Fix findpcre2 cmake file

last remaining warning
Merge branch 'develop' of github.com:PDB-REDO/libcifpp into develop
2026-06-04 22:14:24 +08:00 · 2025-09-02 13:12:20 +02:00 · 2025-09-02 12:57:08 +02:00 · 2025-09-02 12:54:03 +02:00 · 2025-09-02 12:54:07 +02:00 · 2025-09-02 11:57:21 +02:00
36 changed files with 1393 additions and 985 deletions
--- a/.gitignore
+++ b/.gitignore
@@ -13,3 +13,6 @@ docs/api
 docs/conf.py
 build_ci/
 data/components.cif
+perf.data*
+.cache/
+
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -24,29 +24,25 @@

 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 8.0.1
-	LANGUAGES CXX)
+	VERSION 9.0.0
+	LANGUAGES CXX C)

 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(FetchContent)
 include(ExternalProject)
-
-# FindBoost, take care of it now.
-if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.30)
-	cmake_policy(SET CMP0167 NEW)
-endif()
+include(FetchContent)

 # When building with ninja-multiconfig, build both debug and release by default
 if(CMAKE_GENERATOR STREQUAL "Ninja Multi-Config")
@@ -63,25 +59,23 @@ elseif(MSVC)
 endif()

 # Build documentation?
-option(BUILD_DOCUMENTATION "Build the documentation" OFF)
+set(BUILD_DOCUMENTATION OFF CACHE BOOL "Build the documentation")

 # Optionally build a version to be installed inside CCP4
-option(BUILD_FOR_CCP4 "Build a version to be installed in CCP4")
+set(BUILD_FOR_CCP4 OFF CACHE BOOL "Build a version to be installed in CCP4")

 # Building shared libraries?
 if(NOT(BUILD_FOR_CCP4 AND WIN32))
-	option(BUILD_SHARED_LIBS "Build a shared library instead of a static one" OFF)
+	set(BUILD_SHARED_LIBS OFF CACHE BOOL "Build a shared library instead of a static one")
 endif()

 if(PROJECT_IS_TOP_LEVEL AND NOT BUILD_FOR_CCP4)
 	# Lots of code depend on the availability of the components.cif file
-	option(CIFPP_DOWNLOAD_CCD
-		"Download the CCD file components.cif during installation" ON)
+	set(CIFPP_DOWNLOAD_CCD ON CACHE BOOL "Download the CCD file components.cif during installation")

 	# An optional cron script can be installed to keep the data files up-to-date
 	if(UNIX AND NOT APPLE)
-		option(CIFPP_INSTALL_UPDATE_SCRIPT
-			"Install the script to update CCD and dictionary files" ON)
+		set(CIFPP_INSTALL_UPDATE_SCRIPT ON CACHE BOOL "Install the script to update CCD and dictionary files")
 	endif()
 else()
 	unset(CIFPP_DOWNLOAD_CCD)
@@ -91,14 +85,13 @@ endif()
 # When CCP4 is sourced in the environment, we can recreate the symmetry
 # operations table
 if(EXISTS "$ENV{CCP4}/lib/data/syminfo.lib")
-	option(CIFPP_RECREATE_SYMOP_DATA
-		"Recreate SymOp data table in case it is out of date" ON)
+	set(CIFPP_RECREATE_SYMOP_DATA ON CACHE BOOL "Recreate SymOp data table in case it is out of date")
 endif()

 # CCP4 build
 if(BUILD_FOR_CCP4)
 	if("$ENV{CCP4}" STREQUAL "" OR NOT EXISTS $ENV{CCP4})
-		message(FATAL_ERROR "A CCP4 built was requested but CCP4 was not sourced")
+		message(FATAL_ERROR "cifpp: A CCP4 built was requested but CCP4 was not sourced")
 	else()
 		list(PREPEND CMAKE_MODULE_PATH "$ENV{CCP4}")
 		list(PREPEND CMAKE_PREFIX_PATH "$ENV{CCP4}")
@@ -128,9 +121,6 @@ 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()
@@ -150,51 +140,8 @@ 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)
@@ -221,11 +168,22 @@ if(MSVC)
 	endforeach()
 endif()

-find_package(ZLIB QUIET)
+# 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 "fmt not found, compiler too old, you're out of luck")
+	endif()
+endif()
+
 find_package(Threads)
+include(FindPCRE2)
+find_package(ZLIB QUIET)

 if(NOT ZLIB_FOUND)
-	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)")
+	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()

 # Using Eigen3 is a bit of a thing. We don't want to build it completely since
@@ -239,15 +197,17 @@ if(Eigen3_FOUND AND TARGET Eigen3::Eigen)
 else()
 	# Use ExternalProject since FetchContent always tries to install the result...
 	ExternalProject_Add(my-eigen3
-		GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
-		GIT_TAG 3.4.0
+		URL https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.zip
+		DOWNLOAD_EXTRACT_TIMESTAMP TRUE
+		CONFIGURE_COMMAND ""
+		BUILD_COMMAND ""
 		INSTALL_COMMAND "")
-	
+
 	ExternalProject_Get_Property(my-eigen3 SOURCE_DIR)
 	set(EIGEN_INCLUDE_DIR ${SOURCE_DIR})
 endif()

-message(STATUS "Eigen include dir is ${EIGEN_INCLUDE_DIR}")
+message(STATUS "cifpp: Eigen include dir is ${EIGEN_INCLUDE_DIR}")

 # Create a revision file, containing the current git version info
 include(VersionString)
@@ -351,19 +311,9 @@ 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()
@@ -374,9 +324,14 @@ target_include_directories(
 	cifpp
 	PUBLIC "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
 	"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
-	PRIVATE "${BOOST_REGEX_INCLUDE_DIR}" "${EIGEN_INCLUDE_DIR}")
+	PRIVATE "${EIGEN_INCLUDE_DIR}")

-target_link_libraries(cifpp PUBLIC Threads::Threads ZLIB::ZLIB $<$<TARGET_EXISTS:std::atomic>:std::atomic>)
+target_link_libraries(cifpp
+	PUBLIC Threads::Threads ZLIB::ZLIB $<$<TARGET_EXISTS:std::atomic>:std::atomic> $<BUILD_INTERFACE:pcre2-8>)
+
+if(fmt_FOUND)
+	target_link_libraries(cifpp PUBLIC fmt)
+endif()

 if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
 	target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
@@ -390,7 +345,7 @@ if(CIFPP_DOWNLOAD_CCD)
 		file(SIZE ${COMPONENTS_CIF} CCD_FILE_SIZE)

 		if(CCD_FILE_SIZE EQUAL 0)
-			message(STATUS "Removing empty ${COMPONENTS_CIF} file")
+			message(STATUS "cifpp: Removing empty ${COMPONENTS_CIF} file")
 			file(REMOVE "${COMPONENTS_CIF}")
 		endif()
 	endif()
@@ -429,7 +384,7 @@ if(CIFPP_DOWNLOAD_CCD)

 		if(CCD_FETCH_STATUS_CODE)
 			message(
-				FATAL_ERROR "Error trying to download CCD file: ${CCD_FETCH_STATUS}")
+				FATAL_ERROR "cifpp: Error trying to download CCD file: ${CCD_FETCH_STATUS}")
 		endif()
 	endif()
 endif()
@@ -493,7 +448,7 @@ file(GLOB OLD_CONFIG_FILES

 if(OLD_CONFIG_FILES)
 	message(
-		STATUS "Installation will remove old config files: ${OLD_CONFIG_FILES}")
+		STATUS "cifpp: Installation will remove old config files: ${OLD_CONFIG_FILES}")
 	install(CODE "file(REMOVE ${OLD_CONFIG_FILES})")
 endif()

@@ -514,6 +469,7 @@ 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
@@ -559,7 +515,7 @@ if(CIFPP_INSTALL_UPDATE_SCRIPT)
 			PERMISSIONS OWNER_EXECUTE OWNER_READ GROUP_EXECUTE GROUP_READ WORLD_EXECUTE
 			WORLD_READ)
 	else()
-		message(FATAL_ERROR "Don't know where to install the update script")
+		message(FATAL_ERROR "cifpp: Don't know where to install the update script")
 	endif()

 	# a config file, to make it complete
@@ -573,7 +529,7 @@ if(CIFPP_INSTALL_UPDATE_SCRIPT)
 		install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf
 			DESTINATION ${CMAKE_INSTALL_SYSCONFDIR})
 		install(
-			CODE "message(\"A configuration file has been written to ${CIFPP_ETC_DIR}/libcifpp.conf, please edit this file to enable automatic updates\")"
+			CODE "message(\"cifpp: A configuration file has been written to ${CIFPP_ETC_DIR}/libcifpp.conf, please edit this file to enable automatic updates\")"
 		)

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

 ### Building

--- a/9
+++ b/9
@@ -1,3 +1,12 @@
+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
--- a/cmake/FindPCRE2.cmake
+++ b/cmake/FindPCRE2.cmake
@@ -0,0 +1,27 @@
+set(PCRE2_USE_STATIC_LIBS ON)
+
+# The cmake config files for pcre2 are broken
+
+include(FindPkgConfig)
+
+if(PKG_CONFIG_FOUND)
+	pkg_check_modules(PCRE2 IMPORTED_TARGET libpcre2-8)
+
+	if(PCRE2_FOUND)
+		message(STATUS "Using pcre2 found using pkg-config")
+
+		add_library(pcre2-8 ALIAS PkgConfig::PCRE2)
+	endif()
+endif()
+
+if(NOT PCRE2_FOUND)
+	find_path(PCRE2_INCLUDEDIR NAMES pcre2.h HINTS "C:/Program Files (x86)/PCRE2/include" REQUIRED)
+	find_library(PCRE2_LIBRARY NAMES pcre2-8-static 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)
+	# target_link_libraries(pcre2-8 INTERFACE ${PCRE2_LIBRARY})
+	set_target_properties(pcre2-8 PROPERTIES IMPORTED_LOCATION ${PCRE2_LIBRARY})
+	set_target_properties(pcre2-8 PROPERTIES IMPORTED_IMPLIB ${PCRE2_LIBRARY})
+endif()
--- a/cmake/cifpp-config.cmake.in
+++ b/cmake/cifpp-config.cmake.in
@@ -8,5 +8,8 @@ include(CMakeFindDependencyMacro)

 find_dependency(Threads)
 find_dependency(ZLIB REQUIRED)
+if(@REQUIRE_FMT@)
+    find_dependency(fmt REQUIRED)
+endif()

 check_required_components(cifpp)
--- a/cmake/test-rx.cpp
+++ b/cmake/test-rx.cpp
@@ -1,18 +0,0 @@
-// See: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=86164
-
-#include <iostream>
-#include <regex>
-
-int main()
-{
-	std::string s(100'000, '*');
-	std::smatch m;
-	std::regex r("^(.*?)$");
-
-	std::regex_search(s, m, r);
-
-	std::cout << s.substr(0, 10) << '\n';
-	std::cout << m.str(1).substr(0, 10) << '\n';
-
-	return 0;
-}
--- a/include/cif++/category.hpp
+++ b/include/cif++/category.hpp
@@ -157,7 +157,7 @@ class category
 		emplace(std::forward<row_initializer>(rows));
 	}

-	category(const category &rhs);   ///< Copy constructor
+	category(const category &rhs); ///< Copy constructor

 	category(category &&rhs) noexcept ///< Move constructor
 	{
@@ -223,6 +223,11 @@ class category
 	/// @return Returns true is all validations pass
 	bool validate_links() const;

+	/**
+	 * @brief Strip removes items from this category that are invalid according to the assigned validator
+	 */
+	void strip();
+
 	/// @brief Equality operator, returns true if @a rhs is equal to this
 	/// @param rhs The object to compare with
 	/// @return True if the data contained is equal
@@ -327,8 +332,16 @@ class category
 	// --------------------------------------------------------------------
 	// A category can have a key, as defined by the validator/dictionary

+	/// @brief The type of an element of the key_type
+	struct key_element_type
+	{
+		std::string name;         ///< Name of the item
+		std::string value;        ///< Value to be found
+		bool may_be_null = false; ///< If true, value should be same or empty
+	};
+
 	/// @brief The key type
-	using key_type = row_initializer;
+	using key_type = std::vector<key_element_type>;

 	/// @brief Return a row_handle for the row specified by \a key
 	/// @param key The value for the key, items specified in the dictionary should have a value
@@ -1244,7 +1257,7 @@ class category
 		{
 		}

-// TODO: NEED TO FIX THIS!
+		// TODO: NEED TO FIX THIS!
 		category *linked;
 		const link_validator *v;
 	};
--- a/include/cif++/compound.hpp
+++ b/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;
@@ -290,6 +290,13 @@ class compound_factory

 	void report_missing_compound(std::string_view compound_id);

+	bool get_report_missing() const { return m_report_missing; }
+
+	void set_report_missing(bool report)
+	{
+		m_report_missing = report;
+	}
+
  private:
 	compound_factory();

@@ -301,6 +308,7 @@ class compound_factory
 	static bool s_use_thread_local_instance;

 	std::shared_ptr<compound_factory_impl> m_impl;
+	bool m_report_missing = true;
 };

 // --------------------------------------------------------------------
--- a/include/cif++/condition.hpp
+++ b/include/cif++/condition.hpp
@@ -27,6 +27,7 @@
 #pragma once

 #include "cif++/row.hpp"
+#include "cif++/format.hpp"

 #include <cassert>
 #include <concepts>
@@ -49,49 +50,49 @@
 * @code {.cpp}
 * cif::condition c = cif::key("id") == 1;
 * @endcode
- * 
+ *
 * That will find rows where the ID item contains the number 1. If
 * using cif::key is a bit too much typing, you can also write:
- * 
+ *
 * @code{.cpp}
 * using namespace cif::literals;
- * 
+ *
 * cif::condition c2 = "id"_key == 1;
 * @endcode
- * 
+ *
 * Now if you want both ID = 1 and ID = 2 in the result:
- * 
+ *
 * @code{.cpp}
 * auto c3 = "id"_key == 1 or "id"_key == 2;
 * @endcode
- * 
+ *
 * There are some special values you can use. To find rows with item that
 * do not have a value:
- * 
+ *
 * @code{.cpp}
 * auto c4 = "type"_key == cif::null;
- * @endcode 
- * 
+ * @endcode
+ *
 * Of if it should not be NULL:
- * 
+ *
 * @code{.cpp}
 * auto c5 = "type"_key != cif::null;
- * @endcode 
- * 
+ * @endcode
+ *
 * There's even a way to find all records:
- * 
+ *
 * @code{.cpp}
 * auto c6 = cif::all;
 * @endcode
- * 
+ *
 * And when you want to search for any item containing the value 'foo':
- * 
+ *
 * @code{.cpp}
 * auto c7 = cif::any == "foo";
- * @endcode 
- * 
+ * @endcode
+ *
 * All these conditions can be chained together again:
- * 
+ *
 * @code{.cpp}
 * auto c8 = std::move(c3) and std::move(c5);
 * @endcode
@@ -106,7 +107,7 @@ namespace cif

 /**
 * @brief Get the items that can be used as key in conditions for a category
- * 
+ *
 * @param cat The category whose items to return
 * @return iset The set of key item names
 */
@@ -115,7 +116,7 @@ iset get_category_fields(const category &cat);

 /**
 * @brief Get the items that can be used as key in conditions for a category
- * 
+ *
 * @param cat The category whose items to return
 * @return iset The set of key field names
 */
@@ -123,7 +124,7 @@ iset get_category_items(const category &cat);

 /**
 * @brief Get the item index for item @a col in category @a cat
- * 
+ *
 * @param cat The category
 * @param col The name of the item
 * @return uint16_t The index
@@ -132,7 +133,7 @@ uint16_t get_item_ix(const category &cat, std::string_view col);

 /**
 * @brief Return whether the item @a col in category @a cat has a primitive type of *uchar*
- * 
+ *
 * @param cat The category
 * @param col The item name
 * @return true If the primitive type is of type *uchar*
@@ -175,14 +176,13 @@ namespace detail
 class condition
 {
  public:
-
 	/** @cond */
 	using condition_impl = detail::condition_impl;
 	/** @endcond */

 	/**
 	 * @brief Construct a new, empty condition object
-	 * 
+	 *
 	 */
 	condition()
 		: m_impl(nullptr)
@@ -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
@@ -752,28 +752,9 @@ namespace detail
 				delete sub;
 		}

-		condition_impl *prepare(const category &c) override
-		{
-			for (auto &sub : m_sub)
-				sub = sub->prepare(c);
-			return this;
-		}
+		condition_impl *prepare(const category &c) override;

-		bool test(row_handle r) const override
-		{
-			bool result = true;
-
-			for (auto sub : m_sub)
-			{
-				if (sub->test(r))
-					continue;
-
-				result = false;
-				break;
-			}
-
-			return result;
-		}
+		bool test(row_handle r) const override;

 		void str(std::ostream &os) const override
 		{
@@ -820,6 +801,7 @@ namespace detail
 		static condition_impl *combine_equal(std::vector<and_condition_impl *> &subs, or_condition_impl *oc);

 		std::vector<condition_impl *> m_sub;
+		std::optional<row_handle> m_single; // Potential result of index lookup
 	};

 	struct or_condition_impl : public condition_impl
@@ -977,9 +959,9 @@ inline condition operator or(condition &&a, condition &&b)
 			if (ci->m_item_name == ce->m_item_name)
 				return condition(new detail::key_equals_or_empty_condition_impl(ci));
 		}
-		
+
 		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);
@@ -997,9 +979,9 @@ 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);
@@ -1019,7 +1001,7 @@ inline condition operator or(condition &&a, condition &&b)

 /**
 * @brief A helper class to make it possible to search for empty items (NULL)
- * 
+ *
 * @code{.cpp}
 * "id"_key == cif::empty_type();
 * @endcode
@@ -1031,7 +1013,7 @@ struct empty_type

 /**
 * @brief A helper to make it possible to have conditions like
- * 
+ *
 * @code{.cpp}
 * "id"_key == cif::null;
 * @endcode
@@ -1041,14 +1023,14 @@ inline constexpr empty_type null = empty_type();

 /**
 * @brief Class to use in creating conditions, creates a reference to a item or item
- * 
+ *
 */
 struct key
 {
 	/**
 	 * @brief Construct a new key object using @a item_name as name
-	 * 
-	 * @param item_name 
+	 *
+	 * @param item_name
 	 */
 	explicit key(const std::string &item_name)
 		: m_item_name(item_name)
@@ -1057,8 +1039,8 @@ struct key

 	/**
 	 * @brief Construct a new key object using @a item_name as name
-	 * 
-	 * @param item_name 
+	 *
+	 * @param item_name
 	 */
 	explicit key(const char *item_name)
 		: m_item_name(item_name)
@@ -1067,8 +1049,8 @@ struct key

 	/**
 	 * @brief Construct a new key object using @a item_name as name
-	 * 
-	 * @param item_name 
+	 *
+	 * @param item_name
 	 */
 	explicit key(std::string_view item_name)
 		: m_item_name(item_name)
@@ -1090,7 +1072,8 @@ 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)
 {
-	return condition(new detail::key_equals_number_condition_impl(key.m_item_name, v));
+	// TODO: change key_equals_etc... to use std::variant<double,int64_t> or something
+	return condition(new detail::key_equals_number_condition_impl(key.m_item_name, static_cast<double>(v)));
 }

 /**
@@ -1137,13 +1120,10 @@ 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; },
-		s.str()));
+		cif::format(" > {}", v)));
 }

 /**
@@ -1152,13 +1132,10 @@ 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; },
-		s.str()));
+		cif::format(" >= {}", v)));
 }

 /**
@@ -1167,13 +1144,10 @@ 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; },
-		s.str()));
+		cif::format(" < {}", v)));
 }

 /**
@@ -1182,13 +1156,10 @@ 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; },
-		s.str()));
+		cif::format(" <= {}", v)));
 }

 /**
@@ -1196,13 +1167,10 @@ 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; },
-		s.str()));
+		cif::format(" > {}", v)));
 }

 /**
@@ -1210,13 +1178,10 @@ 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; },
-		s.str()));
+		cif::format(" >= {}", v)));
 }

 /**
@@ -1224,13 +1189,10 @@ 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; },
-		s.str()));
+		cif::format(" < {}", v)));
 }

 /**
@@ -1238,13 +1200,10 @@ 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; },
-		s.str()));
+		cif::format(" <= {}", v)));
 }

 /**
@@ -1345,7 +1304,7 @@ 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
--- a/include/cif++/datablock.hpp
+++ b/include/cif++/datablock.hpp
@@ -128,15 +128,6 @@ 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
@@ -146,6 +137,14 @@ 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();
+
 	// --------------------------------------------------------------------

 	/**
@@ -184,6 +183,15 @@ 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
--- a/include/cif++/format.hpp
+++ b/include/cif++/format.hpp
@@ -26,138 +26,28 @@

 #pragma once

+#if __has_include(<format>)
+#include <format>
+#define USE_STD_FORMAT 1
+#else
+#include <fmt/format.h>
+#endif
+
 #include <string>

 /**  \file format.hpp
 * 
- * File containing a basic reimplementation of boost::format
- * but then a bit more simplistic. Still this allowed me to move my code
- * from using boost::format to something without external dependency easily.
+ * Now using cif::format instead of a home grown rip off
 */

 namespace cif
 {

-namespace detail
-{
-	template <typename T>
-	struct to_varg
-	{
-		using type = T;
-
-		to_varg(const T &v)
-			: m_value(v)
-		{
-		}
-
-		type operator*() { return m_value; }
-
-		T m_value;
-	};
-
-	template <>
-	struct to_varg<const char *>
-	{
-		using type = const char *;
-
-		to_varg(const char *v)
-			: m_value(v)
-		{
-		}
-
-		type operator*() { return m_value.c_str(); }
-
-		std::string m_value;
-	};
-
-	template <>
-	struct to_varg<std::string>
-	{
-		using type = const char *;
-
-		to_varg(const std::string &v)
-			: m_value(v)
-		{
-		}
-
-		type operator*() { return m_value.c_str(); }
-
-		std::string m_value;
-	};
-
-} // namespace
-
-/** @cond */
-
-template <typename... Args>
-class format_plus_arg
-{
-  public:
-	using args_vector_type = std::tuple<detail::to_varg<Args>...>;
-	using vargs_vector_type = std::tuple<typename detail::to_varg<Args>::type...>;
-
-	format_plus_arg(const format_plus_arg &) = delete;
-	format_plus_arg &operator=(const format_plus_arg &) = delete;
-
-
-	format_plus_arg(std::string_view fmt, Args... args)
-		: m_fmt(fmt)
-		, m_args(std::forward<Args>(args)...)
-	{
-		auto ix = std::make_index_sequence<sizeof...(Args)>();
-		copy_vargs(ix);
-	}
-
-	std::string str()
-	{
-		char buffer[1024];
-		std::string::size_type r = std::apply(snprintf, std::tuple_cat(std::make_tuple(buffer, sizeof(buffer), m_fmt.c_str()), m_vargs));
-		return { buffer, r };
-	}
-
-	friend std::ostream &operator<<(std::ostream &os, const format_plus_arg &f)
-	{
-		char buffer[1024];
-		std::string::size_type r = std::apply(snprintf, std::tuple_cat(std::make_tuple(buffer, sizeof(buffer), f.m_fmt.c_str()), f.m_vargs));
-		os.write(buffer, r);
-		return os;
-	}
-
-  private:
-
-	template <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)...);
-}
+#if USE_STD_FORMAT
+using std::format;
+#else
+using fmt::format;
+#endif

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

 #pragma once

--- a/include/cif++/item.hpp
+++ b/include/cif++/item.hpp
@@ -250,6 +250,8 @@ class item
 			return value();
 	}

+	auto operator<=>(const item &rhs) const = default;
+
  private:
 	std::string_view m_name;
 	std::string m_value;
--- a/include/cif++/model.hpp
+++ b/include/cif++/model.hpp
@@ -106,8 +106,6 @@ class atom

 		atom_impl(const atom_impl &i) = default;

-		void prefetch();
-
 		int compare(const atom_impl &b) const;

 		// bool getAnisoU(float anisou[6]) const;
@@ -345,7 +343,7 @@ 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("auth_alt_id"); }        ///< Return the auth_alt_id property
+	std::string get_auth_alt_id() const { return get_property("pdbx_auth_alt_id"); }   ///< Return the auth_alt_id property
 	std::string get_auth_comp_id() const { return get_property("auth_comp_id"); }      ///< Return the auth_comp_id property
 	std::string get_pdb_ins_code() const { return get_property("pdbx_PDB_ins_code"); } ///< Return the pdb_ins_code property

@@ -481,8 +479,8 @@ class residue
 		, m_compound_id(compoundID)
 		, m_asym_id(asymID)
 		, m_seq_id(seqID)
-		, m_auth_asym_id(authAsymID)
-		, m_auth_seq_id(authSeqID)
+		, m_pdb_strand_id(authAsymID)
+		, m_pdb_seq_num(authSeqID)
 		, m_pdb_ins_code(pdbInsCode)
 	{
 	}
@@ -509,9 +507,9 @@ class residue
 	const std::string &get_asym_id() const { return m_asym_id; } ///< Return the asym_id
 	int get_seq_id() const { return m_seq_id; }                  ///< Return the seq_id

-	const std::string get_auth_asym_id() const { return m_auth_asym_id; } ///< Return the auth_asym_id
-	const std::string get_auth_seq_id() const { return m_auth_seq_id; }   ///< Return the auth_seq_id
-	std::string get_pdb_ins_code() const { return m_pdb_ins_code; }       ///< Return the pdb_ins_code
+	const std::string get_pdb_strand_id() const { return m_pdb_strand_id; } ///< Return the pdb_strand_id
+	const std::string get_pdb_seq_num() const { return m_pdb_seq_num; }     ///< Return the pdb_seq_num
+	std::string get_pdb_ins_code() const { return m_pdb_ins_code; }         ///< Return the pdb_ins_code

 	const std::string &get_compound_id() const { return m_compound_id; } ///< Return the compound_id
 	void set_compound_id(const std::string &id) { m_compound_id = id; }  ///< Set the compound_id to @a id
@@ -580,7 +578,7 @@ 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_auth_seq_id == rhs.m_auth_seq_id);
+								   m_pdb_seq_num == rhs.m_pdb_seq_num);
 	}

 	/// @brief Create a new atom and add it to the list
@@ -594,7 +592,7 @@ class residue
 	structure *m_structure = nullptr;
 	std::string m_compound_id, m_asym_id;
 	int m_seq_id = 0;
-	std::string m_auth_asym_id, m_auth_seq_id, m_pdb_ins_code;
+	std::string m_pdb_strand_id, m_pdb_seq_num, m_pdb_ins_code;
 	std::vector<atom> m_atoms;
 	/** @endcond */
 };
@@ -714,15 +712,15 @@ class polymer : public std::vector<monomer>

 	structure *get_structure() const { return m_structure; } ///< Return the structure

-	std::string get_asym_id() const { return m_asym_id; }           ///< Return the asym_id
-	std::string get_auth_asym_id() const { return m_auth_asym_id; } ///< Return the PDB chain ID, actually
-	std::string get_entity_id() const { return m_entity_id; }       ///< Return the entity_id
+	std::string get_asym_id() const { return m_asym_id; }             ///< Return the asym_id
+	std::string get_pdb_strand_id() const { return m_pdb_strand_id; } ///< Return the PDB chain ID, actually
+	std::string get_entity_id() const { return m_entity_id; }         ///< Return the entity_id

  private:
 	structure *m_structure;
 	std::string m_entity_id;
 	std::string m_asym_id;
-	std::string m_auth_asym_id;
+	std::string m_pdb_strand_id;
 };

 // --------------------------------------------------------------------
@@ -760,7 +758,7 @@ class sugar : public residue
 	int num() const
 	{
 		int result;
-		auto r = std::from_chars(m_auth_seq_id.data(), m_auth_seq_id.data() + m_auth_seq_id.length(), result);
+		auto r = std::from_chars(m_pdb_seq_num.data(), m_pdb_seq_num.data() + m_pdb_seq_num.length(), result);
 		if ((bool)r.ec)
 			throw std::runtime_error("The auth_seq_id should be a number for a sugar");
 		return result;
@@ -859,19 +857,38 @@ class branch : public std::vector<sugar>
 	std::string m_asym_id, m_entity_id;
 };

-// --------------------------------------------------------------------
-
-/// \brief A still very limited set of options for reading structures
-enum class StructureOpenOptions
+/** @brief Enumeration for controlling atom selection based on occupancy. */
+enum class occupancy_policy
 {
-	SkipHydrogen = 1 << 0 ///< Do not include hydrogen atoms in the structure object
+	/** @brief Include all atoms regardless of their occupancy factor. */
+	ALL = 0,
+
+	/** @brief Select only alternate atoms with the maximum occupancy factor.
+	 * If multiple atoms have the same maximum occupancy, choose the one with the minimum B-factor.
+	 * If multiple atoms share both the maximum occupancy and the minimum B-factor, select the first encountered atom.
+	 */
+	MAX = 1,
+
+	/** @brief Select only alternate atoms with the minimum occupancy factor.
+	 * Similar to MAX, if multiple atoms have the same minimum occupancy, choose the one with the minimum B-factor.
+	 * If multiple atoms share both the minimum occupancy and the minimum B-factor, select the first encountered atom.
+	 */
+	MIN = 2,
+
+	/** @brief Exclude all atoms with an occupancy factor greater than zero. */
+	UNOCCUPIED = 3
 };

-/// \brief A way to combine two options. Not very useful as there is only one...
-constexpr inline bool operator&(StructureOpenOptions a, StructureOpenOptions b)
+struct structure_open_options
 {
-	return static_cast<int>(a) bitand static_cast<int>(b);
-}
+	bool skip_hydrogen = false;                              ///< Do not include hydrogen atoms in the structure object
+	bool skip_hetatom = false;                               ///< Do not include HET atoms in the structure object
+	bool skip_water = false;                                 ///< Do not include water atoms in the structure object
+	occupancy_policy occupancy_mode = occupancy_policy::ALL; ///< By default, the occupancy policy is set to occupancy_policy::ALL
+	std::vector<std::string> asyms;                          ///< The asyms to load, if empty load all
+	std::optional<float> min_b_factor;                       ///< Only load atoms with at least this b_factor
+	std::optional<float> max_b_factor;                       ///< Only load atoms with at most this b_factor
+};

 // --------------------------------------------------------------------

@@ -885,10 +902,10 @@ class structure
 {
  public:
 	/// \brief Read the structure from cif::file @a p
-	structure(file &p, std::size_t modelNr = 1, StructureOpenOptions options = {});
+	structure(file &p, std::size_t modelNr = 1, structure_open_options options = {});

 	/// \brief Load the structure from already parsed mmCIF data in @a db
-	structure(datablock &db, std::size_t modelNr = 1, StructureOpenOptions options = {});
+	structure(datablock &db, std::size_t modelNr = 1, structure_open_options options = {});

 	/** @cond */
 	structure(structure &&s) = default;
@@ -1118,7 +1135,7 @@ class structure
 	friend polymer;
 	friend residue;

-	void load_atoms_for_model(StructureOpenOptions options);
+	void load_atoms_for_model(structure_open_options options);

 	std::string insert_compound(const std::string &compoundID, bool is_entity);

--- a/include/cif++/pdb.hpp
+++ b/include/cif++/pdb.hpp
@@ -104,6 +104,27 @@ 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.
--- a/include/cif++/utilities.hpp
+++ b/include/cif++/utilities.hpp
@@ -53,6 +53,7 @@
 #pragma warning(disable : 4068) // unknown pragma
 #pragma warning(disable : 4100) // unreferenced formal parameter
 #pragma warning(disable : 4101) // unreferenced local variable
+#pragma warning(disable : 4702) // unreachable code (too bad, this one. Happens in for loops)
 #define _SILENCE_CXX17_CODECVT_HEADER_DEPRECATION_WARNING 1
 #endif

--- a/rsrc/mmcif_pdbx.dic
+++ b/rsrc/mmcif_pdbx.dic
@@ -9,7 +9,7 @@ _datablock.description
 #
 _dictionary.title         mmcif_pdbx.dic
 _dictionary.datablock_id  mmcif_pdbx.dic
-_dictionary.version       5.403
+_dictionary.version       5.404
 #
 loop_
 _dictionary_history.version
@@ -3292,6 +3292,18 @@ Changes (ep):
  + Add 'M' to _em_software.name enumeration.
 ;
  
+5.404  2025-06-01  
+;
+Changes (ep):
+  + Add DeepEMhancer to _em_software.name enumeration
+  + Add HexAuFoil to _em_sample_support.grid_type enumeration
+  + Add "PSI JUNGFRAU 9M" and "PSI JUNGFRAU 10M" detectors to
+    _diffrn_detector.type
+  + Add "N6-benzoyllysine", "N6-isonicotinyllysine",
+    and "N6-methacryllysine" to enumeration list for
+    _pdbx_chem_comp_pcm.type and _pdbx_modification_feature.type
+;
+  
 #
 loop_
 _sub_category.id
@@ -3838,13 +3850,13 @@ _pdbx_dictionary_component.datablock_id
 _pdbx_dictionary_component.dictionary_component_id
 _pdbx_dictionary_component.title
 _pdbx_dictionary_component.version
-mmcif_pdbx-base.dic                     mmcif_pdbx-base.dic                     "mmCIF/PDBx base dictionary"                   0.39   
+mmcif_pdbx-base.dic                     mmcif_pdbx-base.dic                     "mmCIF/PDBx base dictionary"                   0.40   
 mmcif_xfel_extensions-v3.dic            mmcif_xfel_extensions-v3.dic            "PDBx/mmCIF XFELDictionary License Extension"  0.0.2  
 mmcif_pdbx_audit_support-extension.dic  mmcif_pdbx_audit_support-extension.dic  "mmCIF/PDBx Audit support extension"           0.24   
 mmcif_pdbx_sifts.dic                    mmcif_pdbx_sifts.dic                    "PDBx/mmCIF Dictionary Sifts Extension"        0.0.2  
 mmcif_pdbx_license.dic                  mmcif_pdbx_license.dic                  "PDBx/mmCIF Dictionary License Extension"      0.0.1  
 initial-model-extension.dic             initial-model-extension.dic             "PDBx/mmCIF Initial model extension"           0.10   
-ptm-extension.dic                       ptm-extension.dic                       "PDBx/mmCIF PTM extension"                     0.10   
+ptm-extension.dic                       ptm-extension.dic                       "PDBx/mmCIF PTM extension"                     0.11   
 #
 loop_
 _pdbx_dictionary_component_history.dictionary_component_id
@@ -4181,6 +4193,15 @@ Changes (ep):
  + Add 'M' to _em_software.name enumeration.
 ;
  
+mmcif_pdbx-base.dic                     0.40   2025-06-01  
+;
+Changes (ep):
+  + Add DeepEMhancer to _em_software.name enumeration
+  + Add HexAuFoil to _em_sample_support.grid_type enumeration
+  + Add "PSI JUNGFRAU 9M" and "PSI JUNGFRAU 10M" detectors to
+    _diffrn_detector.type
+;
+  
 mmcif_xfel_extensions-v3.dic            0.0.1  2023-05-31  
 ;
 Changes (ep):
@@ -4606,6 +4627,16 @@ ptm-extension.dic                       0.10   2024-11-26
      _pdbx_modification_feature.type
 ;
  
+ptm-extension.dic                       0.11   2024-06-01  
+;
+  Changes (dh/ep)
+  + added "N6-benzoyllysine", "N6-isonicotinyllysine",
+    and "N6-methacryllysine" 
+    type to enumeration list for
+      _pdbx_chem_comp_pcm.type
+      _pdbx_modification_feature.type
+;
+  
 #
 loop_
 _pdbx_item_linked_group.category_id
@@ -21911,6 +21942,8 @@ save__diffrn_detector.type
     "_diffrn_detector.type"  "PSI JUNGFRAU 1M"                  PIXEL  
     "_diffrn_detector.type"  "PSI JUNGFRAU 4M"                  PIXEL  
     "_diffrn_detector.type"  "PSI JUNGFRAU 8M"                  PIXEL  
+     "_diffrn_detector.type"  "PSI JUNGFRAU 9M"                  PIXEL  
+     "_diffrn_detector.type"  "PSI JUNGFRAU 10M"                 PIXEL  
     "_diffrn_detector.type"  "PSI JUNGFRAU 16M"                 PIXEL  
     "_diffrn_detector.type"  "PSI PILATUS 6M"                   PIXEL  
     "_diffrn_detector.type"  "RAYONIX MX-225"                   CCD  
@@ -117761,6 +117794,7 @@ save__em_sample_support.grid_type
     "_em_sample_support.grid_type"  "Quantifoil Active R2/1"                    .  
     "_em_sample_support.grid_type"  "Quantifoil Active R1.6/0.9"                .  
     "_em_sample_support.grid_type"  "Quantifoil Active R1.2/0.8"                .  
+     "_em_sample_support.grid_type"  HexAuFoil                                   .  
     "_em_sample_support.grid_type"  UltrAuFoil                                  .  
     "_em_sample_support.grid_type"  "UltrAuFoil R0./1"                          .  
     "_em_sample_support.grid_type"  "UltrAuFoil R1.2/1.3"                       .  
@@ -126147,6 +126181,7 @@ save__em_software.name
     "_em_software.name"  CTFPHASEFLIP                    .  
     "_em_software.name"  CTFTILT                         .  
     "_em_software.name"  DE-IM                           .  
+     "_em_software.name"  DeepEMhancer                    .  
     "_em_software.name"  DIALS                           .  
     "_em_software.name"  DigitalMicrograph               .  
     "_em_software.name"  DireX                           .  
@@ -168351,6 +168386,9 @@ save__pdbx_chem_comp_pcm.type
     Methylsulfanylation                                .  
     Methylsulfation                                    .  
     Myristoylation                                     .  
+     N6-benzoyllysine                                   .  
+     N6-isonicotinyllysine                              .  
+     N6-methacryllysine                                 .  
     "N-pyruvic acid 2-iminylation"                     .  
     N-methylcarbamoylation                             .  
     Nitration                                          .  
@@ -169337,6 +169375,9 @@ save__pdbx_modification_feature.type
     Methylsulfanylation                                .  
     Methylsulfation                                    .  
     Myristoylation                                     .  
+     N6-benzoyllysine                                   .  
+     N6-isonicotinyllysine                              .  
+     N6-methacryllysine                                 .  
     "N-pyruvic acid 2-iminylation"                     .  
     N-methylcarbamoylation                             .  
     Nitration                                          .  
--- a/src/category.cpp
+++ b/src/category.cpp
@@ -92,7 +92,7 @@ class row_comparator
 		return d;
 	}

-	int operator()(const category &cat, const row_initializer &a, const row *b) const
+	int operator()(const category &cat, const category::key_type &a, const row *b) const
 	{
 		assert(b);

@@ -105,10 +105,11 @@ class row_comparator
 		{
 			assert(ai != a.end());

-			std::string_view ka = ai->value();
+			std::string_view ka = ai->value;
 			std::string_view kb = rhb[k].text();

-			d = f(ka, kb);
+			if (not (ai->may_be_null and rhb[k].empty()))
+				d = f(ka, kb);

 			if (d != 0)
 				break;
@@ -142,7 +143,7 @@ class category_index
 	}

 	row *find(const category &cat, row *k) const;
-	row *find_by_value(const category &cat, row_initializer k) const;
+	row *find_by_value(const category &cat, const category::key_type &k) const;

 	void insert(category &cat, row *r);
 	void erase(category &cat, row *r);
@@ -352,19 +353,19 @@ row *category_index::find(const category &cat, row *k) const
 	return r ? r->m_row : nullptr;
 }

-row *category_index::find_by_value(const category &cat, row_initializer k) const
+row *category_index::find_by_value(const category &cat, const category::key_type &k) const
 {
 	// sort the values in k first

-	row_initializer k2;
+	category::key_type k2;
 	for (auto &f : cat.key_item_indices())
 	{
 		auto fld = cat.get_item_name(f);

 		auto ki = find_if(k.begin(), k.end(), [&fld](auto &i)
-			{ return i.name() == fld; });
+			{ return i.name == fld; });
 		if (ki == k.end())
-			k2.emplace_back(fld, "");
+			k2.emplace_back(std::string{ fld }, "");
 		else
 			k2.emplace_back(*ki);
 	}
@@ -914,6 +915,24 @@ bool category::validate_links() const
 	return result;
 }

+void category::strip()
+{
+	std::vector<std::string> to_be_removed;
+
+	for (auto &item : m_items)
+	{
+		if (item.m_validator == nullptr)
+			to_be_removed.push_back(item.m_name);
+	}
+
+	for (auto item : to_be_removed)
+	{
+		if (cif::VERBOSE > 0)
+			std::clog << "Dropping item " << m_name << '.' << item << '\n';
+		remove_item(item);
+	}
+}
+
 // --------------------------------------------------------------------

 row_handle category::operator[](const key_type &key)
@@ -1320,8 +1339,7 @@ std::string category::get_unique_value(std::string_view item_name)
 		// brain-dead implementation
 		for (std::size_t ix = 0; ix < size(); ++ix)
 		{
-			// result = m_name + "-" + std::to_string(ix);
-			result = cif_id_for_number(ix);
+			result = cif_id_for_number(static_cast<int>(ix));
 			if (not contains(key(item_name) == result))
 				break;
 		}
--- a/src/compound.cpp
+++ b/src/compound.cpp
@@ -480,10 +480,13 @@ compound *local_compound_factory_impl::create(const std::string &id)

 			try
 			{
-				const auto &[id, name, threeLetterCode, group] =
+				const auto &[id2, name, threeLetterCode, group] =
 					chem_comp->front().get<std::string, std::string, std::string, std::string>("id", "name", "three_letter_code", "group");

-				result = construct_compound(db, id, name, threeLetterCode, group);
+				if (id == id2)
+					result = construct_compound(db, id, name, threeLetterCode, group);
+				else
+					throw std::runtime_error("Compound ID's don't match: id 1=" + id + ", id 2=" + id2);
 			}
 			catch (const std::exception &ex)
 			{
@@ -757,8 +760,7 @@ bool compound_factory::is_monomer(std::string_view res_name) const

 void compound_factory::report_missing_compound(std::string_view compound_id)
 {
-	static bool s_reported = false;
-	if (std::exchange(s_reported, true) == false)
+	if (std::exchange(m_report_missing, false))
 	{
 		using namespace cif::colour;

--- a/src/condition.cpp
+++ b/src/condition.cpp
@@ -24,8 +24,8 @@
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

-#include "cif++/category.hpp"
 #include "cif++/condition.hpp"
+#include "cif++/category.hpp"
 #include "cif++/validate.hpp"

 namespace cif
@@ -61,6 +61,52 @@ bool is_item_type_uchar(const category &cat, std::string_view col)

 namespace detail
 {
+	// 	// index lookup
+	// 	struct index_lookup_condition_impl : public condition_impl
+	// 	{
+	// 		index_lookup_condition_impl(row_initializer &&key_values)
+	// 			: m_key_values(std::move(key_values))
+	// 		{
+	// 		}
+	//
+	// 		condition_impl *prepare(const category &c) override
+	// 		{
+	// 			m_single_hit = c[m_key_values];
+	// 			return this;
+	// 		}
+	//
+	// 		bool test(row_handle r) const override
+	// 		{
+	// 			return m_single_hit == r;
+	// 		}
+	//
+	// 		void str(std::ostream &os) const override
+	// 		{
+	// 			os << "index scan";
+	// 		}
+	//
+	// 		virtual std::optional<row_handle> single() const override
+	// 		{
+	// 			return m_single_hit;
+	// 		}
+	//
+	// 		virtual bool equals(const condition_impl *rhs) const override
+	// 		{
+	// 			if (typeid(*rhs) == typeid(index_lookup_condition_impl))
+	// 			{
+	// 				auto ri = static_cast<const index_lookup_condition_impl *>(rhs);
+	// 				if (m_single_hit or ri->m_single_hit)
+	// 					return m_single_hit == ri->m_single_hit;
+	// 				else
+	// 					// watch out, both m_item_ix might be the same while item_names might be diffent (in case they both do not exist in the category)
+	// 					return m_key_values == ri->m_key_values;
+	// 			}
+	// 			return this == rhs;
+	// 		}
+	//
+	// 		row_initializer m_key_values;
+	// 		row_handle m_single_hit;
+	// 	};

 	condition_impl *key_equals_condition_impl::prepare(const category &c)
 	{
@@ -85,7 +131,8 @@ namespace detail
 			c.key_item_indices().contains(m_item_ix) and
 			c.key_item_indices().size() == 1)
 		{
-			m_single_hit = c[{ { m_item_name, m_value } }];
+			item v(m_item_name, m_value);
+			m_single_hit = c[{ { m_item_name, std::string{ v.value() }, false } }];
 		}

 		return this;
@@ -99,7 +146,8 @@ namespace detail
 		{
 			auto &cs = (*s)->m_sub;

-			if (find_if(cs.begin(), cs.end(), [c](const condition_impl *i) { return i->equals(c); }) == cs.end())
+			if (find_if(cs.begin(), cs.end(), [c](const condition_impl *i)
+					{ return i->equals(c); }) == cs.end())
 			{
 				result = false;
 				break;
@@ -119,7 +167,8 @@ 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;
 			}
@@ -137,11 +186,12 @@ 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;
@@ -158,6 +208,99 @@ namespace detail
 		return oc;
 	}

+	condition_impl *and_condition_impl::prepare(const category &c)
+	{
+		for (auto &sub : m_sub)
+			sub = sub->prepare(c);
+
+		if (auto cv = c.get_cat_validator(); cv != nullptr)
+		{
+			// See if we can collapse a search part of this and_condition into a single index lookup
+
+			cif::iset keys{ cv->m_keys.begin(), cv->m_keys.end() };
+			category::key_type lookup;
+			std::vector<condition_impl *> subs;
+			std::vector<std::string> may_be_empty;
+
+			for (auto &sub : m_sub)
+			{
+				if (auto s = dynamic_cast<const key_equals_condition_impl *>(sub); s != nullptr)
+				{
+					if (keys.contains(s->m_item_name))
+					{
+						lookup.emplace_back(s->m_item_name, s->m_value);
+						subs.emplace_back(sub);
+					}
+					continue;
+				}
+
+				if (auto s = dynamic_cast<const key_equals_number_condition_impl *>(sub); s != nullptr)
+				{
+					if (keys.contains(s->m_item_name))
+					{
+						item v{ s->m_item_name, s->m_value };
+						lookup.emplace_back(s->m_item_name, std::string{ v.value() } );
+						subs.emplace_back(sub);
+					}
+					continue;
+				}
+
+				if (auto s = dynamic_cast<const key_equals_or_empty_condition_impl *>(sub); s != nullptr)
+				{
+					if (keys.contains(s->m_item_name))
+					{
+						lookup.emplace_back(s->m_item_name, s->m_value, true);
+						subs.emplace_back(sub);
+						may_be_empty.emplace_back(s->m_item_name);
+					}
+					continue;
+				}
+
+				if (auto s = dynamic_cast<const key_equals_number_or_empty_condition_impl *>(sub); s != nullptr)
+				{
+					if (keys.contains(s->m_item_name))
+					{
+						item v{ s->m_item_name, s->m_value };
+						lookup.emplace_back(s->m_item_name, std::string{ v.value() }, true );
+						subs.emplace_back(sub);
+					}
+					continue;
+				}
+			}
+
+			if (lookup.size() == keys.size())
+			{
+				m_single = c[lookup];
+
+				for (auto s : subs)
+					m_sub.erase(std::remove(m_sub.begin(), m_sub.end(), s), m_sub.end());
+			}
+		}
+
+		return this;
+	}
+
+	bool and_condition_impl::test(row_handle r) const
+	{
+		bool result = true;
+
+		if (m_single.has_value() and *m_single != r)
+			result = false;
+		else
+		{
+			for (auto sub : m_sub)
+			{
+				if (sub->test(r))
+					continue;
+
+				result = false;
+				break;
+			}
+		}
+
+		return result;
+	}
+
 	condition_impl *or_condition_impl::prepare(const category &c)
 	{
 		std::vector<and_condition_impl *> and_conditions;
@@ -181,7 +324,7 @@ void condition::prepare(const category &c)
 {
 	if (m_impl)
 		m_impl = m_impl->prepare(c);
-	
+
 	m_prepared = true;
 }

--- a/src/datablock.cpp
+++ b/src/datablock.cpp
@@ -78,17 +78,41 @@ bool datablock::is_valid() const
 	return result;
 }

-bool datablock::is_valid()
+bool datablock::validate_links() const
 {
-	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;
+		const_cast<category &>(cat).update_links(*this);
+
+	for (auto &cat : *this)
+		result = cat.validate_links() and result;
+
+	return result;
+}
+
+bool datablock::strip()
+{
+	bool result = true;
+
+	// remove all categories that have no validator
+	erase(std::remove_if(begin(), end(), [](category &c) {
+		bool result = false;
+		if (c.get_cat_validator() == nullptr)
+		{
+			if (cif::VERBOSE > 0)
+				std::clog << "Dropping category " << c.name() << '\n';
+			result = true;
+		}
+		return result;
+	}), end());
+
+	// then strip the remaining categories
+	for (auto &cat : *this)
+		cat.strip();

 	// Add or remove the audit_conform block here.
-	if (result)
+	if (is_valid())
 	{
 		// If the dictionary declares an audit_conform category, put it in,
 		// but only if it does not exist already!
@@ -101,22 +125,7 @@ bool datablock::is_valid()
 		}
 	}
 	else
-		erase(std::find_if(begin(), end(), [](category &cat)
-				  { return cat.name() == "audit_conform"; }),
-			end());
-
-	return result;
-}
-
-bool datablock::validate_links() const
-{
-	bool result = true;
-
-	for (auto &cat : *this)
-		const_cast<category &>(cat).update_links(*this);
-
-	for (auto &cat : *this)
-		result = cat.validate_links() and result;
+		result = false;

 	return result;
 }
--- a/src/file.cpp
+++ b/src/file.cpp
@@ -25,6 +25,7 @@
 */

 #include "cif++/file.hpp"
+#include "cif++/condition.hpp"
 #include "cif++/gzio.hpp"

 namespace cif
@@ -46,8 +47,16 @@ bool file::is_valid()
 {
 	bool result = not empty();

-	for (auto &d : *this)
-		result = d.is_valid() and result;
+	for (bool first = true; auto &d : *this)
+	{
+		if (first)
+		{
+			result = d.is_valid() and result;
+			first = false;
+		}
+		else if (d.get_validator() != nullptr)
+			result = d.is_valid() and result;
+	}

 	if (result)
 		result = validate_links();
--- a/src/model.cpp
+++ b/src/model.cpp
@@ -47,15 +47,10 @@ void atom::atom_impl::moveTo(const point &p)

 	auto r = row();

-#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
+	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);
+
 	m_location = p;
 }

@@ -102,18 +97,18 @@ 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 = 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);
+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"));

-// 	return d;
-// }
+	return d;
+}

 // bool atom::atom_impl::getAnisoU(float anisou[6]) const
 // {
@@ -149,145 +144,6 @@ 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())
@@ -319,8 +175,8 @@ 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_auth_asym_id = a.get_auth_asym_id();
-	m_auth_seq_id = a.get_auth_seq_id();
+	m_pdb_strand_id = a.get_auth_asym_id();
+	m_pdb_seq_num = a.get_auth_seq_id();
 	m_pdb_ins_code = a.get_pdb_ins_code();

 	for (auto atom : atoms)
@@ -371,10 +227,10 @@ 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_auth_asym_id },
+		{ "auth_asym_id", m_pdb_strand_id },
 		{ "auth_atom_id", inAtomID },
 		{ "auth_comp_id", m_compound_id },
-		{ "auth_seq_id", m_auth_seq_id },
+		{ "auth_seq_id", m_pdb_seq_num },
 		{ "occupancy", 1.0f, 2 },
 		{ "B_iso_or_equiv", 20.0f },
 		{ "pdbx_PDB_model_num", m_structure->get_model_nr() },
@@ -541,8 +397,8 @@ 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_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() << ']';
+	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() << ']';

 	return os;
 }
@@ -551,7 +407,7 @@ 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_auth_asym_id(), authSeqID, pdbInsCode)
+	: residue(*polymer.get_structure(), compoundID, polymer.get_asym_id(), seqID, polymer.get_pdb_strand_id(), authSeqID, pdbInsCode)
 	, m_polymer(&polymer)
 	, m_index(index)
 {
@@ -970,7 +826,7 @@ 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_auth_asym_id(auth_asym_id)
+	, m_pdb_strand_id(auth_asym_id)
 {
 	using namespace cif::literals;

@@ -982,12 +838,8 @@ 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::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::string compoundID, pdbSeqNum, pdbInsCode;
+		cif::tie(seqID, pdbSeqNum, compoundID, pdbInsCode) = r.get("seq_id", "pdb_seq_num", "mon_id", "pdb_ins_code");

 		std::size_t index = size();

@@ -995,11 +847,11 @@ 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, authSeqID, pdbInsCode, compoundID);
+			emplace_back(*this, index, seqID, pdbSeqNum, pdbInsCode, compoundID);
 		}
 		else if (VERBOSE > 0)
 		{
-			monomer m{ *this, index, seqID, authSeqID, pdbInsCode, compoundID };
+			monomer m{ *this, index, seqID, pdbSeqNum, pdbInsCode, compoundID };
 			std::cerr << "Dropping alternate residue " << m << '\n';
 		}
 	}
@@ -1139,7 +991,7 @@ 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_auth_seq_id });
+	atom_info.set_value({ "auth_seq_id", m_pdb_seq_num });
 	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 });
@@ -1255,12 +1107,12 @@ 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.num() },
+		{ "pdb_seq_num", result.get_pdb_seq_num() },
 		{ "pdb_mon_id", result.get_compound_id() },

-		{ "auth_asym_id", result.get_auth_asym_id() },
+		{ "auth_asym_id", result.get_pdb_strand_id() },
 		{ "auth_mon_id", result.get_compound_id() },
-		{ "auth_seq_num", result.get_auth_seq_id() },
+		{ "auth_seq_num", result.get_pdb_seq_num() },

 		{ "hetero", "n" } });

@@ -1303,7 +1155,7 @@ 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_auth_seq_id())
+		if (not sn.get_link() or sn.get_link().get_auth_seq_id() != s.get_pdb_seq_num())
 			continue;

 		auto n = name(sn) + "-(1-" + sn.get_link().get_label_atom_id().substr(1) + ')';
@@ -1330,19 +1182,19 @@ float branch::weight() const
 // --------------------------------------------------------------------
 //	structure

-structure::structure(file &p, std::size_t modelNr, StructureOpenOptions options)
+structure::structure(file &p, std::size_t modelNr, structure_open_options options)
 	: structure(p.front(), modelNr, options)
 {
 }

-structure::structure(datablock &db, std::size_t modelNr, StructureOpenOptions options)
+structure::structure(datablock &db, std::size_t modelNr, structure_open_options options)
 	: m_db(db)
 	, m_model_nr(modelNr)
 {
 	if (db.get_validator() == nullptr)
 		db.load_dictionary();

-	auto &atomCat = db["atom_site"];
+	auto &atom_site = db["atom_site"];

 	load_atoms_for_model(options);

@@ -1350,7 +1202,7 @@ structure::structure(datablock &db, std::size_t modelNr, StructureOpenOptions op
 	if (m_atoms.empty() and m_model_nr == 1)
 	{
 		std::optional<std::size_t> model_nr;
-		cif::tie(model_nr) = atomCat.front().get("pdbx_PDB_model_num");
+		cif::tie(model_nr) = atom_site.front().get("pdbx_PDB_model_num");
 		if (model_nr and *model_nr != m_model_nr)
 		{
 			if (VERBOSE > 0)
@@ -1369,42 +1221,133 @@ structure::structure(datablock &db, std::size_t modelNr, StructureOpenOptions op
 		load_data();
 }

-void structure::load_atoms_for_model(StructureOpenOptions options)
+void structure::load_atoms_for_model(structure_open_options options)
 {
 	using namespace literals;

-	auto &atomCat = m_db["atom_site"];
+	auto &atom_site = 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");

-	for (auto id : atomCat.find<std::string>(std::move(c), "id"))
-		emplace_atom(std::make_shared<atom::atom_impl>(m_db, id));
+	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);
+	
+		}
+	}
+
 }

-// 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 or m_polymers.back().get_entity_id() != entityID)
+		if (m_polymers.empty() or m_polymers.back().get_asym_id() != asym_id)
 			m_polymers.emplace_back(*this, entityID, asym_id, auth_asym_id);
 	}

@@ -1430,18 +1373,18 @@ void structure::load_data()
 	for (auto &poly : m_polymers)
 	{
 		for (auto &res : poly)
-			resMap[{ res.get_asym_id(), res.get_seq_id(), res.get_auth_seq_id() }] = &res;
+			resMap[{ res.get_asym_id(), res.get_seq_id(), res.get_pdb_seq_num() }] = &res;
 	}

 	for (auto &res : m_non_polymers)
-		resMap[{ res.get_asym_id(), res.get_seq_id(), res.get_auth_seq_id() }] = &res;
+		resMap[{ res.get_asym_id(), res.get_seq_id(), res.get_pdb_seq_num() }] = &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_auth_seq_id() }] = &sugar;
+			resMap[{ sugar.get_asym_id(), sugar.get_seq_id(), sugar.get_pdb_seq_num() }] = &sugar;
 			sugars.insert(sugar.get_compound_id());
 		}
 	}
@@ -1516,30 +1459,6 @@ 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());
@@ -1688,7 +1607,7 @@ 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_auth_seq_id() == authSeqID))
+			if (res.get_asym_id() == asym_id and (authSeqID.empty() or res.get_pdb_seq_num() == authSeqID))
 				return res;
 		}
 	}
@@ -1712,7 +1631,7 @@ 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_auth_seq_id() == authSeqID)
+			if (sugar.get_asym_id() == asym_id and sugar.get_pdb_seq_num() == authSeqID)
 				return sugar;
 		}
 	}
@@ -1734,7 +1653,7 @@ 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_auth_seq_id() == authSeqID and res.get_compound_id() == compID)
+			if (res.get_asym_id() == asym_id and res.get_pdb_seq_num() == authSeqID and res.get_compound_id() == compID)
 				return res;
 		}
 	}
@@ -1758,7 +1677,7 @@ 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_auth_seq_id() == authSeqID and sugar.get_compound_id() == compID)
+			if (sugar.get_asym_id() == asym_id and sugar.get_pdb_seq_num() == authSeqID and sugar.get_compound_id() == compID)
 				return sugar;
 		}
 	}
@@ -2108,7 +2027,7 @@ 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_auth_seq_id() == auth_seq_id))
+			if (res.get_asym_id() == asym_id and (auth_seq_id.empty() or res.get_pdb_seq_num() == auth_seq_id))
 			{
 				remove_residue(res);
 				return;
@@ -2138,7 +2057,7 @@ 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_auth_seq_id() == auth_seq_id)
+			if (sugar.get_asym_id() == asym_id and sugar.get_pdb_seq_num() == auth_seq_id)
 			{
 				remove_residue(sugar);
 				return;
@@ -2271,7 +2190,7 @@ 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_auth_seq_id() },
+				{ "auth_seq_num", sugar.get_pdb_seq_num() },

 				{ "hetero", "n" } });
 		}
@@ -2357,8 +2276,8 @@ 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_auth_seq_id() },
-		{ "auth_seq_num", res.get_auth_seq_id() },
+		{ "pdb_seq_num", res.get_pdb_seq_num() },
+		{ "auth_seq_num", res.get_pdb_seq_num() },
 		{ "pdb_mon_id", comp_id },
 		{ "auth_mon_id", comp_id },
 		{ "pdb_strand_id", asym_id },
@@ -2418,8 +2337,8 @@ 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_auth_seq_id() },
-		{ "auth_seq_num", res.get_auth_seq_id() },
+		{ "pdb_seq_num", res.get_pdb_seq_num() },
+		{ "auth_seq_num", res.get_pdb_seq_num() },
 		{ "pdb_mon_id", comp_id },
 		{ "auth_mon_id", comp_id },
 		{ "pdb_strand_id", asym_id },
@@ -2733,11 +2652,11 @@ 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_auth_seq_id() },
+				{ "entity_branch_list_num_1", s1.get_pdb_seq_num() },
 				{ "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_auth_seq_id() },
+				{ "entity_branch_list_num_2", s2.get_pdb_seq_num() },
 				{ "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() },
@@ -2950,7 +2869,7 @@ static int compare_numbers(std::string_view a, std::string_view b)

 int compare_cif_id(const std::string &a, const std::string &b)
 {
-	int d = a.length() - b.length();
+	int d = static_cast<int>(a.length() - b.length());
 	if (d == 0)
 		d = a.compare(b);
 	return d;
--- a/src/pdb/cif2pdb.cpp
+++ b/src/pdb/cif2pdb.cpp
@@ -33,7 +33,6 @@
 #include <regex>
 #include <set>

-
 namespace cif::pdb
 {

@@ -58,9 +57,9 @@ std::string cif2pdbDate(const std::string &d)
 		int month = std::stoi(m[2].str());

 		if (m[3].matched)
-			result = cif::format("%02.2d-%3.3s-%02.2d", stoi(m[3].str()), kMonths[month - 1], (year % 100)).str();
+			result = cif::format("{:02}-{:3.3}-{:02}", stoi(m[3].str()), kMonths[month - 1], (year % 100));
 		else
-			result = cif::format("%3.3s-%02.2d", kMonths[month - 1], (year % 100)).str();
+			result = cif::format("{:3.3}-{:02}", kMonths[month - 1], (year % 100));
 	}

 	return result;
@@ -258,16 +257,14 @@ std::size_t WriteCitation(std::ostream &pdbFile, const datablock &db, row_handle
 	{
 		to_upper(pubname);

-		const std::string kRefHeader = s1 + "REF %2.2s %-28.28s  %2.2s%4.4s %5.5s %4.4s";
-		pdbFile << cif::format(kRefHeader, "" /* continuation */, pubname, (volume.empty() ? "" : "V."), volume, pageFirst, year)
+		pdbFile << s1 << cif::format("REF {:2.2s} {:<28.28s}  {:2.2s}{:>4.4s} {:>5.5s} {:4.4s}", "" /* continuation */, pubname, (volume.empty() ? "" : "V."), volume, pageFirst, year)
 				<< '\n';
 		++result;
 	}

 	if (not issn.empty())
 	{
-		const std::string kRefHeader = s1 + "REFN                   ISSN %-25.25s";
-		pdbFile << cif::format(kRefHeader, issn) << '\n';
+		pdbFile << s1 << cif::format("REFN                   ISSN {:<25.25s}", issn) << '\n';
 		++result;
 	}

@@ -276,27 +273,25 @@ 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).str()
+	//						% issn)
 	//					<< '\n';
 	//		}

 	if (not pmid.empty())
 	{
-		const std::string kPMID = s1 + "PMID   %-60.60s ";
-		pdbFile << cif::format(kPMID, pmid) << '\n';
+		pdbFile << s1 << cif::format("PMID   {:<60.60s} ", pmid) << '\n';
 		++result;
 	}

 	if (not doi.empty())
 	{
-		const std::string kDOI = s1 + "DOI    %-60.60s ";
-		pdbFile << cif::format(kDOI, doi) << '\n';
+		pdbFile << s1 << cif::format("DOI    {:<60.60s} ", doi) << '\n';
 		++result;
 	}

@@ -307,10 +302,10 @@ void write_header_lines(std::ostream &pdbFile, const datablock &db)
 {
 	//    0         1         2         3         4         5         6         7         8
 	//    HEADER    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxDDDDDDDDD   IIII
-	const char kHeader[] =
-		"HEADER    %-40.40s"
-		"%-9.9s"
-		"   %-4.4s";
+	// const char kHeader[] =
+	// 	"HEADER    {:<40.40s}"
+	// 	"{:<9.9s}"
+	// 	"   {:<4.4s}";

 	// HEADER

@@ -345,7 +340,12 @@ void write_header_lines(std::ostream &pdbFile, const datablock &db)
 		}
 	}

-	pdbFile << cif::format(kHeader, keywords, date, db.name()) << '\n';
+	pdbFile << cif::format(/* kHeader */
+		"HEADER    {:<40.40s}"
+		"{:<9.9s}"
+		"   {:<4.4s}"
+	
+	, keywords, date, db.name()) << '\n';

 	// TODO: implement
 	// OBSLTE (skip for now)
@@ -535,7 +535,6 @@ void WriteTitle(std::ostream &pdbFile, const datablock &db)
 	write_header_lines(pdbFile, db);

 	// REVDAT
-	const char kRevDatFmt[] = "REVDAT %3d%2.2s %9.9s %4.4s    %1d      ";
 	auto &cat2 = db["database_PDB_rev"];
 	std::vector<row_handle> rev(cat2.begin(), cat2.end());
 	sort(rev.begin(), rev.end(), [](row_handle a, row_handle b) -> bool
@@ -559,9 +558,9 @@ void WriteTitle(std::ostream &pdbFile, const datablock &db)
 		{
 			std::string cs = ++continuation > 1 ? std::to_string(continuation) : std::string();

-			pdbFile << cif::format(kRevDatFmt, revNum, cs, date, db.name(), modType);
+			pdbFile << cif::format("REVDAT {:3}{:2.2s} {:9.9s} {:4.4s}    {:1}      ", revNum, cs, date, db.name(), modType);
 			for (std::size_t i = 0; i < 4; ++i)
-				pdbFile << cif::format(" %-6.6s", (i < types.size() ? types[i] : std::string()));
+				pdbFile << cif::format(" {:<6.6s}", (i < types.size() ? types[i] : std::string()));
 			pdbFile << '\n';

 			if (types.size() > 4)
@@ -614,7 +613,7 @@ void WriteRemark2(std::ostream &pdbFile, const datablock &db)
 		{
 			float resHigh = refine.front()["ls_d_res_high"].as<float>();
 			pdbFile << "REMARK   2\n"
-					<< cif::format("REMARK   2 RESOLUTION. %7.2f ANGSTROMS.", resHigh) << '\n';
+					<< cif::format("REMARK   2 RESOLUTION. {:7.2f} ANGSTROMS.", resHigh) << '\n';
 		}
 		catch (...)
 		{ /* skip it */
@@ -761,10 +760,7 @@ class Fs : public FBase
 		else
 		{
 			os << '\n';
-
-			std::stringstream ss;
-			ss << "REMARK " << std::setw(3) << std::right << mNr << ' ';
-			WriteOneContinuedLine(os, ss.str(), 0, s);
+			WriteOneContinuedLine(os, cif::format("REMARK {:3} ", mNr), 0, s);
 		}
 	}

@@ -1617,7 +1613,7 @@ void WriteRemark3Phenix(std::ostream &pdbFile, const datablock &db)

 		percent_reflns_obs /= 100;

-		pdbFile << RM3("  ") << cif::format("%3d %7.4f - %7.4f    %4.2f %8d %5d  %6.4f %6.4f", bin++, d_res_low, d_res_high, percent_reflns_obs, number_reflns_R_work, number_reflns_R_free, R_factor_R_work, R_factor_R_free) << '\n';
+		pdbFile << RM3("  ") << cif::format("{:3} {:7.4f} - {:7.4f}    {:4.2f} {:8} {:5}  {:6.4f} {:6.4f}", bin++, d_res_low, d_res_high, percent_reflns_obs, number_reflns_R_work, number_reflns_R_free, R_factor_R_work, R_factor_R_free) << '\n';
 	}

 	pdbFile << RM3("") << '\n'
@@ -2585,7 +2581,7 @@ void WriteRemark465(std::ostream &pdbFile, const datablock &db)
 		cif::tie(modelNr, resName, chainID, iCode, seqNr) =
 			r.get("PDB_model_num", "auth_comp_id", "auth_asym_id", "PDB_ins_code", "auth_seq_id");

-		pdbFile << cif::format("REMARK 465 %3.3s %3.3s %1.1s %5d%1.1s", modelNr, resName, chainID, seqNr, iCode) << '\n';
+		pdbFile << cif::format("REMARK 465 {:3.3s} {:3.3s} {:1.1s} {:5}{:1.1s}", modelNr, resName, chainID, seqNr, iCode) << '\n';
 	}
 }

@@ -2632,7 +2628,7 @@ void WriteRemark470(std::ostream &pdbFile, const datablock &db)

 			while (not a.second.empty())
 			{
-				pdbFile << cif::format("REMARK 470 %3.3s %3.3s %1.1s%4d%1.1s  ", modelNr, resName, chainID, seqNr, iCode) << "  ";
+				pdbFile << cif::format("REMARK 470 {:>3.3s} {:3.3s} {:1.1s}{:4}{:1.1s}  ", modelNr, resName, chainID, seqNr, iCode) << "  ";

 				for (std::size_t i = 0; i < 6 and not a.second.empty(); ++i)
 				{
@@ -2730,16 +2726,16 @@ int WritePrimaryStructure(std::ostream &pdbFile, const datablock &db)

 			if (dbAccession.length() > 8 or db_code.length() > 12 or atoi(dbseqEnd.c_str()) >= 100000)
 				pdbFile << cif::format(
-							   "DBREF1 %4.4s %1.1s %4.4s%1.1s %4.4s%1.1s %-6.6s               %-20.20s",
+							   "DBREF1 {:>4.4s} {:1.1s} {:>4.4s}{:1.1s} {:>4.4s}{:1.1s} {:<6.6s}               {:<20.20s}",
 							   idCode, chainID, seqBegin, insertBegin, seqEnd, insertEnd, db_name, db_code)
 						<< '\n'
 						<< cif::format(
-							   "DBREF2 %4.4s %1.1s     %-22.22s     %10.10s  %10.10s",
+							   "DBREF2 {:>4.4s} {:1.1s}     {:<22.22s}     {:10.10s}  {:10.10s}",
 							   idCode, chainID, dbAccession, dbseqBegin, dbseqEnd)
 						<< '\n';
 			else
 				pdbFile << cif::format(
-							   "DBREF  %4.4s %1.1s %4.4s%1.1s %4.4s%1.1s %-6.6s %-8.8s %-12.12s %5.5s%1.1s %5.5s%1.1s",
+							   "DBREF  {:>4.4s} {:1.1s} {:>4.4s}{:1.1s} {:>4.4s}{:1.1s} {:<6.6s} {:<8.8s} {:<12.12s} {:>5.5s}{:1.1s} {:>5.5s}{:1.1s}",
 							   idCode, chainID, seqBegin, insertBegin, seqEnd, insertEnd, db_name, dbAccession, db_code, dbseqBegin, dbinsBeg, dbseqEnd, dbinsEnd)
 						<< '\n';
 		}
@@ -2758,9 +2754,8 @@ int WritePrimaryStructure(std::ostream &pdbFile, const datablock &db)
 		to_upper(conflict);

 		pdbFile << cif::format(
-					   "SEQADV %4.4s %3.3s %1.1s %4.4s%1.1s %-4.4s %-9.9s %3.3s %5.5s %-21.21s",
+					   "SEQADV {:4.4s} {:3.3s} {:1.1s} {:>4.4s}{:1.1s} {:<4.4s} {:<9.9s} {:3.3s} {:>5.5s} {:<21.21s}",
 					   idCode, resName, chainID, seqNum, iCode, database, dbAccession, dbRes, dbSeq, conflict)
-					   .str()
 				<< '\n';
 	}

@@ -2788,7 +2783,7 @@ int WritePrimaryStructure(std::ostream &pdbFile, const datablock &db)
 				t = 13;

 			pdbFile << cif::format(
-						   "SEQRES %3d %1.1s %4d  %-51.51s          ",
+						   "SEQRES {:3} {:1.1s} {:4}  {:<51.51s}          ",
 						   n++, std::string{ chainID }, seqresl[chainID], join(seq.begin(), seq.begin() + t, " "))
 					<< '\n';

@@ -2808,9 +2803,8 @@ int WritePrimaryStructure(std::ostream &pdbFile, const datablock &db)
 			r.get("auth_asym_id", "auth_seq_id", "auth_comp_id", "PDB_ins_code", "parent_comp_id", "details");

 		pdbFile << cif::format(
-					   "MODRES %4.4s %3.3s %1.1s %4.4s%1.1s %3.3s  %-41.41s",
+					   "MODRES {:4.4s} {:3.3s} {:1.1s} {:4.4s}{:1.1s} {:3.3s}  {:<41.41s}",
 					   db.name(), resName, chainID, seqNum, iCode, stdRes, comment)
-					   .str()
 				<< '\n';
 	}

@@ -2925,7 +2919,7 @@ int WriteHeterogen(std::ostream &pdbFile, const datablock &db)
 	{
 		if (h.water)
 			continue;
-		pdbFile << cif::format("HET    %3.3s  %c%4d%c  %5d", h.hetID, h.chainID, h.seqNum, h.iCode, h.numHetAtoms) << '\n';
+		pdbFile << cif::format("HET    {:3.3s}  {:1c}{:4}{:1c}  {:5}", h.hetID, h.chainID, h.seqNum, h.iCode, h.numHetAtoms) << '\n';
 		++numHet;
 	}

@@ -2940,7 +2934,7 @@ int WriteHeterogen(std::ostream &pdbFile, const datablock &db)

 		for (;;)
 		{
-			pdbFile << cif::format("HETNAM  %2.2s %3.3s ", (c > 1 ? std::to_string(c) : std::string()), id);
+			pdbFile << cif::format("HETNAM  {:2.2s} {:3.3s} ", (c > 1 ? std::to_string(c) : std::string()), id);
 			++c;

 			if (name.length() > 55)
@@ -3032,7 +3026,7 @@ int WriteHeterogen(std::ostream &pdbFile, const datablock &db)
 			{
 				std::stringstream fs;

-				fs << cif::format("FORMUL  %2d  %3.3s %2.2s%c", componentNr, hetID, (c > 1 ? std::to_string(c) : std::string()), (hetID == water_comp_id ? '*' : ' '));
+				fs << cif::format("FORMUL  {:2}  {:3.3s} {:2.2s}{:1c}", componentNr, hetID, (c > 1 ? std::to_string(c) : std::string()), (hetID == water_comp_id ? '*' : ' '));
 				++c;

 				if (formula.length() > 51)
@@ -3099,7 +3093,7 @@ std::tuple<int, int> WriteSecondaryStructure(std::ostream &pdbFile, const databl
 				"pdbx_PDB_helix_class", "pdbx_PDB_helix_length", "beg_auth_seq_id", "end_auth_seq_id");

 		++numHelix;
-		pdbFile << cif::format("HELIX  %3d %3.3s %3.3s %1.1s %4d%1.1s %3.3s %1.1s %4d%1.1s%2d%-30.30s %5d",
+		pdbFile << cif::format("HELIX  {:3} {:>3.3s} {:3.3s} {:1.1s} {:4}{:1.1s} {:3.3s} {:1.1s} {:4}{:1.1s}{:2}{:<30.30s} {:5}",
 					   numHelix, pdbx_PDB_helix_id, beg_label_comp_id, beg_auth_asym_id, beg_auth_seq_id, pdbx_beg_PDB_ins_code, end_label_comp_id, end_auth_asym_id, end_auth_seq_id, pdbx_end_PDB_ins_code, pdbx_PDB_helix_class, details, pdbx_PDB_helix_length)
 				<< '\n';
 	}
@@ -3136,7 +3130,7 @@ std::tuple<int, int> WriteSecondaryStructure(std::ostream &pdbFile, const databl
 					"pdbx_end_PDB_ins_code", "beg_auth_comp_id", "beg_auth_asym_id", "beg_auth_seq_id",
 					"end_auth_comp_id", "end_auth_asym_id", "end_auth_seq_id");

-				pdbFile << cif::format("SHEET  %3.3s %3.3s%2d %3.3s %1.1s%4d%1.1s %3.3s %1.1s%4d%1.1s%2d", rangeID1, sheetID, numStrands, initResName, initChainID, initSeqNum, initICode, endResName, endChainID, endSeqNum, endICode, 0) << '\n';
+				pdbFile << cif::format("SHEET  {:>3.3s} {:>3.3s}{:2} {:3.3s} {:1.1s}{:4}{:1.1s} {:3.3s} {:1.1s}{:4}{:1.1s}{:2}", rangeID1, sheetID, numStrands, initResName, initChainID, initSeqNum, initICode, endResName, endChainID, endSeqNum, endICode, 0) << '\n';

 				first = false;
 			}
@@ -3155,7 +3149,7 @@ std::tuple<int, int> WriteSecondaryStructure(std::ostream &pdbFile, const databl

 			if (h.empty())
 			{
-				pdbFile << cif::format("SHEET  %3.3s %3.3s%2d %3.3s %1.1s%4d%1.1s %3.3s %1.1s%4d%1.1s%2d", rangeID2, sheetID, numStrands, initResName, initChainID, initSeqNum, initICode, endResName, endChainID, endSeqNum, endICode, sense) << '\n';
+				pdbFile << cif::format("SHEET  {:>3.3s} {:>3.3s}{:2} {:3.3s} {:1.1s}{:4}{:1.1s} {:3.3s} {:1.1s}{:4}{:1.1s}{:2}", rangeID2, sheetID, numStrands, initResName, initChainID, initSeqNum, initICode, endResName, endChainID, endSeqNum, endICode, sense) << '\n';
 			}
 			else
 			{
@@ -3168,8 +3162,8 @@ std::tuple<int, int> WriteSecondaryStructure(std::ostream &pdbFile, const databl
 				curAtom = cif2pdbAtomName(curAtom, compID[0], db);
 				prevAtom = cif2pdbAtomName(prevAtom, compID[1], db);

-				pdbFile << cif::format("SHEET  %3.3s %3.3s%2d %3.3s %1.1s%4d%1.1s %3.3s %1.1s%4d%1.1s%2d "
-										"%-4.4s%3.3s %1.1s%4d%1.1s %-4.4s%3.3s %1.1s%4d%1.1s",
+				pdbFile << cif::format("SHEET  {:>3.3s} {:>3.3s}{:2} {:3.3s} {:1.1s}{:4}{:1.1s} {:3.3s} {:1.1s}{:4}{:1.1s}{:2} "
+										"{:<4.4s}{:3.3s} {:1.1s}{:4}{:1.1s} {:<4.4s}{:3.3s} {:1.1s}{:4}{:1.1s}",
 							   rangeID2, sheetID, numStrands, initResName, initChainID, initSeqNum, initICode, endResName, endChainID, endSeqNum, endICode, sense, curAtom, curResName, curChainID, curResSeq, curICode, prevAtom, prevResName, prevChainID, prevResSeq, prevICode)
 						<< '\n';
 			}
@@ -3207,7 +3201,7 @@ void WriteConnectivity(std::ostream &pdbFile, const datablock &db)
 		sym1 = cif2pdbSymmetry(sym1);
 		sym2 = cif2pdbSymmetry(sym2);

-		pdbFile << cif::format("SSBOND %3d CYS %1.1s %4d%1.1s   CYS %1.1s %4d%1.1s                       %6.6s %6.6s %5.2f", nr, chainID1, seqNum1, icode1, chainID2, seqNum2, icode2, sym1, sym2, Length) << '\n';
+		pdbFile << cif::format("SSBOND {:3} CYS {:1.1s} {:4}{:1.1s}   CYS {:1.1s} {:4}{:1.1s}                       {:6.6s} {:6.6s} {:5.2f}", nr, chainID1, seqNum1, icode1, chainID2, seqNum2, icode2, sym1, sym2, Length) << '\n';

 		++nr;
 	}
@@ -3234,10 +3228,10 @@ void WriteConnectivity(std::ostream &pdbFile, const datablock &db)
 		sym1 = cif2pdbSymmetry(sym1);
 		sym2 = cif2pdbSymmetry(sym2);

-		pdbFile << cif::format("LINK        %-4.4s%1.1s%3.3s %1.1s%4d%1.1s               %-4.4s%1.1s%3.3s %1.1s%4d%1.1s  %6.6s %6.6s", name1, altLoc1, resName1, chainID1, resSeq1, iCode1, name2, altLoc2, resName2, chainID2, resSeq2, iCode2, sym1, sym2);
+		pdbFile << cif::format("LINK        {:<4.4s}{:1.1s}{:3.3s} {:1.1s}{:4}{:1.1s}               {:<4.4s}{:1.1s}{:3.3s} {:1.1s}{:4}{:1.1s}  {:>6.6s} {:>6.6s}", name1, altLoc1, resName1, chainID1, resSeq1, iCode1, name2, altLoc2, resName2, chainID2, resSeq2, iCode2, sym1, sym2);

 		if (not Length.empty())
-			pdbFile << cif::format(" %5.2f", stod(Length));
+			pdbFile << cif::format(" {:5.2f}", stod(Length));

 		pdbFile << '\n';
 	}
@@ -3255,7 +3249,7 @@ void WriteConnectivity(std::ostream &pdbFile, const datablock &db)
 				"pdbx_label_comp_id_2", "pdbx_auth_asym_id_2", "pdbx_auth_seq_id_2", "pdbx_PDB_ins_code_2",
 				"pdbx_PDB_model_num", "pdbx_omega_angle");

-		pdbFile << cif::format("CISPEP %3.3s %3.3s %1.1s %4d%1.1s   %3.3s %1.1s %4d%1.1s       %3.3s       %6.2f",
+		pdbFile << cif::format("CISPEP {:3.3s} {:3.3s} {:1.1s} {:4}{:1.1s}   {:3.3s} {:1.1s} {:4}{:1.1s}       {:3.3s}       {:6.2f}",
 			serNum, pep1, chainID1, seqNum1, icode1, pep2, chainID2, seqNum2, icode2, modNum, measure) << '\n';
 	}
 }
@@ -3276,7 +3270,7 @@ int WriteMiscellaneousFeatures(std::ostream &pdbFile, const datablock &db)
 		cif::tie(siteID, resName, chainID, seq, iCode) =
 			r.get("site_id", "auth_comp_id", "auth_asym_id", "auth_seq_id", "pdbx_auth_ins_code");

-		sites[siteID].push_back(cif::format("%3.3s %1.1s%4d%1.1s ", resName, chainID, seq, iCode).str());
+		sites[siteID].push_back(cif::format("{:3.3s} {:1.1s}{:4}{:1.1s} ", resName, chainID, seq, iCode));
 	}

 	for (auto s : sites)
@@ -3289,7 +3283,7 @@ int WriteMiscellaneousFeatures(std::ostream &pdbFile, const datablock &db)
 		int nr = 1;
 		while (res.empty() == false)
 		{
-			pdbFile << cif::format("SITE   %3d %3.3s %2d ", nr, siteID, numRes);
+			pdbFile << cif::format("SITE   {:3} {:3.3s} {:2} ", nr, siteID, numRes);

 			for (int i = 0; i < 4; ++i)
 			{
@@ -3318,7 +3312,7 @@ void WriteCrystallographic(std::ostream &pdbFile, const datablock &db)

 	r = db["cell"].find_first(key("entry_id") == db.name());

-	pdbFile << cif::format("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11.11s%4d", r["length_a"].as<double>(), r["length_b"].as<double>(), r["length_c"].as<double>(), r["angle_alpha"].as<double>(), r["angle_beta"].as<double>(), r["angle_gamma"].as<double>(), symmetry, r["Z_PDB"].as<int>()) << '\n';
+	pdbFile << cif::format("CRYST1{:9.3f}{:9.3f}{:9.3f}{:7.2f}{:7.2f}{:7.2f} {:<11.11s}{:4}", r["length_a"].as<double>(), r["length_b"].as<double>(), r["length_c"].as<double>(), r["angle_alpha"].as<double>(), r["angle_beta"].as<double>(), r["angle_gamma"].as<double>(), symmetry, r["Z_PDB"].as<int>()) << '\n';
 }

 int WriteCoordinateTransformation(std::ostream &pdbFile, const datablock &db)
@@ -3327,18 +3321,18 @@ int WriteCoordinateTransformation(std::ostream &pdbFile, const datablock &db)

 	for (auto r : db["database_PDB_matrix"])
 	{
-		pdbFile << cif::format("ORIGX%1d    %10.6f%10.6f%10.6f     %10.5f", 1, r["origx[1][1]"].as<float>(), r["origx[1][2]"].as<float>(), r["origx[1][3]"].as<float>(), r["origx_vector[1]"].as<float>()) << '\n';
-		pdbFile << cif::format("ORIGX%1d    %10.6f%10.6f%10.6f     %10.5f", 2, r["origx[2][1]"].as<float>(), r["origx[2][2]"].as<float>(), r["origx[2][3]"].as<float>(), r["origx_vector[2]"].as<float>()) << '\n';
-		pdbFile << cif::format("ORIGX%1d    %10.6f%10.6f%10.6f     %10.5f", 3, r["origx[3][1]"].as<float>(), r["origx[3][2]"].as<float>(), r["origx[3][3]"].as<float>(), r["origx_vector[3]"].as<float>()) << '\n';
+		pdbFile << cif::format("ORIGX{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 1, r["origx[1][1]"].as<float>(), r["origx[1][2]"].as<float>(), r["origx[1][3]"].as<float>(), r["origx_vector[1]"].as<float>()) << '\n';
+		pdbFile << cif::format("ORIGX{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 2, r["origx[2][1]"].as<float>(), r["origx[2][2]"].as<float>(), r["origx[2][3]"].as<float>(), r["origx_vector[2]"].as<float>()) << '\n';
+		pdbFile << cif::format("ORIGX{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 3, r["origx[3][1]"].as<float>(), r["origx[3][2]"].as<float>(), r["origx[3][3]"].as<float>(), r["origx_vector[3]"].as<float>()) << '\n';
 		result += 3;
 		break;
 	}

 	for (auto r : db["atom_sites"])
 	{
-		pdbFile << cif::format("SCALE%1d    %10.6f%10.6f%10.6f     %10.5f", 1, r["fract_transf_matrix[1][1]"].as<float>(), r["fract_transf_matrix[1][2]"].as<float>(), r["fract_transf_matrix[1][3]"].as<float>(), r["fract_transf_vector[1]"].as<float>()) << '\n';
-		pdbFile << cif::format("SCALE%1d    %10.6f%10.6f%10.6f     %10.5f", 2, r["fract_transf_matrix[2][1]"].as<float>(), r["fract_transf_matrix[2][2]"].as<float>(), r["fract_transf_matrix[2][3]"].as<float>(), r["fract_transf_vector[2]"].as<float>()) << '\n';
-		pdbFile << cif::format("SCALE%1d    %10.6f%10.6f%10.6f     %10.5f", 3, r["fract_transf_matrix[3][1]"].as<float>(), r["fract_transf_matrix[3][2]"].as<float>(), r["fract_transf_matrix[3][3]"].as<float>(), r["fract_transf_vector[3]"].as<float>()) << '\n';
+		pdbFile << cif::format("SCALE{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 1, r["fract_transf_matrix[1][1]"].as<float>(), r["fract_transf_matrix[1][2]"].as<float>(), r["fract_transf_matrix[1][3]"].as<float>(), r["fract_transf_vector[1]"].as<float>()) << '\n';
+		pdbFile << cif::format("SCALE{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 2, r["fract_transf_matrix[2][1]"].as<float>(), r["fract_transf_matrix[2][2]"].as<float>(), r["fract_transf_matrix[2][3]"].as<float>(), r["fract_transf_vector[2]"].as<float>()) << '\n';
+		pdbFile << cif::format("SCALE{:1}    {:10.6f}{:10.6f}{:10.6f}     {:10.5f}", 3, r["fract_transf_matrix[3][1]"].as<float>(), r["fract_transf_matrix[3][2]"].as<float>(), r["fract_transf_matrix[3][3]"].as<float>(), r["fract_transf_vector[3]"].as<float>()) << '\n';
 		result += 3;
 		break;
 	}
@@ -3348,9 +3342,9 @@ int WriteCoordinateTransformation(std::ostream &pdbFile, const datablock &db)
 	{
 		std::string given = r["code"] == "given" ? "1" : "";

-		pdbFile << cif::format("MTRIX%1d %3d%10.6f%10.6f%10.6f     %10.5f    %1.1s", 1, nr, r["matrix[1][1]"].as<float>(), r["matrix[1][2]"].as<float>(), r["matrix[1][3]"].as<float>(), r["vector[1]"].as<float>(), given) << '\n';
-		pdbFile << cif::format("MTRIX%1d %3d%10.6f%10.6f%10.6f     %10.5f    %1.1s", 2, nr, r["matrix[2][1]"].as<float>(), r["matrix[2][2]"].as<float>(), r["matrix[2][3]"].as<float>(), r["vector[2]"].as<float>(), given) << '\n';
-		pdbFile << cif::format("MTRIX%1d %3d%10.6f%10.6f%10.6f     %10.5f    %1.1s", 3, nr, r["matrix[3][1]"].as<float>(), r["matrix[3][2]"].as<float>(), r["matrix[3][3]"].as<float>(), r["vector[3]"].as<float>(), given) << '\n';
+		pdbFile << cif::format("MTRIX{:1} {:3}{:10.6f}{:10.6f}{:10.6f}     {:10.5f}    {:1.1s}", 1, nr, r["matrix[1][1]"].as<float>(), r["matrix[1][2]"].as<float>(), r["matrix[1][3]"].as<float>(), r["vector[1]"].as<float>(), given) << '\n';
+		pdbFile << cif::format("MTRIX{:1} {:3}{:10.6f}{:10.6f}{:10.6f}     {:10.5f}    {:1.1s}", 2, nr, r["matrix[2][1]"].as<float>(), r["matrix[2][2]"].as<float>(), r["matrix[2][3]"].as<float>(), r["vector[2]"].as<float>(), given) << '\n';
+		pdbFile << cif::format("MTRIX{:1} {:3}{:10.6f}{:10.6f}{:10.6f}     {:10.5f}    {:1.1s}", 3, nr, r["matrix[3][1]"].as<float>(), r["matrix[3][2]"].as<float>(), r["matrix[3][3]"].as<float>(), r["vector[3]"].as<float>(), given) << '\n';

 		++nr;
 		result += 3;
@@ -3369,10 +3363,6 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab

 	auto &atom_site = db["atom_site"];
 	auto &atom_site_anisotrop = db["atom_site_anisotrop"];
-	auto &entity = db["entity"];
-	// auto &pdbx_poly_seq_scheme = db["pdbx_poly_seq_scheme"];
-	// auto &pdbx_nonpoly_scheme = db["pdbx_nonpoly_scheme"];
-	auto &pdbx_branch_scheme = db["pdbx_branch_scheme"];

 	int serial = 1;
 	auto ri = atom_site.begin();
@@ -3417,7 +3407,7 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab

 			if (terminate)
 			{
-				pdbFile << cif::format("TER   %5d      %3.3s %1.1s%4d%1.1s",  serial,  resName,  chainID,  resSeq,  iCode) << '\n';
+				pdbFile << cif::format("TER   {:5}      {:3.3s} {:1.1s}{:4}{:1.1s}",  serial,  resName,  chainID,  resSeq,  iCode) << '\n';

 				++serial;
 				terminatedChains.insert(chainID);
@@ -3446,26 +3436,6 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 			r.get("id", "group_PDB", "label_atom_id", "label_alt_id", "auth_comp_id", "auth_asym_id", "auth_seq_id",
 				"pdbx_PDB_ins_code", "Cartn_x", "Cartn_y", "Cartn_z", "occupancy", "B_iso_or_equiv", "type_symbol", "pdbx_formal_charge");

-		if (resName != "HOH")
-		{
-			int entity_id = r.get<int>("label_entity_id");
-			try
-			{
-				auto type = entity.find1<std::string>("id"_key == entity_id, "type");
-
-				if (type == "branched")	// find the real auth_seq_num, since sugars have their auth_seq_num reused as sugar number... sigh.
-					resSeq = pdbx_branch_scheme.find1<int>("asym_id"_key == r.get<std::string>("label_asym_id") and "pdb_seq_num"_key == resSeq, "auth_seq_num");
-				// else if (type == "non-polymer")	// same for non-polymers
-				// 	resSeq = pdbx_nonpoly_scheme.find1<int>("asym_id"_key == r.get<std::string>("label_asym_id") and "pdb_seq_num"_key == resSeq, "auth_seq_num");
-				// else if (type == "polymer")
-				// 	resSeq = pdbx_poly_seq_scheme.find1<int>("asym_id"_key == r.get<std::string>("label_asym_id") and "pdb_seq_num"_key == resSeq, "auth_seq_num");
-			}
-			catch (const std::exception &ex)
-			{
-				std::cerr << "Oops, there was not exactly one entity with id " << entity_id << '\n';
-			}
-		}
-		
 		if (chainID.length() > 1)
 			throw std::runtime_error("Chain ID " + chainID + " won't fit into a PDB file");

@@ -3476,7 +3446,8 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 		if (charge != 0)
 			sCharge = std::to_string(charge) + (charge > 0 ? '+' : '-');

-		pdbFile << cif::format("%-6.6s%5d %-4.4s%1.1s%3.3s %1.1s%4d%1.1s   %8.3f%8.3f%8.3f%6.2f%6.2f          %2.2s%2.2s", group, serial, name, altLoc, resName, chainID, resSeq, iCode, x, y, z, occupancy, tempFactor, element, sCharge) << '\n';
+		pdbFile << cif::format("{:<6.6s}{:5} {:<4.4s}{:1.1s}{:3.3s} {:1.1s}{:4}{:1.1s}   {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f}          {:>2.2s}{:2.2s}",
+			group, serial, name, altLoc, resName, chainID, resSeq, iCode, x, y, z, occupancy, tempFactor, element, sCharge) << '\n';

 		++numCoord;

@@ -3491,7 +3462,7 @@ std::tuple<int, int> WriteCoordinatesForModel(std::ostream &pdbFile, const datab
 			tie(u11, u22, u33, u12, u13, u23) =
 				ai.get("U[1][1]", "U[2][2]", "U[3][3]", "U[1][2]", "U[1][3]", "U[2][3]");

-			pdbFile << cif::format("ANISOU%5d %-4.4s%1.1s%3.3s %1.1s%4d%1.1s %7d%7d%7d%7d%7d%7d      %2.2s%2.2s", serial, name, altLoc, resName, chainID, resSeq, iCode, std::lrintf(u11 * 10000), std::lrintf(u22 * 10000), std::lrintf(u33 * 10000), std::lrintf(u12 * 10000), std::lrintf(u13 * 10000), std::lrintf(u23 * 10000), element, sCharge) << '\n';
+			pdbFile << cif::format("ANISOU{:5} {:<4.4s}{:1.1s}{:3.3s} {:1.1s}{:4}{:1.1s} {:7}{:7}{:7}{:7}{:7}{:7}      {:2.2s}{:2.2s}", serial, name, altLoc, resName, chainID, resSeq, iCode, std::lrintf(u11 * 10000), std::lrintf(u22 * 10000), std::lrintf(u33 * 10000), std::lrintf(u12 * 10000), std::lrintf(u13 * 10000), std::lrintf(u23 * 10000), element, sCharge) << '\n';
 		}

 		++serial;
@@ -3543,7 +3514,7 @@ std::tuple<int, int> WriteCoordinate(std::ostream &pdbFile, const datablock &db)
 		for (int model_nr : models)
 		{
 			if (models.size() > 1)
-				pdbFile << cif::format("MODEL     %4d",  model_nr) << '\n';
+				pdbFile << cif::format("MODEL     {:4}",  model_nr) << '\n';

 			std::set<std::string> TERminatedChains;
 			auto n = WriteCoordinatesForModel(pdbFile, db, last_resseq_for_chain_map, TERminatedChains, model_nr);
@@ -3615,7 +3586,7 @@ std::string get_HEADER_line(const datablock &db, std::string::size_type truncate
 		}
 	}

-	return FixStringLength(cif::format("HEADER    %-40.40s%-9.9s   %-4.4s", keywords, date, db.name()).str(), truncate_at);
+	return FixStringLength(cif::format("HEADER    {:<40.40s}{:<9.9s}   {:<4.4s}", keywords, date, db.name()), truncate_at);
 }

 std::string get_COMPND_line(const datablock &db, std::string::size_type truncate_at)
@@ -3788,7 +3759,7 @@ void write(std::ostream &os, const datablock &db)
 	numXform = WriteCoordinateTransformation(os, db);
 	std::tie(numCoord, numTer) = WriteCoordinate(os, db);

-	os << cif::format("MASTER    %5d    0%5d%5d%5d%5d%5d%5d%5d%5d%5d%5d",  numRemark,  numHet,  numHelix,  numSheet,  numTurn,  numSite,  numXform,  numCoord,  numTer,  numConect,  numSeq) << '\n'
+	os << cif::format("MASTER    {:5}    0{:5}{:5}{:5}{:5}{:5}{:5}{:5}{:5}{:5}{:5}",  numRemark,  numHet,  numHelix,  numSheet,  numTurn,  numSite,  numXform,  numCoord,  numTer,  numConect,  numSeq) << '\n'
 			<< "END\n";
 }

--- a/src/pdb/pdb2cif.cpp
+++ b/src/pdb/pdb2cif.cpp
@@ -32,6 +32,7 @@
 #include <map>
 #include <set>
 #include <stack>
+#include <stdexcept>

 using cif::category;
 using cif::datablock;
@@ -895,12 +896,7 @@ class PDBFileParser
 				if (year < 1950)
 					year += 100;

-				std::stringstream ss;
-				ss << std::setw(4) << std::setfill('0') << year << '-'
-				   << std::setw(2) << std::setfill('0') << month << '-'
-				   << std::setw(2) << std::setfill('0') << day;
-
-				s = ss.str();
+				s = cif::format("{:04}-{:02}-{:02}", year, month, day);
 			}
 			else if (regex_match(s, m, rx2))
 			{
@@ -912,7 +908,7 @@ class PDBFileParser
 				if (year < 1950)
 					year += 100;

-				s = cif::format("%04d-%02d", year, month).str();
+				s = cif::format("{:04}-{:02}", year, month);
 			}
 			else
 				ec = error::make_error_code(error::pdbErrors::invalidDate);
@@ -3341,18 +3337,18 @@ void PDBFileParser::ParseRemark350()
 								{ "type", type },
 								// { "name", "" },
 							    // { "symmetryOperation", "" },
-								{ "matrix[1][1]", cif::format("%12.10f", mat[0]).str() },
-								{ "matrix[1][2]", cif::format("%12.10f", mat[1]).str() },
-								{ "matrix[1][3]", cif::format("%12.10f", mat[2]).str() },
-								{ "vector[1]", cif::format("%12.10f", vec[0]).str() },
-								{ "matrix[2][1]", cif::format("%12.10f", mat[3]).str() },
-								{ "matrix[2][2]", cif::format("%12.10f", mat[4]).str() },
-								{ "matrix[2][3]", cif::format("%12.10f", mat[5]).str() },
-								{ "vector[2]", cif::format("%12.10f", vec[1]).str() },
-								{ "matrix[3][1]", cif::format("%12.10f", mat[6]).str() },
-								{ "matrix[3][2]", cif::format("%12.10f", mat[7]).str() },
-								{ "matrix[3][3]", cif::format("%12.10f", mat[8]).str() },
-								{ "vector[3]", cif::format("%12.10f", vec[2]).str() }
+								{ "matrix[1][1]", cif::format("{:12.10f}", mat[0]) },
+								{ "matrix[1][2]", cif::format("{:12.10f}", mat[1]) },
+								{ "matrix[1][3]", cif::format("{:12.10f}", mat[2]) },
+								{ "vector[1]", cif::format("{:12.10f}", vec[0]) },
+								{ "matrix[2][1]", cif::format("{:12.10f}", mat[3]) },
+								{ "matrix[2][2]", cif::format("{:12.10f}", mat[4]) },
+								{ "matrix[2][3]", cif::format("{:12.10f}", mat[5]) },
+								{ "vector[2]", cif::format("{:12.10f}", vec[1]) },
+								{ "matrix[3][1]", cif::format("{:12.10f}", mat[6]) },
+								{ "matrix[3][2]", cif::format("{:12.10f}", mat[7]) },
+								{ "matrix[3][3]", cif::format("{:12.10f}", mat[8]) },
+								{ "vector[3]", cif::format("{:12.10f}", vec[2]) }
 							});
 																			// clang-format on

@@ -4318,7 +4314,7 @@ void PDBFileParser::ConstructEntities()
 	}

 	// build sugar trees first
-	ConstructSugarTrees(asymNr);
+	// ConstructSugarTrees(asymNr);

 	// done with the sugar, resume operation as before

@@ -5772,6 +5768,9 @@ void PDBFileParser::ParseCoordinate(int modelNr)
 		std::string element = vS(77, 78);    //	77 - 78        LString(2)    element      Element symbol, right-justified.
 		std::string charge = vS(79, 80);     //	79 - 80        LString(2)    charge       Charge  on the atom.

+		if (element.empty())
+			throw std::runtime_error("Empty element column in PDB file at line " + std::to_string(mRec->mLineNr));
+
 		std::string entityID = mAsymID2EntityID[asymID];

 		charge = pdb2cifCharge(charge);
@@ -5850,7 +5849,7 @@ void PDBFileParser::ParseCoordinate(int modelNr)

 			auto f = [](float f) -> std::string
 			{
-				return cif::format("%6.4f", f).str();
+				return cif::format("{:6.4f}", f);
 			};

 			// clang-format off
@@ -6406,7 +6405,7 @@ file read(std::istream &is)
 		if (std::isalpha(ch) and std::toupper(ch) != 'D')
 		{
 			read_pdb_file(is, result);
-			reconstruct_pdbx(result);
+			fixup_pdbx(result);
 		}
 		else
 		{
@@ -6419,22 +6418,37 @@ 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."));
 			}

-			// 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.
-			try
+			if (not(result.empty() or result.front().empty()))
 			{
-				cif::mm::structure s(result);
-			}
-			catch (const std::exception &e)
-			{
-				reconstruct_pdbx(result);
+				if (auto &db = result.front(); db.get("audit_conform") == nullptr)
+					reconstruct_pdbx(result);
+				else
+				{
+					try
+					{
+						// Try to see if we can create an mm::structure out of this data.
+						// If that fails, we need to reconstruct a PDBx file out of it.
+
+						cif::mm::structure s(result);
+					}
+					catch (const std::exception &e)
+					{
+						reconstruct_pdbx(result);
+					}
+				}
 			}
 		}
 	}

 	// Must be a PDB like file, right?
-	if (not result.empty() and result.front().get_validator() == nullptr)
-		result.front().set_validator(&validator_factory::instance().get("mmcif_pdbx.dic"));
+	if (not result.empty())
+	{
+		auto &db = result.front();
+		if (db.get_validator() == nullptr)
+			db.set_validator(&validator_factory::instance().get("mmcif_pdbx.dic"));
+		if (db.is_valid())
+			db.get_validator()->fill_audit_conform(db["audit_conform"]);
+	}

 	return result;
 }
--- a/src/pdb/reconstruct.cpp
+++ b/src/pdb/reconstruct.cpp
@@ -25,6 +25,7 @@
 */

 #include "cif++.hpp"
+#include "cif++/row.hpp"

 // --------------------------------------------------------------------

@@ -138,15 +139,15 @@ void checkEntities(datablock &db)
 				auto compound = cf.create(comp_id);
 				if (compound)
 					formula_weight += compound->formula_weight();
-				else if (cif::VERBOSE > 0)
-					std::clog << "missing information for compound " + comp_id << '\n';
+				// else if (cif::VERBOSE > 0)
+				// 	std::clog << "missing information for compound " + comp_id << '\n';
 				++n;
 			}

-			formula_weight -= (n - 1) * 18.015;
+			formula_weight -= (n - 1) * 18.015f;
 		}
 		else if (type == "water")
-			formula_weight = 18.015;
+			formula_weight = 18.015f;
 		else if (type == "branched")
 		{
 			int n = 0;
@@ -156,12 +157,12 @@ void checkEntities(datablock &db)
 				auto compound = cf.create(comp_id);
 				if (compound)
 					formula_weight += compound->formula_weight();
-				else if (cif::VERBOSE > 0)
-					std::clog << "missing information for compound " + comp_id << '\n';
+				// else if (cif::VERBOSE > 0)
+				// 	std::clog << "missing information for compound " + comp_id << '\n';
 				++n;
 			}

-			formula_weight -= (n - 1) * 18.015;
+			formula_weight -= (n - 1) * 18.015f;
 		}
 		else if (type == "non-polymer")
 		{
@@ -171,7 +172,7 @@ void checkEntities(datablock &db)
 				auto compound = cf.create(*comp_id);
 				if (not compound)
 				{
-					std::cerr << "missing information for compound " << *comp_id << "\n";
+					// std::cerr << "missing information for compound " << *comp_id << "\n";
 					continue;
 				}
 				formula_weight = compound->formula_weight();
@@ -264,8 +265,8 @@ void createEntityIDs(datablock &db)

 		std::string comp_id = get_comp_id(k);

-		for (auto &k : e)
-			atom_site.update_value(get_condition(k), "label_entity_id", entity_id);
+		for (auto &k2 : e)
+			atom_site.update_value(get_condition(k2), "label_entity_id", entity_id);
 	}

 	if (not waters.empty())
@@ -319,7 +320,7 @@ void fillLabelAsymID(category &atom_site)
 		{
 			if (not mapAuthAsymIDAndEntityToLabelAsymID.contains(key))
 			{
-				std::string asym_id = cif_id_for_number(mapAuthAsymIDAndEntityToLabelAsymID.size());
+				std::string asym_id = cif_id_for_number(static_cast<int>(mapAuthAsymIDAndEntityToLabelAsymID.size()));
 				mapAuthAsymIDAndEntityToLabelAsymID[key] = asym_id;
 			}
 		}
@@ -484,7 +485,8 @@ void checkAtomRecords(datablock &db)
 		if (not compound)
 		{
 			missingCompounds.insert(comp_id);
-			std::cerr << "Missing compound information for " << comp_id << "\n";
+			// if (cif::VERBOSE > 0)
+			// 	std::cerr << "Missing compound information for " << comp_id << "\n";
 			continue;
 		}

@@ -542,7 +544,7 @@ void checkAtomRecords(datablock &db)

 		// Rewrite the coordinates and other items that look better in a fixed format
 		// Be careful not to nuke invalidly formatted data here
-		for (auto [item_name, prec] : std::vector<std::tuple<std::string_view, std::string::size_type>>{
+		for (auto [item_name, prec] : std::vector<std::tuple<std::string_view, int>>{
 				 { "cartn_x", 3 },
 				 { "cartn_y", 3 },
 				 { "cartn_z", 3 },
@@ -557,11 +559,11 @@ void checkAtomRecords(datablock &db)
 			if (auto [ptr, ec] = cif::from_chars(s.data(), s.data() + s.length(), v); (bool)ec)
 				continue;

-			if (s.length() < prec + 1 or s[s.length() - prec - 1] != '.')
+			if (s.length() < prec + 1UL or s[s.length() - prec - 1] != '.')
 			{
 				char b[12];

-				if (auto [ptr, ec] = cif::to_chars(b, b + sizeof(b), v, cif::chars_format::fixed, prec); (bool)ec)
+				if (auto [ptr, ec] = cif::to_chars(b, b + sizeof(b), v, cif::chars_format::fixed, prec); ec == std::errc{})
 					row.assign(item_name, { b, static_cast<std::string::size_type>(ptr - b) }, false, false);
 			}
 		}
@@ -628,13 +630,13 @@ void checkAtomAnisotropRecords(datablock &db)

 		if (row["pdbx_auth_alt_id"].empty() and not parent["pdbx_auth_alt_id"].empty())
 			row["pdbx_auth_alt_id"] = parent["pdbx_auth_alt_id"].text();
-		if (row["pdbx_label_seq_id"].empty() and not parent["pdbx_label_seq_id"].empty())
+		if (row["pdbx_label_seq_id"].empty() and not parent["label_seq_id"].empty())
 			row["pdbx_label_seq_id"] = parent["label_seq_id"].text();
-		if (row["pdbx_label_asym_id"].empty() and not parent["pdbx_label_asym_id"].empty())
+		if (row["pdbx_label_asym_id"].empty() and not parent["label_asym_id"].empty())
 			row["pdbx_label_asym_id"] = parent["label_asym_id"].text();
-		if (row["pdbx_label_atom_id"].empty() and not parent["pdbx_label_atom_id"].empty())
+		if (row["pdbx_label_atom_id"].empty() and not parent["label_atom_id"].empty())
 			row["pdbx_label_atom_id"] = parent["label_atom_id"].text();
-		if (row["pdbx_label_comp_id"].empty() and not parent["pdbx_label_comp_id"].empty())
+		if (row["pdbx_label_comp_id"].empty() and not parent["label_comp_id"].empty())
 			row["pdbx_label_comp_id"] = parent["label_comp_id"].text();
 		// if (row["pdbx_PDB_model_num"].empty() and not parent["pdbx_PDB_model_num"].empty())
 		// 	row["pdbx_PDB_model_num"] = parent["pdbx_PDB_model_num"].text();
@@ -722,7 +724,7 @@ void createEntity(datablock &db)

 		std::string type, desc;
 		float weight = 0;
-		int count = 0;
+		size_t count = 0;

 		auto first_comp_id = std::get<0>(content.front());

@@ -1167,7 +1169,7 @@ void createPdbxNonpolyScheme(datablock &db)
 		for (int ndb_nr = 1; auto row : atom_site.find("label_entity_id"_key == entity_id and "label_comp_id"_key == comp_id))
 		{
 			// Skip existing records
-			auto linked = atom_site.get_linked(row, pdbx_nonpoly_scheme);
+			auto linked = atom_site.get_children(row, pdbx_nonpoly_scheme);
 			if (not linked.empty())
 				continue;

@@ -1242,6 +1244,101 @@ void createPdbxBranchScheme(datablock &db)
 	}
 }

+void reconstruct_index_for_category(const validator &validator, category &cat, datablock &db)
+{
+	auto cv = validator.get_validator_for_category(cat.name());
+
+	enum class State
+	{
+		Start,
+		MissingKeys,
+		DuplicateKeys
+	} state = State::Start;
+
+	for (;;)
+	{
+		// See if we can build an index
+		try
+		{
+			cat.set_validator(&validator, db);
+		}
+		catch (const missing_key_error &ex)
+		{
+			if (state == State::MissingKeys)
+			{
+				if (cif::VERBOSE > 0)
+					std::clog << "Repairing failed for category " << cat.name() << ", missing keys remain: " << ex.what() << '\n';
+
+				throw;
+			}
+
+			state = State::MissingKeys;
+
+			auto key = ex.get_key();
+
+			if (cif::VERBOSE > 1)
+				std::clog << "Need to add key " << key << " to category " << cat.name() << '\n';
+
+			for (auto row : cat)
+			{
+				auto ord = row.get<std::string>(key.c_str());
+				if (ord.empty())
+					row.assign({ //
+						{ key, cat.get_unique_value(key) } });
+			}
+
+			continue;
+		}
+		catch (const duplicate_key_error &ex)
+		{
+			if (state == State::DuplicateKeys)
+			{
+				if (cif::VERBOSE > 0)
+					std::clog << "Repairing failed for category " << cat.name() << ", duplicate keys remain: " << ex.what() << '\n';
+
+				throw;
+			}
+
+			state = State::DuplicateKeys;
+
+			if (cif::VERBOSE > 0)
+				std::clog << "Attempt to fix " << cat.name() << " failed: " << ex.what() << '\n';
+
+			// replace items that do not define a relation to a parent
+
+			std::set<std::string> replaceableKeys;
+			for (auto key : cv->m_keys)
+			{
+				bool replaceable = true;
+				for (auto lv : validator.get_links_for_child(cat.name()))
+				{
+					if (find(lv->m_child_keys.begin(), lv->m_child_keys.end(), key) != lv->m_child_keys.end())
+					{
+						replaceable = false;
+						break;
+					}
+				}
+
+				if (replaceable)
+					replaceableKeys.insert(key);
+			}
+
+			if (replaceableKeys.empty())
+				throw std::runtime_error("Cannot repair category " + cat.name() + " since it contains duplicate keys that cannot be replaced");
+
+			for (auto key : replaceableKeys)
+			{
+				for (auto row : cat)
+					row.assign(key, cat.get_unique_value(key), false, false);
+			}
+
+			continue;
+		}
+
+		break;
+	}
+}
+
 bool reconstruct_pdbx(file &file)
 {
 	if (file.empty())
@@ -1337,7 +1434,7 @@ bool reconstruct_pdbx(file &file, const validator &validator)
 				              iv->m_type != nullptr and
 				              iv->m_type->m_primitive_type == cif::DDL_PrimitiveType::Numb;

-				for (std::size_t ix = 0; auto row : cat)
+				for (int ix = 0; auto row : cat)
 				{
 					if (number)
 						row.assign(key, std::to_string(++ix), false, false);
@@ -1408,95 +1505,7 @@ bool reconstruct_pdbx(file &file, const validator &validator)
 				}
 			}

-			enum class State
-			{
-				Start,
-				MissingKeys,
-				DuplicateKeys
-			} state = State::Start;
-
-			for (;;)
-			{
-				// See if we can build an index
-				try
-				{
-					cat.set_validator(&validator, db);
-				}
-				catch (const missing_key_error &ex)
-				{
-					if (state == State::MissingKeys)
-					{
-						if (cif::VERBOSE > 0)
-							std::clog << "Repairing failed for category " << cat.name() << ", missing keys remain: " << ex.what() << '\n';
-
-						throw;
-					}
-
-					state = State::MissingKeys;
-
-					auto key = ex.get_key();
-
-					if (cif::VERBOSE > 0)
-						std::clog << "Need to add key " << key << " to category " << cat.name() << '\n';
-
-					for (auto row : cat)
-					{
-						auto ord = row.get<std::string>(key.c_str());
-						if (ord.empty())
-							row.assign({ //
-								{ key, cat.get_unique_value(key) } });
-					}
-
-					continue;
-				}
-				catch (const duplicate_key_error &ex)
-				{
-					if (state == State::DuplicateKeys)
-					{
-						if (cif::VERBOSE > 0)
-							std::clog << "Repairing failed for category " << cat.name() << ", duplicate keys remain: " << ex.what() << '\n';
-
-						throw;
-					}
-
-					state = State::DuplicateKeys;
-
-					if (cif::VERBOSE > 0)
-						std::clog << "Attempt to fix " << cat.name() << " failed: " << ex.what() << '\n';
-
-					// replace items that do not define a relation to a parent
-
-					std::set<std::string> replaceableKeys;
-					for (auto key : cv->m_keys)
-					{
-						bool replaceable = true;
-						for (auto lv : validator.get_links_for_child(cat.name()))
-						{
-							if (find(lv->m_child_keys.begin(), lv->m_child_keys.end(), key) != lv->m_child_keys.end())
-							{
-								replaceable = false;
-								break;
-							}
-						}
-
-						if (replaceable)
-							replaceableKeys.insert(key);
-					}
-
-					if (replaceableKeys.empty())
-						throw std::runtime_error("Cannot repair category " + cat.name() + " since it contains duplicate keys that cannot be replaced");
-
-					for (auto key : replaceableKeys)
-					{
-						for (auto row : cat)
-							row.assign(key, cat.get_unique_value(key), false, false);
-					}
-
-					continue;
-				}
-
-				break;
-			}
+			reconstruct_index_for_category(validator, cat, db);
 		}
 		catch (const std::exception &ex)
 		{
@@ -1537,7 +1546,7 @@ bool reconstruct_pdbx(file &file, const validator &validator)

 	if (auto cat = db.get("ndb_poly_seq_scheme"); cat == nullptr or cat->empty())
 		comparePolySeqSchemes(db);
-	
+
 	createPdbxNonpolyScheme(db);

 	// Create a minimal set of branch records
@@ -1554,4 +1563,111 @@ bool reconstruct_pdbx(file &file, const validator &validator)
 	return valid and is_valid_pdbx_file(file, validator);
 }

+// --------------------------------------------------------------------
+
+void fixup_pdbx(file &file)
+{
+	if (file.empty())
+		throw std::runtime_error("Cannot reconstruct PDBx, file seems to be empty");
+
+	auto &db = file.front();
+
+	if (auto ac = db.get("audit_conform"); ac != nullptr)
+		fixup_pdbx(file, validator_factory::instance().get(*ac));
+	else
+		fixup_pdbx(file, validator_factory::instance().get("mmcif_pdbx.dic"));
+}
+
+void fixup_pdbx(file &file, const validator &validator)
+{
+	if (file.empty())
+		throw std::runtime_error("Cannot reconstruct PDBx, file seems to be empty");
+
+	// assuming the first datablock contains the entry ...
+	auto &db = file.front();
+
+	if (auto cat = db.get("atom_site"); cat == nullptr or cat->empty())
+		throw std::runtime_error("Cannot reconstruct PDBx file, atom data missing");
+
+	// ... and any additional datablock will contain compound information
+	cif::compound_source cs(file);
+
+	// Be silent about missing compound info in fixup
+	auto &cf = compound_factory::instance();
+	bool save_report = cf.get_report_missing();
+	cf.set_report_missing(cif::VERBOSE > 1);
+
+	std::string entry_id;
+
+	// Phenix files do not have an entry record
+	if (auto cat = db.get("entry"); cat == nullptr or cat->empty())
+	{
+		entry_id = db.name();
+		category entry("entry");
+		entry.emplace({ { "id", entry_id } });
+		db.emplace_back(std::move(entry));
+	}
+	else
+	{
+		auto &entry = db["entry"];
+		if (entry.size() != 1)
+			throw std::runtime_error("Unexpected size of entry category");
+
+		entry_id = entry.front().get<std::string>("id");
+	}
+
+	// Start with chem_comp, it is often missing many fields
+	// that can easily be filled in.
+	checkChemCompRecords(db);
+
+	// If the data is really horrible, it might not contain entities
+	if (not db["atom_site"].find_first(key("label_entity_id") != null))
+		createEntityIDs(db);
+
+	// Now see if atom records make sense at all, but in a silent way, this time
+	checkAtomRecords(db);
+
+	db["chem_comp"].reorder_by_index();
+
+	// See if we can easily reconstruct missing data fields in order to create an index
+	for (auto &cat : db)
+	{
+		try
+		{
+			cat.set_validator(&validator, db);
+		}
+		catch (const missing_key_error &)
+		{
+			reconstruct_index_for_category(validator, cat, db);
+		}
+	}
+
+	db.set_validator(&validator);
+
+	// Now create any missing categories
+	// Next make sure we have struct_asym records
+	if (auto cat = db.get("struct_asym"); cat == nullptr or cat->empty())
+		createStructAsym(db);
+
+	if (auto cat = db.get("entity"); cat == nullptr or cat->empty())
+		createEntity(db);
+
+	if (auto cat = db.get("pdbx_poly_seq_scheme"); cat == nullptr or cat->empty())
+		createPdbxPolySeqScheme(db);
+
+	if (auto cat = db.get("ndb_poly_seq_scheme"); cat == nullptr or cat->empty())
+		comparePolySeqSchemes(db);
+
+	createPdbxNonpolyScheme(db);
+
+	// Create a minimal set of branch records
+	createPdbxBranchScheme(db);
+
+	// fill in missing formula_weight, e.g.
+	checkEntities(db);
+
+	// That's it
+	cf.set_report_missing(save_report);
+}
+
 } // namespace cif::pdb
--- a/src/pdb/validate-pdbx.cpp
+++ b/src/pdb/validate-pdbx.cpp
@@ -61,8 +61,6 @@ 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;
 }
@@ -92,7 +90,7 @@ bool is_valid_pdbx_file(const file &file, const validator &validator, std::error
 {
 	using namespace cif::literals;

-	bool result = true;
+	bool result = true, warned_missing_parents = false;

 	try
 	{
@@ -129,10 +127,18 @@ bool is_valid_pdbx_file(const file &file, const validator &validator, std::error
 			if (not cf.is_monomer(comp_id))
 				continue;

-			auto p = pdbx_poly_seq_scheme.find(get_parents_condition(validator, r, pdbx_poly_seq_scheme));
+			auto cond = get_parents_condition(validator, r, pdbx_poly_seq_scheme);
+			if (not cond)
+			{
+				if (VERBOSE > 0 and std::exchange(warned_missing_parents, true) == false)
+					std::cerr << "warning: missing links for atom_site/pdbx_poly_seq_scheme\n";
+				continue;
+			}
+
+			auto p = pdbx_poly_seq_scheme.find(std::move(cond));
 			if (p.size() != 1)
 			{
-				if (cif::VERBOSE > 0)
+				if (VERBOSE > 0)
 					std::clog << "In atom_site record: " << r["id"].text() << '\n';
 				throw std::runtime_error("For each monomer in atom_site there should be exactly one pdbx_poly_seq_scheme record");
 			}
@@ -274,7 +280,7 @@ bool is_valid_pdbx_file(const file &file, const validator &validator, std::error

 			if (not seq.has_value())
 			{
-				if (cif::VERBOSE > 0)
+				if (VERBOSE > 0)
 					std::clog << "Warning: entity_poly has no sequence for entity_id " << entity_id << '\n';
 			}
 			else
@@ -287,7 +293,7 @@ bool is_valid_pdbx_file(const file &file, const validator &validator, std::error

 			if (not seq_can.has_value())
 			{
-				if (cif::VERBOSE > 1)
+				if (VERBOSE > 1)
 					std::clog << "Warning: entity_poly has no canonical sequence for entity_id " << entity_id << '\n';
 			}
 			else
@@ -304,7 +310,7 @@ bool is_valid_pdbx_file(const file &file, const validator &validator, std::error
 	catch (const std::exception &ex)
 	{
 		result = false;
-		if (cif::VERBOSE > 0)
+		if (VERBOSE > 0)
 			std::clog << ex.what() << '\n';
 		ec = make_error_code(validation_error::not_valid_pdbx);
 	}
--- a/src/symmetry.cpp
+++ b/src/symmetry.cpp
@@ -32,6 +32,11 @@

 #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
@@ -90,10 +95,10 @@ float cell::get_volume() const
 	auto cos_beta = std::cos(beta);
 	auto cos_gamma = std::cos(gamma);

-	auto vol = m_a * m_b * m_c;
+	double vol = m_a * m_b * m_c;
 	vol *= std::sqrt(1.0f - cos_alpha * cos_alpha - cos_beta * cos_beta - cos_gamma * cos_gamma + 2.0f * cos_alpha * cos_beta * cos_gamma);

-	return vol;
+	return static_cast<float>(vol);
 }

 // --------------------------------------------------------------------
--- a/src/validate.cpp
+++ b/src/validate.cpp
@@ -36,16 +36,11 @@

 // The validator depends on regular expressions. Unfortunately,
 // the implementation of std::regex in g++ is buggy and crashes
-// on reading the pdbx dictionary. Therefore, in case g++ is used
-// the code will use boost::regex instead.
+// on reading the pdbx dictionary. We used to use boost regex
+// instead but using pcre2 is even easier and faster.

-#if USE_BOOST_REGEX
-# include <boost/regex.hpp>
-using boost::regex;
-#else
-# include <regex>
-using std::regex;
-#endif
+#define PCRE2_CODE_UNIT_WIDTH 8
+#include <pcre2.h>

 namespace cif
 {
@@ -67,14 +62,67 @@ validation_exception::validation_exception(std::error_code ec, std::string_view

 // --------------------------------------------------------------------

-struct regex_impl : public regex
+// struct regex_impl : public regex
+// {
+// 	regex_impl(std::string_view rx)
+// 		: regex(rx.begin(), rx.end(), regex::extended | regex::optimize)
+// 	{
+// 	}
+// };
+
+struct regex_impl
 {
-	regex_impl(std::string_view rx)
-		: regex(rx.begin(), rx.end(), regex::extended | regex::optimize)
-	{
-	}
+	regex_impl(std::string_view rx);
+	~regex_impl();
+
+	regex_impl(const regex_impl &) = delete;
+	regex_impl &operator=(const regex_impl &) = delete;
+
+	bool match(std::string_view v) const;
+
+  private:
+
+	pcre2_code *m_rx = nullptr;
+	pcre2_match_data *m_data = nullptr;
 };

+regex_impl::regex_impl(std::string_view rx)
+{
+	int err_code;
+	size_t err_offset;
+	m_rx = pcre2_compile((PCRE2_SPTR)rx.data(), rx.length(), 0, &err_code, &err_offset, nullptr);
+	if (m_rx == nullptr)
+	{
+		PCRE2_UCHAR buffer[256];
+		int n = pcre2_get_error_message(err_code, buffer, sizeof(buffer));
+
+		throw std::runtime_error(std::string("PCRE2 compilation failed: ") + std::string{ (char *)buffer, (char *)buffer + n });
+	}
+
+	m_data = pcre2_match_data_create_from_pattern(m_rx, nullptr);
+}
+
+regex_impl::~regex_impl()
+{
+	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;
+}
+
 // --------------------------------------------------------------------

 DDL_PrimitiveType map_to_primitive_type(std::string_view s, std::error_code &ec) noexcept
@@ -233,7 +281,7 @@ 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 regex_match(value.begin(), value.end(), *m_type->m_rx))
+		if (m_type != nullptr and not m_type->m_rx->match(value))
 			ec = make_error_code(validation_error::value_does_not_match_rx);
 		else if (not m_enums.empty() and m_enums.count(std::string{ value }) == 0)
 			ec = make_error_code(validation_error::value_is_not_in_enumeration_list);
@@ -552,6 +600,9 @@ const validator &validator_factory::get(const category &audit_conform)
 validator validator_factory::construct_validator(std::string_view name, std::optional<std::string> version)
 {
 	auto data = load_resource(name);
+	if (not data and name == "mmcif_pdbx_v50")
+		data = load_resource("mmcif_pdbx.dic");
+
 	if (not data)
 		throw std::runtime_error("Could not load dictionary " + std::string{ name });

--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -22,13 +22,14 @@ list(
 	CIFPP_tests
 	unit-v2
 	unit-3d
-	format
 	model
+	query
 	rename-compound
 	sugar
 	spinner
 	# reconstruction
-	validate-pdbx)
+	validate-pdbx
+	)

 add_library(test-main OBJECT "${CMAKE_CURRENT_SOURCE_DIR}/test-main.cpp")

--- a/test/model-test.cpp
+++ b/test/model-test.cpp
@@ -431,3 +431,169 @@ TEST_CASE("remove_residue_1")

 	REQUIRE_NOTHROW(s.validate_atoms());
 }
+
+// --------------------------------------------------------------------
+// Tests for structure_open_options
+
+TEST_CASE("options_1")
+{
+	using namespace cif::literals;
+
+	const std::filesystem::path example(gTestDir / ".." / "examples" / "1cbs.cif.gz");
+	cif::file file(example.string());
+
+	auto &cf = cif::compound_factory::instance();
+
+	SECTION("skip_water")
+	{
+		cif::mm::structure s(file, 1, { .skip_water = true });
+
+		REQUIRE_NOTHROW(s.validate_atoms());
+
+		for (auto a : s.atoms())
+			CHECK_FALSE(a.is_water());
+	}
+
+	SECTION("skip_hetatom")
+	{
+		cif::mm::structure s(file, 1, { .skip_hetatom = true });
+
+		REQUIRE_NOTHROW(s.validate_atoms());
+
+		for (auto a : s.atoms())
+			CHECK((a.is_water() or cf.is_peptide(a.get_label_comp_id()) or cf.is_base(a.get_label_comp_id())));
+	}
+
+	SECTION("selected_asyms")
+	{
+		cif::mm::structure s(file, 1, { .asyms = { "A" } });
+
+		REQUIRE_NOTHROW(s.validate_atoms());
+
+		for (auto a : s.atoms())
+			CHECK(a.get_label_asym_id() == "A");
+	}
+
+	SECTION("min-b-factor")
+	{
+		cif::mm::structure s(file, 1, { .min_b_factor = 20.f });
+
+		REQUIRE_NOTHROW(s.validate_atoms());
+
+		for (auto a : s.atoms())
+			CHECK(a.get_property_float("B_iso_or_equiv") >= 20.f);
+	}
+
+	SECTION("max-b-factor")
+	{
+		cif::mm::structure s(file, 1, { .max_b_factor = 20.f });
+
+		REQUIRE_NOTHROW(s.validate_atoms());
+
+		for (auto a : s.atoms())
+			CHECK(a.get_property_float("B_iso_or_equiv") <= 20.f);
+	}
+}
+
+TEST_CASE("options_2")
+{
+
+	auto data = R"(
+data_TEST
+# 
+_pdbx_nonpoly_scheme.asym_id         A 
+_pdbx_nonpoly_scheme.ndb_seq_num     1 
+_pdbx_nonpoly_scheme.entity_id       1 
+_pdbx_nonpoly_scheme.mon_id          HEM 
+_pdbx_nonpoly_scheme.pdb_seq_num     1 
+_pdbx_nonpoly_scheme.auth_seq_num    1 
+_pdbx_nonpoly_scheme.pdb_mon_id      HEM 
+_pdbx_nonpoly_scheme.auth_mon_id     HEM 
+_pdbx_nonpoly_scheme.pdb_strand_id   A 
+_pdbx_nonpoly_scheme.pdb_ins_code    . 
+#
+loop_
+_atom_site.id
+_atom_site.auth_asym_id
+_atom_site.label_alt_id
+_atom_site.label_asym_id
+_atom_site.label_atom_id
+_atom_site.label_comp_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.type_symbol
+_atom_site.group_PDB
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.B_iso_or_equiv
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_comp_id
+_atom_site.auth_atom_id
+_atom_site.pdbx_PDB_model_num
+1 A A A CHA HEM 1 . C HETATM ? -5.248 39.769 -0.250 0.75 7.67 ? 1 HEM CHA 1
+3 A A A CHB HEM 1 . C HETATM ? -3.774 36.790 3.280  0.75 7.05 ? 1 HEM CHB 1
+2 A A A CHC HEM 1 . C HETATM ? -2.879 33.328 0.013  0.75 7.69 ? 1 HEM CHC 1
+4 A A A CHD HEM 1 . C HETATM ? -4.342 36.262 -3.536 0.75 8.00 ? 1 HEM CHD 1
+5 A B A CHA HEM 1 . C HETATM ? -5.248 39.769 -0.250 0.25 7.67 ? 1 HEM CHA 1
+6 A B A CHB HEM 1 . C HETATM ? -3.774 36.790 3.280  0.25 7.05 ? 1 HEM CHB 1
+7 A B A CHC HEM 1 . C HETATM ? -2.879 33.328 0.013  0.25 7.69 ? 1 HEM CHC 1
+8 A B A CHD HEM 1 . C HETATM ? -4.342 36.262 -3.536 0.25 8.00 ? 1 HEM CHD 1
+#
+_chem_comp.id               HEM
+_chem_comp.type             NON-POLYMER
+_chem_comp.name             'PROTOPORPHYRIN IX CONTAINING FE'
+_chem_comp.formula          'C34 H32 Fe N4 O4'
+_chem_comp.formula_weight   616.487000
+#
+_pdbx_entity_nonpoly.entity_id   1
+_pdbx_entity_nonpoly.name        'PROTOPORPHYRIN IX CONTAINING FE'
+_pdbx_entity_nonpoly.comp_id     HEM
+#
+_entity.id                 1
+_entity.type               non-polymer
+_entity.pdbx_description   'PROTOPORPHYRIN IX CONTAINING FE'
+_entity.formula_weight     616.487000
+#
+_struct_asym.id                            A
+_struct_asym.entity_id                     1
+_struct_asym.pdbx_blank_PDB_chainid_flag   N
+_struct_asym.pdbx_modified                 N
+_struct_asym.details                       ?
+#
+)"_cf;
+
+	data.front().set_validator(&cif::validator_factory::instance().get("mmcif_pdbx.dic"));
+
+	SECTION("max")
+	{
+		cif::mm::structure s(data, 1, {
+			.occupancy_mode = cif::mm::occupancy_policy::MAX
+		});
+
+		REQUIRE(s.atoms().size() == 4);
+		CHECK(s.atoms().front().get_label_alt_id() == "A");
+	}
+
+	SECTION("min")
+	{
+		cif::mm::structure s(data, 1, {
+			.occupancy_mode = cif::mm::occupancy_policy::MIN
+		});
+
+		REQUIRE(s.atoms().size() == 4);
+		CHECK(s.atoms().front().get_label_alt_id() == "B");
+	}
+
+	SECTION("unoccupied")
+	{
+		cif::mm::structure s(data, 1, {
+			.occupancy_mode = cif::mm::occupancy_policy::UNOCCUPIED
+		});
+
+		CHECK(s.atoms().empty());
+	}
+}
--- a/test/format-test.cpp
+++ b/test/format-test.cpp
@@ -1,17 +1,17 @@
 /*-
 * SPDX-License-Identifier: BSD-2-Clause
- *
- * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
- *
+ * 
+ * Copyright (c) 2025 NKI/AVL, Netherlands Cancer Institute
+ * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
- *
+ * 
 * 1. Redistributions of source code must retain the above copyright notice, this
 *    list of conditions and the following disclaimer
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
- *
+ * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
@@ -24,38 +24,31 @@
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

-
 #include "test-main.hpp"

-#include <stdexcept>
-
 #include <cif++.hpp>

-// --------------------------------------------------------------------
+#include <iostream>
+#include <fstream>

-TEST_CASE("fmt_1")
+TEST_CASE("q-1")
 {
-	std::ostringstream os;
+	using namespace cif::literals;

-	std::string world("world");
-	os << cif::format("Hello, %-10.10s, the magic number is %d and pi is %g", world, 42, cif::kPI);
-	REQUIRE(os.str() == "Hello, world     , the magic number is 42 and pi is 3.14159");
+	cif::compound_factory::instance().push_dictionary(gTestDir / "REA.cif");
+
+	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);
+	}
+	

-	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';
-}
--- a/test/unit-3d-test.cpp
+++ b/test/unit-3d-test.cpp
@@ -30,6 +30,11 @@

 #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>

 // --------------------------------------------------------------------
@@ -296,7 +301,7 @@ TEST_CASE("m2q_0a")
 		auto d = cif::kSymopNrTable[i].symop().data();

 		Eigen::Matrix3f rot;
-		rot << d[0], d[1], d[2], d[3], d[4], d[5], d[6], d[7], d[8];
+		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]);

 		// check to see if this matrix contains a true rotation
 		if (rot * rot.transpose() != Eigen::Matrix3f::Identity() or rot.determinant() != 1)
@@ -435,11 +440,11 @@ TEST_CASE("symm_4")

 	// based on 2b8h
 	auto sg = cif::spacegroup(154); // p 32 2 1
-	auto c = cif::cell(107.516, 107.516, 338.487, 90.00, 90.00, 120.00);
+	auto c = cif::cell(107.516f, 107.516f, 338.487f, 90.00f, 90.00f, 120.00f);

-	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
+	cif::point a{ -8.688f, 79.351f, 10.439f };  // O6 NAG A 500
+	cif::point b{ -35.356f, 33.693f, -3.236f }; // CG2 THR D 400
+	cif::point sb(-6.916f, 79.34f, 3.236f);     // 4_565 copy of b

 	CHECK_THAT(distance(a, sg(a, c, "1_455"_symop)), Catch::Matchers::WithinRel(static_cast<float>(c.get_a()), 0.01f));
 	CHECK_THAT(distance(a, sg(a, c, "1_545"_symop)), Catch::Matchers::WithinRel(static_cast<float>(c.get_b()), 0.01f));
@@ -466,7 +471,7 @@ TEST_CASE("symm_4wvp_1")

 	cif::crystal c(db);

-	cif::point p{ -78.722, 98.528, 11.994 };
+	cif::point p{ -78.722f, 98.528f, 11.994f };
 	auto a = s.get_residue("A", 10, "").get_atom_by_atom_id("O");

 	auto sp1 = c.symmetry_copy(a.get_location(), "2_565"_symop);
--- a/test/unit-v2-test.cpp
+++ b/test/unit-v2-test.cpp
@@ -228,13 +228,13 @@ TEST_CASE("item_2")
 	cif::item i1("test1", std:: optional<float>());
 	REQUIRE(i1.value() == "?");

-	cif::item i2("test1", std::make_optional<float>(1));
+	cif::item i2("test1", std::make_optional<float>(1.f));
 	REQUIRE(i2.value() == "1");

 	cif::item i3("test1", std::optional<float>(), 2);
 	REQUIRE(i3.value() == "?");

-	cif::item i4("test1", std::make_optional<float>(1), 2);
+	cif::item i4("test1", std::make_optional<float>(1.f), 2);
 	REQUIRE(i4.value() == "1.00");
 }

@@ -3355,10 +3355,10 @@ _cat_1.id_2
 	using test_tuple_type = std::tuple<key_type,bool>;

 	test_tuple_type TESTS[] = {
-		{ {{"id", 1}, {"id_2", 10}}, true },
-		{ {{"id_2", 10}, {"id", 1}}, true },
-		{ {{"id", 1}, {"id_2", 20}}, false },
-		{ {{"id", 3} }, true },
+		{ {{"id", "1"}, {"id_2", "10"}}, true },
+		{ {{"id_2", "10"}, {"id", "1"}}, true },
+		{ {{"id", "1"}, {"id_2", "20"}}, false },
+		{ {{"id", "3"} }, true },
 	};

 	for (const auto &[key, test] : TESTS)
--- a/tools/depends.cmd
+++ b/tools/depends.cmd
@@ -1,10 +1,13 @@
@ECHO OFF
 SET ZLIB_VERSION=1.3
+SET PCRE2_VERSION=10.45

 IF NOT EXIST build_ci\libs (
  MKDIR build_ci\libs
 )
 CD build_ci\libs
+
+@REM Install ZLib
 IF NOT EXIST zlib-%ZLIB_VERSION%.zip (
  ECHO Downloading https://github.com/libarchive/zlib/archive/v%ZLIB_VERSION%.zip
  curl -L -o zlib-%ZLIB_VERSION%.zip https://github.com/libarchive/zlib/archive/v%ZLIB_VERSION%.zip || EXIT /b 1
@@ -14,9 +17,24 @@ IF NOT EXIST zlib-%ZLIB_VERSION% (
  C:\windows\system32\tar.exe -x -f zlib-%ZLIB_VERSION%.zip || EXIT /b 1
 )
 CD zlib-%ZLIB_VERSION%
-cmake -G "Visual Studio 17 2022" . || EXIT /b 1
-cmake --build . --target ALL_BUILD --config Release || EXIT /b 1
-cmake --build . --target RUN_TESTS --config Release || EXIT /b 1
-cmake --build . --target INSTALL --config Release || EXIT /b 1
+cmake -B build || EXIT /b 1
+cmake --build build --target ALL_BUILD --config Release || EXIT /b 1
+cmake --build build --target RUN_TESTS --config Release || EXIT /b 1
+cmake --build build --target INSTALL --config Release || EXIT /b 1
+
+@REM Install PCRE2
+IF NOT EXIST pcre2-%PCRE2_VERSION%.zip (
+  ECHO Downloading https://github.com/PCRE2Project/pcre2/releases/download/pcre2-%PCRE2_VERSION%/pcre2-%PCRE2_VERSION%.zip
+  curl -L -o pcre2-%PCRE2_VERSION%.zip https://github.com/PCRE2Project/pcre2/releases/download/pcre2-%PCRE2_VERSION%/pcre2-%PCRE2_VERSION%.zip || EXIT /b 1
+)
+IF NOT EXIST pcre2-%PCRE2_VERSION% (
+  ECHO Unpacking pcre2-%PCRE2_VERSION%.zip
+  C:\windows\system32\tar.exe -x -f pcre2-%PCRE2_VERSION%.zip || EXIT /b 1
+)
+CD pcre2-%PCRE2_VERSION%
+cmake -B build -DPCRE2_BUILD_PCRE2GREP=OFF || EXIT /b 1
+cmake --build build --target ALL_BUILD --config Release || EXIT /b 1
+@REM cmake --build build --target RUN_TESTS --config Release || EXIT /b 1
+cmake --build build --target INSTALL --config Release || EXIT /b 1

@EXIT /b 0
Author	SHA1	Message	Date
Maarten L. Hekkelman	1de973ddcb	Fix findpcre2 cmake file	2025-09-02 13:12:20 +02:00
Maarten L. Hekkelman	eecc801203	last remaining warning	2025-09-02 12:57:08 +02:00
Maarten L. Hekkelman	5c50154ea4	Merge branch 'develop' of github.com:PDB-REDO/libcifpp into develop	2025-09-02 12:54:03 +02:00
Maarten L. Hekkelman	0fa3d6aa94	Removing warning using MSVC	2025-09-02 12:54:07 +02:00
Maarten L. Hekkelman	01f5242bfb	Revert "Add formatting file" This reverts commit `af6d8d4f71`.	2025-09-02 11:57:21 +02:00
Maarten L. Hekkelman	af6d8d4f71	Add formatting file	2025-09-02 11:47:50 +02:00
Maarten L. Hekkelman	fa8285fc0f	use std::format anyway, even if __cpp_lib_format is not defined.	2025-09-02 10:23:00 +02:00
Maarten L. Hekkelman	2e7f6b8337	cross platform check for lib format	2025-09-02 10:03:36 +02:00
Maarten L. Hekkelman	a6a55020eb	Merge branch 'develop' of github.com:PDB-REDO/libcifpp into develop	2025-09-01 10:54:09 +02:00
Maarten L. Hekkelman	0e84ea454d	fmt fix	2025-09-01 10:53:29 +02:00
Maarten L. Hekkelman	f3bf211d45	pdb formatting	2025-09-01 09:34:07 +02:00
Maarten L. Hekkelman	f5ef44836c	pdb formatting	2025-09-01 09:31:22 +02:00
Maarten L. Hekkelman	070124b6e1	fix cif2pdb	2025-08-29 14:00:27 +02:00
Maarten L. Hekkelman	c8a46fcdd9	Stop when element is missing in reading PDB input	2025-08-29 13:17:17 +02:00
Maarten L. Hekkelman	5306b59fd8	Do not write zero seq ID's in PDB files	2025-08-29 10:08:56 +02:00
Maarten L. Hekkelman	90c5df832a	Check only first datablock	2025-08-29 09:49:27 +02:00
Maarten L. Hekkelman	2aa439d51f	test for fmt	2025-08-28 08:48:20 +02:00
Maarten L. Hekkelman	ac2b68517c	conditional fmt	2025-08-27 16:08:51 +02:00
Maarten L. Hekkelman	e56b568c42	use cif::format... sigh	2025-08-27 15:46:41 +02:00
Maarten L. Hekkelman	63c49b2e04	Fix writing pdb files	2025-08-27 15:20:20 +02:00
Maarten L. Hekkelman	559fd18a20	Fix std::format usage	2025-08-27 08:57:40 +02:00
Maarten L. Hekkelman	beb7585261	fix std::format usage	2025-08-27 08:24:07 +02:00
Maarten L. Hekkelman	8b0f92aa9a	Merge remote-tracking branch 'github/using-fmt' into develop	2025-08-27 07:43:22 +02:00
Maarten L. Hekkelman	0d8beeae5b	No longer needed	2025-08-26 16:04:31 +02:00
Maarten L. Hekkelman	e3da654e67	Speed up build when eigen3 is not available	2025-08-26 15:54:55 +02:00
Maarten L. Hekkelman	dc9e151d89	remove warning	2025-08-26 15:37:22 +02:00
Maarten L. Hekkelman	7cfaf051ba	should now work on windows	2025-08-26 15:16:01 +02:00
Maarten L. Hekkelman	7920491309	hope to find pcre2.h	2025-08-26 14:07:47 +02:00
Maarten L. Hekkelman	0ee493a3fb	implib?	2025-08-26 13:55:25 +02:00
Maarten L. Hekkelman	7e23bc0c0b	finding pcre2 on windows	2025-08-26 13:46:03 +02:00
Maarten L. Hekkelman	579f859562	no find_packge for pcre2	2025-08-26 13:42:14 +02:00
Maarten L. Hekkelman	752938ca44	using find_package?	2025-08-26 13:38:37 +02:00
Maarten L. Hekkelman	fce58c02fe	no pcre2grep please, no tests either	2025-08-26 13:34:43 +02:00
Maarten L. Hekkelman	924f7c1505	finding pcre2, yet another attempt	2025-08-26 13:31:12 +02:00
Maarten L. Hekkelman	8944906fd2	fix warning, pcre2	2025-08-26 12:41:08 +02:00
Maarten L. Hekkelman	cb02969604	Using std::format	2025-08-25 16:31:00 +02:00
Maarten L. Hekkelman	31090c6ec5	attempt 2	2025-08-25 11:25:10 +02:00
Maarten L. Hekkelman	9e30d2bc1a	finding pcre2	2025-08-25 10:39:48 +02:00
Maarten L. Hekkelman	93d703f7a1	Do not buld pcre tests	2025-08-20 20:40:08 +02:00
Maarten L. Hekkelman	3c241048a5	do not install pcre	2025-08-20 17:02:40 +02:00
Maarten L. Hekkelman	2788536799	this should work	2025-08-20 16:58:52 +02:00
Maarten L. Hekkelman	314d435a18	Another way of importing pcre	2025-08-20 16:49:12 +02:00
Maarten L. Hekkelman	37edcd8666	Finding and optionally building pcre	2025-08-20 15:47:49 +02:00
Maarten L. Hekkelman	10e290fbdf	pcre2 in github actions?	2025-08-20 14:40:50 +02:00
Maarten L. Hekkelman	58cda1241e	cleanup	2025-08-20 13:41:45 +02:00
Maarten L. Hekkelman	3659aaabff	remove unneeded allocations	2025-08-20 13:35:15 +02:00
Maarten L. Hekkelman	727a39cc54	Finishing up replacing boost with pcre	2025-08-20 13:28:24 +02:00
Maarten L. Hekkelman	fd9ccdfff9	Using pcre instead of boost::regex	2025-08-19 16:16:43 +02:00
Maarten L. Hekkelman	aabee270b3	update .gitignore	2025-08-19 14:28:51 +02:00
Maarten L. Hekkelman	647c58f8ec	allow code to be built with older compilers...	2025-08-19 12:44:41 +02:00
Maarten L. Hekkelman	0b8024d19c	Optimise query processing	2025-08-19 12:24:33 +02:00
Maarten L. Hekkelman	d59b0bf27f	Remove wrong warnings	2025-08-13 11:30:53 +02:00
Maarten L. Hekkelman	398c16eac2	Merge branch 'develop' of github.com:PDB-REDO/libcifpp into develop	2025-08-13 09:02:10 +02:00
Maarten L. Hekkelman	fa869bdc7d	lightweight fixup	2025-08-13 09:01:50 +02:00
Maarten L. Hekkelman	c20d0d2a30	lightweight fixup	2025-08-12 16:45:19 +02:00
Maarten L. Hekkelman	000f2736c2	Merge branch 'develop' into clebreto-feature/enrich_structure_options	2025-08-11 10:13:20 +02:00
Maarten L. Hekkelman	cfcc81bb62	verbose messages	2025-08-11 10:13:07 +02:00
Maarten L. Hekkelman	82eae05868	changed b-factor options for structure loading	2025-06-11 14:17:50 +02:00
Maarten L. Hekkelman	e8fb53c49b	Alternate implementation of structure_open_options	2025-06-11 13:35:58 +02:00
Maarten L. Hekkelman	604c97afe1	Merge branch 'develop' into clebreto-feature/enrich_structure_options	2025-06-11 11:43:01 +02:00
Maarten L. Hekkelman	7e60cdf272	remove redundant statement	2025-06-11 11:42:26 +02:00
Maarten L. Hekkelman	9ea7cfcc80	Remove test	2025-06-11 09:56:26 +02:00
Maarten L. Hekkelman	a7a4a16f79	remove debug code	2025-06-11 09:45:45 +02:00
Maarten L. Hekkelman	6717059934	Revert renaming compound_id to mon_id in residue	2025-06-11 09:41:49 +02:00
Maarten L. Hekkelman	714747c280	version bump	2025-06-11 09:32:36 +02:00
Maarten L. Hekkelman	81cd305c80	rename mm::polymer fields and methods to better match mmcif_pdbx naming. fix building mm::structure using pdb_seq_num instead of auth_seq_num	2025-06-11 09:30:54 +02:00
Maarten L. Hekkelman	5de872bbb3	Version bump, update mmcif_pdbx.dic	2025-06-10 09:17:30 +02:00
Maarten L. Hekkelman	ce6a75a920	right...	2025-06-10 09:11:26 +02:00
Maarten L. Hekkelman	874a5cb2f2	missing code added	2025-06-02 15:09:49 +02:00
Maarten L. Hekkelman	6e2202d4f1	More verbose strip	2025-06-02 09:10:58 +02:00
Maarten L. Hekkelman	bcf33df701	Added strip, removed dangerous datablock::is_valid (non-const version)	2025-06-02 08:52:58 +02:00
Maarten L. Hekkelman	3bdcf21c69	Merge commit '4b36bdc' into develop	2025-05-29 16:14:15 +02:00
Maarten L. Hekkelman	4b36bdc58c	work around incorrect mmcif_pdbx name	2025-05-29 16:13:28 +02:00
Maarten L. Hekkelman	6d9008ee8c	Merge branch 'trunk' into develop	2025-05-29 15:15:41 +02:00
Maarten L. Hekkelman	ee93692707	comment formatting	2025-05-29 14:15:13 +02:00
Maarten L. Hekkelman	2bcc368bce	reconstruct when audit_conform is missing	2025-05-29 14:07:45 +02:00
Maarten L. Hekkelman	6cc4467d53	options	2025-05-27 13:55:13 +02:00
Maarten L. Hekkelman	41c0521480	Merge branch 'feature/enrich_structure_options' of github.com:clebreto/libcifpp into clebreto-feature/enrich_structure_options	2025-04-02 13:58:01 +02:00
LE BRETON Come	7d33d56c0e	Update docs	2025-03-07 15:59:19 +01:00
LE BRETON Come	f86f34e5e1	WIP Enrich StructureOpenOptions	2025-03-07 15:54:30 +01:00