
-	for (auto &a : m_atoms)
-	{
-		if (auto a_alt_id = a.get_label_alt_id(); a.get_label_atom_id() == atomID and (a_alt_id.empty() or a_alt_id == altID))
-		{
-			result = a;
-			break;
-		}
-	}
-
-	if (not result and VERBOSE > 1)
-		std::cerr << "atom with atom_id " << atomID << " and alt_id " << altID << " not found in residue " << m_asym_id << ':' << m_seq_id << '\n';
-
-	return result;
-}
-
 // residue is a single entity if the atoms for the asym with m_asym_id is equal
 // to the number of atoms in this residue...  hope this is correct....
 bool residue::is_entity() const
@@ -398,8 +518,8 @@ std::ostream &operator<<(std::ostream &os, const residue &res)
 {
 	os << res.get_compound_id() << ' ' << res.get_asym_id() << ':' << res.get_seq_id();
 
-	if (res.get_pdb_strand_id() != res.get_asym_id() or res.get_pdb_seq_num() != std::to_string(res.get_seq_id()))
-		os << " [" << res.get_pdb_strand_id() << ':' << res.get_pdb_seq_num() << ']';
+	if (res.get_auth_asym_id() != res.get_asym_id() or res.get_auth_seq_id() != std::to_string(res.get_seq_id()))
+		os << " [" << res.get_auth_asym_id() << ':' << res.get_auth_seq_id() << ']';
 
 	return os;
 }
@@ -408,7 +528,7 @@ std::ostream &operator<<(std::ostream &os, const residue &res)
 // monomer
 
 monomer::monomer(const polymer &polymer, std::size_t index, int seqID, const std::string &authSeqID, const std::string &pdbInsCode, const std::string &compoundID)
-	: residue(*polymer.get_structure(), compoundID, polymer.get_asym_id(), seqID, polymer.get_pdb_strand_id(), authSeqID, pdbInsCode)
+	: residue(*polymer.get_structure(), compoundID, polymer.get_asym_id(), seqID, polymer.get_auth_asym_id(), authSeqID, pdbInsCode)
 	, m_polymer(&polymer)
 	, m_index(index)
 {
@@ -442,16 +562,6 @@ bool monomer::is_last_in_chain() const
 	return m_index + 1 == m_polymer->size();
 }
 
-const monomer &monomer::prev() const
-{
-	return m_polymer->at(m_index - 1);
-}
-
-const monomer &monomer::next() const
-{
-	return m_polymer->at(m_index + 1);
-}
-
 bool monomer::has_alpha() const
 {
 	return m_index >= 1 and m_index + 2 < m_polymer->size();
@@ -468,7 +578,7 @@ float monomer::phi() const
 
 	if (m_index > 0)
 	{
-		auto &prev = m_polymer->at(m_index - 1);
+		auto &prev = m_polymer->operator[](m_index - 1);
 		if (prev.m_seq_id + 1 == m_seq_id)
 		{
 			auto a1 = prev.C();
@@ -490,7 +600,7 @@ float monomer::psi() const
 
 	if (m_index + 1 < m_polymer->size())
 	{
-		auto &next = m_polymer->at(m_index + 1);
+		auto &next = m_polymer->operator[](m_index + 1);
 		if (m_seq_id + 1 == next.m_seq_id)
 		{
 			auto a1 = N();
@@ -514,9 +624,9 @@ float monomer::alpha() const
 	{
 		if (m_index >= 1 and m_index + 2 < m_polymer->size())
 		{
-			auto &prev = m_polymer->at(m_index - 1);
-			auto &next = m_polymer->at(m_index + 1);
-			auto &nextNext = m_polymer->at(m_index + 2);
+			auto &prev = m_polymer->operator[](m_index - 1);
+			auto &next = m_polymer->operator[](m_index + 1);
+			auto &nextNext = m_polymer->operator[](m_index + 2);
 
 			result = static_cast<float>(dihedral_angle(prev.CAlpha().get_location(), CAlpha().get_location(), next.CAlpha().get_location(), nextNext.CAlpha().get_location()));
 		}
@@ -538,8 +648,8 @@ float monomer::kappa() const
 	{
 		if (m_index >= 2 and m_index + 2 < m_polymer->size())
 		{
-			auto &prevPrev = m_polymer->at(m_index - 2);
-			auto &nextNext = m_polymer->at(m_index + 2);
+			auto &prevPrev = m_polymer->operator[](m_index - 2);
+			auto &nextNext = m_polymer->operator[](m_index + 2);
 
 			if (prevPrev.m_seq_id + 4 == nextNext.m_seq_id)
 			{
@@ -567,7 +677,7 @@ float monomer::tco() const
 	{
 		if (m_index > 0)
 		{
-			auto &prev = m_polymer->at(m_index - 1);
+			auto &prev = m_polymer->operator[](m_index - 1);
 			if (prev.m_seq_id + 1 == m_seq_id)
 				result = static_cast<float>(cosinus_angle(C().get_location(), O().get_location(), prev.C().get_location(), prev.O().get_location()));
 		}
@@ -589,7 +699,7 @@ float monomer::omega() const
 	try
 	{
 		if (not is_last_in_chain())
-			result = omega(*this, m_polymer->at(m_index + 1));
+			result = omega(*this, m_polymer->operator[](m_index + 1));
 	}
 	catch (const std::exception &ex)
 	{
@@ -685,7 +795,7 @@ bool monomer::is_cis() const
 
 	if (m_index + 1 < m_polymer->size())
 	{
-		auto &next = m_polymer->at(m_index + 1);
+		auto &next = m_polymer->operator[](m_index + 1);
 
 		result = monomer::is_cis(*this, next);
 	}
@@ -827,7 +937,7 @@ polymer::polymer(structure &s, const std::string &entityID, const std::string &a
 	: m_structure(const_cast<structure *>(&s))
 	, m_entity_id(entityID)
 	, m_asym_id(asym_id)
-	, m_pdb_strand_id(auth_asym_id)
+	, m_auth_asym_id(auth_asym_id)
 {
 	using namespace cif::literals;
 
@@ -839,8 +949,12 @@ polymer::polymer(structure &s, const std::string &entityID, const std::string &a
 	for (auto r : poly_seq_scheme.find("asym_id"_key == asym_id))
 	{
 		int seqID;
-		std::string compoundID, pdbSeqNum, pdbInsCode;
-		cif::tie(seqID, pdbSeqNum, compoundID, pdbInsCode) = r.get("seq_id", "pdb_seq_num", "mon_id", "pdb_ins_code");
+		std::optional<int> pdbSeqNum;
+		std::string compoundID, authSeqID, pdbInsCode;
+		cif::tie(seqID, authSeqID, compoundID, pdbInsCode, pdbSeqNum) = r.get("seq_id", "auth_seq_num", "mon_id", "pdb_ins_code", "pdb_seq_num");
+
+		if (authSeqID.empty() and pdbSeqNum.has_value())
+			authSeqID = std::to_string(*pdbSeqNum);
 
 		std::size_t index = size();
 
@@ -848,11 +962,11 @@ polymer::polymer(structure &s, const std::string &entityID, const std::string &a
 		if (not ix.count(seqID))
 		{
 			ix[seqID] = index;
-			emplace_back(*this, index, seqID, pdbSeqNum, pdbInsCode, compoundID);
+			emplace_back(*this, index, seqID, authSeqID, pdbInsCode, compoundID);
 		}
 		else if (VERBOSE > 0)
 		{
-			monomer m{ *this, index, seqID, pdbSeqNum, pdbInsCode, compoundID };
+			monomer m{ *this, index, seqID, authSeqID, pdbInsCode, compoundID };
 			std::cerr << "Dropping alternate residue " << m << '\n';
 		}
 	}
@@ -992,7 +1106,7 @@ cif::mm::atom sugar::add_atom(row_initializer atom_info)
 	atom_info.set_value({ "label_alt_id", "." });
 	atom_info.set_value({ "auth_asym_id", m_branch->get_asym_id() });
 	atom_info.set_value({ "auth_comp_id", m_compound_id });
-	atom_info.set_value({ "auth_seq_id", m_pdb_seq_num });
+	atom_info.set_value({ "auth_seq_id", m_auth_seq_id });
 	atom_info.set_value({ "occupancy", 1.0, 2 });
 	atom_info.set_value({ "B_iso_or_equiv", 30.0, 2 });
 	atom_info.set_value({ "pdbx_PDB_model_num", 1 });
@@ -1108,12 +1222,12 @@ sugar &branch::construct_sugar(const std::string &compound_id)
 		{ "mon_id", result.get_compound_id() },
 
 		{ "pdb_asym_id", result.get_asym_id() },
-		{ "pdb_seq_num", result.get_pdb_seq_num() },
+		{ "pdb_seq_num", result.num() },
 		{ "pdb_mon_id", result.get_compound_id() },
 
-		{ "auth_asym_id", result.get_pdb_strand_id() },
+		{ "auth_asym_id", result.get_auth_asym_id() },
 		{ "auth_mon_id", result.get_compound_id() },
-		{ "auth_seq_num", result.get_pdb_seq_num() },
+		{ "auth_seq_num", result.get_auth_seq_id() },
 
 		{ "hetero", "n" } });
 
@@ -1156,7 +1270,7 @@ std::string branch::name(const sugar &s) const
 
 	for (auto &sn : *this)
 	{
-		if (not sn.get_link() or sn.get_link().get_auth_seq_id() != s.get_pdb_seq_num())
+		if (not sn.get_link() or sn.get_link().get_auth_seq_id() != s.get_auth_seq_id())
 			continue;
 
 		auto n = name(sn) + "-(1-" + sn.get_link().get_label_atom_id().substr(1) + ')';
@@ -1183,19 +1297,16 @@ float branch::weight() const
 // --------------------------------------------------------------------
 //	structure
 
-structure::structure(file &p, std::size_t modelNr, structure_open_options options)
+structure::structure(file &p, std::size_t modelNr, StructureOpenOptions options)
 	: structure(p.front(), modelNr, options)
 {
 }
 
-structure::structure(datablock &db, std::size_t modelNr, structure_open_options options)
+structure::structure(datablock &db, std::size_t modelNr, StructureOpenOptions options)
 	: m_db(db)
 	, m_model_nr(modelNr)
 {
-	if (db.get_validator() == nullptr)
-		db.load_dictionary();
-
-	auto &atom_site = db["atom_site"];
+	auto &atomCat = db["atom_site"];
 
 	load_atoms_for_model(options);
 
@@ -1203,7 +1314,7 @@ structure::structure(datablock &db, std::size_t modelNr, structure_open_options
 	if (m_atoms.empty() and m_model_nr == 1)
 	{
 		std::optional<std::size_t> model_nr;
-		cif::tie(model_nr) = atom_site.front().get("pdbx_PDB_model_num");
+		cif::tie(model_nr) = atomCat.front().get("pdbx_PDB_model_num");
 		if (model_nr and *model_nr != m_model_nr)
 		{
 			if (VERBOSE > 0)
@@ -1222,131 +1333,42 @@ structure::structure(datablock &db, std::size_t modelNr, structure_open_options
 		load_data();
 }
 
-void structure::load_atoms_for_model(structure_open_options options)
+void structure::load_atoms_for_model(StructureOpenOptions options)
 {
 	using namespace literals;
 
-	auto &atom_site = m_db["atom_site"];
+	auto &atomCat = m_db["atom_site"];
 
 	condition c = "pdbx_PDB_model_num"_key == null or "pdbx_PDB_model_num"_key == m_model_nr;
+	if (options bitand StructureOpenOptions::SkipHydrogen)
+		c = std::move(c) and ("type_symbol"_key != "H" and "type_symbol"_key != "D");
 
-	if (options.skip_hydrogen)
-		c = std::move(c) and (cif::key("type_symbol") != "H" and cif::key("type_symbol") != "D");
-
-	if (options.skip_water)
-		c = std::move(c) and (cif::key("auth_comp_id") != "HOH" and cif::key("auth_comp_id") != "H20" and cif::key("auth_comp_id") != "WAT");
-
-	if (options.skip_hetatom)
-	{
-		if (options.skip_water)
-			c = std::move(c) and cif::key("group_PDB") != "HETATM";
-		else
-			c = std::move(c) and (cif::key("group_PDB") != "HETATM" or (cif::key("auth_comp_id") == "HOH" or cif::key("auth_comp_id") == "H20" or cif::key("auth_comp_id") == "WAT"));
-	}
-
-	if (options.min_b_factor.has_value())
-		c = std::move(c) and cif::key("B_iso_or_equiv") >= *options.min_b_factor;
-
-	if (options.max_b_factor.has_value())
-		c = std::move(c) and cif::key("B_iso_or_equiv") <= *options.max_b_factor;
-
-	if (not options.asyms.empty())
-	{
-		condition tmp_c;
-		for (auto asym_id : options.asyms)
-			tmp_c = std::move(tmp_c) or cif::key("label_asym_id") == asym_id;
-		c = std::move(c) and std::move(tmp_c);
-	}
-
-	if (options.occupancy_mode == occupancy_policy::ALL)
-	{
-		for (auto id : atom_site.find<std::string>(std::move(c), "id"))
-			emplace_atom(std::make_shared<atom::atom_impl>(m_db, id));
-	}
-	else if (options.occupancy_mode == occupancy_policy::UNOCCUPIED)
-	{
-		for (auto id : atom_site.find<std::string>(std::move(c), "id"))
-		{
-			auto a = std::make_shared<atom::atom_impl>(m_db, id);
-			if (a->get_property_float("occupancy") > 0)
-				continue;
-			emplace_atom(a);
-		}
-	}
-	else
-	{
-		std::vector<cif::mm::atom> atoms;
-		std::map<std::tuple<std::string, int>, std::map<std::string, float>> alts;
-
-		for (auto id : atom_site.find<std::string>(std::move(c), "id"))
-		{
-			auto a = atoms.emplace_back(std::make_shared<atom::atom_impl>(m_db, id));
-
-			if (a.is_alternate())
-			{
-				auto key = std::make_tuple(a.get_label_asym_id(), a.get_label_seq_id());
-				auto alt_id = a.get_label_alt_id();
-
-				if (auto i = alts.find(key); i != alts.end())
-					i->second[alt_id] += a.get_occupancy();
-				else
-					alts[key][alt_id] = a.get_occupancy();
-			}
-		}
-
-		for (auto &&[key, value] : alts)
-		{
-			// const auto &[asym_id, seq_id] = key;
-
-			// select highest occupancy for this residue's alternates
-			std::string alt_id;
-			float occupancy = options.occupancy_mode == occupancy_policy::MAX ? 0.f : std::numeric_limits<float>::max();
-			for (const auto &[alt_key, alt_value] : value)
-			{
-				if (options.occupancy_mode == occupancy_policy::MAX)
-				{
-					if (occupancy < alt_value)
-					{
-						alt_id = alt_key;
-						occupancy = alt_value;
-					}
-				}
-				else
-				{
-					if (occupancy > alt_value)
-					{
-						alt_id = alt_key;
-						occupancy = alt_value;
-					}
-				}
-			}
-
-			value.clear();
-			value.emplace(alt_id, occupancy);
-		}
-
-		for (auto a : atoms)
-		{
-			if (a.is_alternate())
-			{
-				auto key = std::make_tuple(a.get_label_asym_id(), a.get_label_seq_id());
-
-				if (alts[key].contains(a.get_label_alt_id()))
-					emplace_atom(a);
-			}
-			else
-				emplace_atom(a);
-		}
-	}
+	for (auto id : atomCat.find<std::string>(std::move(c), "id"))
+		emplace_atom(std::make_shared<atom::atom_impl>(m_db, id));
 }
 
+// structure::structure(const structure &s)
+// 	: m_db(s.m_db)
+// 	, m_model_nr(s.m_model_nr)
+// {
+// 	m_atoms.reserve(s.m_atoms.size());
+// 	for (auto &atom : s.m_atoms)
+// 		emplace_atom(atom.clone());
+
+// 	load_data();
+// }
+
+// structure::~structure()
+// {
+// }
+
 void structure::load_data()
 {
 	auto &polySeqScheme = m_db["pdbx_poly_seq_scheme"];
 
 	for (const auto &[asym_id, auth_asym_id, entityID] : polySeqScheme.rows<std::string, std::string, std::string>("asym_id", "pdb_strand_id", "entity_id"))
 	{
-		if (m_polymers.empty() or m_polymers.back().get_asym_id() != asym_id)
+		if (m_polymers.empty() or m_polymers.back().get_asym_id() != asym_id or m_polymers.back().get_entity_id() != entityID)
 			m_polymers.emplace_back(*this, entityID, asym_id, auth_asym_id);
 	}
 
@@ -1372,18 +1394,18 @@ void structure::load_data()
 	for (auto &poly : m_polymers)
 	{
 		for (auto &res : poly)
-			resMap[{ res.get_asym_id(), res.get_seq_id(), res.get_pdb_seq_num() }] = &res;
+			resMap[{ res.get_asym_id(), res.get_seq_id(), res.get_auth_seq_id() }] = &res;
 	}
 
 	for (auto &res : m_non_polymers)
-		resMap[{ res.get_asym_id(), res.get_seq_id(), res.get_pdb_seq_num() }] = &res;
+		resMap[{ res.get_asym_id(), res.get_seq_id(), res.get_auth_seq_id() }] = &res;
 
 	std::set<std::string> sugars;
 	for (auto &branch : m_branches)
 	{
 		for (auto &sugar : branch)
 		{
-			resMap[{ sugar.get_asym_id(), sugar.get_seq_id(), sugar.get_pdb_seq_num() }] = &sugar;
+			resMap[{ sugar.get_asym_id(), sugar.get_seq_id(), sugar.get_auth_seq_id() }] = &sugar;
 			sugars.insert(sugar.get_compound_id());
 		}
 	}
@@ -1458,6 +1480,30 @@ EntityType structure::get_entity_type_for_asym_id(const std::string asym_id) con
 	return get_entity_type_for_entity_id(entityID);
 }
 
+// std::vector<atom> structure::waters() const
+// {
+// 	using namespace literals;
+
+// 	std::vector<atom> result;
+
+// 	auto &db = datablock();
+
+// 	// Get the entity id for water. Watch out, structure may not have water at all
+// 	auto &entityCat = db["entity"];
+// 	for (const auto &[waterEntityID] : entityCat.find<std::string>("type"_key == "water", "id"))
+// 	{
+// 		for (auto &a : m_atoms)
+// 		{
+// 			if (a.get_property("label_entity_id") == waterEntityID)
+// 				result.push_back(a);
+// 		}
+
+// 		break;
+// 	}
+
+// 	return result;
+// }
+
 bool structure::has_atom_id(const std::string &id) const
 {
 	assert(m_atoms.size() == m_atom_index.size());
@@ -1606,7 +1652,7 @@ residue &structure::get_residue(const std::string &asym_id, int seqID, const std
 	{
 		for (auto &res : m_non_polymers)
 		{
-			if (res.get_asym_id() == asym_id and (authSeqID.empty() or res.get_pdb_seq_num() == authSeqID))
+			if (res.get_asym_id() == asym_id and (authSeqID.empty() or res.get_auth_seq_id() == authSeqID))
 				return res;
 		}
 	}
@@ -1630,7 +1676,7 @@ residue &structure::get_residue(const std::string &asym_id, int seqID, const std
 
 		for (auto &sugar : branch)
 		{
-			if (sugar.get_asym_id() == asym_id and sugar.get_pdb_seq_num() == authSeqID)
+			if (sugar.get_asym_id() == asym_id and sugar.get_auth_seq_id() == authSeqID)
 				return sugar;
 		}
 	}
@@ -1652,7 +1698,7 @@ residue &structure::get_residue(const std::string &asym_id, const std::string &c
 	{
 		for (auto &res : m_non_polymers)
 		{
-			if (res.get_asym_id() == asym_id and res.get_pdb_seq_num() == authSeqID and res.get_compound_id() == compID)
+			if (res.get_asym_id() == asym_id and res.get_auth_seq_id() == authSeqID and res.get_compound_id() == compID)
 				return res;
 		}
 	}
@@ -1676,7 +1722,7 @@ residue &structure::get_residue(const std::string &asym_id, const std::string &c
 
 		for (auto &sugar : branch)
 		{
-			if (sugar.get_asym_id() == asym_id and sugar.get_pdb_seq_num() == authSeqID and sugar.get_compound_id() == compID)
+			if (sugar.get_asym_id() == asym_id and sugar.get_auth_seq_id() == authSeqID and sugar.get_compound_id() == compID)
 				return sugar;
 		}
 	}
@@ -1897,12 +1943,13 @@ void structure::swap_atoms(atom a1, atom a2)
 		auto r1 = atomSites.find1(key("id") == a1.id());
 		auto r2 = atomSites.find1(key("id") == a2.id());
 
-		for (std::string fld : std::initializer_list<std::string>{ "label_atom_id", "auth_atom_id", "type_symbol" })
-		{
-			auto l1 = r1[fld];
-			auto l2 = r2[fld];
-			l1.swap(l2);
-		}
+		auto l1 = r1["label_atom_id"];
+		auto l2 = r2["label_atom_id"];
+		l1.swap(l2);
+
+		auto l3 = r1["auth_atom_id"];
+		auto l4 = r2["auth_atom_id"];
+		l3.swap(l4);
 	}
 	catch (const std::exception &ex)
 	{
@@ -2025,7 +2072,7 @@ void structure::remove_residue(const std::string &asym_id, int seq_id, const std
 	{
 		for (auto &res : m_non_polymers)
 		{
-			if (res.get_asym_id() == asym_id and (auth_seq_id.empty() or res.get_pdb_seq_num() == auth_seq_id))
+			if (res.get_asym_id() == asym_id and (auth_seq_id.empty() or res.get_auth_seq_id() == auth_seq_id))
 			{
 				remove_residue(res);
 				return;
@@ -2055,7 +2102,7 @@ void structure::remove_residue(const std::string &asym_id, int seq_id, const std
 
 		for (auto &sugar : branch)
 		{
-			if (sugar.get_asym_id() == asym_id and sugar.get_pdb_seq_num() == auth_seq_id)
+			if (sugar.get_asym_id() == asym_id and sugar.get_auth_seq_id() == auth_seq_id)
 			{
 				remove_residue(sugar);
 				return;
@@ -2188,7 +2235,7 @@ void structure::remove_sugar(sugar &s)
 				// TODO: need fix, collect from nag_atoms?
 				{ "auth_asym_id", asym_id },
 				{ "auth_mon_id", sugar.get_compound_id() },
-				{ "auth_seq_num", sugar.get_pdb_seq_num() },
+				{ "auth_seq_num", sugar.get_auth_seq_id() },
 
 				{ "hetero", "n" } });
 		}
@@ -2274,8 +2321,8 @@ std::string structure::create_non_poly(const std::string &entity_id, const std::
 		{ "entity_id", entity_id },
 		{ "mon_id", comp_id },
 		{ "ndb_seq_num", ndb_nr },
-		{ "pdb_seq_num", res.get_pdb_seq_num() },
-		{ "auth_seq_num", res.get_pdb_seq_num() },
+		{ "pdb_seq_num", res.get_auth_seq_id() },
+		{ "auth_seq_num", res.get_auth_seq_id() },
 		{ "pdb_mon_id", comp_id },
 		{ "auth_mon_id", comp_id },
 		{ "pdb_strand_id", asym_id },
@@ -2335,8 +2382,8 @@ std::string structure::create_non_poly(const std::string &entity_id, std::vector
 		{ "entity_id", entity_id },
 		{ "mon_id", comp_id },
 		{ "ndb_seq_num", ndb_nr },
-		{ "pdb_seq_num", res.get_pdb_seq_num() },
-		{ "auth_seq_num", res.get_pdb_seq_num() },
+		{ "pdb_seq_num", res.get_auth_seq_id() },
+		{ "auth_seq_num", res.get_auth_seq_id() },
 		{ "pdb_mon_id", comp_id },
 		{ "auth_mon_id", comp_id },
 		{ "pdb_strand_id", asym_id },
@@ -2410,61 +2457,6 @@ void structure::create_water(row_initializer atom)
 	});
 }
 
-std::string structure::create_link(atom a1, atom a2, const std::string &link_type, const std::string &role)
-{
-	using namespace literals;
-
-	auto &struct_conn = m_db["struct_conn"];
-	auto &struct_conn_type = m_db["struct_conn_type"];
-
-	// This will validate link_type :-)
-	if (not struct_conn_type.contains("id"_key == link_type))
-		struct_conn_type.emplace({ { "id", link_type } });
-
-	std::string link_id = struct_conn.get_unique_id(link_type + '_');
-
-	item label_seq_id_1("ptnr1_label_seq_id");
-	if (int nr = a1.get_label_seq_id(); nr != 0)
-		label_seq_id_1.value(std::to_string(nr));
-
-	item label_seq_id_2("ptnr2_label_seq_id");
-	if (int nr = a2.get_label_seq_id(); nr != 0)
-		label_seq_id_2.value(std::to_string(nr));
-
-	struct_conn.emplace(
-		{ //
-			{ "id", link_id },
-			{ "conn_type_id", link_type },
-			{ "pdbx_leaving_atom_flag", "one" },
-
-			{ "ptnr1_label_asym_id", a1.get_label_asym_id() },
-			{ "ptnr1_label_comp_id", a1.get_label_comp_id() },
-			label_seq_id_1,
-			{ "ptnr1_label_atom_id", a1.get_label_atom_id() },
-			{ "pdbx_ptnr1_label_alt_id", a1.get_label_alt_id() },
-			{ "pdbx_ptnr1_PDB_ins_code", a1.get_pdb_ins_code() },
-			{ "ptnr1_auth_asym_id", a1.get_auth_asym_id() },
-			{ "ptnr1_auth_comp_id", a1.get_auth_comp_id() },
-			{ "ptnr1_auth_seq_id", a1.get_auth_seq_id() },
-			{ "ptnr1_symmetry", a1.symmetry() },
-
-			{ "ptnr2_label_asym_id", a2.get_label_asym_id() },
-			{ "ptnr2_label_comp_id", a2.get_label_comp_id() },
-			label_seq_id_2,
-			{ "ptnr2_label_atom_id", a2.get_label_atom_id() },
-			{ "pdbx_ptnr2_label_alt_id", a2.get_label_alt_id() },
-			{ "pdbx_ptnr2_PDB_ins_code", a2.get_pdb_ins_code() },
-			{ "ptnr2_auth_asym_id", a2.get_auth_asym_id() },
-			{ "ptnr2_auth_comp_id", a2.get_auth_comp_id() },
-			{ "ptnr2_auth_seq_id", a2.get_auth_seq_id() },
-			{ "ptnr2_symmetry", a2.symmetry() },
-
-			{ "pdbx_dist_value", distance(a1.get_location(), a2.get_location()), 3 },
-			{ "pdbx_role", role } });
-
-	return link_id;
-}
-
 branch &structure::create_branch()
 {
 	auto &entity = m_db["entity"];
@@ -2705,11 +2697,11 @@ std::string structure::create_entity_for_branch(branch &branch)
 
 			pdbx_entity_branch_link.emplace({ { "link_id", pdbx_entity_branch_link.get_unique_id("") },
 				{ "entity_id", entityID },
-				{ "entity_branch_list_num_1", s1.get_pdb_seq_num() },
+				{ "entity_branch_list_num_1", s1.get_auth_seq_id() },
 				{ "comp_id_1", s1.get_compound_id() },
 				{ "atom_id_1", l1.get_label_atom_id() },
 				{ "leaving_atom_id_1", "O1" },
-				{ "entity_branch_list_num_2", s2.get_pdb_seq_num() },
+				{ "entity_branch_list_num_2", s2.get_auth_seq_id() },
 				{ "comp_id_2", s2.get_compound_id() },
 				{ "atom_id_2", l2.get_label_atom_id() },
 				{ "leaving_atom_id_2", "H" + l2.get_label_atom_id() },
@@ -2722,12 +2714,9 @@ std::string structure::create_entity_for_branch(branch &branch)
 
 void structure::cleanup_empty_categories()
 {
-
 	using namespace literals;
 
 	auto &atomSite = m_db["atom_site"];
-	auto &pdbxPolySeqScheme = m_db["pdbx_poly_seq_scheme"];
-	auto &entityPolySeq = m_db["entity_poly_seq"];
 
 	// Remove chem_comp's for which there are no atoms at all
 	auto &chem_comp = m_db["chem_comp"];
@@ -2736,12 +2725,8 @@ void structure::cleanup_empty_categories()
 	for (auto chemComp : chem_comp)
 	{
 		std::string compID = chemComp["id"].as<std::string>();
-		if (atomSite.contains("label_comp_id"_key == compID or "auth_comp_id"_key == compID) or
-			pdbxPolySeqScheme.contains("mon_id"_key == compID or "auth_mon_id"_key == compID or "pdb_mon_id"_key == compID) or
-			entityPolySeq.contains("mon_id"_key == compID))
-		{
+		if (atomSite.contains("label_comp_id"_key == compID or "auth_comp_id"_key == compID))
 			continue;
-		}
 
 		obsoleteChemComps.push_back(chemComp);
 	}
@@ -2898,8 +2883,8 @@ static int compare_numbers(std::string_view a, std::string_view b)
 
 	std::from_chars_result ra, rb;
 
-	ra = from_chars(a.data(), a.data() + a.length(), da);
-	rb = from_chars(b.data(), b.data() + b.length(), db);
+	ra = selected_charconv<double>::from_chars(a.data(), a.data() + a.length(), da);
+	rb = selected_charconv<double>::from_chars(b.data(), b.data() + b.length(), db);
 
 	if (not(bool) ra.ec and not(bool) rb.ec)
 	{
@@ -2920,14 +2905,6 @@ static int compare_numbers(std::string_view a, std::string_view b)
 	return result;
 }
 
-int compare_cif_id(const std::string &a, const std::string &b)
-{
-	int d = static_cast<int>(a.length() - b.length());
-	if (d == 0)
-		d = a.compare(b);
-	return d;
-}
-
 void structure::reorder_atoms()
 {
 	auto &atom_site = m_db["atom_site"];
@@ -2939,7 +2916,7 @@ void structure::reorder_atoms()
 			// First by model number
 			d = a.get<int>("pdbx_PDB_model_num") - b.get<int>("pdbx_PDB_model_num");
 			if (d == 0)
-				d = compare_cif_id(a.get<std::string>("label_asym_id"), b.get<std::string>("label_asym_id"));
+				d = a.get<std::string>("label_asym_id").compare(b.get<std::string>("label_asym_id"));
 			if (d == 0)
 			{
 				auto na = a.get<std::optional<int>>("label_seq_id");

src/pdb/cif2pdb.cpp

@@ -33,6 +33,7 @@
 #include <regex>
 #include <set>
 
+
 namespace cif::pdb
 {
 
@@ -57,9 +58,9 @@ std::string cif2pdbDate(const std::string &d)
 		int month = std::stoi(m[2].str());
 
 		if (m[3].matched)
-			result = cif::format("{:02}-{:3.3}-{:02}", stoi(m[3].str()), kMonths[month - 1], (year % 100));
+			result = cif::format("%02.2d-%3.3s-%02.2d", stoi(m[3].str()), kMonths[month - 1], (year % 100)).str();
 		else
-			result = cif::format("{:3.3}-{:02}", kMonths[month - 1], (year % 100));
+			result = cif::format("%3.3s-%02.2d", kMonths[month - 1], (year % 100)).str();
 	}
 
 	return result;
@@ -257,14 +258,16 @@ std::size_t WriteCitation(std::ostream &pdbFile, const datablock &db, row_handle
 	{
 		to_upper(pubname);
 
-		pdbFile << s1 << cif::format("REF {:2.2s} {:<28.28s}  {:2.2s}{:>4.4s} {:>5.5s} {:4.4s}", "" /* continuation */, pubname, (volume.empty() ? "" : "V."), volume, pageFirst, year)
+		const std::string kRefHeader = s1 + "REF %2.2s %-28.28s  %2.2s%4.4s %5.5s %4.4s";
+		pdbFile << cif::format(kRefHeader, "" /* continuation */, pubname, (volume.empty() ? "" : "V."), volume, pageFirst, year)
 				<< '\n';
 		++result;
 	}
 
 	if (not issn.empty())
 	{
-		pdbFile << s1 << cif::format("REFN                   ISSN {:<25.25s}", issn) << '\n';
+		const std::string kRefHeader = s1 + "REFN                   ISSN %-25.25s";
+		pdbFile << cif::format(kRefHeader, issn) << '\n';
 		++result;
 	}
 
@@ -273,25 +276,27 @@ std::size_t WriteCitation(std::ostream &pdbFile, const datablock &db, row_handle
 	////    0         1         2         3         4         5         6         7         8
 	////    HEADER    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxDDDDDDDDD   IIII
 	// const char kRefHeader[] =
-	//          "REMARK   1  REFN    {:4.4s} {:<6.6s}  {:2.2s} {:<25.25s}";
+	//          "REMARK   1  REFN    %4.4s %-6.6s  %2.2s %-25.25s";
 	//
 	//			pdbFile << (boost::cif::format(kRefHeader)
 	//						% (astm.empty() ? "" : "ASTN")
 	//						% astm
 	//						% country
-	//						% issn)
+	//						% issn).str()
 	//					<< '\n';
 	//		}
 
 	if (not pmid.empty())
 	{
-		pdbFile << s1 << cif::format("PMID   {:<60.60s} ", pmid) << '\n';
+		const std::string kPMID = s1 + "PMID   %-60.60s ";
+		pdbFile << cif::format(kPMID, pmid) << '\n';
 		++result;
 	}
 
 	if (not doi.empty())
 	{
-		pdbFile << s1 << cif::format("DOI    {:<60.60s} ", doi) << '\n';
+		const std::string kDOI = s1 + "DOI    %-60.60s ";
+		pdbFile << cif::format(kDOI, doi) << '\n';
 		++result;
 	}
 
@@ -302,10 +307,10 @@ void write_header_lines(std::ostream &pdbFile, const datablock &db)
 {
 	//    0         1         2         3         4         5         6         7         8
 	//    HEADER    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxDDDDDDDDD   IIII
-	// const char kHeader[] =
-	// 	"HEADER    {:<40.40s}"
-	// 	"{:<9.9s}"
-	// 	"   {:<4.4s}";
+	const char kHeader[] =
+		"HEADER    %-40.40s"
+		"%-9.9s"
+		"   %-4.4s";
 
 	// HEADER
 
@@ -340,12 +345,7 @@ void write_header_lines(std::ostream &pdbFile, const datablock &db)
 		}
 	}
 
-	pdbFile << cif::format(/* kHeader */
-		"HEADER    {:<40.40s}"
-		"{:<9.9s}"
-		"   {:<4.4s}"
-	
-	, keywords, date, db.name()) << '\n';
+	pdbFile << cif::format(kHeader, keywords, date, db.name()) << '\n';
 
 	// TODO: implement
 	// OBSLTE (skip for now)
@@ -535,6 +535,7 @@ void WriteTitle(std::ostream &pdbFile, const datablock &db)
 	write_header_lines(pdbFile, db);
 
 	// REVDAT
+	const char kRevDatFmt[] = "REVDAT %3d%2.2s %9.9s %4.4s    %1d      ";
 	auto &cat2 = db["database_PDB_rev"];
 	std::vector<row_handle> rev(cat2.begin(), cat2.end());
 	sort(rev.begin(), rev.end(), [](row_handle a, row_handle b) -> bool
@@ -558,9 +559,9 @@ void WriteTitle(std::ostream &pdbFile, const datablock &db)
 		{
 			std::string cs = ++continuation > 1 ? std::to_string(continuation) : std::string();
 
-			pdbFile << cif::format("REVDAT {:3}{:2.2s} {:9.9s} {:4.4s}    {:1}      ", revNum, cs, date, db.name(), modType);
+			pdbFile << cif::format(kRevDatFmt, revNum, cs, date, db.name(), modType);
 			for (std::size_t i = 0; i < 4; ++i)
-				pdbFile << cif::format(" {:<6.6s}", (i < types.size() ? types[i] : std::string()));
+				pdbFile << cif::format(" %-6.6s", (i < types.size() ? types[i] : std::string()));
 			pdbFile << '\n';
 
 			if (types.size() > 4)
@@ -613,7 +614,7 @@ void WriteRemark2(std::ostream &pdbFile, const datablock &db)
 		{
 			float resHigh = refine.front()["ls_d_res_high"].as<float>();
 			pdbFile << "REMARK   2\n"
-					<< cif::format("REMARK   2 RESOLUTION. {:7.2f} ANGSTROMS.", resHigh) << '\n';
+					<< cif::format("REMARK   2 RESOLUTION. %7.2f ANGSTROMS.", resHigh) << '\n';
 		}
 		catch (...)
 		{ /* skip it */
@@ -760,7 +761,10 @@ class Fs : public FBase
 		else
 		{
 			os << '\n';
-			WriteOneContinuedLine(os, cif::format("REMARK {:3} ", mNr), 0, s);
+
+			std::stringstream ss;
+			ss << "REMARK " << std::setw(3) << std::right << mNr << ' ';
+			WriteOneContinuedLine(os, ss.str(), 0, s);
 		}
 	}
 
@@ -1613,7 +1617,7 @@ void WriteRemark3Phenix(std::ostream &pdbFile, const datablock &db)
 
 		percent_reflns_obs /= 100;
 
-		pdbFile << RM3("  ") << cif::format("{:3} {:7.4f} - {:7.4f}    {:4.2f} {:8} {:5}  {:6.4f} {:6.4f}", bin++, d_res_low, d_res_high, percent_reflns_obs, number_reflns_R_work, number_reflns_R_free, R_factor_R_work, R_factor_R_free) << '\n';
+		pdbFile << RM3("  ") << cif::format("%3d %7.4f - %7.4f    %4.2f %8d %5d  %6.4f %6.4f", bin++, d_res_low, d_res_high, percent_reflns_obs, number_reflns_R_work, number_reflns_R_free, R_factor_R_work, R_factor_R_free) << '\n';
 	}
 
 	pdbFile << RM3("") << '\n'
@@ -2581,7 +2585,7 @@ void WriteRemark465(std::ostream &pdbFile, const datablock &db)
 		cif::tie(modelNr, resName, chainID, iCode, seqNr) =
 			r.get("PDB_model_num", "auth_comp_id", "auth_asym_id", "PDB_ins_code", "auth_seq_id");
 
-		pdbFile << cif::format("REMARK 465 {:3.3s} {:3.3s} {:1.1s} {:5}{:1.1s}", modelNr, resName, chainID, seqNr, iCode) << '\n';
+		pdbFile << cif::format("REMARK 465 %3.3s %3.3s %1.1s %5d%1.1s", modelNr, resName, chainID, seqNr, iCode) << '\n';
 	}
 }
 
@@ -2628,7 +2632,7 @@ void WriteRemark470(std::ostream &pdbFile, const datablock &db)
 
 			while (not a.second.empty())
 			{
-				pdbFile << cif::format("REMARK 470 {:>3.3s} {:3.3s} {:1.1s}{:4}{:1.1s}  ", modelNr, resName, chainID, seqNr, iCode) << "  ";
+				pdbFile << cif::format("REMARK 470 %3.3s %3.3s %1.1s%4d%1.1s  ", modelNr, resName, chainID, seqNr, iCode) << "  ";
 
 				for (std::size_t i = 0; i < 6 and not a.second.empty(); ++i)
 				{
@@ -2726,16 +2730,16 @@ int WritePrimaryStructure(std::ostream &pdbFile, const datablock &db)
 
 			if (dbAccession.length() > 8 or db_code.length() > 12 or atoi(dbseqEnd.c_str()) >= 100000)
 				pdbFile << cif::format(
-							   "DBREF1 {:>4.4s} {:1.1s} {:>4.4s}{:1.1s} {:>4.4s}{:1.1s} {:<6.6s}               {:<20.20s}",
+							   "DBREF1 %4.4s %1.1s %4.4s%1.1s %4.4s%1.1s %-6.6s               %-20.20s",
 							   idCode, chainID, seqBegin, insertBegin, seqEnd, insertEnd, db_name, db_code)
 						<< '\n'
 						<< cif::format(
-							   "DBREF2 {:>4.4s} {:1.1s}     {:<22.22s}     {:10.10s}  {:10.10s}",
+							   "DBREF2 %4.4s %1.1s     %-22.22s     %10.10s  %10.10s",
 							   idCode, chainID, dbAccession, dbseqBegin, dbseqEnd)
 						<< '\n';
 			else
 				pdbFile << cif::format(
-							   "DBREF  {:>4.4s} {:1.1s} {:>4.4s}{:1.1s} {:>4.4s}{:1.1s} {:<6.6s} {:<8.8s} {:<12.12s} {:>5.5s}{:1.1s} {:>5.5s}{:1.1s}",
+							   "DBREF  %4.4s %1.1s %4.4s%1.1s %4.4s%1.1s %-6.6s %-8.8s %-12.12s %5.5s%1.1s %5.5s%1.1s",
 							   idCode, chainID, seqBegin, insertBegin, seqEnd, insertEnd, db_name, dbAccession, db_code, dbseqBegin, dbinsBeg, dbseqEnd, dbinsEnd)
 						<< '\n';
 		}
@@ -2754,8 +2758,9 @@ int WritePrimaryStructure(std::ostream &pdbFile, const datablock &db)
 		to_upper(conflict);
 
 		pdbFile << cif::format(
-					   "SEQADV {:4.4s} {:3.3s} {:1.1s} {:>4.4s}{:1.1s} {:<4.4s} {:<9.9s} {:3.3s} {:>5.5s} {:<21.21s}",
+					   "SEQADV %4.4s %3.3s %1.1s %4.4s%1.1s %-4.4s %-9.9s %3.3s %5.5s %-21.21s",
 					   idCode, resName, chainID, seqNum, iCode, database, dbAccession, dbRes, dbSeq, conflict)
+					   .str()
 				<< '\n';
 	}
 
@@ -2783,7 +2788,7 @@ int WritePrimaryStructure(std::ostream &pdbFile, const datablock &db)
 				t = 13;
 
 			pdbFile << cif::format(
-						   "SEQRES {:3} {:1.1s} {:4}  {:<51.51s}          ",
+						   "SEQRES %3d %1.1s %4d  %-51.51s          ",
 						   n++, std::string{ chainID }, seqresl[chainID], join(seq.begin(), seq.begin() + t, " "))
 					<< '\n';
 
@@ -2803,8 +2808,9 @@ int WritePrimaryStructure(std::ostream &pdbFile, const datablock &db)
 			r.get("auth_asym_id", "auth_seq_id", "auth_comp_id", "PDB_ins_code", "parent_comp_id", "details");
 
 		pdbFile << cif::format(
-					   "MODRES {:4.4s} {:3.3s} {:1.1s} {:4.4s}{:1.1s} {:3.3s}  {:<41.41s}",
+					   "MODRES %4.4s %3.3s %1.1s %4.4s%1.1s %3.3s  %-41.41s",
 					   db.name(), resName, chainID, seqNum, iCode, stdRes, comment)
+					   .str()
 				<< '\n';
 	}
 
@@ -2919,7 +2925,7 @@ int WriteHeterogen(std::ostream &pdbFile, const datablock &db)
 	{
 		if (h.water)
 			continue;
-		pdbFile << cif::format("HET    {:3.3s}  {:1c}{:4}{:1c}  {:5}", h.hetID, h.chainID, h.seqNum, h.iCode, h.numHetAtoms) << '\n';
+		pdbFile << cif::format("HET    %3.3s  %c%4d%c  %5d", h.hetID, h.chainID, h.seqNum, h.iCode, h.numHetAtoms) << '\n';
 		++numHet;
 	}
 
@@ -2934,7 +2940,7 @@ int WriteHeterogen(std::ostream &pdbFile, const datablock &db)
 
 		for (;;)
 		{
-			pdbFile << cif::format("HETNAM  {:2.2s} {:3.3s} ", (c > 1 ? std::to_string(c) : std::string()), id);
+			pdbFile << cif::format("HETNAM  %2.2s %3.3s ", (c > 1 ? std::to_string(c) : std::string()), id);
 			++c;
 
 			if (name.length() > 55)
@@ -3026,7 +3032,7 @@ int WriteHeterogen(std::ostream &pdbFile, const datablock &db)
 			{
 				std::stringstream fs;
 
-				fs << cif::format("FORMUL  {:2}  {:3.3s} {:2.2s}{:1c}", componentNr, hetID, (c > 1 ? std::to_string(c) : std::string()), (hetID == water_comp_id ? '*' : ' '));
+				fs << cif::format("FORMUL  %2d  %3.3s %2.2s%c", componentNr, hetID, (c > 1 ? std::to_string(c) : std::string()), (hetID == water_comp_id ? '*' : ' '));
 				++c;
 
 				if (formula.length() > 51)
@@ -3093,7 +3099,7 @@ std::tuple<int, int> WriteSecondaryStructure(std::ostream &pdbFile, const databl
 				"pdbx_PDB_helix_class", "pdbx_PDB_helix_length", "beg_auth_seq_id", "end_auth_seq_id");
 
 		++numHelix;
-		pdbFile << cif::format("HELIX  {:3} {:>3.3s} {:3.3s} {:1.1s} {:4}{:1.1s} {:3.3s} {:1.1s} {:4}{:1.1s}{:2}{:<30.30s} {:5}",
+		pdbFile << cif::format("HELIX  %3d %3.3s %3.3s %1.1s %4d%1.1s %3.3s %1.1s %4d%1.1s%2d%-30.30s %5d",
 					   numHelix, pdbx_PDB_helix_id, beg_label_comp_id, beg_auth_asym_id, beg_auth_seq_id, pdbx_beg_PDB_ins_code, end_label_comp_id, end_auth_asym_id, end_auth_seq_id, pdbx_end_PDB_ins_code, pdbx_PDB_helix_class, details, pdbx_PDB_helix_length)
 				<< '\n';
 	}
@@ -3130,7 +3136,7 @@ std::tuple<int, int> WriteSecondaryStructure(std::ostream &pdbFile, const databl
 					"pdbx_end_PDB_ins_code", "beg_auth_comp_id", "beg_auth_asym_id", "beg_auth_seq_id",
 					"end_auth_comp_id", "end_auth_asym_id", "end_auth_seq_id");
 
-				pdbFile << cif::format("SHEET  {:>3.3s} {:>3.3s}{:2} {:3.3s} {:1.1s}{:4}{:1.1s} {:3.3s} {:1.1s}{:4}{:1.1s}{:2}", rangeID1, sheetID, numStrands, initResName, initChainID, initSeqNum, initICode, endResName, endChainID, endSeqNum, endICode, 0) << '\n';
+				pdbFile << cif::format("SHEET  %3.3s %3.3s%2d %3.3s %1.1s%4d%1.1s %3.3s %1.1s%4d%1.1s%2d", rangeID1, sheetID, numStrands, initResName, initChainID, initSeqNum, initICode, endResName, endChainID, endSeqNum, endICode, 0) << '\n';
 
 				first = false;
 			}
@@ -3149,7 +3155,7 @@ std::tuple<int, int> WriteSecondaryStructure(std::ostream &pdbFile, const databl
 
 			if (h.empty())
 			{
-				pdbFile << cif::format("SHEET  {:>3.3s} {:>3.3s}{:2} {:3.3s} {:1.1s}{:4}{:1.1s} {:3.3s} {:1.1s}{:4}{:1.1s}{:2}", rangeID2, sheetID, numStrands, initResName, initChainID, initSeqNum, initICode, endResName, endChainID, endSeqNum, endICode, sense) << '\n';
+				pdbFile << cif::format("SHEET  %3.3s %3.3s%2d %3.3s %1.1s%4d%1.1s %3.3s %1.1s%4d%1.1s%2d", rangeID2, sheetID, numStrands, initResName, initChainID, initSeqNum, initICode, endResName, endChainID, endSeqNum, endICode, sense) << '\n';
 			}
 			else
 			{
@@ -3162,8 +3168,8 @@ std::tuple<int, int> WriteSecondaryStructure(std::ostream &pdbFile, const databl
 				curAtom = cif2pdbAtomName(curAtom, compID[0], db);
 				prevAtom = cif2pdbAtomName(prevAtom, compID[1], db);
 
-				pdbFile << cif::format("SHEET  {:>3.3s} {:>3.3s}{:2} {:3.3s} {:1.1s}{:4}{:1.1s} {:3.3s} {:1.1s}{:4}{:1.1s}{:2} "
-										"{:<4.4s}{:3.3s} {:1.1s}{:4}{:1.1s} {:<4.4s}{:3.3s} {:1.1s}{:4}{:1.1s}",
+				pdbFile << cif::format("SHEET  %3.3s %3.3s%2d %3.3s %1.1s%4d%1.1s %3.3s %1.1s%4d%1.1s%2d "
+										"%-4.4s%3.3s %1.1s%4d%1.1s %-4.4s%3.3s %1.1s%4d%1.1s",
 							   rangeID2, sheetID, numStrands, initResName, initChainID, initSeqNum, initICode, endResName, endChainID, endSeqNum, endICode, sense, curAtom, curResName, curChainID, curResSeq, curICode, prevAtom, prevResName, prevChainID, prevResSeq, prevICode)
 						<< '\n';
 			}
@@ -3201,7 +3207,7 @@ void WriteConnectivity(std::ostream &pdbFile, const datablock &db)
 		sym1 = cif2pdbSymmetry(sym1);
 		sym2 = cif2pdbSymmetry(sym2);
 
-		pdbFile << cif::format("SSBOND {:3} CYS {:1.1s} {:4}{:1.1s}   CYS {:1.1s} {:4}{:1.1s}                       {:6.6s} {:6.6s} {:5.2f}", nr, chainID1, seqNum1, icode1, chainID2, seqNum2, icode2, sym1, sym2, Length) << '\n';
+		pdbFile << cif::format("SSBOND %3d CYS %1.1s %4d%1.1s   CYS %1.1s %4d%1.1s                       %6.6s %6.6s %5.2f", nr, chainID1, seqNum1, icode1, chainID2, seqNum2, icode2, sym1, sym2, Length) << '\n';
 
 		++nr;
 	}
@@ -3228,10 +3234,10 @@ void WriteConnectivity(std::ostream &pdbFile, const datablock &db)
 		sym1 = cif2pdbSymmetry(sym1);
 		sym2 = cif2pdbSymmetry(sym2);
 
-		pdbFile << cif::format("LINK        {:<4.4s}{:1.1s}{:3.3s} {:1.1s}{:4}{:1.1s}               {:<4.4s}{:1.1s}{:3.3s} {:1.1s}{:4}{:1.1s}  {:>6.6s} {:>6.6s}", name1, altLoc1, resName1, chainID1, resSeq1, iCode1, name2, altLoc2, resName2, chainID2, resSeq2, iCode2, sym1, sym2);
+		pdbFile << cif::format("LINK        %-4.4s%1.1s%3.3s %1.1s%4d%1.1s               %-4.4s%1.1s%3.3s %1.1s%4d%1.1s  %6.6s %6.6s", name1, altLoc1, resName1, chainID1, resSeq1, iCode1, name2, altLoc2, resName2, chainID2, resSeq2, iCode2, sym1, sym2);
 
 		if (not Length.empty())
-			pdbFile << cif::format(" {:5.2f}", stod(Length));
+			pdbFile << cif::format(" %5.2f", stod(Length));
 
 		pdbFile << '\n';
 	}
@@ -3249,7 +3255,7 @@ void WriteConnectivity(std::ostream &pdbFile, const datablock &db)
 				"pdbx_label_comp_id_2", "pdbx_auth_asym_id_2", "pdbx_auth_seq_id_2", "pdbx_PDB_ins_code_2",
 				"pdbx_PDB_model_num", "pdbx_omega_angle");
 
-		pdbFile << cif::format("CISPEP {:3.3s} {:3.3s} {:1.1s} {:4}{:1.1s}   {:3.3s} {:1.1s} {:4}{:1.1s}       {:3.3s}       {:6.2f}",
+		pdbFile << cif::format("CISPEP %3.3s %3.3s %1.1s %4d%1.1s   %3.3s %1.1s %4d%1.1s       %3.3s       %6.2f",
 			serNum, pep1, chainID1, seqNum1, icode1, pep2, chainID2, seqNum2, icode2, modNum, measure) << '\n';
 	}
 }
@@ -3270,7 +3276,7 @@ int WriteMiscellaneousFeatures(std::ostream &pdbFile, const datablock &db)
 		cif::tie(siteID, resName, chainID, seq, iCode) =
 			r.get("site_id", "auth_comp_id", "auth_asym_id", "auth_seq_id", "pdbx_auth_ins_code");
 
-		sites[siteID].push_back(cif::format("{:3.3s} {:1.1s}{:4}{:1.1s} ", resName, chainID, seq, iCode));
+		sites[siteID].push_back(cif::format("%3.3s %1.1s%4d%1.1s ", resName, chainID, seq, iCode).str());
 	}
 
 	for (auto s : sites)
@@ -3283,7 +3289,7 @@ int WriteMiscellaneousFeatures(std::ostream &pdbFile, const datablock &db)
 		int nr = 1;
 		while (res.empty() == false)
 		{
-			pdbFile << cif::format("SITE   {:3} {:3.3s} {:2} ", nr, siteID, numRes);
+			pdbFile << cif::format("SITE   %3d %3.3s %2d ", nr, siteID, numRes);
 
 			for (int i = 0; i < 4; ++i)
 			{
@@ -3312,7 +3318,7 @@ void WriteCrystallographic(std::ostream &pdbFile, const datablock &db)
 
 	r = db["cell"].find_first(key("entry_id") == db.name());
 
-	pdbFile << cif::format("CRYST1{:9.3f}{:9.3f}{:9.3f}{:7.2f}{:7.2f}{:7.2f} {:<11.11s}{:4}", r["length_a"].as<double>(), r["length_b"].as<double>(), r["length_c"].as<double>(), r["angle_alpha"].as<double>(), r["angle_beta"].as<double>(), r["angle_gamma"].as<double>(), symmetry, r["Z_PDB"].as<int>()) << '\n';
+	pdbFile << cif::format("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11.11s%4d", r["length_a"].as<double>(), r["length_b"].as<double>(), r["length_c"].as<double>(), r["angle_alpha"].as<double>(), r["angle_beta"].as<double>(), r["angle_gamma"].as<double>(), symmetry, r["Z_PDB"].as<int>()) << '\n';
 }
 
 int WriteCoordinateTransformation(std::ostream &pdbFile, const datablock &db)
@@ -3321,18 +3327,18 @@ int WriteCoordinateTransformation(std::ostream &pdbFile, const datablock &db)
 
 	for (auto r : db["database_PDB_matrix"])
 	{
-		pdbFile << cif::format("ORIGX{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 1, r["origx[1][1]"].as<float>(), r["origx[1][2]"].as<float>(), r["origx[1][3]"].as<float>(), r["origx_vector[1]"].as<float>()) << '\n';
-		pdbFile << cif::format("ORIGX{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 2, r["origx[2][1]"].as<float>(), r["origx[2][2]"].as<float>(), r["origx[2][3]"].as<float>(), r["origx_vector[2]"].as<float>()) << '\n';
-		pdbFile << cif::format("ORIGX{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 3, r["origx[3][1]"].as<float>(), r["origx[3][2]"].as<float>(), r["origx[3][3]"].as<float>(), r["origx_vector[3]"].as<float>()) << '\n';
+		pdbFile << cif::format("ORIGX%1d    %10.6f%10.6f%10.6f     %10.5f", 1, r["origx[1][1]"].as<float>(), r["origx[1][2]"].as<float>(), r["origx[1][3]"].as<float>(), r["origx_vector[1]"].as<float>()) << '\n';
+		pdbFile << cif::format("ORIGX%1d    %10.6f%10.6f%10.6f     %10.5f", 2, r["origx[2][1]"].as<float>(), r["origx[2][2]"].as<float>(), r["origx[2][3]"].as<float>(), r["origx_vector[2]"].as<float>()) << '\n';
+		pdbFile << cif::format("ORIGX%1d    %10.6f%10.6f%10.6f     %10.5f", 3, r["origx[3][1]"].as<float>(), r["origx[3][2]"].as<float>(), r["origx[3][3]"].as<float>(), r["origx_vector[3]"].as<float>()) << '\n';
 		result += 3;
 		break;
 	}
 
 	for (auto r : db["atom_sites"])
 	{
-		pdbFile << cif::format("SCALE{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 1, r["fract_transf_matrix[1][1]"].as<float>(), r["fract_transf_matrix[1][2]"].as<float>(), r["fract_transf_matrix[1][3]"].as<float>(), r["fract_transf_vector[1]"].as<float>()) << '\n';
-		pdbFile << cif::format("SCALE{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 2, r["fract_transf_matrix[2][1]"].as<float>(), r["fract_transf_matrix[2][2]"].as<float>(), r["fract_transf_matrix[2][3]"].as<float>(), r["fract_transf_vector[2]"].as<float>()) << '\n';
-		pdbFile << cif::format("SCALE{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 3, r["fract_transf_matrix[3][1]"].as<float>(), r["fract_transf_matrix[3][2]"].as<float>(), r["fract_transf_matrix[3][3]"].as<float>(), r["fract_transf_vector[3]"].as<float>()) << '\n';
+		pdbFile << cif::format("SCALE%1d    %10.6f%10.6f%10.6f     %10.5f", 1, r["fract_transf_matrix[1][1]"].as<float>(), r["fract_transf_matrix[1][2]"].as<float>(), r["fract_transf_matrix[1][3]"].as<float>(), r["fract_transf_vector[1]"].as<float>()) << '\n';
+		pdbFile << cif::format("SCALE%1d    %10.6f%10.6f%10.6f     %10.5f", 2, r["fract_transf_matrix[2][1]"].as<float>(), r["fract_transf_matrix[2][2]"].as<float>(), r["fract_transf_matrix[2][3]"].as<float>(), r["fract_transf_vector[2]"].as<float>()) << '\n';
+		pdbFile << cif::format("SCALE%1d    %10.6f%10.6f%10.6f     %10.5f", 3, r["fract_transf_matrix[3][1]"].as<float>(), r["fract_transf_matrix[3][2]"].as<float>(), r["fract_transf_matrix[3][3]"].as<float>(), r["fract_transf_vector[3]"].as<float>()) << '\n';
 		result += 3;
 		break;
 	}
@@ -3342,9 +3348,9 @@ int WriteCoordinateTransformation(std::ostream &pdbFile, const datablock &db)
 	{
 		std::string given = r["code"] == "given" ? "1" : "";
 
-		pdbFile << cif::format("MTRIX{:1} {:3}{:10.6f}{:10.6f}{:10.6f}     {:10.5f}    {:1.1s}", 1, nr, r["matrix[1][1]"].as<float>(), r["matrix[1][2]"].as<float>(), r["matrix[1][3]"].as<float>(), r["vector[1]"].as<float>(), given) << '\n';
-		pdbFile << cif::format("MTRIX{:1} {:3}{:10.6f}{:10.6f}{:10.6f}     {:10.5f}    {:1.1s}", 2, nr, r["matrix[2][1]"].as<float>(), r["matrix[2][2]"].as<float>(), r["matrix[2][3]"].as<float>(), r["vector[2]"].as<float>(), given) << '\n';
-		pdbFile << cif::format("MTRIX{:1} {:3}{:10.6f}{:10.6f}{:10.6f}     {:10.5f}    {:1.1s}", 3, nr, r["matrix[3][1]"].as<float>(), r["matrix[3][2]"].as<float>(), r["matrix[3][3]"].as<float>(), r["vector[3]"].as<float>(), given) << '\n';
+		pdbFile << cif::format("MTRIX%1d %3d%10.6f%10.6f%10.6f     %10.5f    %1.1s", 1, nr, r["matrix[1][1]"].as<float>(), r["matrix[1][2]"].as<float>(), r["matrix[1][3]"].as<float>(), r["vector[1]"].as<float>(), given) << '\n';
+		pdbFile << cif::format("MTRIX%1d %3d%10.6f%10.6f%10.6f     %10.5f    %1.1s", 2, nr, r["matrix[2][1]"].as<float>(), r["matrix[2][2]"].as<float>(), r["matrix[2][3]"].as<float>(), r["vector[2]"].as<float>(), given) << '\n';
+		pdbFile << cif::format("MTRIX%1d %3d%10.6f%10.6f%10.6f     %10.5f    %1.1s", 3, nr, r["matrix[3][1]"].as<float>(), r["matrix[3][2]"].as<float>(), r["matrix[3][3]"].as<float>(), r["vector[3]"].as<float>(), given) << '\n';
 
 		++nr;
 		result += 3;
@@ -3363,6 +3369,10 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 
 	auto &atom_site = db["atom_site"];
 	auto &atom_site_anisotrop = db["atom_site_anisotrop"];
+	auto &entity = db["entity"];
+	// auto &pdbx_poly_seq_scheme = db["pdbx_poly_seq_scheme"];
+	// auto &pdbx_nonpoly_scheme = db["pdbx_nonpoly_scheme"];
+	auto &pdbx_branch_scheme = db["pdbx_branch_scheme"];
 
 	int serial = 1;
 	auto ri = atom_site.begin();
@@ -3407,7 +3417,7 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 
 			if (terminate)
 			{
-				pdbFile << cif::format("TER   {:5}      {:3.3s} {:1.1s}{:4}{:1.1s}",  serial,  resName,  chainID,  resSeq,  iCode) << '\n';
+				pdbFile << cif::format("TER   %5d      %3.3s %1.1s%4d%1.1s",  serial,  resName,  chainID,  resSeq,  iCode) << '\n';
 
 				++serial;
 				terminatedChains.insert(chainID);
@@ -3436,6 +3446,26 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 			r.get("id", "group_PDB", "label_atom_id", "label_alt_id", "auth_comp_id", "auth_asym_id", "auth_seq_id",
 				"pdbx_PDB_ins_code", "Cartn_x", "Cartn_y", "Cartn_z", "occupancy", "B_iso_or_equiv", "type_symbol", "pdbx_formal_charge");
 
+		if (resName != "HOH")
+		{
+			int entity_id = r.get<int>("label_entity_id");
+			try
+			{
+				auto type = entity.find1<std::string>("id"_key == entity_id, "type");
+
+				if (type == "branched")	// find the real auth_seq_num, since sugars have their auth_seq_num reused as sugar number... sigh.
+					resSeq = pdbx_branch_scheme.find1<int>("asym_id"_key == r.get<std::string>("label_asym_id") and "pdb_seq_num"_key == resSeq, "auth_seq_num");
+				// else if (type == "non-polymer")	// same for non-polymers
+				// 	resSeq = pdbx_nonpoly_scheme.find1<int>("asym_id"_key == r.get<std::string>("label_asym_id") and "pdb_seq_num"_key == resSeq, "auth_seq_num");
+				// else if (type == "polymer")
+				// 	resSeq = pdbx_poly_seq_scheme.find1<int>("asym_id"_key == r.get<std::string>("label_asym_id") and "pdb_seq_num"_key == resSeq, "auth_seq_num");
+			}
+			catch (const std::exception &ex)
+			{
+				std::cerr << "Oops, there was not exactly one entity with id " << entity_id << '\n';
+			}
+		}
+		
 		if (chainID.length() > 1)
 			throw std::runtime_error("Chain ID " + chainID + " won't fit into a PDB file");
 
@@ -3446,8 +3476,7 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 		if (charge != 0)
 			sCharge = std::to_string(charge) + (charge > 0 ? '+' : '-');
 
-		pdbFile << cif::format("{:<6.6s}{:5} {:<4.4s}{:1.1s}{:3.3s} {:1.1s}{:4}{:1.1s}   {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f}          {:>2.2s}{:2.2s}",
-			group, serial, name, altLoc, resName, chainID, resSeq, iCode, x, y, z, occupancy, tempFactor, element, sCharge) << '\n';
+		pdbFile << cif::format("%-6.6s%5d %-4.4s%1.1s%3.3s %1.1s%4d%1.1s   %8.3f%8.3f%8.3f%6.2f%6.2f          %2.2s%2.2s", group, serial, name, altLoc, resName, chainID, resSeq, iCode, x, y, z, occupancy, tempFactor, element, sCharge) << '\n';
 
 		++numCoord;
 
@@ -3462,7 +3491,7 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 			tie(u11, u22, u33, u12, u13, u23) =
 				ai.get("U[1][1]", "U[2][2]", "U[3][3]", "U[1][2]", "U[1][3]", "U[2][3]");
 
-			pdbFile << cif::format("ANISOU{:5} {:<4.4s}{:1.1s}{:3.3s} {:1.1s}{:4}{:1.1s} {:7}{:7}{:7}{:7}{:7}{:7}      {:2.2s}{:2.2s}", serial, name, altLoc, resName, chainID, resSeq, iCode, std::lrintf(u11 * 10000), std::lrintf(u22 * 10000), std::lrintf(u33 * 10000), std::lrintf(u12 * 10000), std::lrintf(u13 * 10000), std::lrintf(u23 * 10000), element, sCharge) << '\n';
+			pdbFile << cif::format("ANISOU%5d %-4.4s%1.1s%3.3s %1.1s%4d%1.1s %7d%7d%7d%7d%7d%7d      %2.2s%2.2s", serial, name, altLoc, resName, chainID, resSeq, iCode, std::lrintf(u11 * 10000), std::lrintf(u22 * 10000), std::lrintf(u33 * 10000), std::lrintf(u12 * 10000), std::lrintf(u13 * 10000), std::lrintf(u23 * 10000), element, sCharge) << '\n';
 		}
 
 		++serial;
@@ -3514,7 +3543,7 @@ std::tuple<int, int> WriteCoordinate(std::ostream &pdbFile, const datablock &db)
 		for (int model_nr : models)
 		{
 			if (models.size() > 1)
-				pdbFile << cif::format("MODEL     {:4}",  model_nr) << '\n';
+				pdbFile << cif::format("MODEL     %4d",  model_nr) << '\n';
 
 			std::set<std::string> TERminatedChains;
 			auto n = WriteCoordinatesForModel(pdbFile, db, last_resseq_for_chain_map, TERminatedChains, model_nr);
@@ -3586,7 +3615,7 @@ std::string get_HEADER_line(const datablock &db, std::string::size_type truncate
 		}
 	}
 
-	return FixStringLength(cif::format("HEADER    {:<40.40s}{:<9.9s}   {:<4.4s}", keywords, date, db.name()), truncate_at);
+	return FixStringLength(cif::format("HEADER    %-40.40s%-9.9s   %-4.4s", keywords, date, db.name()).str(), truncate_at);
 }
 
 std::string get_COMPND_line(const datablock &db, std::string::size_type truncate_at)
@@ -3759,7 +3788,7 @@ void write(std::ostream &os, const datablock &db)
 	numXform = WriteCoordinateTransformation(os, db);
 	std::tie(numCoord, numTer) = WriteCoordinate(os, db);
 
-	os << cif::format("MASTER    {:5}    0{:5}{:5}{:5}{:5}{:5}{:5}{:5}{:5}{:5}{:5}",  numRemark,  numHet,  numHelix,  numSheet,  numTurn,  numSite,  numXform,  numCoord,  numTer,  numConect,  numSeq) << '\n'
+	os << cif::format("MASTER    %5d    0%5d%5d%5d%5d%5d%5d%5d%5d%5d%5d",  numRemark,  numHet,  numHelix,  numSheet,  numTurn,  numSite,  numXform,  numCoord,  numTer,  numConect,  numSeq) << '\n'
 			<< "END\n";
 }
 

src/pdb/pdb2cif.cpp

@@ -32,7 +32,6 @@
 #include <map>
 #include <set>
 #include <stack>
-#include <stdexcept>
 
 using cif::category;
 using cif::datablock;
@@ -896,7 +895,12 @@ class PDBFileParser
 				if (year < 1950)
 					year += 100;
 
-				s = cif::format("{:04}-{:02}-{:02}", year, month, day);
+				std::stringstream ss;
+				ss << std::setw(4) << std::setfill('0') << year << '-'
+				   << std::setw(2) << std::setfill('0') << month << '-'
+				   << std::setw(2) << std::setfill('0') << day;
+
+				s = ss.str();
 			}
 			else if (regex_match(s, m, rx2))
 			{
@@ -908,7 +912,7 @@ class PDBFileParser
 				if (year < 1950)
 					year += 100;
 
-				s = cif::format("{:04}-{:02}", year, month);
+				s = cif::format("%04d-%02d", year, month).str();
 			}
 			else
 				ec = error::make_error_code(error::pdbErrors::invalidDate);
@@ -1958,7 +1962,7 @@ void PDBFileParser::ParseRemarks()
 			switch (remarkNr)
 			{
 				case 1:
-					while (mRec->is("REMARK   1") or mRec->is("REMARK 001"))
+					while (mRec->is("REMARK   1"))
 					{
 						if (mRec->mVlen > 15 and vS(12, 20) == "REFERENCE")
 						{
@@ -3330,27 +3334,38 @@ void PDBFileParser::ParseRemark350()
 
 						std::string type = mat == std::vector<double>{ 1, 0, 0, 0, 1, 0, 0, 0, 1 } and vec == std::vector<double>{ 0, 0, 0 } ? "identity operation" : "crystal symmetry operation";
 
-						auto pdbx_struct_oper_list = getCategory("pdbx_struct_oper_list");
-						if (not pdbx_struct_oper_list->contains(cif::key("id") == operID))
-							getCategory("pdbx_struct_oper_list")->emplace({ // clang-format off
+						// if (type == "identity operation")
+						// {
+
+						// }
+						// else
+						try
+						{
+							// clang-format off
+							getCategory("pdbx_struct_oper_list")->emplace({
 								{ "id", operID },
 								{ "type", type },
 								// { "name", "" },
 							    // { "symmetryOperation", "" },
-								{ "matrix[1][1]", cif::format("{:12.10f}", mat[0]) },
-								{ "matrix[1][2]", cif::format("{:12.10f}", mat[1]) },
-								{ "matrix[1][3]", cif::format("{:12.10f}", mat[2]) },
-								{ "vector[1]", cif::format("{:12.10f}", vec[0]) },
-								{ "matrix[2][1]", cif::format("{:12.10f}", mat[3]) },
-								{ "matrix[2][2]", cif::format("{:12.10f}", mat[4]) },
-								{ "matrix[2][3]", cif::format("{:12.10f}", mat[5]) },
-								{ "vector[2]", cif::format("{:12.10f}", vec[1]) },
-								{ "matrix[3][1]", cif::format("{:12.10f}", mat[6]) },
-								{ "matrix[3][2]", cif::format("{:12.10f}", mat[7]) },
-								{ "matrix[3][3]", cif::format("{:12.10f}", mat[8]) },
-								{ "vector[3]", cif::format("{:12.10f}", vec[2]) }
+								{ "matrix[1][1]", cif::format("%12.10f", mat[0]).str() },
+								{ "matrix[1][2]", cif::format("%12.10f", mat[1]).str() },
+								{ "matrix[1][3]", cif::format("%12.10f", mat[2]).str() },
+								{ "vector[1]", cif::format("%12.10f", vec[0]).str() },
+								{ "matrix[2][1]", cif::format("%12.10f", mat[3]).str() },
+								{ "matrix[2][2]", cif::format("%12.10f", mat[4]).str() },
+								{ "matrix[2][3]", cif::format("%12.10f", mat[5]).str() },
+								{ "vector[2]", cif::format("%12.10f", vec[1]).str() },
+								{ "matrix[3][1]", cif::format("%12.10f", mat[6]).str() },
+								{ "matrix[3][2]", cif::format("%12.10f", mat[7]).str() },
+								{ "matrix[3][3]", cif::format("%12.10f", mat[8]).str() },
+								{ "vector[3]", cif::format("%12.10f", vec[2]).str() }
 							});
-																			// clang-format on
+							// clang-format on
+						}
+						catch (duplicate_key_error &ex)
+						{
+							// so what?
+						}
 
 						mat.clear();
 						vec.clear();
@@ -4285,8 +4300,6 @@ void PDBFileParser::ConstructEntities()
 			type = "polypeptide(L)";
 		else if (mightBeDNA and not mightBePolyPeptide)
 			type = "polyribonucleotide";
-		else
-			type = "other";
 
 		// clang-format off
 		getCategory("entity_poly")->emplace({
@@ -4314,7 +4327,7 @@ void PDBFileParser::ConstructEntities()
 	}
 
 	// build sugar trees first
-	// ConstructSugarTrees(asymNr);
+	ConstructSugarTrees(asymNr);
 
 	// done with the sugar, resume operation as before
 
@@ -4492,7 +4505,7 @@ void PDBFileParser::ConstructEntities()
 	int modResID = 1;
 	std::set<std::string> modResSet;
 	for (auto rec = FindRecord("MODRES"); rec != nullptr and rec->is("MODRES");
-		rec = rec->mNext)                      //	 1 -  6        Record name   "MODRES"
+		 rec = rec->mNext)                     //	 1 -  6        Record name   "MODRES"
 	{                                          //	 8 - 11        IDcode        idCode      ID code of this datablock.
 		std::string resName = rec->vS(13, 15); //	13 - 15        Residue name  resName     Residue name used in this datablock.
 		char chainID = rec->vC(17);            //	17             Character     chainID     Chain identifier.
@@ -5614,7 +5627,7 @@ void PDBFileParser::ParseCoordinateTransformation()
 			igiven = vC(60) == '1';   //	60             Integer       iGiven        1 if coordinates for the  representations
 			                          //	                                           which  are approximately related by the
 			GetNextRecord();          //	                                           transformations  of the molecule are
-		} //	                                           contained in the datablock. Otherwise, blank.
+		}                             //	                                           contained in the datablock. Otherwise, blank.
 
 		// clang-format off
 		getCategory("struct_ncs_oper")->emplace({
@@ -5768,9 +5781,6 @@ void PDBFileParser::ParseCoordinate(int modelNr)
 		std::string element = vS(77, 78);    //	77 - 78        LString(2)    element      Element symbol, right-justified.
 		std::string charge = vS(79, 80);     //	79 - 80        LString(2)    charge       Charge  on the atom.
 
-		if (element.empty())
-			throw std::runtime_error("Empty element column in PDB file at line " + std::to_string(mRec->mLineNr));
-
 		std::string entityID = mAsymID2EntityID[asymID];
 
 		charge = pdb2cifCharge(charge);
@@ -5849,7 +5859,7 @@ void PDBFileParser::ParseCoordinate(int modelNr)
 
 			auto f = [](float f) -> std::string
 			{
-				return cif::format("{:6.4f}", f);
+				return cif::format("%6.4f", f).str();
 			};
 
 			// clang-format off
@@ -6366,20 +6376,11 @@ void read_pdb_file(std::istream &pdbFile, cif::file &cifFile)
 
 	p.Parse(pdbFile, cifFile);
 
-	if (cifFile.empty())
-	{
-		if (VERBOSE >= 0)
-			std::cerr << "PDB is empty!\n";
-	}
-	else
-	{
-		cifFile.front().load_dictionary();
-		if (cifFile.front().get_validator() == nullptr)
-			cifFile.front().set_validator(&validator_factory::instance().get("mmcif_pdbx.dic"));
+	if (not cifFile.empty() and cifFile.front().get_validator() == nullptr)
+		cifFile.front().load_dictionary("mmcif_pdbx.dic");
 
-		if (not cifFile.is_valid() and cif::VERBOSE >= 0)
-			std::cerr << "Resulting mmCIF file is not valid!\n";
-	}
+	if (not cifFile.is_valid() and cif::VERBOSE >= 0)
+		std::cerr << "Resulting mmCIF file is not valid!\n";
 }
 
 // --------------------------------------------------------------------
@@ -6403,10 +6404,7 @@ file read(std::istream &is)
 		// apart from the letter 'd', the test has changed into the following:
 
 		if (std::isalpha(ch) and std::toupper(ch) != 'D')
-		{
 			read_pdb_file(is, result);
-			fixup_pdbx(result);
-		}
 		else
 		{
 			try
@@ -6417,38 +6415,16 @@ file read(std::istream &is)
 			{
 				std::throw_with_nested(std::runtime_error("Since the file did not start with a valid PDB HEADER line mmCIF was assumed, but that failed."));
 			}
-
-			if (not(result.empty() or result.front().empty()))
-			{
-				if (auto &db = result.front(); db.get("audit_conform") == nullptr)
-					reconstruct_pdbx(result);
-				else
-				{
-					try
-					{
-						// Try to see if we can create an mm::structure out of this data.
-						// If that fails, we need to reconstruct a PDBx file out of it.
-
-						cif::mm::structure s(result);
-					}
-					catch (const std::exception &e)
-					{
-						reconstruct_pdbx(result);
-					}
-				}
-			}
 		}
+
+		// Since we're using the cif::pdb way of reading the file, the data may need
+		// reconstruction
+		reconstruct_pdbx(result);
 	}
 
 	// Must be a PDB like file, right?
-	if (not result.empty())
-	{
-		auto &db = result.front();
-		if (db.get_validator() == nullptr)
-			db.set_validator(&validator_factory::instance().get("mmcif_pdbx.dic"));
-		if (db.is_valid())
-			db.get_validator()->fill_audit_conform(db["audit_conform"]);
-	}
+	if (not result.empty() and result.front().get_validator() == nullptr)
+		result.front().load_dictionary("mmcif_pdbx.dic");
 
 	return result;
 }

src/pdb/pdb2cif_remark_3.cpp

@@ -1478,8 +1478,6 @@ bool Remark3Parser::parse(const std::string &expMethod, PDBRecord *r, cif::datab
 
 		best.parser->fixup();
 
-		auto &validator = cif::validator_factory::instance().get("mmcif_pdbx.dic");
-
 		for (auto &cat1 : best.parser->mDb)
 		{
 			if (cat1.empty())
@@ -1498,15 +1496,8 @@ bool Remark3Parser::parse(const std::string &expMethod, PDBRecord *r, cif::datab
 					auto r1 = cat1.front();
 					auto r2 = cat2.front();
 
-					auto cv = cat1.get_cat_validator();
-					if (cv == nullptr)
-						cv = validator.get_validator_for_category(cat1.name());
-					
-					if (cv == nullptr)
-						continue;
-
-					for (auto &iv : cv->m_item_validators)
-						r2[iv.m_item_name] = r1[iv.m_item_name].text();
+					for (auto item : cat1.key_items())
+						r2[item] = r1[item].text();
 				}
 			}
 			else

src/pdb/validate-pdbx.cpp

@@ -61,15 +61,17 @@ condition get_parents_condition(const validator &validator, row_handle rh, const
 			result = std::move(result) or std::move(cond);
 		}
 	}
+	else if (cif::VERBOSE > 0)
+		std::cerr << "warning: no child to parent links were found for child " << childName << " and parent " << parentName << '\n';
 
 	return result;
 }
 
-bool is_valid_pdbx_file(const file &file, const validator &v)
+bool is_valid_pdbx_file(const file &file, std::string_view dictionary)
 {
 	std::error_code ec;
-	bool result = is_valid_pdbx_file(file, v, ec);
-	return result and not(bool) ec;
+	bool result = is_valid_pdbx_file(file, dictionary, ec);
+	return result and not (bool)ec;
 }
 
 bool is_valid_pdbx_file(const file &file, std::error_code &ec)
@@ -78,23 +80,42 @@ bool is_valid_pdbx_file(const file &file, std::error_code &ec)
 
 	if (file.empty())
 		ec = make_error_code(validation_error::empty_file);
-	else if (auto ac = file.front().get("audit_conform"); ac != nullptr)
-		result = is_valid_pdbx_file(file, validator_factory::instance().get(*ac), ec);
 	else
-		result = is_valid_pdbx_file(file, validator_factory::instance().get("mmcif_pdbx.dic"), ec);
+	{
+		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, const validator &validator, std::error_code &ec)
+bool is_valid_pdbx_file(const file &file, std::string_view dictionary, std::error_code &ec)
 {
 	using namespace cif::literals;
 
-	bool result = true, warned_missing_parents = false;
+	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");
@@ -127,18 +148,10 @@ bool is_valid_pdbx_file(const file &file, const validator &validator, std::error
 			if (not cf.is_monomer(comp_id))
 				continue;
 
-			auto cond = get_parents_condition(validator, r, pdbx_poly_seq_scheme);
-			if (not cond)
-			{
-				if (VERBOSE > 0 and std::exchange(warned_missing_parents, true) == false)
-					std::cerr << "warning: missing links for atom_site/pdbx_poly_seq_scheme\n";
-				continue;
-			}
-
-			auto p = pdbx_poly_seq_scheme.find(std::move(cond));
+			auto p = pdbx_poly_seq_scheme.find(get_parents_condition(validator, r, pdbx_poly_seq_scheme));
 			if (p.size() != 1)
 			{
-				if (VERBOSE > 0)
+				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");
 			}
@@ -167,7 +180,7 @@ bool is_valid_pdbx_file(const file &file, const validator &validator, std::error
 
 			const auto entity_poly_type = entity_poly.find1<std::string>("entity_id"_key == entity_id, "type");
 
-			std::map<int, std::set<std::string>> mon_per_seq_id;
+			std::map<int,std::set<std::string>> mon_per_seq_id;
 
 			for (const auto &[num, mon_id, hetero] : entity_poly_seq.find<int, std::string, bool>("entity_id"_key == entity_id, "num", "mon_id", "hetero"))
 			{
@@ -202,37 +215,28 @@ bool is_valid_pdbx_file(const file &file, const validator &validator, std::error
 					throw std::runtime_error("Mismatch between the hetero flag in the poly seq schemes and the number residues per seq_id");
 			}
 
-			// This code proved to take too much time ...
-
-			// for (const auto &[seq_id, mon_ids] : mon_per_seq_id)
-			// {
-			// 	for (auto asym_id : struct_asym.find<std::string>("entity_id"_key == entity_id, "id"))
-			// 	{
-			// 		condition cond;
-
-			// 		for (auto mon_id : mon_ids)
-			// 			cond = std::move(cond) or "label_comp_id"_key == mon_id;
-
-			// 		cond = "label_entity_id"_key == entity_id and
-			// 			"label_asym_id"_key == asym_id and
-			// 			"label_seq_id"_key == seq_id and not std::move(cond);
-
-			// 		if (atom_site.contains(std::move(cond)))
-			// 			throw std::runtime_error("An atom_site record exists that has no parent in the poly seq scheme categories");
-			// 	}
-			// }
-
-			// ... so we're using this instead, should be almost the same...
-
-			for (const auto &[comp_id, seq_id] :
-				atom_site.find<std::string, int>("label_entity_id"_key == entity_id, "label_comp_id", "label_seq_id"))
+			for (const auto &[seq_id, mon_ids] : mon_per_seq_id)
 			{
-				if (not mon_per_seq_id[seq_id].contains(comp_id))
-					throw std::runtime_error("An atom_site record exists that has no parent in the poly seq scheme categories");
+				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)
 			{
@@ -269,8 +273,8 @@ bool is_valid_pdbx_file(const file &file, const validator &validator, std::error
 							else
 								letter = '(' + comp_id + ')';
 						}
-
-						if (iequals(std::string{ si, si + letter.length() }, letter))
+						
+						if (iequals(std::string{si, si + letter.length()}, letter))
 						{
 							match = true;
 							si += letter.length();
@@ -289,14 +293,12 @@ bool is_valid_pdbx_file(const file &file, const validator &validator, std::error
 
 			if (not seq.has_value())
 			{
-				if (VERBOSE > 0)
+				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());
+				seq->erase(std::remove_if(seq->begin(), seq->end(), [](char ch) { return std::isspace(ch); }), seq->end());
 
 				if (not seq_match(false, seq->begin(), seq->end()))
 					throw std::runtime_error("Sequences do not match for entity " + entity_id);
@@ -304,14 +306,12 @@ bool is_valid_pdbx_file(const file &file, const validator &validator, std::error
 
 			if (not seq_can.has_value())
 			{
-				if (VERBOSE > 1)
+				if (cif::VERBOSE > 1)
 					std::clog << "Warning: entity_poly has no canonical sequence for entity_id " << entity_id << '\n';
 			}
 			else
 			{
-				seq_can->erase(std::remove_if(seq_can->begin(), seq_can->end(), [](char ch)
-								   { return std::isspace(ch); }),
-					seq_can->end());
+				seq_can->erase(std::remove_if(seq_can->begin(), seq_can->end(), [](char ch) { return std::isspace(ch); }), seq_can->end());
 
 				if (not seq_match(true, seq_can->begin(), seq_can->end()))
 					throw std::runtime_error("Canonical sequences do not match for entity " + entity_id);
@@ -323,15 +323,16 @@ bool is_valid_pdbx_file(const file &file, const validator &validator, std::error
 	catch (const std::exception &ex)
 	{
 		result = false;
-		if (VERBOSE > 0)
+		if (cif::VERBOSE > 0)
 			std::clog << ex.what() << '\n';
 		ec = make_error_code(validation_error::not_valid_pdbx);
 	}
 
-	if (not result and (bool) ec)
+	if (not result and (bool)ec)
 		ec = make_error_code(validation_error::not_valid_pdbx);
 
 	return result;
 }
 
 } // namespace cif::pdb
+  

src/symmetry.cpp

@@ -32,11 +32,6 @@
 
 #include "symop_table_data.hpp"
 
-#if defined(_MSC_VER)
-#pragma warning (disable : 5054)	// warning C5054: operator '&': deprecated between enumerations of different types
-#pragma warning (disable : 4127)	// conditional expression is constant
-#endif
-
 #include <Eigen/Eigen>
 
 namespace cif
@@ -95,10 +90,10 @@ float cell::get_volume() const
 	auto cos_beta = std::cos(beta);
 	auto cos_gamma = std::cos(gamma);
 
-	double vol = m_a * m_b * m_c;
+	auto vol = m_a * m_b * m_c;
 	vol *= std::sqrt(1.0f - cos_alpha * cos_alpha - cos_beta * cos_beta - cos_gamma * cos_gamma + 2.0f * cos_alpha * cos_beta * cos_gamma);
 
-	return static_cast<float>(vol);
+	return vol;
 }
 
 // --------------------------------------------------------------------

src/text.cpp

@@ -29,11 +29,6 @@
 #include <algorithm>
 #include <cassert>
 
-#if __has_include("fast_float/fast_float.h")
-#include "fast_float/fast_float.h"
-#endif
-
-
 namespace cif
 {
 
@@ -517,22 +512,4 @@ std::vector<std::string> word_wrap(const std::string &text, std::size_t width)
 	return result;
 }
 
-#if __has_include("fast_float/fast_float.h")
-
-template<>
-std::from_chars_result ff_charconv<float>::from_chars(const char *a, const char *b, float &v)
-{
-	auto r = fast_float::from_chars(a, b, v);
-	return { r.ptr, r.ec };
-}
-
-template<>
-std::from_chars_result ff_charconv<double>::from_chars(const char *a, const char *b, double &v)
-{
-	auto r = fast_float::from_chars(a, b, v);
-	return { r.ptr, r.ec };
-}
-
-#endif
-
 } // namespace cif

src/utilities.cpp

@@ -34,20 +34,14 @@
 #include <condition_variable>
 #include <cstring>
 #include <deque>
-#include <format>
 #include <fstream>
+#include <functional>
 #include <iomanip>
 #include <iostream>
 #include <map>
 #include <mutex>
 #include <sstream>
-#include <string>
 #include <thread>
-#include <utility>
-
-#if __cpp_lib_jthread >= 201911L
-#include <stop_token>
-#endif
 
 namespace fs = std::filesystem;
 
@@ -71,50 +65,27 @@ std::string get_version_nr()
 
 #if defined(_WIN32) or defined(__MINGW32__)
 }
-// clang-format off
-# include <windows.h>
-# include <libloaderapi.h>
-# include <wincon.h>
-// clang-format on
+#include <windows.h>
+#include <libloaderapi.h>
+#include <wincon.h>
+
+#include <codecvt>
 
 namespace cif
 {
 
 uint32_t get_terminal_width()
 {
-	CONSOLE_SCREEN_BUFFER_INFO csbi;
-	return ::GetConsoleScreenBufferInfo(::GetStdHandle(STD_OUTPUT_HANDLE), &csbi)
-	           ? csbi.srWindow.Right - csbi.srWindow.Left + 1
-	           : 80;
-}
-
-void write_to_console(const std::string &s)
-{
-	auto h = ::GetStdHandle(STD_OUTPUT_HANDLE);
-	CONSOLE_SCREEN_BUFFER_INFO csbi;
-
-	if (auto l = ::MultiByteToWideChar(CP_UTF8, 0, s.data(), s.length(), nullptr, 0);
-		l > 0 and ::GetConsoleScreenBufferInfo(::GetStdHandle(STD_OUTPUT_HANDLE), &csbi))
-	{
-		std::u16string ws(l, 0);
-
-		::MultiByteToWideChar(CP_UTF8, 0, s.data(), s.length(), (LPWSTR)ws.data(), l);
-
-		DWORD w;
-		::WriteConsoleW(h, ws.data(), ws.length(), &w, nullptr);
-	}
-	else
-	{
-		std::cout.write(s.data(), s.length());
-		std::cout.flush();
-	}
+    CONSOLE_SCREEN_BUFFER_INFO csbi;
+    ::GetConsoleScreenBufferInfo(::GetStdHandle(STD_OUTPUT_HANDLE), &csbi);
+    return csbi.srWindow.Right - csbi.srWindow.Left + 1;
 }
 
 #else
 
-# include <limits.h>
-# include <sys/ioctl.h>
-# include <termios.h>
+#include <sys/ioctl.h>
+#include <termios.h>
+#include <limits.h>
 
 uint32_t get_terminal_width()
 {
@@ -129,220 +100,59 @@ uint32_t get_terminal_width()
 	return result;
 }
 
-inline void write_to_console(const std::string &s)
-{
-	std::cout << s << std::flush;
-}
-
 #endif
 
 // --------------------------------------------------------------------
 
 struct progress_bar_impl
 {
-	progress_bar_impl(uint64_t max_value, const std::string &message)
-		: m_max_value(max_value)
+	progress_bar_impl(int64_t inMax, const std::string &inAction)
+		: m_max_value(inMax)
 		, m_consumed(0)
-		, m_action(message)
-		, m_message(message)
+		, m_action(inAction)
+		, m_message(inAction)
+		, m_thread(std::bind(&progress_bar_impl::run, this))
 	{
 	}
 
-	virtual ~progress_bar_impl() {}
+	progress_bar_impl(const progress_bar_impl&) = delete;
+	progress_bar_impl &operator=(const progress_bar_impl &) = delete;
 
-	virtual void consumed(uint64_t n);
-	virtual void progress(uint64_t p);
-	virtual void message(const std::string &msg);
-	virtual void print_done();
+	~progress_bar_impl();
+
+	void run();
+
+	void consumed(int64_t n);
+	void progress(int64_t p);
+	void message(const std::string &msg);
+
+	void print_progress();
+	void print_done();
 
 	using time_point = std::chrono::time_point<std::chrono::system_clock>;
 
-	uint64_t m_max_value;
-	std::atomic<uint64_t> m_consumed;
+	int64_t m_max_value;
+	std::atomic<int64_t> m_consumed;
+	int64_t m_last_consumed = 0;
+	int m_spinner_index = 0;
 	std::string m_action, m_message;
-	time_point m_start = std::chrono::system_clock::now();
-};
-
-void progress_bar_impl::consumed(uint64_t n)
-{
-	m_consumed += n;
-}
-
-void progress_bar_impl::progress(uint64_t p)
-{
-	m_consumed = p;
-}
-
-void progress_bar_impl::message(const std::string &msg)
-{
-	m_message = msg;
-}
-
-void progress_bar_impl::print_done()
-{
-	std::chrono::duration<double> elapsed = std::chrono::system_clock::now() - m_start;
-	std::string days, hours, minutes, seconds;
-
-	uint64_t s = static_cast<uint64_t>(std::trunc(elapsed.count()));
-	if (s > 24 * 60 * 60)
-	{
-		days = std::format("{:d}d ", s / (24 * 60 * 60));
-		s %= 24 * 60 * 60;
-	}
-
-	if (s > 60 * 60)
-	{
-		hours = std::format("{:2d}h ", s / (60 * 60));
-		s %= 60 * 60;
-	}
-
-	if (s > 60)
-	{
-		minutes = std::format("{:2d}m ", s / 60);
-		s %= 60;
-	}
-
-	std::string msg = std::format("{} done in {}{}{}{:.1f}s", m_action, days, hours, minutes, s + 1e-6 * (elapsed.count() - s));
-
-	uint32_t width = get_terminal_width();
-
-	if (msg.length() < width)
-		msg += std::string(width - msg.length(), ' ');
-
-	write_to_console(msg += '\n');
-}
-
-// --------------------------------------------------------------------
-
-struct simple_progress_bar_impl : public progress_bar_impl
-{
-	simple_progress_bar_impl(uint64_t max_value, const std::string &message)
-		: progress_bar_impl(max_value, message)
-	{
-	}
-
-	~simple_progress_bar_impl()
-	{
-		if (m_printed_any)
-			print_done();
-	}
-
-	void consumed(uint64_t n) override
-	{
-		using namespace std::literals;
-
-		progress_bar_impl::consumed(n);
-
-		// print at most 10 steps, but only if it took long enough
-
-		int percentile = static_cast<int>(std::floor(10.f * m_consumed / m_max_value));
-		if (percentile > m_last_percentile and (m_printed_any or std::chrono::system_clock::now() - m_start >= 1s))
-		{
-			if (not std::exchange(m_printed_any, true))
-				write_to_console(m_action + ": ");
-
-			write_to_console(std::format("...{:d}0%", percentile));
-			m_last_percentile = percentile;
-		}
-	}
-
-	void progress(uint64_t p) override
-	{
-		consumed(p - m_consumed);
-	}
-
-	void print_done() override
-	{
-		if (m_printed_any)
-		{
-			write_to_console("\n");
-			progress_bar_impl::print_done();
-		}
-	}
-
-	bool m_printed_any = false;
-	int m_last_percentile = 0;
-};
-
-// --------------------------------------------------------------------
-
-struct fancy_progress_bar_impl : public progress_bar_impl
-{
-	fancy_progress_bar_impl(uint64_t max_value, const std::string &message)
-		: progress_bar_impl(max_value, message)
-		, m_thread(
-#if __cpp_lib_jthread >= 201911L
-			  [this](std::stop_token stoken)
-			  { this->run(stoken); }
-#else
-			  [this]()
-			  { this->run(); }
-#endif
-		  )
-	{
-	}
-
-	~fancy_progress_bar_impl();
-
-#if __cpp_lib_jthread >= 201911L
-	void run(std::stop_token stoken);
-#else
-	void run();
-#endif
-
-	void consumed(uint64_t n) override;
-	void progress(uint64_t p) override;
-	void message(const std::string &msg) override;
-
-	void print_progress();
-
 	std::mutex m_mutex;
-	std::condition_variable m_cv;
-
-	float m_progress;
-	uint32_t m_width, m_bar_width;
-	uint32_t m_steps, m_last_steps = 0;
-	uint64_t m_last_consumed = 0;
-#if __cpp_lib_jthread >= 201911L
-	std::jthread m_thread;
-#else
 	std::thread m_thread;
+	time_point m_start = std::chrono::system_clock::now();
+	time_point m_last = std::chrono::system_clock::now();
 	bool m_stop = false;
-#endif
 };
 
-const char *kBlocks[] = {
-	" ",
-	"▏",
-	"▎",
-	"▍",
-	"▌",
-	"▋",
-	"▊",
-	"▉",
-	"█",
-};
-
-const size_t kBlockCount = sizeof(kBlocks) / sizeof(void *) - 1;
-
-fancy_progress_bar_impl::~fancy_progress_bar_impl()
+progress_bar_impl::~progress_bar_impl()
 {
 	using namespace std::literals;
 	assert(m_thread.joinable());
 
-#if __cpp_lib_jthread >= 201911L
-	m_thread.request_stop();
-#else
 	m_stop = true;
-#endif
 	m_thread.join();
 }
 
-#if __cpp_lib_jthread >= 201911L
-void fancy_progress_bar_impl::run(std::stop_token stoken)
-#else
-void fancy_progress_bar_impl::run()
-#endif
+void progress_bar_impl::run()
 {
 	using namespace std::literals;
 
@@ -350,44 +160,25 @@ void fancy_progress_bar_impl::run()
 
 	try
 	{
-		for (;;)
+		while (not m_stop)
 		{
-			std::unique_lock lock(m_mutex);
-
-			m_cv.wait_for(lock, 25ms);
-
-#if __cpp_lib_jthread >= 201911L
-			if (stoken.stop_requested())
-				break;
-#else
-			if (m_stop)
-				break;
-#endif
-
 			auto now = std::chrono::system_clock::now();
 
-			if (m_consumed == m_last_consumed or now - m_start < 1s)
+			if (now - m_start < 2s or now - m_last < 100ms)
+			{
+				std::this_thread::sleep_for(10ms);
 				continue;
+			}
 
-			m_last_consumed = m_consumed;
+			std::lock_guard lock(m_mutex);
 
-			// See if we need to do work
-			m_width = get_terminal_width();
-			m_progress = static_cast<float>(m_consumed) / m_max_value;
-			m_bar_width = 7 * m_width / 10; // 70% of the width of the terminal
-			m_steps = static_cast<uint32_t>(std::ceil(m_progress * m_bar_width * kBlockCount));
-
-			if (m_steps == m_last_steps)
-				continue;
-
-			m_last_steps = m_steps;
-
-			if (not printedAny)
-				write_to_console("\x1b[?25l");
+			if (not printedAny and isatty(STDOUT_FILENO))
+				std::cout << "\x1b[?25l";
 
 			print_progress();
 
 			printedAny = true;
+			m_last = std::chrono::system_clock::now();
 		}
 	}
 	catch (...)
@@ -396,94 +187,161 @@ void fancy_progress_bar_impl::run()
 
 	if (printedAny)
 	{
-		write_to_console("\r\x1b[?25h");
 		print_done();
+		if (isatty(STDOUT_FILENO))
+			std::cout << "\x1b[?25h";
 	}
 }
 
-void fancy_progress_bar_impl::consumed(uint64_t n)
+void progress_bar_impl::consumed(int64_t n)
 {
-	progress_bar_impl::consumed(n);
-	// m_cv.notify_one();
+	m_consumed += n;
 }
 
-void fancy_progress_bar_impl::progress(uint64_t p)
+void progress_bar_impl::progress(int64_t p)
 {
-	progress_bar_impl::progress(p);
-	// m_cv.notify_one();
+	m_consumed = p;
 }
 
-void fancy_progress_bar_impl::message(const std::string &msg)
+void progress_bar_impl::message(const std::string &msg)
 {
 	std::unique_lock lock(m_mutex);
-	progress_bar_impl::message(msg);
-	// m_cv.notify_one();
+	m_message = msg;
 }
 
+const char* kSpinner[] = {
+	// ".", "o", "O", "0", "O", "o", ".", " "
+	// "⢄", "⢂", "⢁", "⡁", "⡈", "⡐", "⡠"
+	 ".", "o", "O", "0", "@", "*", " "
+};
+
+const std::size_t kSpinnerCount = sizeof(kSpinner) / sizeof(char*);
+
+const int kSpinnerTimeInterval = 100;
+
 const uint32_t kMinBarWidth = 40, kMinMsgWidth = 12;
 
-void fancy_progress_bar_impl::print_progress()
+void progress_bar_impl::print_progress()
 {
-	const uint32_t pct_width = 5;
-	uint32_t msg_width = m_width - m_bar_width - pct_width - 1;
+	const char *kBlocks[] = {
+		// "▯", // 0
+		// "▮", // 1
+		"=",
+		"-"
+	};
 
-	if (msg_width < kMinMsgWidth)
+	uint32_t width = get_terminal_width();
+
+	float progress = static_cast<float>(m_consumed) / m_max_value;
+	
+	if (width < kMinBarWidth)
+		std::cout << (100 * progress) << "%\n";
+	else
 	{
-		m_bar_width += kMinMsgWidth - msg_width;
-		msg_width = kMinMsgWidth;
-	}
+		uint32_t bar_width = 7 * width / 10;
+		uint32_t pct_width = 7;
+		uint32_t msg_width = width - bar_width - pct_width - 1;
 
-	std::string bar;
-	bar.reserve(m_bar_width * 4);
+		if (msg_width < kMinMsgWidth)
+		{
+			bar_width += kMinMsgWidth - msg_width;
+			msg_width = kMinMsgWidth;
+		}
 
-	for (uint32_t i = 0; i < m_bar_width; ++i)
-	{
-		if (i * kBlockCount <= m_steps)
-			bar += kBlocks[kBlockCount];
-		else if (i * kBlockCount > m_steps + kBlockCount)
-			bar += kBlocks[0];
+		std::ostringstream msg;
+
+		if (m_message.length() <= msg_width)
+		{
+			msg << m_message;
+			if (m_message.length() < msg_width)
+				msg << std::string(msg_width - m_message.length(), ' ');
+		}
 		else
-			bar += kBlocks[1 + m_steps % kBlockCount];
+			msg << m_message.substr(0, msg_width - 3) << "...";
+
+		msg << ' ';
+
+		uint32_t pi = static_cast<uint32_t>(std::ceil(progress * bar_width));
+
+		for (uint32_t i = 0; i < bar_width; ++i)
+			msg << kBlocks[i > pi ? 1 : 0];
+
+		msg << ' ';
+
+		msg << std::setw(3) << static_cast<int>(std::ceil(progress * 100)) << "% ";
+
+		auto now = std::chrono::system_clock::now();
+		m_spinner_index = (std::chrono::duration_cast<std::chrono::milliseconds>(now - m_start).count() / kSpinnerTimeInterval) % kSpinnerCount;
+
+		msg << kSpinner[m_spinner_index];
+
+		std::cout << '\r' << msg.str();
+		std::cout.flush();
 	}
-
-	// make the bar more colorfull
-	struct color_type
-	{
-		uint8_t r, g, b;
-	} fg{ 0, 3, 5 }, bg{ 0, 1, 2 };
-
-	auto esc_1 = std::format("\x1b[38;5;{}m\x1b[48;5;{}m",
-		16 + (fg.r * 36) + (fg.g * 6) + fg.b,
-		16 + (bg.r * 36) + (bg.g * 6) + bg.b);
-	std::string esc_2("\x1b[0m");
-
-	bar = esc_1 + bar + esc_2;
-
-	std::string msg = m_message.length() <= msg_width
-	                      ? m_message
-	                      : m_message.substr(0, msg_width - 3) + "...";
-
-	write_to_console(std::format("{:{}} {} {:3d}%\r", msg, msg_width, bar,
-		static_cast<int>(std::ceil(m_progress * 100))));
 }
 
-// --------------------------------------------------------------------
+namespace
+{
 
-progress_bar::progress_bar(int64_t max_value, const std::string &message)
+	std::ostream &operator<<(std::ostream &os, const std::chrono::duration<double> &t)
+	{
+		uint64_t s = static_cast<uint64_t>(std::trunc(t.count()));
+		if (s > 24 * 60 * 60)
+		{
+			auto days = s / (24 * 60 * 60);
+			os << days << "d ";
+			s %= 24 * 60 * 60;
+		}
+
+		if (s > 60 * 60)
+		{
+			auto hours = s / (60 * 60);
+			os << hours << "h ";
+			s %= 60 * 60;
+		}
+
+		if (s > 60)
+		{
+			auto minutes = s / 60;
+			os << minutes << "m ";
+			s %= 60;
+		}
+
+		double ss = s + 1e-6 * (t.count() - s);
+
+		os << std::fixed << std::setprecision(1) << ss << 's';
+
+		return os;
+	}
+
+} // namespace
+
+void progress_bar_impl::print_done()
+{
+	std::chrono::duration<double> elapsed = std::chrono::system_clock::now() - m_start;
+
+	std::ostringstream msgstr;
+	msgstr << m_action << " done in " << elapsed << " seconds";
+	auto msg = msgstr.str();
+
+	uint32_t width = get_terminal_width();
+
+	if (msg.length() < width)
+		msg += std::string(width - msg.length(), ' ');
+
+	std::cout << '\r' << msg << '\n';
+}
+
+progress_bar::progress_bar(int64_t inMax, const std::string &inAction)
 	: m_impl(nullptr)
 {
-	if (VERBOSE >= 0)
-	{
-		if (isatty(STDOUT_FILENO) and get_terminal_width() > kMinBarWidth)
-			m_impl = new fancy_progress_bar_impl(max_value, message);
-		else
-			m_impl = new simple_progress_bar_impl(max_value, message);
-	}
+	if (isatty(STDOUT_FILENO) and VERBOSE >= 0)
+		m_impl = new progress_bar_impl(inMax, inAction);
 }
 
 progress_bar::~progress_bar()
 {
-	flush();
+	delete m_impl;
 }
 
 void progress_bar::consumed(int64_t inConsumed)
@@ -492,25 +350,16 @@ void progress_bar::consumed(int64_t inConsumed)
 		m_impl->consumed(inConsumed);
 }
 
-void progress_bar::progress(int64_t value)
+void progress_bar::progress(int64_t inProgress)
 {
 	if (m_impl != nullptr)
-		m_impl->progress(value);
+		m_impl->progress(inProgress);
 }
 
-void progress_bar::message(const std::string &message)
+void progress_bar::message(const std::string &inMessage)
 {
 	if (m_impl != nullptr)
-		m_impl->message(message);
-}
-
-void progress_bar::flush()
-{
-	if (m_impl)
-	{
-		delete m_impl;
-		m_impl = nullptr;
-	}
+		m_impl->message(inMessage);
 }
 
 } // namespace cif
@@ -538,13 +387,13 @@ struct rsrc_imp
 
 #if _WIN32
 
-# if __MINGW32__
+#if __MINGW32__
 
 extern "C" __attribute__((weak, alias("gResourceIndexDefault"))) const mrsrc::rsrc_imp gResourceIndex[];
 extern "C" __attribute__((weak, alias("gResourceDataDefault"))) const char gResourceData[];
 extern "C" __attribute__((weak, alias("gResourceNameDefault"))) const char gResourceName[];
 
-# else
+#else
 
 extern "C" const mrsrc::rsrc_imp *gResourceIndexDefault[1] = {};
 extern "C" const char *gResourceDataDefault[1] = {};
@@ -554,11 +403,11 @@ extern "C" const mrsrc::rsrc_imp gResourceIndex[];
 extern "C" const char gResourceData[];
 extern "C" const char gResourceName[];
 
-#  pragma comment(linker, "/alternatename:gResourceIndex=gResourceIndexDefault")
-#  pragma comment(linker, "/alternatename:gResourceData=gResourceDataDefault")
-#  pragma comment(linker, "/alternatename:gResourceName=gResourceNameDefault")
+#pragma comment(linker, "/alternatename:gResourceIndex=gResourceIndexDefault")
+#pragma comment(linker, "/alternatename:gResourceData=gResourceDataDefault")
+#pragma comment(linker, "/alternatename:gResourceName=gResourceNameDefault")
 
-# endif
+#endif
 
 #else
 extern const __attribute__((weak)) mrsrc::rsrc_imp gResourceIndex[];

src/validate.cpp

@@ -25,7 +25,6 @@
  */
 
 #include "cif++/validate.hpp"
-#include "cif++/category.hpp"
 #include "cif++/dictionary_parser.hpp"
 #include "cif++/gzio.hpp"
 #include "cif++/utilities.hpp"
@@ -36,11 +35,16 @@
 
 // The validator depends on regular expressions. Unfortunately,
 // the implementation of std::regex in g++ is buggy and crashes
-// on reading the pdbx dictionary. We used to use boost regex
-// instead but using pcre2 is even easier and faster.
+// on reading the pdbx dictionary. Therefore, in case g++ is used
+// the code will use boost::regex instead.
 
-#define PCRE2_CODE_UNIT_WIDTH 8
-#include <pcre2.h>
+#if USE_BOOST_REGEX
+# include <boost/regex.hpp>
+using boost::regex;
+#else
+# include <regex>
+using std::regex;
+#endif
 
 namespace cif
 {
@@ -62,57 +66,13 @@ validation_exception::validation_exception(std::error_code ec, std::string_view
 
 // --------------------------------------------------------------------
 
-struct regex_impl
+struct regex_impl : public regex
 {
-	regex_impl(std::string_view rx);
-	~regex_impl();
-
-	regex_impl(const regex_impl &) = delete;
-	regex_impl &operator=(const regex_impl &) = delete;
-
-	bool match(std::string_view v) const;
-
-  private:
-	pcre2_code *m_rx = nullptr;
-	pcre2_match_data *m_data = nullptr;
-};
-
-regex_impl::regex_impl(std::string_view rx)
-{
-	int err_code;
-	size_t err_offset;
-	m_rx = pcre2_compile((PCRE2_SPTR)rx.data(), rx.length(), 0, &err_code, &err_offset, nullptr);
-	if (m_rx == nullptr)
+	regex_impl(std::string_view rx)
+		: regex(rx.begin(), rx.end(), regex::extended | regex::optimize)
 	{
-		PCRE2_UCHAR buffer[256];
-		int n = pcre2_get_error_message(err_code, buffer, sizeof(buffer));
-
-		throw std::runtime_error(std::string("PCRE2 compilation failed: ") + std::string{ (char *)buffer, (char *)buffer + n });
 	}
-
-	m_data = pcre2_match_data_create_from_pattern(m_rx, nullptr);
-}
-
-regex_impl::~regex_impl()
-{
-	if (m_data)
-		pcre2_match_data_free(m_data);
-
-	if (m_rx)
-		pcre2_code_free(m_rx);
-}
-
-bool regex_impl::match(std::string_view v) const
-{
-	bool result = false;
-
-	if (int rc = pcre2_match(m_rx, (PCRE2_SPTR)v.data(), v.length(), 0, 0, m_data, nullptr); rc >= 0)
-		result = true;
-	else if (rc != PCRE2_ERROR_NOMATCH)
-		std::cerr << "Error matching with pcre\n";
-
-	return result;
-}
+};
 
 // --------------------------------------------------------------------
 
@@ -149,15 +109,9 @@ type_validator::type_validator(std::string_view name, DDL_PrimitiveType type, st
 {
 }
 
-type_validator::type_validator(const type_validator &tv)
-	: m_name(tv.m_name)
-	, m_primitive_type(tv.m_primitive_type)
-	, m_rx(tv.m_rx)
-{
-}
-
 type_validator::~type_validator()
 {
+	delete m_rx;
 }
 
 int type_validator::compare(std::string_view a, std::string_view b) const
@@ -181,8 +135,8 @@ int type_validator::compare(std::string_view a, std::string_view b) const
 
 				std::from_chars_result ra, rb;
 
-				ra = from_chars(a.data(), a.data() + a.length(), da);
-				rb = from_chars(b.data(), b.data() + b.length(), db);
+				ra = selected_charconv<double>::from_chars(a.data(), a.data() + a.length(), da);
+				rb = selected_charconv<double>::from_chars(b.data(), b.data() + b.length(), db);
 
 				if (not(bool) ra.ec and not(bool) rb.ec)
 				{
@@ -272,7 +226,7 @@ bool item_validator::validate_value(std::string_view value, std::error_code &ec)
 
 	if (not value.empty() and value != "?" and value != ".")
 	{
-		if (m_type != nullptr and not m_type->m_rx->match(value))
+		if (m_type != nullptr and not regex_match(value.begin(), value.end(), *m_type->m_rx))
 			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);
@@ -288,7 +242,7 @@ void category_validator::add_item_validator(item_validator &&v)
 	if (v.m_mandatory)
 		m_mandatory_items.insert(v.m_item_name);
 
-	v.m_category = m_name;
+	v.m_category = this;
 
 	auto r = m_item_validators.insert(std::move(v));
 	if (not r.second and VERBOSE >= 4)
@@ -330,29 +284,6 @@ const item_validator *category_validator::get_validator_for_aliased_item(std::st
 
 // --------------------------------------------------------------------
 
-validator::validator(const validator &rhs)
-	: m_audit_conform(rhs.m_audit_conform)
-	, m_strict(rhs.m_strict)
-	, m_type_validators(rhs.m_type_validators)
-	, m_category_validators(rhs.m_category_validators)
-	, m_link_validators(rhs.m_link_validators)
-{
-}
-
-void swap(validator &a, validator &b) noexcept
-{
-	std::swap(a.m_audit_conform, b.m_audit_conform);
-	std::swap(a.m_strict, b.m_strict);
-	std::swap(a.m_type_validators, b.m_type_validators);
-	std::swap(a.m_category_validators, b.m_category_validators);
-	std::swap(a.m_link_validators, b.m_link_validators);
-}
-
-void validator::parse(std::istream &is)
-{
-	parse_dictionary(*this, is);
-}
-
 void validator::add_type_validator(type_validator &&v)
 {
 	auto r = m_type_validators.insert(std::move(v));
@@ -485,48 +416,6 @@ void validator::report_error(std::error_code ec, std::string_view category,
 		std::cerr << ex.what() << '\n';
 }
 
-void validator::fill_audit_conform(category &audit_conform) const
-{
-	audit_conform.clear();
-	audit_conform.emplace(m_audit_conform.begin(), m_audit_conform.end());
-}
-
-bool validator::matches_audit_conform(const category &audit_conform) const
-{
-	if (audit_conform.empty())
-		return false;
-
-	auto ai = m_audit_conform.begin();
-	auto bi = audit_conform.begin();
-
-	while (ai != m_audit_conform.end() and bi != audit_conform.end())
-	{
-		const auto &[name_a, version_a] = ai->get<std::string, std::optional<std::string>>("dict_name", "dict_version");
-		const auto &[name_b, version_b] = bi->get<std::string, std::optional<std::string>>("dict_name", "dict_version");
-
-		++ai;
-		++bi;
-
-		if (name_a != name_b)
-			return false;
-
-		if (not version_b.has_value() or not version_a.has_value())
-			continue;
-
-		if (validator_factory::check_version(name_a, *version_b, *version_a) == false)
-			return false;
-	}
-
-	return ai == m_audit_conform.end() and bi == audit_conform.end();
-}
-
-void validator::append_audit_conform(const std::string &name, const std::optional<std::string> &version)
-{
-	m_audit_conform.emplace({ //
-		{ "dict_name", name },
-		{ "dict_version", version } });
-}
-
 // --------------------------------------------------------------------
 
 validator_factory &validator_factory::instance()
@@ -535,127 +424,113 @@ validator_factory &validator_factory::instance()
 	return s_instance;
 }
 
-const validator &validator_factory::get(std::string_view dictionary_name)
+const validator &validator_factory::operator[](std::string_view dictionary_name)
 {
-	category audit_conform("audit_conform");
-	for (auto part : cif::split(dictionary_name, ";", true))
-		audit_conform.emplace({ { "dict_name", part } });
-
-	return get(audit_conform);
-}
-
-const validator &validator_factory::get(const category &audit_conform)
-{
-	if (audit_conform.empty())
-		throw std::runtime_error("Empty audit_conform category, cannot create a validator");
-
-	std::lock_guard lock(m_mutex);
-
-	// Check existing first
-	for (auto &v : m_validators)
+	try
 	{
-		if (v.matches_audit_conform(audit_conform))
-			return v;
-	}
+		std::lock_guard lock(m_mutex);
 
-	// If the audit conform contains only one record, this is easy
-	if (audit_conform.size() == 1)
-	{
-		const auto &[name, version] =
-			audit_conform.front().get<std::string, std::optional<std::string>>("dict_name", "dict_version");
-		if (not name.empty())
-			return m_validators.emplace_back(construct_validator(name, version));
-	}
-
-	// A new, merged dictionary
-
-	std::optional<validator> v;
-	for (const auto &[name, version] : audit_conform.rows<std::string, std::optional<std::string>>("dict_name", "dict_version"))
-	{
-		if (name.empty())
-			continue;
-
-		if (not v)
-			v = construct_validator(name, version);
-		else
+		for (auto &validator : m_validators)
 		{
-			auto data = load_resource(name);
+			if (iequals(validator.name(), dictionary_name))
+				return validator;
+		}
+
+		// not found, try to see if it helps if we tweak the name a little
+
+		// too bad clang version 10 did not have a constructor for std::filesystem::path that accepts a std::string_view
+		std::filesystem::path dictionary(dictionary_name.data(), dictionary_name.data() + dictionary_name.length());
+
+		if (dictionary.extension() != ".dic")
+		{
+			auto dict_name = dictionary.filename().string() + ".dic";
+
+			for (auto &validator : m_validators)
+			{
+				if (iequals(validator.name(), dict_name))
+					return validator;
+			}
+		}
+
+		// not found, add it
+
+		validator v(dictionary_name);
+
+		for (bool first = true; auto part_name : cif::split(dictionary_name, ";", true))
+		{
+			auto data = load_resource(part_name);
+			dictionary.assign(part_name.begin(), part_name.end());
+
+			if (not data and dictionary.extension().string() != ".dic")
+				data = load_resource(dictionary.parent_path() / (dictionary.filename().string() + ".dic"));
+
 			if (not data)
-				throw std::runtime_error("Could not load dictionary " + std::string{ name });
+			{
+				std::error_code ec;
 
-			v->parse(*data);
+				// might be a compressed dictionary on disk
+				std::filesystem::path p = dictionary;
+				if (p.extension() == ".dic")
+					p = p.parent_path() / (p.filename().string() + ".gz");
+				else
+					p = p.parent_path() / (p.filename().string() + ".dic.gz");
+
+#if defined(CACHE_DIR) or defined(DATA_DIR)
+				if (not std::filesystem::exists(p, ec) or ec)
+				{
+					for (const char *dir : {
+# if defined(CACHE_DIR)
+							 CACHE_DIR,
+# endif
+# if defined(DATA_DIR)
+							 DATA_DIR
+# endif
+						 })
+					{
+						auto p2 = std::filesystem::path(dir) / p;
+						if (std::filesystem::exists(p2, ec) and not ec)
+						{
+							swap(p, p2);
+							break;
+						}
+					}
+				}
+#endif
+
+				if (std::filesystem::exists(p, ec) and not ec)
+				{
+					auto in = std::make_unique<gzio::ifstream>(p);
+
+					if (not in->is_open())
+						throw std::runtime_error("Could not open dictionary (" + p.string() + ")");
+
+					data.reset(in.release());
+				}
+				else
+					throw std::runtime_error("Dictionary not found or defined (" + dictionary.string() + ")");
+			}
+
+			if (std::exchange(first, false))
+				v = parse_dictionary(part_name, *data);
+			else
+				extend_dictionary(v, *data);
 		}
+
+		m_validators.emplace_back(std::move(v));
+
+		return m_validators.back();
+	}
+	catch (const std::exception &ex)
+	{
+		std::string msg = "Error while loading dictionary ";
+		msg += dictionary_name;
+		std::throw_with_nested(std::runtime_error(msg));
 	}
-
-	if (not v)
-		throw std::runtime_error("Missing dictionary information?");
-
-	return m_validators.emplace_back(std::move(*v));
 }
 
-validator validator_factory::construct_validator(std::string_view name, std::optional<std::string> version)
+const validator &validator_factory::construct_validator(std::string_view name, std::istream &is)
 {
-	auto data = load_resource(name);
-	if (not data and name == "mmcif_pdbx_v50")
-		data = load_resource("mmcif_pdbx.dic");
-
-	if (not data)
-		throw std::runtime_error("Could not load dictionary " + std::string{ name });
-
-	validator v;
-	v.parse(*data);
-
-	if (version.has_value() and VERBOSE >= 0 and
-		not v.matches_audit_conform(category{ "audit_conform", //
-			{ { "dict_name", name }, { "dict_version", version } } }))
-	{
-		std::clog << "Loaded dictionary does not match name=" << name << " and version=" << version.value_or("''") << "\n";
-	}
-
-	return v;
-}
-
-bool validator_factory::check_version(std::string_view name, std::string_view expected, std::string_view found)
-{
-	bool result = true;
-	auto el = cif::split(expected, ".");
-	auto fl = cif::split(found, ".");
-
-	auto eli = el.begin();
-	auto fli = fl.begin();
-
-	while (eli != el.end() and fli != fl.end())
-	{
-		int e_int, f_int;
-		if (auto [ptr, ec] = std::from_chars(eli->data(), eli->data() + eli->length(), e_int); ec != std::errc{})
-		{
-			std::clog << "Could not parse requested version string for dictionary " << std::quoted(expected) << "\n";
-			result = false;
-			break;
-		}
-
-		if (auto [ptr, ec] = std::from_chars(fli->data(), fli->data() + fli->length(), f_int); ec != std::errc{})
-		{
-			std::clog << "Could not parse version string in dictionary " << name << " " << std::quoted(found) << "\n";
-			result = false;
-			break;
-		}
-
-		if (f_int > e_int) // newer version, assume this is ok
-			break;
-
-		if (f_int < e_int)
-		{
-			std::clog << "The version in dictionary " << name << " is lower than requested, this may cause validation errors\n";
-			result = false;
-			break;
-		}
-
-		++eli;
-		++fli;
-	}
-
-	return result;
+	return m_validators.emplace_back(parse_dictionary(name, is));
 }
 
 } // namespace cif

test/CMakeLists.txt

@@ -1,39 +1,19 @@
-# SPDX-License-Identifier: BSD-2-Clause
-# 
-# Copyright (c) 2025  NKI/AVL, Netherlands Cancer Institute
-# 
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-# 
-# 1. Redistributions of source code must retain the above copyright notice, this
-#    list of conditions and the following disclaimer
-# 2. Redistributions in binary form must reproduce the above copyright notice,
-#    this list of conditions and the following disclaimer in the documentation
-#    and/or other materials provided with the distribution.
-# 
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+# We're using the older version 2 of Catch2
 
-if(NOT (Catch2_FOUND OR TARGET Catch2))
-	find_package(Catch2 3 QUIET)
+if(NOT(Catch2_FOUND OR TARGET Catch2))
+	find_package(Catch2 QUIET)
 
 	if(NOT Catch2_FOUND)
+		include(FetchContent)
+
 		FetchContent_Declare(
 			Catch2
 			GIT_REPOSITORY https://github.com/catchorg/Catch2.git
-            GIT_TAG v3.4.0)
+			GIT_TAG v2.13.9)
 
 		FetchContent_MakeAvailable(Catch2)
 
-		target_compile_features(Catch2 PRIVATE cxx_std_20)
+		set(Catch2_VERSION "2.13.9")
 	endif()
 endif()
 
@@ -42,19 +22,24 @@ list(
 	CIFPP_tests
 	unit-v2
 	unit-3d
+	format
 	model
-	query
 	rename-compound
 	sugar
 	spinner
-	reconstruction
-	validate-pdbx
-)
+	# reconstruction
+	validate-pdbx)
 
 add_library(test-main OBJECT "${CMAKE_CURRENT_SOURCE_DIR}/test-main.cpp")
 
 target_link_libraries(test-main cifpp::cifpp Catch2::Catch2)
 
+if("${Catch2_VERSION}" VERSION_LESS 3.0.0)
+	target_compile_definitions(test-main PUBLIC CATCH22=1)
+else()
+	target_compile_definitions(test-main PUBLIC CATCH22=0)
+endif()
+
 foreach(CIFPP_TEST IN LISTS CIFPP_tests)
 	set(CIFPP_TEST "${CIFPP_TEST}-test")
 	set(CIFPP_TEST_SOURCE "${CMAKE_CURRENT_SOURCE_DIR}/${CIFPP_TEST}.cpp")
@@ -62,6 +47,12 @@ foreach(CIFPP_TEST IN LISTS CIFPP_tests)
 	add_executable(
 		${CIFPP_TEST} ${CIFPP_TEST_SOURCE} $<TARGET_OBJECTS:test-main>)
 
+	if(${Catch2_VERSION} VERSION_GREATER_EQUAL 3.0.0)
+		target_compile_definitions(${CIFPP_TEST} PUBLIC CATCH22=0)
+	else()
+		target_compile_definitions(${CIFPP_TEST} PUBLIC CATCH22=1)
+	endif()
+
 	target_link_libraries(${CIFPP_TEST} PRIVATE cifpp::cifpp Catch2::Catch2)
 	target_include_directories(${CIFPP_TEST} PRIVATE "${EIGEN_INCLUDE_DIR}")
 
@@ -70,6 +61,15 @@ foreach(CIFPP_TEST IN LISTS CIFPP_tests)
 		target_compile_options(${CIFPP_TEST} PRIVATE /EHsc)
 	endif()
 
-	add_test(NAME ${CIFPP_TEST}
-		COMMAND $<TARGET_FILE:${CIFPP_TEST}> --data-dir ${CMAKE_CURRENT_SOURCE_DIR})
-endforeach()
+	add_custom_target(
+		"run-${CIFPP_TEST}"
+		DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch ${CIFPP_TEST})
+
+	add_custom_command(
+		OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch
+		COMMAND $<TARGET_FILE:${CIFPP_TEST}> --data-dir
+		${CMAKE_CURRENT_SOURCE_DIR})
+
+	add_test(NAME ${CIFPP_TEST} COMMAND $<TARGET_FILE:${CIFPP_TEST}> --data-dir
+		${CMAKE_CURRENT_SOURCE_DIR})
+endforeach()

test/brak.pdb

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

test/format-test.cpp

@@ -1,17 +1,17 @@
 /*-
  * SPDX-License-Identifier: BSD-2-Clause
- * 
- * Copyright (c) 2025 NKI/AVL, Netherlands Cancer Institute
- * 
+ *
+ * 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
@@ -24,31 +24,38 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
+
 #include "test-main.hpp"
 
+#include <stdexcept>
+
 #include <cif++.hpp>
 
-#include <iostream>
-#include <fstream>
+// --------------------------------------------------------------------
 
-TEST_CASE("q-1")
+TEST_CASE("fmt_1")
 {
-	using namespace cif::literals;
+	std::ostringstream os;
 
-	cif::compound_factory::instance().push_dictionary(gTestDir / "REA.cif");
-
-	cif::file a = cif::pdb::read(gTestDir / "pdb1cbs.ent.gz");
-	auto &pdbx_poly_seq_scheme = a.front()["pdbx_poly_seq_scheme"];
-	REQUIRE_FALSE(pdbx_poly_seq_scheme.empty());
-
-	SECTION("s-11")
-	{
-		CHECK(pdbx_poly_seq_scheme.count("asym_id"_key == "A") == 137);
-
-		CHECK(pdbx_poly_seq_scheme.count("asym_id"_key == "A" and "entity_id"_key == 1 and "seq_id"_key == 1 and "mon_id"_key == "PRO") == 1);
-
-		CHECK(pdbx_poly_seq_scheme.count("asym_id"_key == "A" and "entity_id"_key == 1 and "seq_id"_key == 1 and "mon_id"_key == "PRO" and "hetero"_key == false) == 1);
-	}
-	
+	std::string world("world");
+	os << cif::format("Hello, %-10.10s, the magic number is %d and pi is %g", world, 42, cif::kPI);
+	REQUIRE(os.str() == "Hello, world     , the magic number is 42 and pi is 3.14159");
 
+	REQUIRE(cif::format("Hello, %-10.10s, the magic number is %d and pi is %g", world, 42, cif::kPI).str() ==
+		"Hello, world     , the magic number is 42 and pi is 3.14159");
 }
+
+// --------------------------------------------------------------------
+
+TEST_CASE("clr_1")
+{
+	using namespace cif::colour;
+
+	std::cout << "Hello, " << cif::coloured("world!", white, red, cif::colour::regular) << '\n'
+			  << "Hello, " << cif::coloured("world!", white, red, bold) << '\n'
+			  << "Hello, " << cif::coloured("world!", black, red) << '\n'
+			  << "Hello, " << cif::coloured("world!", white, green) << '\n'
+			  << "Hello, " << cif::coloured("world!", white, blue) << '\n'
+			  << "Hello, " << cif::coloured("world!", blue, white) << '\n'
+			  << "Hello, " << cif::coloured("world!", red, white, bold) << '\n';
+}

test/model-test.cpp

@@ -54,7 +54,7 @@ TEST_CASE("create_nonpoly_1")
 
 	cif::file file;
 	auto &&[dbi, ignore] = file.emplace("TEST"); // create a datablock
-	dbi->set_validator(&cif::validator_factory::instance().get("mmcif_pdbx.dic"));
+	dbi->load_dictionary("mmcif_pdbx.dic");
 
 	cif::mm::structure structure(file);
 
@@ -82,7 +82,7 @@ _atom_site.pdbx_formal_charge
 # that's enough to test with
 )"_cf;
 
-	atoms.front().set_validator(&cif::validator_factory::instance().get("mmcif_pdbx.dic"));
+	atoms.front().load_dictionary("mmcif_pdbx.dic");
 
 	auto &hem_data = atoms["HEM"];
 	auto &atom_site = hem_data["atom_site"];
@@ -159,7 +159,7 @@ _struct_asym.details                       ?
 _atom_type.symbol   C
 )"_cf;
 
-	expected.front().set_validator(&cif::validator_factory::instance().get("mmcif_pdbx.dic"));
+	expected.front().load_dictionary("mmcif_pdbx.dic");
 
 	if (not(expected.front() == structure.get_datablock()))
 	{
@@ -178,7 +178,7 @@ TEST_CASE("create_nonpoly_2")
 
 	cif::file file;
 	auto &&[dbi, ignore] = file.emplace("TEST"); // create a datablock
-	dbi->set_validator(&cif::validator_factory::instance().get("mmcif_pdbx.dic"));
+	dbi->load_dictionary("mmcif_pdbx.dic");
 
 	cif::mm::structure structure(file);
 
@@ -270,7 +270,7 @@ _struct_asym.details                       ?
 _atom_type.symbol   C
 )"_cf;
 
-	expected.front().set_validator(&cif::validator_factory::instance().get("mmcif_pdbx.dic"));
+	expected.front().load_dictionary("mmcif_pdbx.dic");
 
 	REQUIRE(expected.front() == structure.get_datablock());
 
@@ -354,7 +354,7 @@ _struct_asym.details                       ?
 #
 )"_cf;
 
-	data.front().set_validator(&cif::validator_factory::instance().get("mmcif_pdbx.dic"));
+	data.front().load_dictionary("mmcif_pdbx.dic");
 
 	cif::mm::structure s(data);
 
@@ -431,169 +431,3 @@ TEST_CASE("remove_residue_1")
 
 	REQUIRE_NOTHROW(s.validate_atoms());
 }
-
-// --------------------------------------------------------------------
-// Tests for structure_open_options
-
-TEST_CASE("options_1")
-{
-	using namespace cif::literals;
-
-	const std::filesystem::path example(gTestDir / ".." / "examples" / "1cbs.cif.gz");
-	cif::file file(example.string());
-
-	auto &cf = cif::compound_factory::instance();
-
-	SECTION("skip_water")
-	{
-		cif::mm::structure s(file, 1, { .skip_water = true });
-
-		REQUIRE_NOTHROW(s.validate_atoms());
-
-		for (auto a : s.atoms())
-			CHECK_FALSE(a.is_water());
-	}
-
-	SECTION("skip_hetatom")
-	{
-		cif::mm::structure s(file, 1, { .skip_hetatom = true });
-
-		REQUIRE_NOTHROW(s.validate_atoms());
-
-		for (auto a : s.atoms())
-			CHECK((a.is_water() or cf.is_peptide(a.get_label_comp_id()) or cf.is_base(a.get_label_comp_id())));
-	}
-
-	SECTION("selected_asyms")
-	{
-		cif::mm::structure s(file, 1, { .asyms = { "A" } });
-
-		REQUIRE_NOTHROW(s.validate_atoms());
-
-		for (auto a : s.atoms())
-			CHECK(a.get_label_asym_id() == "A");
-	}
-
-	SECTION("min-b-factor")
-	{
-		cif::mm::structure s(file, 1, { .min_b_factor = 20.f });
-
-		REQUIRE_NOTHROW(s.validate_atoms());
-
-		for (auto a : s.atoms())
-			CHECK(a.get_property_float("B_iso_or_equiv") >= 20.f);
-	}
-
-	SECTION("max-b-factor")
-	{
-		cif::mm::structure s(file, 1, { .max_b_factor = 20.f });
-
-		REQUIRE_NOTHROW(s.validate_atoms());
-
-		for (auto a : s.atoms())
-			CHECK(a.get_property_float("B_iso_or_equiv") <= 20.f);
-	}
-}
-
-TEST_CASE("options_2")
-{
-
-	auto data = R"(
-data_TEST
-# 
-_pdbx_nonpoly_scheme.asym_id         A 
-_pdbx_nonpoly_scheme.ndb_seq_num     1 
-_pdbx_nonpoly_scheme.entity_id       1 
-_pdbx_nonpoly_scheme.mon_id          HEM 
-_pdbx_nonpoly_scheme.pdb_seq_num     1 
-_pdbx_nonpoly_scheme.auth_seq_num    1 
-_pdbx_nonpoly_scheme.pdb_mon_id      HEM 
-_pdbx_nonpoly_scheme.auth_mon_id     HEM 
-_pdbx_nonpoly_scheme.pdb_strand_id   A 
-_pdbx_nonpoly_scheme.pdb_ins_code    . 
-#
-loop_
-_atom_site.id
-_atom_site.auth_asym_id
-_atom_site.label_alt_id
-_atom_site.label_asym_id
-_atom_site.label_atom_id
-_atom_site.label_comp_id
-_atom_site.label_entity_id
-_atom_site.label_seq_id
-_atom_site.type_symbol
-_atom_site.group_PDB
-_atom_site.pdbx_PDB_ins_code
-_atom_site.Cartn_x
-_atom_site.Cartn_y
-_atom_site.Cartn_z
-_atom_site.occupancy
-_atom_site.B_iso_or_equiv
-_atom_site.pdbx_formal_charge
-_atom_site.auth_seq_id
-_atom_site.auth_comp_id
-_atom_site.auth_atom_id
-_atom_site.pdbx_PDB_model_num
-1 A A A CHA HEM 1 . C HETATM ? -5.248 39.769 -0.250 0.75 7.67 ? 1 HEM CHA 1
-3 A A A CHB HEM 1 . C HETATM ? -3.774 36.790 3.280  0.75 7.05 ? 1 HEM CHB 1
-2 A A A CHC HEM 1 . C HETATM ? -2.879 33.328 0.013  0.75 7.69 ? 1 HEM CHC 1
-4 A A A CHD HEM 1 . C HETATM ? -4.342 36.262 -3.536 0.75 8.00 ? 1 HEM CHD 1
-5 A B A CHA HEM 1 . C HETATM ? -5.248 39.769 -0.250 0.25 7.67 ? 1 HEM CHA 1
-6 A B A CHB HEM 1 . C HETATM ? -3.774 36.790 3.280  0.25 7.05 ? 1 HEM CHB 1
-7 A B A CHC HEM 1 . C HETATM ? -2.879 33.328 0.013  0.25 7.69 ? 1 HEM CHC 1
-8 A B A CHD HEM 1 . C HETATM ? -4.342 36.262 -3.536 0.25 8.00 ? 1 HEM CHD 1
-#
-_chem_comp.id               HEM
-_chem_comp.type             NON-POLYMER
-_chem_comp.name             'PROTOPORPHYRIN IX CONTAINING FE'
-_chem_comp.formula          'C34 H32 Fe N4 O4'
-_chem_comp.formula_weight   616.487000
-#
-_pdbx_entity_nonpoly.entity_id   1
-_pdbx_entity_nonpoly.name        'PROTOPORPHYRIN IX CONTAINING FE'
-_pdbx_entity_nonpoly.comp_id     HEM
-#
-_entity.id                 1
-_entity.type               non-polymer
-_entity.pdbx_description   'PROTOPORPHYRIN IX CONTAINING FE'
-_entity.formula_weight     616.487000
-#
-_struct_asym.id                            A
-_struct_asym.entity_id                     1
-_struct_asym.pdbx_blank_PDB_chainid_flag   N
-_struct_asym.pdbx_modified                 N
-_struct_asym.details                       ?
-#
-)"_cf;
-
-	data.front().set_validator(&cif::validator_factory::instance().get("mmcif_pdbx.dic"));
-
-	SECTION("max")
-	{
-		cif::mm::structure s(data, 1, {
-			.occupancy_mode = cif::mm::occupancy_policy::MAX
-		});
-
-		REQUIRE(s.atoms().size() == 4);
-		CHECK(s.atoms().front().get_label_alt_id() == "A");
-	}
-
-	SECTION("min")
-	{
-		cif::mm::structure s(data, 1, {
-			.occupancy_mode = cif::mm::occupancy_policy::MIN
-		});
-
-		REQUIRE(s.atoms().size() == 4);
-		CHECK(s.atoms().front().get_label_alt_id() == "B");
-	}
-
-	SECTION("unoccupied")
-	{
-		cif::mm::structure s(data, 1, {
-			.occupancy_mode = cif::mm::occupancy_policy::UNOCCUPIED
-		});
-
-		CHECK(s.atoms().empty());
-	}
-}

test/reconstruction-test.cpp

@@ -28,7 +28,6 @@
 
 #include <cif++.hpp>
 
-#include <filesystem>
 #include <iostream>
 #include <fstream>
 

test/test-main.cpp

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

test/test-main.hpp

@@ -1,17 +1,17 @@
 /*-
  * SPDX-License-Identifier: BSD-2-Clause
- *
+ * 
  * Copyright (c) 2024 NKI/AVL, Netherlands Cancer Institute
- *
+ * 
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice, this
  *    list of conditions and the following disclaimer
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
  * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
  * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
@@ -26,7 +26,11 @@
 
 #pragma once
 
+#if CATCH22
+#include <catch2/catch.hpp>
+#else
 #include <catch2/catch_all.hpp>
+#endif
 
 #include <filesystem>
 

test/unit-3d-test.cpp

@@ -30,11 +30,6 @@
 
 #include <cif++.hpp>
 
-#if defined(_MSC_VER)
-#pragma warning (disable : 5054)	// warning C5054: operator '&': deprecated between enumerations of different types
-#pragma warning (disable : 4127)	// conditional expression is constant
-#endif
-
 #include <Eigen/Eigenvalues>
 
 // --------------------------------------------------------------------
@@ -95,7 +90,7 @@ TEST_CASE("t1")
 
 	const auto &&[angle, axis] = cif::quaternion_to_angle_axis(q2);
 
-	CHECK_THAT(std::fmod(360 + angle, 360), Catch::Matchers::WithinRel(std::fmod(360 - angle0, 360), 0.01));
+	REQUIRE_THAT(std::fmod(360 + angle, 360), Catch::Matchers::WithinRel(std::fmod(360 - angle0, 360), 0.01));
 
 	for (auto &p : p1)
 		p.rotate(q2);
@@ -121,7 +116,7 @@ TEST_CASE("t2")
 
 	auto &&[angle, axis] = cif::quaternion_to_angle_axis(q);
 
-	CHECK_THAT(angle, Catch::Matchers::WithinRel(45.f, 0.01f));
+	REQUIRE_THAT(angle, Catch::Matchers::WithinRel(45.f, 0.01f));
 }
 
 TEST_CASE("t3")
@@ -145,7 +140,7 @@ TEST_CASE("t3")
 
 	double a = cif::angle(v, p[0], p[1]);
 
-	CHECK_THAT(a, Catch::Matchers::WithinRel(45.f, 0.01f));
+	REQUIRE_THAT(a, Catch::Matchers::WithinRel(45.f, 0.01f));
 }
 
 TEST_CASE("dh_q_0")
@@ -161,7 +156,7 @@ TEST_CASE("dh_q_0")
 	};
 
 	auto a = cif::dihedral_angle(t[0], t[1], t[2], p);
-	CHECK_THAT(a, Catch::Matchers::WithinRel(0.f, 0.01f));
+	REQUIRE_THAT(a, Catch::Matchers::WithinRel(0.f, 0.01f));
 
 	auto q = cif::construct_from_angle_axis(90, axis);
 
@@ -225,7 +220,7 @@ TEST_CASE("dh_q_1")
 		pts[3].rotate(q, pts[2]);
 
 		auto dh = cif::dihedral_angle(pts[0], pts[1], pts[2], pts[3]);
-		CHECK_THAT(dh, Catch::Matchers::WithinRel(angle, 0.1f));
+		REQUIRE_THAT(dh, Catch::Matchers::WithinRel(angle, 0.1f));
 	}
 }
 
@@ -288,9 +283,9 @@ TEST_CASE("dh_q_1")
 
 // 		cif::point p3 = rot * p1;
 
-// 		CHECK_THAT(p2.m_x, Catch::Matchers::WithinRel(p3.m_x, 0.01f));
-// 		CHECK_THAT(p2.m_y, Catch::Matchers::WithinRel(p3.m_y, 0.01f));
-// 		CHECK_THAT(p2.m_z, Catch::Matchers::WithinRel(p3.m_z, 0.01f));
+// 		REQUIRE_THAT(p2.m_x, Catch::Matchers::WithinRel(p3.m_x, 0.01f));
+// 		REQUIRE_THAT(p2.m_y, Catch::Matchers::WithinRel(p3.m_y, 0.01f));
+// 		REQUIRE_THAT(p2.m_z, Catch::Matchers::WithinRel(p3.m_z, 0.01f));
 // 	}
 // }
 
@@ -301,7 +296,7 @@ TEST_CASE("m2q_0a")
 		auto d = cif::kSymopNrTable[i].symop().data();
 
 		Eigen::Matrix3f rot;
-		rot << static_cast<float>(d[0]), static_cast<float>(d[1]), static_cast<float>(d[2]), static_cast<float>(d[3]), static_cast<float>(d[4]), static_cast<float>(d[5]), static_cast<float>(d[6]), static_cast<float>(d[7]), static_cast<float>(d[8]);
+		rot << d[0], d[1], d[2], d[3], d[4], d[5], d[6], d[7], d[8];
 
 		// check to see if this matrix contains a true rotation
 		if (rot * rot.transpose() != Eigen::Matrix3f::Identity() or rot.determinant() != 1)
@@ -316,22 +311,22 @@ TEST_CASE("m2q_0a")
 		p2.rotate(q);
 
 		cif::matrix3x3<float> rot_c({
-			static_cast<float>(d[0]),
-			static_cast<float>(d[1]),
-			static_cast<float>(d[2]),
-			static_cast<float>(d[3]),
-			static_cast<float>(d[4]),
-			static_cast<float>(d[5]),
-			static_cast<float>(d[6]),
-			static_cast<float>(d[7]),
-			static_cast<float>(d[8])
+			rot_c(0, 0) = d[0],
+			rot_c(0, 1) = d[1],
+			rot_c(0, 2) = d[2],
+			rot_c(1, 0) = d[3],
+			rot_c(1, 1) = d[4],
+			rot_c(1, 2) = d[5],
+			rot_c(2, 0) = d[6],
+			rot_c(2, 1) = d[7],
+			rot_c(2, 2) = d[8]
 		});
 
 		cif::point p3 = rot_c * p1;
 
-		CHECK_THAT(p2.m_x, Catch::Matchers::WithinRel(p3.m_x, 0.01f));
-		CHECK_THAT(p2.m_y, Catch::Matchers::WithinRel(p3.m_y, 0.01f));
-		CHECK_THAT(p2.m_z, Catch::Matchers::WithinRel(p3.m_z, 0.01f));
+		REQUIRE_THAT(p2.m_x, Catch::Matchers::WithinRel(p3.m_x, 0.01f));
+		REQUIRE_THAT(p2.m_y, Catch::Matchers::WithinRel(p3.m_y, 0.01f));
+		REQUIRE_THAT(p2.m_z, Catch::Matchers::WithinRel(p3.m_z, 0.01f));
 	}
 }
 
@@ -404,15 +399,15 @@ TEST_CASE("symm_1")
 
 	cif::point f = fractional(p, c);
 
-	CHECK_THAT(f.m_x, Catch::Matchers::WithinRel(0.1f, 0.01f));
-	CHECK_THAT(f.m_y, Catch::Matchers::WithinRel(0.1f, 0.01f));
-	CHECK_THAT(f.m_z, Catch::Matchers::WithinRel(0.1f, 0.01f));
+	REQUIRE_THAT(f.m_x, Catch::Matchers::WithinRel(0.1f, 0.01f));
+	REQUIRE_THAT(f.m_y, Catch::Matchers::WithinRel(0.1f, 0.01f));
+	REQUIRE_THAT(f.m_z, Catch::Matchers::WithinRel(0.1f, 0.01f));
 
 	cif::point o = orthogonal(f, c);
 
-	CHECK_THAT(o.m_x, Catch::Matchers::WithinRel(1.f, 0.01f));
-	CHECK_THAT(o.m_y, Catch::Matchers::WithinRel(1.f, 0.01f));
-	CHECK_THAT(o.m_z, Catch::Matchers::WithinRel(1.f, 0.01f));
+	REQUIRE_THAT(o.m_x, Catch::Matchers::WithinRel(1.f, 0.01f));
+	REQUIRE_THAT(o.m_y, Catch::Matchers::WithinRel(1.f, 0.01f));
+	REQUIRE_THAT(o.m_z, Catch::Matchers::WithinRel(1.f, 0.01f));
 }
 
 TEST_CASE("symm_2")
@@ -440,22 +435,22 @@ TEST_CASE("symm_4")
 
 	// based on 2b8h
 	auto sg = cif::spacegroup(154); // p 32 2 1
-	auto c = cif::cell(107.516f, 107.516f, 338.487f, 90.00f, 90.00f, 120.00f);
+	auto c = cif::cell(107.516, 107.516, 338.487, 90.00, 90.00, 120.00);
 
-	cif::point a{ -8.688f, 79.351f, 10.439f };  // O6 NAG A 500
-	cif::point b{ -35.356f, 33.693f, -3.236f }; // CG2 THR D 400
-	cif::point sb(-6.916f, 79.34f, 3.236f);     // 4_565 copy of b
+	cif::point a{ -8.688, 79.351, 10.439 };  // O6 NAG A 500
+	cif::point b{ -35.356, 33.693, -3.236 }; // CG2 THR D 400
+	cif::point sb(-6.916, 79.34, 3.236);     // 4_565 copy of b
 
-	CHECK_THAT(distance(a, sg(a, c, "1_455"_symop)), Catch::Matchers::WithinRel(static_cast<float>(c.get_a()), 0.01f));
-	CHECK_THAT(distance(a, sg(a, c, "1_545"_symop)), Catch::Matchers::WithinRel(static_cast<float>(c.get_b()), 0.01f));
-	CHECK_THAT(distance(a, sg(a, c, "1_554"_symop)), Catch::Matchers::WithinRel(static_cast<float>(c.get_c()), 0.01f));
+	REQUIRE_THAT(distance(a, sg(a, c, "1_455"_symop)), Catch::Matchers::WithinRel(static_cast<float>(c.get_a()), 0.01f));
+	REQUIRE_THAT(distance(a, sg(a, c, "1_545"_symop)), Catch::Matchers::WithinRel(static_cast<float>(c.get_b()), 0.01f));
+	REQUIRE_THAT(distance(a, sg(a, c, "1_554"_symop)), Catch::Matchers::WithinRel(static_cast<float>(c.get_c()), 0.01f));
 
 	auto sb2 = sg(b, c, "4_565"_symop);
-	CHECK_THAT(sb.m_x, Catch::Matchers::WithinRel(sb2.m_x, 0.01f));
-	CHECK_THAT(sb.m_y, Catch::Matchers::WithinRel(sb2.m_y, 0.01f));
-	CHECK_THAT(sb.m_z, Catch::Matchers::WithinRel(sb2.m_z, 0.01f));
+	REQUIRE_THAT(sb.m_x, Catch::Matchers::WithinRel(sb2.m_x, 0.01f));
+	REQUIRE_THAT(sb.m_y, Catch::Matchers::WithinRel(sb2.m_y, 0.01f));
+	REQUIRE_THAT(sb.m_z, Catch::Matchers::WithinRel(sb2.m_z, 0.01f));
 
-	CHECK_THAT(distance(a, sb2), Catch::Matchers::WithinRel(7.42f, 0.01f));
+	REQUIRE_THAT(distance(a, sb2), Catch::Matchers::WithinRel(7.42f, 0.01f));
 }
 
 // --------------------------------------------------------------------
@@ -471,21 +466,21 @@ TEST_CASE("symm_4wvp_1")
 
 	cif::crystal c(db);
 
-	cif::point p{ -78.722f, 98.528f, 11.994f };
+	cif::point p{ -78.722, 98.528, 11.994 };
 	auto a = s.get_residue("A", 10, "").get_atom_by_atom_id("O");
 
 	auto sp1 = c.symmetry_copy(a.get_location(), "2_565"_symop);
-	CHECK_THAT(sp1.m_x, Catch::Matchers::WithinAbs(p.m_x, 0.5f));
-	CHECK_THAT(sp1.m_y, Catch::Matchers::WithinAbs(p.m_y, 0.5f));
-	CHECK_THAT(sp1.m_z, Catch::Matchers::WithinAbs(p.m_z, 0.5f));
+	REQUIRE_THAT(sp1.m_x, Catch::Matchers::WithinAbs(p.m_x, 0.5f));
+	REQUIRE_THAT(sp1.m_y, Catch::Matchers::WithinAbs(p.m_y, 0.5f));
+	REQUIRE_THAT(sp1.m_z, Catch::Matchers::WithinAbs(p.m_z, 0.5f));
 
 	const auto &[d, sp2, so] = c.closest_symmetry_copy(p, a.get_location());
 
 	REQUIRE(d < 1);
 
-	CHECK_THAT(sp2.m_x, Catch::Matchers::WithinAbs(p.m_x, 0.5f));
-	CHECK_THAT(sp2.m_y, Catch::Matchers::WithinAbs(p.m_y, 0.5f));
-	CHECK_THAT(sp2.m_z, Catch::Matchers::WithinAbs(p.m_z, 0.5f));
+	REQUIRE_THAT(sp2.m_x, Catch::Matchers::WithinAbs(p.m_x, 0.5f));
+	REQUIRE_THAT(sp2.m_y, Catch::Matchers::WithinAbs(p.m_y, 0.5f));
+	REQUIRE_THAT(sp2.m_z, Catch::Matchers::WithinAbs(p.m_z, 0.5f));
 }
 
 TEST_CASE("symm_2bi3_1")
@@ -517,17 +512,17 @@ TEST_CASE("symm_2bi3_1")
 		auto sa1 = c.symmetry_copy(a1.get_location(), cif::sym_op(symm1));
 		auto sa2 = c.symmetry_copy(a2.get_location(), cif::sym_op(symm2));
 
-		CHECK_THAT(cif::distance(sa1, sa2), Catch::Matchers::WithinAbs(dist, 0.5f));
+		REQUIRE_THAT(cif::distance(sa1, sa2), Catch::Matchers::WithinAbs(dist, 0.5f));
 
 		auto pa1 = a1.get_location();
 
 		const auto &[d, p, so] = c.closest_symmetry_copy(pa1, a2.get_location());
 
-		CHECK_THAT(p.m_x, Catch::Matchers::WithinAbs(sa2.m_x, 0.5f));
-		CHECK_THAT(p.m_y, Catch::Matchers::WithinAbs(sa2.m_y, 0.5f));
-		CHECK_THAT(p.m_z, Catch::Matchers::WithinAbs(sa2.m_z, 0.5f));
+		REQUIRE_THAT(p.m_x, Catch::Matchers::WithinAbs(sa2.m_x, 0.5f));
+		REQUIRE_THAT(p.m_y, Catch::Matchers::WithinAbs(sa2.m_y, 0.5f));
+		REQUIRE_THAT(p.m_z, Catch::Matchers::WithinAbs(sa2.m_z, 0.5f));
 
-		CHECK_THAT(d, Catch::Matchers::WithinAbs(dist, 0.5f));
+		REQUIRE_THAT(d, Catch::Matchers::WithinAbs(dist, 0.5f));
 		REQUIRE(so.string() == symm2);
 	}
 }
@@ -564,15 +559,15 @@ TEST_CASE("symm_2bi3_1a")
 		auto sa1 = c.symmetry_copy(p1, cif::sym_op(symm1));
 		auto sa2 = c.symmetry_copy(p2, cif::sym_op(symm2));
 
-		CHECK_THAT(cif::distance(sa1, sa2), Catch::Matchers::WithinAbs(dist, 0.5f));
+		REQUIRE_THAT(cif::distance(sa1, sa2), Catch::Matchers::WithinAbs(dist, 0.5f));
 
 		const auto &[d, p, so] = c.closest_symmetry_copy(p1, p2);
 
-		CHECK_THAT(p.m_x, Catch::Matchers::WithinAbs(sa2.m_x, 0.5f));
-		CHECK_THAT(p.m_y, Catch::Matchers::WithinAbs(sa2.m_y, 0.5f));
-		CHECK_THAT(p.m_z, Catch::Matchers::WithinAbs(sa2.m_z, 0.5f));
+		REQUIRE_THAT(p.m_x, Catch::Matchers::WithinAbs(sa2.m_x, 0.5f));
+		REQUIRE_THAT(p.m_y, Catch::Matchers::WithinAbs(sa2.m_y, 0.5f));
+		REQUIRE_THAT(p.m_z, Catch::Matchers::WithinAbs(sa2.m_z, 0.5f));
 
-		CHECK_THAT(d, Catch::Matchers::WithinAbs(dist, 0.5f));
+		REQUIRE_THAT(d, Catch::Matchers::WithinAbs(dist, 0.5f));
 		REQUIRE(so.string() == symm2);
 	}
 }
@@ -595,7 +590,7 @@ TEST_CASE("symm_3bwh_1")
 
 			const auto &[d, p, so] = c.closest_symmetry_copy(a1.get_location(), a2.get_location());
 
-			CHECK_THAT(d, Catch::Matchers::WithinAbs(distance(a1.get_location(), p), 0.5f));
+			REQUIRE_THAT(d, Catch::Matchers::WithinAbs(distance(a1.get_location(), p), 0.5f));
 		}
 	}
 }
@@ -608,5 +603,5 @@ TEST_CASE("volume_3bwh_1")
 
 	cif::crystal c(db);
 
-	CHECK_THAT(c.get_cell().get_volume(), Catch::Matchers::WithinRel(741009.625f, 0.01f));
+	REQUIRE_THAT(c.get_cell().get_volume(), Catch::Matchers::WithinRel(741009.625f, 0.01f));
 }

test/validate-pdbx-test.cpp

@@ -279,20 +279,6 @@ A 1 5   GLY 5   5   5   GLY GLY A . n
 
 		REQUIRE_FALSE(cif::pdb::is_valid_pdbx_file(f));
 	}
-}
-
-TEST_CASE("extended-dictionary-1")
-{
-	cif::add_file_resource("dssp-extension.dic", gTestDir / "dssp-extension.dic");
-
-	cif::VERBOSE = 2;
-
-	auto f = cif::pdb::read(gTestDir / "1cbs-dssp.cif");
-	CHECK(f.is_valid());
-}
-
-TEST_CASE("brak")
-{
-	auto f = cif::pdb::read(gTestDir / "brak.pdb");
-	CHECK(f.is_valid());
+
+
 }

tools/depends.cmd

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

tools/update-libcifpp-data.in

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