begin with curl

fix building mm::structure using pdb_seq_num instead of auth_seq_num

CMakeLists.txt

@@ -24,10 +24,15 @@
 
 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
+	VERSION 9.0.0
 	LANGUAGES CXX)
 
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
@@ -63,25 +68,26 @@ 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")
+
+# Optionally use libcurl to fetch compound files
+set(USE_CURL_FOR_CCD ON CACHE BOOL "Use curl to fetch missing CCD files")
 
 # 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 +97,13 @@ 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-		"Recreate SymOp data table in case it is out of date" ON)
+	set(CIFPP_RECREATE_SYMOP_DATA ON CACHE BOOL "Recreate SymOp data table in case it is out of date")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 +133,6 @@ 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()
@@ -164,7 +166,7 @@ int main(int argc, char *argv[]) { return 0; }"
 
 if(GXX_LIBSTDCPP)
 	message(
-		STATUS "Testing for known regex bug, since you're using GNU libstdc++")
+		STATUS "cifpp: Testing for known regex bug, since you're using GNU libstdc++")
 
 	try_run(STD_REGEX_RUNNING STD_REGEX_COMPILING
 		${CMAKE_CURRENT_BINARY_DIR}/test
@@ -173,7 +175,7 @@ if(GXX_LIBSTDCPP)
 	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"
+			"cifpp: 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)
@@ -221,11 +223,15 @@ if(MSVC)
 	endforeach()
 endif()
 
+if(USE_CURL_FOR_CCD)
+	find_package(CURL REQUIRED)
+endif()
+
 find_package(ZLIB QUIET)
 find_package(Threads)
 
 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
@@ -242,12 +248,12 @@ else()
 		GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
 		GIT_TAG 3.4.0
 		INSTALL_COMMAND "")
-	
+
 	ExternalProject_Get_Property(my-eigen3 SOURCE_DIR)
 	set(EIGEN_INCLUDE_DIR ${SOURCE_DIR})
 endif()
 
-message(STATUS "Eigen include dir is ${EIGEN_INCLUDE_DIR}")
+message(STATUS "cifpp: Eigen include dir is ${EIGEN_INCLUDE_DIR}")
 
 # Create a revision file, containing the current git version info
 include(VersionString)
@@ -376,7 +382,13 @@ target_include_directories(
 	"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
 	PRIVATE "${BOOST_REGEX_INCLUDE_DIR}" "${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>
+	$<IF:$<BOOL:${USE_CURL_FOR_CCD}>,CURL::libcurl,>)
+
+if (USE_CURL_FOR_CCD)
+	target_compile_definitions(cifpp PUBLIC HAVE_CURL)
+endif()
 
 if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
 	target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
@@ -390,7 +402,7 @@ 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 +441,7 @@ 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 +505,7 @@ 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()
 
@@ -559,7 +571,7 @@ 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 +585,7 @@ 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)

changelog

@@ -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

cmake/cifpp-config.cmake.in

@@ -8,5 +8,6 @@ include(CMakeFindDependencyMacro)
 
 find_dependency(Threads)
 find_dependency(ZLIB REQUIRED)
+find_dependency(CURL REQUIRED)
 
 check_required_components(cifpp)

include/cif++/category.hpp

@@ -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

include/cif++/compound.hpp

@@ -196,6 +196,23 @@ class compound
 // --------------------------------------------------------------------
 // Factory class for compound and Link objects
 
+/// @brief Options available to configure a compound factory
+struct compound_factory_options
+{
+	/// If you have a multithreaded application and want to have different
+	/// compounds in each thread (e.g. a web service processing user requests
+	/// with different sets of compounds) you can set this flag to true.
+	bool use_thread_local_instance_only = false;
+
+#if HAVE_CURL
+	// Various locations for chem_comp data files:
+	// - ftp://files.ebi.ac.uk/pub/databases/pdb/refdata/chem_comp
+	// - https://files.rcsb.org/pub/pdb/refdata/chem_comp/
+
+	std::string remote_chem_comp_url = "ftp://files.ebi.ac.uk/pub/databases/pdb/refdata/chem_comp";
+#endif
+};
+
 /// Use the compound_factory singleton instance to create compound objects
 
 class compound_factory
@@ -208,8 +225,12 @@ class compound_factory
 	/// with different sets of compounds) you can set the \a useThreadLocalInstanceOnly
 	/// flag to true.
 
+	[[deprecated("Use version with compound_factory_options instead")]]
 	static void init(bool useThreadLocalInstanceOnly);
 
+	/// \brief Initialise a singleton instance.
+	static void init(compound_factory_options options = {});
+
 	/// Return the singleton instance. If initialized with local threads, this is the
 	/// instance for the current thread.
 	static compound_factory &instance();
@@ -239,6 +260,8 @@ class compound_factory
 	void push_dictionary(const file &file);
 
 	/// Remove the last pushed dictionary
+
+	// TODO: check if the popped dict is the correct one
 	void pop_dictionary();
 
 	/// Return whether @a res_name is a valid and known peptide
@@ -298,7 +321,7 @@ class compound_factory
 
 	static std::unique_ptr<compound_factory> s_instance;
 	static thread_local std::unique_ptr<compound_factory> tl_instance;
-	static bool s_use_thread_local_instance;
+	static compound_factory_options s_options;
 
 	std::shared_ptr<compound_factory_impl> m_impl;
 };
@@ -320,6 +343,9 @@ class compound_factory
  * @endcode
  */
 
+
+// TODO: check if pushed and popped dicts are the same!
+
 class compound_source
 {
   public:

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

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);
 

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.

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                                          .  

src/category.cpp

@@ -914,6 +914,24 @@ 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)

src/compound.cpp

@@ -26,6 +26,10 @@
 
 #include "cif++.hpp"
 
+#if HAVE_CURL
+# include <curl/curl.h>
+#endif
+
 #include <filesystem>
 #include <fstream>
 #include <map>
@@ -140,7 +144,7 @@ compound::compound(cif::datablock &db)
 
 	cif::tie(m_id, m_name, m_type, m_formula, m_formula_weight, m_formal_charge, one_letter_code, m_parent_id) =
 		chemComp.front().get("id", "name", "type", "formula", "formula_weight", "pdbx_formal_charge", "one_letter_code", "mon_nstd_parent_comp_id");
-	
+
 	if (one_letter_code.length() == 1)
 		m_one_letter_code = one_letter_code.front();
 
@@ -159,7 +163,7 @@ compound::compound(cif::datablock &db)
 		if (stereo_config.empty())
 			atom.stereo_config = stereo_config_type::N;
 		else
-		atom.stereo_config = parse_stereo_config_from_string(stereo_config);
+			atom.stereo_config = parse_stereo_config_from_string(stereo_config);
 		m_atoms.push_back(std::move(atom));
 	}
 
@@ -172,7 +176,7 @@ compound::compound(cif::datablock &db)
 		if (valueOrder.empty())
 			bond.type = bond_type::sing;
 		else
-		bond.type = parse_bond_type_from_string(valueOrder);
+			bond.type = parse_bond_type_from_string(valueOrder);
 		m_bonds.push_back(std::move(bond));
 	}
 }
@@ -231,12 +235,12 @@ float compound::bond_length(const std::string &atomId_1, const std::string &atom
 
 bool compound::is_peptide() const
 {
-	return iequals(m_type, "l-peptide linking")	or iequals(m_type, "peptide linking");
+	return iequals(m_type, "l-peptide linking") or iequals(m_type, "peptide linking");
 }
 
 bool compound::is_base() const
 {
-	return iequals(m_type, "dna linking")	or iequals(m_type, "rna linking");
+	return iequals(m_type, "dna linking") or iequals(m_type, "rna linking");
 }
 
 // --------------------------------------------------------------------
@@ -299,7 +303,7 @@ class compound_factory_impl : public std::enable_shared_from_this<compound_facto
 		std::shared_lock lock(mMutex);
 
 		compound *result = nullptr;
-		
+
 		for (auto impl = shared_from_this(); impl; impl = impl->m_next)
 		{
 			result = impl->create(id);
@@ -363,7 +367,9 @@ compound *compound_factory_impl::create(const std::string &id)
 	if (m_missing.contains(id))
 		return nullptr;
 
-	if (auto i = find_if(m_compounds.begin(), m_compounds.end(), [id](compound *c) { return c->id() == id; }); i != m_compounds.end())
+	if (auto i = find_if(m_compounds.begin(), m_compounds.end(), [id](compound *c)
+			{ return c->id() == id; });
+		i != m_compounds.end())
 		return *i;
 
 	compound *result = nullptr;
@@ -454,7 +460,6 @@ class local_compound_factory_impl : public compound_factory_impl
 	compound *create(const std::string &id) override;
 
   private:
-
 	compound *construct_compound(const datablock &db, const std::string &id, const std::string &name, const std::string &three_letter_code, const std::string &group);
 
 	cif::file m_local_file;
@@ -465,7 +470,9 @@ compound *local_compound_factory_impl::create(const std::string &id)
 	if (m_missing.contains(id))
 		return nullptr;
 
-	if (auto i = find_if(m_compounds.begin(), m_compounds.end(), [id](compound *c) { return c->id() == id; }); i != m_compounds.end())
+	if (auto i = find_if(m_compounds.begin(), m_compounds.end(), [id](compound *c)
+			{ return c->id() == id; });
+		i != m_compounds.end())
 		return *i;
 
 	compound *result = nullptr;
@@ -507,12 +514,10 @@ compound *local_compound_factory_impl::construct_compound(const datablock &rdb,
 
 	float formula_weight = 0;
 	int formal_charge = 0;
-	std::map<std::string,std::size_t> formula_data;
+	std::map<std::string, std::size_t> formula_data;
 
 	for (std::size_t ord = 1; const auto &[atom_id, type_symbol, type, charge, x, y, z, xi, yi, zi] :
-		rdb["chem_comp_atom"].rows<std::string, std::string, std::string, int,
-			std::optional<float>, std::optional<float>, std::optional<float>,
-			std::optional<float>, std::optional<float>, std::optional<float>>(
+		rdb["chem_comp_atom"].rows<std::string, std::string, std::string, int, std::optional<float>, std::optional<float>, std::optional<float>, std::optional<float>, std::optional<float>, std::optional<float>>(
 			"atom_id", "type_symbol", "type", "charge",
 			"model_Cartn_x", "model_Cartn_y", "model_Cartn_z",
 			"pdbx_model_Cartn_x_ideal", "pdbx_model_Cartn_y_ideal", "pdbx_model_Cartn_z_ideal"))
@@ -522,16 +527,14 @@ compound *local_compound_factory_impl::construct_compound(const datablock &rdb,
 
 		formula_data[type_symbol] += 1;
 
-		db["chem_comp_atom"].emplace({
-			{ "comp_id", id },
+		db["chem_comp_atom"].emplace({ { "comp_id", id },
 			{ "atom_id", atom_id },
 			{ "type_symbol", type_symbol },
 			{ "charge", charge },
-			{ "model_Cartn_x",  x.has_value() ? x : xi, 3 },
-			{ "model_Cartn_y",  y.has_value() ? y : yi, 3 },
-			{ "model_Cartn_z",  z.has_value() ? z : zi, 3 },
-			{ "pdbx_ordinal", ord++ }
-		});
+			{ "model_Cartn_x", x.has_value() ? x : xi, 3 },
+			{ "model_Cartn_y", y.has_value() ? y : yi, 3 },
+			{ "model_Cartn_z", z.has_value() ? z : zi, 3 },
+			{ "pdbx_ordinal", ord++ } });
 
 		formal_charge += charge;
 	}
@@ -548,21 +551,19 @@ compound *local_compound_factory_impl::construct_compound(const datablock &rdb,
 		else if (cif::iequals(type, "triple") or cif::iequals(type, "trip"))
 			value_order = "TRIP";
 
-		db["chem_comp_bond"].emplace({
-			{ "comp_id", id },
+		db["chem_comp_bond"].emplace({ { "comp_id", id },
 			{ "atom_id_1", atom_id_1 },
 			{ "atom_id_2", atom_id_2 },
 			{ "value_order", value_order },
 			{ "pdbx_aromatic_flag", aromatic },
 			// TODO: fetch stereo_config info from chem_comp_chir
-			{ "pdbx_ordinal", ord++ }
-		});
+			{ "pdbx_ordinal", ord++ } });
 	}
 
 	db.emplace_back(rdb["pdbx_chem_comp_descriptor"]);
 
 	std::string formula;
-	for (bool first = true; const auto &[symbol, count]: formula_data)
+	for (bool first = true; const auto &[symbol, count] : formula_data)
 	{
 		if (std::exchange(first, false))
 			formula += ' ';
@@ -581,15 +582,13 @@ compound *local_compound_factory_impl::construct_compound(const datablock &rdb,
 	else
 		type = "NON-POLYMER";
 
-	db["chem_comp"].emplace({
-		{ "id", id },
+	db["chem_comp"].emplace({ { "id", id },
 		{ "name", name },
 		{ "type", type },
 		{ "formula", formula },
 		{ "pdbx_formal_charge", formal_charge },
 		{ "formula_weight", formula_weight },
-		{ "three_letter_code", three_letter_code }
-	});
+		{ "three_letter_code", three_letter_code } });
 
 	std::shared_lock lock(mMutex);
 
@@ -602,11 +601,16 @@ compound *local_compound_factory_impl::construct_compound(const datablock &rdb,
 
 std::unique_ptr<compound_factory> compound_factory::s_instance;
 thread_local std::unique_ptr<compound_factory> compound_factory::tl_instance;
-bool compound_factory::s_use_thread_local_instance;
+compound_factory_options compound_factory::s_options;
 
 void compound_factory::init(bool useThreadLocalInstanceOnly)
 {
-	s_use_thread_local_instance = useThreadLocalInstanceOnly;
+	init({ .use_thread_local_instance_only = useThreadLocalInstanceOnly });
+}
+
+void compound_factory::init(compound_factory_options options)
+{
+	s_options = options;
 }
 
 compound_factory::compound_factory()
@@ -625,7 +629,7 @@ compound_factory::~compound_factory()
 
 compound_factory &compound_factory::instance()
 {
-	if (s_use_thread_local_instance)
+	if (s_options.use_thread_local_instance_only)
 	{
 		if (not tl_instance)
 			tl_instance.reset(new compound_factory());
@@ -641,7 +645,7 @@ compound_factory &compound_factory::instance()
 
 void compound_factory::clear()
 {
-	if (s_use_thread_local_instance)
+	if (s_options.use_thread_local_instance_only)
 		tl_instance.reset(nullptr);
 	else
 		s_instance.reset();
@@ -719,7 +723,7 @@ bool compound_factory::is_peptide(std::string_view res_name) const
 	bool result = is_std_peptide(res_name);
 	if (not result and m_impl)
 	{
-		auto compound = const_cast<compound_factory&>(*this).create(res_name);
+		auto compound = const_cast<compound_factory &>(*this).create(res_name);
 		result = compound != nullptr and compound->is_peptide();
 	}
 	return result;
@@ -731,7 +735,7 @@ bool compound_factory::is_base(std::string_view res_name) const
 	bool result = is_std_base(res_name);
 	if (not result and m_impl)
 	{
-		auto compound = const_cast<compound_factory&>(*this).create(res_name);
+		auto compound = const_cast<compound_factory &>(*this).create(res_name);
 		result = compound != nullptr and compound->is_base();
 	}
 	return result;

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;
 }

src/model.cpp

@@ -102,18 +102,18 @@ void atom::atom_impl::set_property(const std::string_view name, const std::strin
 	r.assign(name, value, true, true);
 }
 
-// int atom::atom_impl::compare(const atom_impl &b) const
-// {
-// 	int d = 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 +149,6 @@ 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 +180,8 @@ 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 +232,10 @@ 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 +402,8 @@ 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 +412,7 @@ 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 +831,7 @@ 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 +843,8 @@ 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 +852,11 @@ 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 +996,7 @@ 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 +1112,12 @@ 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 +1160,7 @@ 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 +1187,19 @@ 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 +1207,7 @@ 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 +1226,133 @@ 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 +1378,18 @@ 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 +1464,6 @@ 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 +1612,7 @@ 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 +1636,7 @@ 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 +1658,7 @@ 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 +1682,7 @@ 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 +2032,7 @@ 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 +2062,7 @@ 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 +2195,7 @@ 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 +2281,8 @@ 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 +2342,8 @@ 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 +2657,11 @@ 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() },

src/pdb/pdb2cif.cpp

@@ -6419,15 +6419,24 @@ 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);
+					}
+				}
 			}
 		}
 	}

src/pdb/reconstruct.cpp

@@ -1554,4 +1554,92 @@ 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();
+
+	// ... and any additional datablock will contain compound information
+	cif::compound_source cs(file);
+
+	if (auto cat = db.get("atom_site"); cat == nullptr or cat->empty())
+		throw std::runtime_error("Cannot reconstruct PDBx file, atom data missing");
+
+	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
+	checkAtomRecords(db);
+
+	db["chem_comp"].reorder_by_index();
+
+	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
+}
+
 } // namespace cif::pdb

src/validate.cpp

@@ -552,6 +552,9 @@ 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 });
 

test/CMakeLists.txt

@@ -28,7 +28,8 @@ list(
 	sugar
 	spinner
 	# reconstruction
-	validate-pdbx)
+	validate-pdbx
+	)
 
 add_library(test-main OBJECT "${CMAKE_CURRENT_SOURCE_DIR}/test-main.cpp")
 

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());
+	}
+}