Backporting CMakeLists.txt file from version 3

fix example for new interface

CMakeLists.txt

@@ -25,7 +25,7 @@
 cmake_minimum_required(VERSION 3.16)
 
 # set the project name
-project(cifpp VERSION 2.0.1 LANGUAGES CXX)
+project(cifpp VERSION 2.0.5 LANGUAGES CXX)
 
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 
@@ -37,17 +37,13 @@ include(CheckIncludeFiles)
 include(CheckLibraryExists)
 include(CMakePackageConfigHelpers)
 include(Dart)
-include(FindFilesystem)
 include(GenerateExportHeader)
 
 set(CXX_EXTENSIONS OFF)
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
-find_package(Filesystem REQUIRED)
-
 if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
-	# https://stackoverflow.com/questions/63902528/program-crashes-when-filesystempath-is-destroyed
 	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers")
 elseif(MSVC)
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4")
@@ -87,14 +83,14 @@ endif()
 
 # When CCP4 is sourced in the environment, we can recreate the symmetry operations table
 if(EXISTS "${CCP4}")
-	if(RECREATE_SYMOP_DATA AND NOT EXISTS "${CLIBD}/syminfo.lib")
+	if(CIFPP_RECREATE_SYMOP_DATA AND NOT EXISTS "${CLIBD}/syminfo.lib")
 		message(WARNING "Symop data table recreation requested, but file syminfo.lib was not found in ${CLIBD}")
-		set(RECREATE_SYMOP_DATA OFF)
+		set(CIFPP_RECREATE_SYMOP_DATA OFF)
 	else()
-		option(RECREATE_SYMOP_DATA "Recreate SymOp data table in case it is out of date" ON)
+		option(CIFPP_RECREATE_SYMOP_DATA "Recreate SymOp data table in case it is out of date" ON)
 	endif()
 else()
-	set(RECREATE_SYMOP_DATA OFF)
+	set(CIFPP_RECREATE_SYMOP_DATA OFF)
 	message("Not trying to recreate SymOpTable_data.hpp since CCP4 is not defined")
 endif()
 
@@ -122,22 +118,6 @@ if(MSVC)
 		message(STATUS "The library and auxiliary files will be installed in $ENV{LOCALAPPDATA}/${PROJECT_NAME}")
 		set(CMAKE_INSTALL_PREFIX "$ENV{LOCALAPPDATA}/${PROJECT_NAME}" CACHE PATH "..." FORCE)
 	endif()
-
-	# Find out the processor type for the target
-	if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "AMD64")
-		set(COFF_TYPE "x64")
-	elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "i386")
-		set(COFF_TYPE "x86")
-	elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "ARM64")
-		set(COFF_TYPE "arm64")
-	else()
-		message(FATAL_ERROR "Unsupported or unknown processor type ${CMAKE_SYSTEM_PROCESSOR}")
-	endif()	
-
-	set(COFF_SPEC "--coff=${COFF_TYPE}")
-
-	# for mrc, just in case
-	list(APPEND CMAKE_PREFIX_PATH "$ENV{LOCALAPPDATA}/mrc")
 endif()
 
 if(UNIX AND NOT APPLE AND NOT BUILD_FOR_CCP4 AND CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
@@ -151,19 +131,19 @@ endif()
 if(WIN32 AND BUILD_SHARED_LIBS)
 	message("Not using resources when building shared libraries for Windows")
 else()
-	find_program(MRC mrc)
+	find_package(Mrc)
 
-	if(MRC)
+	if(MRC_FOUND)
 		option(USE_RSRC "Use mrc to create resources" ON)
 	else()
-		message("Using resources not possible since mrc was not found")
+		message(WARNING "Not using resources since mrc was not found")
 	endif()
 
-	if(USE_RSRC STREQUAL "ON")
-		set(USE_RSRC 1)
+	if(CIFPP_USE_RSRC STREQUAL "ON")
+		set(CIFPP_USE_RSRC 1)
 
 		message("Using resources compiled with ${MRC}")
-		add_compile_definitions(USE_RSRC)
+		add_compile_definitions(CIFPP_USE_RSRC)
 	endif()
 endif()
 
@@ -173,43 +153,30 @@ set(CMAKE_THREAD_PREFER_PTHREAD)
 set(THREADS_PREFER_PTHREAD_FLAG)
 find_package(Threads)
 
-set(Boost_DETAILED_FAILURE_MSG ON)
-if(NOT BUILD_SHARED_LIBS)
-	set(Boost_USE_STATIC_LIBS ON)
-endif()
 find_package(Boost 1.70.0 REQUIRED COMPONENTS system iostreams regex program_options)
 
 if(NOT MSVC AND Boost_USE_STATIC_LIBS)
 	find_package(ZLIB REQUIRED)
-	find_package(BZip2 REQUIRED)
+	list(APPEND CIFPP_REQUIRED_LIBRARIES ZLIB::ZLIB)
 endif()
 
+include(FindFilesystem)
+list(APPEND CIFPP_REQUIRED_LIBRARIES ${STDCPPFS_LIBRARY})
+
+include(FindAtomic)
+list(APPEND CIFPP_REQUIRED_LIBRARIES ${STDCPPATOMIC_LIBRARY})
+
 # Create a revision file, containing the current git version info
-
-find_package(Git)
-if(GIT_FOUND AND EXISTS "${CMAKE_SOURCE_DIR}/.git")
-	include(GetGitRevisionDescription)
-    get_git_head_revision(REFSPEC COMMITHASH)
-
-	# Generate our own version string
-	git_describe_working_tree(BUILD_VERSION_STRING --match=build --dirty)
-else()
-    message(WARNING "Git not found, cannot set version info")
-
-    SET(BUILD_VERSION_STRING ${PROJECT_VERSION})
-endif()
-
-# generate version.h
-string(TIMESTAMP BUILD_DATE_TIME "%Y-%m-%dT%H:%M:%SZ" UTC)
-configure_file("${CMAKE_SOURCE_DIR}/src/revision.hpp.in" "${CMAKE_BINARY_DIR}/revision.hpp" @ONLY)
+include(VersionString)
+write_version_header("LibCIFPP")
 
 # SymOp data table
-if(RECREATE_SYMOP_DATA)
+if(CIFPP_RECREATE_SYMOP_DATA)
 	# The tool to create the table
 
 	add_executable(symop-map-generator "${CMAKE_SOURCE_DIR}/tools/symop-map-generator.cpp")
 
-	target_link_libraries(symop-map-generator Threads::Threads ${Boost_LIBRARIES} std::filesystem ${ZLIB_LIBRARIES} ${BZip2_LIBRARIES})
+	target_link_libraries(symop-map-generator Threads::Threads ${Boost_LIBRARIES} ${CIFPP_REQUIRED_LIBRARIES})
 	if(Boost_INCLUDE_DIR)
 		target_include_directories(symop-map-generator PUBLIC ${Boost_INCLUDE_DIR})
 	endif()
@@ -256,7 +223,6 @@ set(project_headers
 	${PROJECT_SOURCE_DIR}/include/cif++/CifUtils.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/CifValidator.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/Compound.hpp
-	${PROJECT_SOURCE_DIR}/include/cif++/Matrix.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/PDB2Cif.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/PDB2CifRemark3.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/Point.hpp
@@ -281,14 +247,15 @@ target_include_directories(cifpp
 	${CMAKE_BINARY_DIR}
 )
 
-target_link_libraries(cifpp Threads::Threads ${Boost_LIBRARIES} std::filesystem ${ZLIB_LIBRARIES} ${BZip2_LIBRARIES})
+target_link_libraries(cifpp PUBLIC Threads::Threads Boost::regex Boost::iostreams ${CIFPP_REQUIRED_LIBRARIES})
+# target_link_libraries(cifpp PRIVATE)
 
 if (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
     target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
 endif (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
 
-option(DOWNLOAD_CCD "Download the CCD file components.cif during installation" OFF)
-if(DOWNLOAD_CCD)
+option(CIFPP_DOWNLOAD_CCD "Download the CCD file components.cif during installation" OFF)
+if(CIFPP_DOWNLOAD_CCD)
 	# download the components.cif file from CCD
 	set(COMPONENTS_CIF ${PROJECT_SOURCE_DIR}/data/components.cif)
 
@@ -316,13 +283,9 @@ if(DOWNLOAD_CCD)
 endif()
 
 if(UNIX)
-	option(INSTALL_UPDATE_SCRIPT "Install the script to update CCD and dictionary files" OFF)
-	if(INSTALL_UPDATE_SCRIPT)
-		set(CIFPP_CACHE_DIR "/var/cache/libcifpp")
-		if(NOT "${CIFPP_CACHE_DIR}" STREQUAL "OFF")
-			target_compile_definitions(cifpp PUBLIC CACHE_DIR="${CIFPP_CACHE_DIR}")
-		endif()
-	endif()
+	option(CIFPP_INSTALL_UPDATE_SCRIPT "Install the script to update CCD and dictionary files" OFF)
+	set(CIFPP_CACHE_DIR "/var/cache/libcifpp" CACHE STRING "The cache directory to use")
+	target_compile_definitions(cifpp PUBLIC CACHE_DIR="${CIFPP_CACHE_DIR}")
 endif()
 
 generate_export_header(cifpp
@@ -332,7 +295,9 @@ set(INCLUDE_INSTALL_DIR ${CMAKE_INSTALL_INCLUDEDIR} )
 set(LIBRARY_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR} )
 set(SHARE_INSTALL_DIR ${CMAKE_INSTALL_DATADIR}/libcifpp)
 
-target_compile_definitions(cifpp PUBLIC DATA_DIR="${CMAKE_INSTALL_PREFIX}/${SHARE_INSTALL_DIR}")
+set(CIFPP_DATA_DIR "${CMAKE_INSTALL_PREFIX}/${SHARE_INSTALL_DIR}" CACHE STRING "The directory containing the provided data files")
+
+target_compile_definitions(cifpp PUBLIC DATA_DIR="${CIFPP_DATA_DIR}")
 
 # Install rules
 
@@ -343,6 +308,13 @@ install(TARGETS cifpp
 	RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
 	INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 
+if(MSVC AND BUILD_SHARED_LIBS)
+	install(
+		FILES $<TARGET_PDB_FILE:${PROJECT_NAME}>
+		DESTINATION ${CMAKE_INSTALL_LIBDIR}
+		OPTIONAL)
+endif()
+
 install(EXPORT cifppTargets
 	FILE "cifppTargets.cmake"
 	NAMESPACE cifpp::
@@ -364,7 +336,7 @@ install(
 install(FILES
 	${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
 	${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx_v50.dic
-	${PROJECT_SOURCE_DIR}/data/components.cif
+	${COMPONENTS_CIF}
 	DESTINATION ${SHARE_INSTALL_DIR}
 )
 
@@ -416,13 +388,6 @@ option(CIFPP_BUILD_TESTS "Build test exectuables" OFF)
 
 if(CIFPP_BUILD_TESTS)
 
-	if(USE_RSRC)
-		add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/cifpp_test_rsrc.obj
-			COMMAND ${MRC} -o ${CMAKE_CURRENT_BINARY_DIR}/cifpp_test_rsrc.obj ${CMAKE_SOURCE_DIR}/rsrc/mmcif_pdbx_v50.dic ${COFF_SPEC}
-		)
-		set(CIFPP_TEST_RESOURCE ${CMAKE_CURRENT_BINARY_DIR}/cifpp_test_rsrc.obj)
-	endif()
-
 	list(APPEND CIFPP_tests
 		# pdb2cif
 		rename-compound
@@ -433,15 +398,19 @@ if(CIFPP_BUILD_TESTS)
 		set(CIFPP_TEST "${CIFPP_TEST}-test")
 		set(CIFPP_TEST_SOURCE "${CMAKE_CURRENT_SOURCE_DIR}/test/${CIFPP_TEST}.cpp")
 
-		add_executable(${CIFPP_TEST} ${CIFPP_TEST_SOURCE} ${CIFPP_TEST_RESOURCE})
+		add_executable(${CIFPP_TEST} ${CIFPP_TEST_SOURCE})
 
 		target_include_directories(${CIFPP_TEST} PRIVATE
 			${CMAKE_CURRENT_SOURCE_DIR}/include
 			${CMAKE_CURRENT_BINARY_DIR}  # for config.h
 		)
 
-		target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp ${Boost_LIBRARIES} std::filesystem ${ZLIB_LIBRARIES} ${BZip2_LIBRARIES})
-	
+		target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp )
+
+		if(CIFPP_USE_RSRC)
+			mrc_target_resources(${CIFPP_TEST} ${CMAKE_SOURCE_DIR}/rsrc/mmcif_pdbx_v50.dic)
+		endif()
+
 		if(MSVC)
 			# Specify unwind semantics so that MSVC knowns how to handle exceptions
 			target_compile_options(${CIFPP_TEST} PRIVATE /EHsc)
@@ -451,10 +420,10 @@ if(CIFPP_BUILD_TESTS)
 
 		add_custom_command(
 			OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/Run${CIFPP_TEST}.touch
-			COMMAND $<TARGET_FILE:${CIFPP_TEST}> -- ${PROJECT_SOURCE_DIR}/test)
+			COMMAND $<TARGET_FILE:${CIFPP_TEST}> -- ${CMAKE_SOURCE_DIR}/test)
 
 		add_test(NAME ${CIFPP_TEST}
-			COMMAND $<TARGET_FILE:${CIFPP_TEST}> -- ${PROJECT_SOURCE_DIR}/test)
+			COMMAND $<TARGET_FILE:${CIFPP_TEST}> -- ${CMAKE_SOURCE_DIR}/test)
 
 	endforeach()
 endif()
@@ -463,7 +432,7 @@ message("Will install in ${CMAKE_INSTALL_PREFIX}")
 
 # Optionally install the update scripts for CCD and dictionary files
 
-if(INSTALL_UPDATE_SCRIPT)
+if(CIFPP_INSTALL_UPDATE_SCRIPT)
 	set(CIFPP_CRON_DIR "$ENV{DESTDIR}/etc/cron.weekly")
 
 	configure_file(${CMAKE_SOURCE_DIR}/tools/update-libcifpp-data.in update-libcifpp-data @ONLY)

Config.cmake.in

@@ -1,10 +1,10 @@
 @PACKAGE_INIT@
 
 include(CMakeFindDependencyMacro)
-find_dependency(Boost 1.70.0 REQUIRED COMPONENTS system iostreams regex program_options)
+find_dependency(Threads)
+find_dependency(Boost 1.70.0 REQUIRED COMPONENTS system iostreams regex)
 if(NOT WIN32)
 find_dependency(ZLIB)
-find_dependency(BZip2)
 endif()
 
 INCLUDE("${CMAKE_CURRENT_LIST_DIR}/cifppTargets.cmake")

changelog

@@ -1,3 +1,20 @@
+Version 2.0.5
+- Backporting updated CMakeLists.txt file
+
+Version 2.0.4
+- Reverted a too strict test when reading cif files.
+
+Version 2.0.3
+- Fixed reading mmCIF files where model numbers are used and
+  model number 1 is missing.
+
+Version 2.0.2
+- Added configuration flag to disable downloading CCD data during build
+  Note that there are now two flags for CCD data:
+  DOWNLOAD_CCD to enable downloading during build
+  INSTALL_UPDATE_SCRIPT to install an update mechanism for this file
+- Updated unit tests to work even if no CCD data is available
+
 Version 2.0.1
 - Fixed the generator for the symmetry operator table
 

cmake/FindAtomic.cmake

@@ -0,0 +1,64 @@
+# Simple check to see if we need a library for std::atomic
+
+if(TARGET std::atomic)
+	return()
+endif()
+
+cmake_minimum_required(VERSION 3.10)
+
+include(CMakePushCheckState)
+include(CheckIncludeFileCXX)
+include(CheckCXXSourceRuns)
+
+cmake_push_check_state()
+
+set(CMAKE_CXX_STANDARD 17)
+
+check_include_file_cxx("atomic" _CXX_ATOMIC_HAVE_HEADER)
+mark_as_advanced(_CXX_ATOMIC_HAVE_HEADER)
+
+set(code [[
+#include <atomic>
+int main(int argc, char** argv) {
+  std::atomic<long long> s;
+  ++s;
+  return 0;
+}
+]])
+
+check_cxx_source_runs("${code}" _CXX_ATOMIC_BUILTIN)
+
+if(_CXX_ATOMIC_BUILTIN)
+	set(_found 1)
+else()
+  list(APPEND CMAKE_REQUIRED_LIBRARIES atomic)
+  list(APPEND FOLLY_LINK_LIBRARIES atomic)
+
+  check_cxx_source_runs("${code}" _CXX_ATOMIC_LIB_NEEDED)
+  if (NOT _CXX_ATOMIC_LIB_NEEDED)
+    message(FATAL_ERROR "unable to link C++ std::atomic code: you may need \
+      to install GNU libatomic")
+  else()
+	set(_found 1)
+  endif()
+endif()
+
+if(_found)
+	add_library(std::atomic INTERFACE IMPORTED)
+	set_property(TARGET std::atomic APPEND PROPERTY INTERFACE_COMPILE_FEATURES cxx_std_14)
+
+	if(_CXX_ATOMIC_BUILTIN)
+		# Nothing to add...
+	elseif(_CXX_ATOMIC_LIB_NEEDED)
+		set_target_properties(std::atomic PROPERTIES IMPORTED_LIBNAME atomic)
+		set(STDCPPATOMIC_LIBRARY atomic)
+	endif()
+endif()
+
+cmake_pop_check_state()
+
+set(Atomic_FOUND ${_found} CACHE BOOL "TRUE if we can run a program using std::atomic" FORCE)
+
+if(Atomic_FIND_REQUIRED AND NOT Atomic_FOUND)
+    message(FATAL_ERROR "Cannot run simple program using std::atomic")
+endif()

cmake/VersionString.cmake

@@ -0,0 +1,77 @@
+# SPDX-License-Identifier: BSD-2-Clause
+
+# Copyright (c) 2021 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.
+
+cmake_minimum_required(VERSION 3.15)
+
+# Create a revision file, containing the current git version info, if any
+function(write_version_header)
+	include(GetGitRevisionDescription)
+	if(NOT(GIT-NOTFOUND OR HEAD-HASH-NOTFOUND))
+		git_describe_working_tree(BUILD_VERSION_STRING --match=build --dirty)
+
+		if(BUILD_VERSION_STRING MATCHES "build-([0-9]+)-g([0-9a-f]+)(-dirty)?")
+			set(BUILD_GIT_TAGREF "${CMAKE_MATCH_2}")
+			if(CMAKE_MATCH_3)
+				set(BUILD_VERSION_STRING "${CMAKE_MATCH_1}*")
+			else()
+				set(BUILD_VERSION_STRING "${CMAKE_MATCH_1}")
+			endif()
+		endif()
+	else()
+		set(BUILD_VERSION_STRING "no git info available")
+	endif()
+
+	include_directories(${CMAKE_BINARY_DIR} PRIVATE)
+	string(TIMESTAMP BUILD_DATE_TIME "%Y-%m-%dT%H:%M:%SZ" UTC)
+
+	if(ARGC GREATER 0)
+		set(VAR_PREFIX "${ARGV0}")
+	endif()
+
+	file(WRITE "${CMAKE_BINARY_DIR}/revision.hpp.in" [[// Generated revision file
+
+#pragma once
+
+#include <ostream>
+
+const char k@VAR_PREFIX@ProjectName[] = "@PROJECT_NAME@";
+const char k@VAR_PREFIX@VersionNumber[] = "@PROJECT_VERSION@";
+const char k@VAR_PREFIX@VersionGitTag[] = "@BUILD_GIT_TAGREF@";
+const char k@VAR_PREFIX@BuildInfo[] = "@BUILD_VERSION_STRING@";
+const char k@VAR_PREFIX@BuildDate[] = "@BUILD_DATE_TIME@";
+
+inline void write_version_string(std::ostream &os, bool verbose)
+{
+	os << k@VAR_PREFIX@ProjectName << " version " << k@VAR_PREFIX@VersionNumber << std::endl;
+	if (verbose)
+	{
+		os << "build: " << k@VAR_PREFIX@BuildInfo << ' ' << k@VAR_PREFIX@BuildDate << std::endl;
+		if (k@VAR_PREFIX@VersionGitTag[0] != 0)
+			os << "git tag: " << k@VAR_PREFIX@VersionGitTag << std::endl;
+	}
+}
+]])
+	configure_file("${CMAKE_BINARY_DIR}/revision.hpp.in" "${CMAKE_BINARY_DIR}/revision.hpp" @ONLY)
+endfunction()
+

examples/example.cpp

@@ -22,9 +22,7 @@ int main()
 		<< "residues with an OXT are:" << std::endl;
 	
 	for (const auto& [asym, comp, seqnr]: db.find<std::string,std::string,int>(
-			cif::Key("label_atom_id") == "OXT",
-			{ "label_asym_id", "label_comp_id", "label_seq_id" }
-		))
+			cif::Key("label_atom_id") == "OXT", "label_asym_id", "label_comp_id", "label_seq_id"))
 	{
 		std::cout << asym << ' ' << comp << ' ' << seqnr << std::endl;
 	}

include/cif++/Structure.hpp

@@ -533,6 +533,8 @@ class Structure
 	void loadData();
 	void updateAtomIndex();
 
+	void loadAtomsForModel(StructureOpenOptions options);
+
 	File &mFile;
 	size_t mModelNr;
 	AtomView mAtoms;

libcifpp.pc.in

@@ -8,5 +8,5 @@ Name: libcifpp
 Description: C++ library for the manipulation of mmCIF files.
 Version: @PACKAGE_VERSION@
 
-Libs: -L${libdir} -lcifpp @PRIVATE_LIBS@
-Cflags: -I${includedir} @PRIVATE_INC_DIRS@
+Libs: -L${libdir} -lcifpp -lboost_regex -lboost_iostreams
+Cflags: -I${includedir} -pthread

src/CifUtils.cpp

@@ -49,6 +49,7 @@
 #include <boost/algorithm/string.hpp>
 
 #include "cif++/CifUtils.hpp"
+#include "revision.hpp"
 
 namespace ba = boost::algorithm;
 namespace fs = std::filesystem;
@@ -64,39 +65,9 @@ extern int VERBOSE;
 
 std::string get_version_nr()
 {
-	const std::regex
-		rxVersionNr1(R"(build-(\d+)-g[0-9a-f]{7}(-dirty)?)"),
-		rxVersionNr2(R"(libcifpp-version: (\d+\.\d+\.\d+))");
-
-#include "revision.hpp"
-
-	struct membuf : public std::streambuf
-	{
-		membuf(char *data, size_t length) { this->setg(data, data, data + length); }
-	} buffer(const_cast<char *>(kRevision), sizeof(kRevision));
-
-	std::istream is(&buffer);
-
-	std::string line, result;
-
-	while (getline(is, line))
-	{
-		std::smatch m;
-
-		if (std::regex_match(line, m, rxVersionNr1))
-		{
-			result = m[1];
-			if (m[2].matched)
-				result += '*';
-			break;
-		}
-
-		// always the first, replace with more specific if followed by the other info
-		if (std::regex_match(line, m, rxVersionNr2))
-			result = m[1];
-	}
-
-	return result;
+	std::ostringstream s;
+	write_version_string(s, false);
+	return s.str();
 }
 
 // --------------------------------------------------------------------
@@ -1243,6 +1214,9 @@ void addDataDirectory(std::filesystem::path dataDir)
 
 void addFileResource(const std::string &name, std::filesystem::path dataFile)
 {
+	if (not fs::exists(dataFile))
+		throw std::runtime_error("Attempt to add a file resource for " + name + " that does not exist: " + dataFile.string());
+
 	gLocalResources[name] = dataFile;
 }
 

src/Compound.cpp

@@ -125,6 +125,9 @@ Compound::Compound(cif::Datablock &db)
 	cif::tie(mID, mName, mType, mFormula, mFormulaWeight, mFormalCharge) =
 		chemComp.front().get("id", "name", "type", "formula", "formula_weight", "pdbx_formal_charge");
 
+	// The name should not contain newline characters since that triggers validation errors later on
+	ba::replace_all(mName, "\n", "");
+
 	auto &chemCompAtom = db["chem_comp_atom"];
 	for (auto row : chemCompAtom)
 	{
@@ -636,17 +639,18 @@ void CompoundFactory::init(bool useThreadLocalInstanceOnly)
 CompoundFactory::CompoundFactory()
 	: mImpl(nullptr)
 {
+	auto ccd = cif::loadResource("components.cif");
+	if (ccd)
+		mImpl.reset(new CCDCompoundFactoryImpl(mImpl));
+	else if (cif::VERBOSE)
+		std::cerr << "CCD components.cif file was not found" << std::endl;
+
 	const char *clibd_mon = getenv("CLIBD_MON");
 	if (clibd_mon != nullptr and fs::is_directory(clibd_mon))
 		mImpl.reset(new CCP4CompoundFactoryImpl(clibd_mon));
 	else if (cif::VERBOSE)
 		std::cerr << "CCP4 monomers library not found, CLIBD_MON is not defined" << std::endl;
 
-	auto ccd = cif::loadResource("components.cif");
-	if (ccd)
-		mImpl.reset(new CCDCompoundFactoryImpl(mImpl));
-	else if (cif::VERBOSE)
-		std::cerr << "CCD components.cif file was not found" << std::endl;
 }
 
 CompoundFactory::~CompoundFactory()

src/Structure.cpp

@@ -1790,6 +1790,33 @@ Structure::Structure(File &f, size_t modelNr, StructureOpenOptions options)
 
 	auto &atomCat = (*db)["atom_site"];
 
+	loadAtomsForModel(options);
+
+	// Check to see if we should actually load another model?
+	if (mAtoms.empty() and mModelNr == 1)
+	{
+		std::optional<size_t> model_nr;
+		cif::tie(model_nr) = atomCat.front().get("pdbx_PDB_model_num");
+		if (model_nr and *model_nr != mModelNr)
+		{
+			if (cif::VERBOSE)
+				std::cerr << "No atoms loaded for model 1, trying model " << *model_nr << std::endl;
+			mModelNr = *model_nr;
+			loadAtomsForModel(options);
+		}
+	}
+
+	if (mAtoms.empty())
+		std::cerr << "Warning: no atoms loaded" << std::endl;
+	else
+		loadData();
+}
+
+void Structure::loadAtomsForModel(StructureOpenOptions options)
+{
+	auto db = mFile.impl().mDb;
+	auto &atomCat = (*db)["atom_site"];
+
 	for (auto &a : atomCat)
 	{
 		std::string id, type_symbol;
@@ -1805,10 +1832,9 @@ Structure::Structure(File &f, size_t modelNr, StructureOpenOptions options)
 
 		mAtoms.emplace_back(new AtomImpl(*db, id, a));
 	}
-
-	loadData();
 }
 
+
 Structure::Structure(const Structure &s)
 	: mFile(s.mFile)
 	, mModelNr(s.mModelNr)

test/HEM.cif

@@ -0,0 +1,253 @@
+data_HEM
+#
+
+_chem_comp.id                                   HEM
+_chem_comp.name                                 "PROTOPORPHYRIN IX CONTAINING FE"
+_chem_comp.type                                 NON-POLYMER
+_chem_comp.pdbx_type                            HETAIN
+_chem_comp.formula                              "C34 H32 Fe N4 O4"
+_chem_comp.mon_nstd_parent_comp_id              ?
+_chem_comp.pdbx_synonyms                        HEME
+_chem_comp.pdbx_formal_charge                   0
+_chem_comp.pdbx_initial_date                    1999-07-08
+_chem_comp.pdbx_modified_date                   2020-06-17
+_chem_comp.pdbx_ambiguous_flag                  Y
+_chem_comp.pdbx_release_status                  REL
+_chem_comp.pdbx_replaced_by                     ?
+_chem_comp.pdbx_replaces                        MHM
+_chem_comp.formula_weight                       616.487
+_chem_comp.one_letter_code                      ?
+_chem_comp.three_letter_code                    HEM
+_chem_comp.pdbx_model_coordinates_details       ?
+_chem_comp.pdbx_model_coordinates_missing_flag  N
+_chem_comp.pdbx_ideal_coordinates_details       Corina
+_chem_comp.pdbx_ideal_coordinates_missing_flag  N
+_chem_comp.pdbx_model_coordinates_db_code       3IA3
+_chem_comp.pdbx_subcomponent_list               ?
+_chem_comp.pdbx_processing_site                 RCSB
+#   #
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.alt_atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.charge
+_chem_comp_atom.pdbx_align
+_chem_comp_atom.pdbx_aromatic_flag
+_chem_comp_atom.pdbx_leaving_atom_flag
+_chem_comp_atom.pdbx_stereo_config
+_chem_comp_atom.model_Cartn_x
+_chem_comp_atom.model_Cartn_y
+_chem_comp_atom.model_Cartn_z
+_chem_comp_atom.pdbx_model_Cartn_x_ideal
+_chem_comp_atom.pdbx_model_Cartn_y_ideal
+_chem_comp_atom.pdbx_model_Cartn_z_ideal
+_chem_comp_atom.pdbx_component_atom_id
+_chem_comp_atom.pdbx_component_comp_id
+_chem_comp_atom.pdbx_ordinal
+HEM  CHA   CHA   C   0  1  N  N  N   2.748  -19.531  39.896  -2.161  -0.125   0.490  CHA   HEM   1  
+HEM  CHB   CHB   C   0  1  N  N  N   3.258  -17.744  35.477   1.458  -3.419   0.306  CHB   HEM   2  
+HEM  CHC   CHC   C   0  1  N  N  N   1.703  -21.900  33.637   4.701   0.169  -0.069  CHC   HEM   3  
+HEM  CHD   CHD   C   0  1  N  N  N   1.149  -23.677  38.059   1.075   3.460   0.018  CHD   HEM   4  
+HEM  C1A   C1A   C   0  1  Y  N  N   3.031  -18.673  38.872  -1.436  -1.305   0.380  C1A   HEM   5  
+HEM  C2A   C2A   C   0  1  Y  N  N   3.578  -17.325  39.013  -2.015  -2.587   0.320  C2A   HEM   6  
+HEM  C3A   C3A   C   0  1  Y  N  N   3.705  -16.820  37.785  -1.009  -3.500   0.270  C3A   HEM   7  
+HEM  C4A   C4A   C   0  1  Y  N  N   3.256  -17.863  36.862   0.216  -2.803   0.298  C4A   HEM   8  
+HEM  CMA   CMA   C   0  1  N  N  N   4.227  -15.469  37.393  -1.175  -4.996   0.197  CMA   HEM   9  
+HEM  CAA   CAA   C   0  1  N  N  N   3.945  -16.670  40.296  -3.490  -2.893   0.314  CAA   HEM  10  
+HEM  CBA   CBA   C   0  1  N  N  N   5.391  -17.138  40.581  -3.998  -2.926  -1.129  CBA   HEM  11  
+HEM  CGA   CGA   C   0  1  N  N  N   6.095  -16.663  41.825  -5.473  -3.232  -1.136  CGA   HEM  12  
+HEM  O1A   O1A   O   0  1  N  N  N   7.098  -15.928  41.683  -6.059  -3.405  -0.094  O1A   HEM  13  
+HEM  O2A   O2A   O   0  1  N  N  N   5.657  -17.040  42.940  -6.137  -3.311  -2.300  O2A   HEM  14  
+HEM  C1B   C1B   C   0  1  N  N  N   2.888  -18.698  34.579   2.664  -2.707   0.308  C1B   HEM  15  
+HEM  C2B   C2B   C   0  1  N  N  N   2.933  -18.535  33.146   3.937  -3.328   0.418  C2B   HEM  16  
+HEM  C3B   C3B   C   0  1  N  N  N   2.499  -19.716  32.632   4.874  -2.341   0.314  C3B   HEM  17  
+HEM  C4B   C4B   C   0  1  N  N  N   2.187  -20.580  33.743   4.117  -1.079   0.139  C4B   HEM  18  
+HEM  CMB   CMB   C   0  1  N  N  N   3.391  -17.290  32.422   4.203  -4.798   0.613  CMB   HEM  19  
+HEM  CAB   CAB   C   0  1  N  N  N   2.345  -20.140  31.217   6.339  -2.497   0.365  CAB   HEM  20  
+HEM  CBB   CBB   C   0  1  N  N  N   1.755  -19.492  30.233   6.935  -3.419  -0.385  CBB   HEM  21  
+HEM  C1C   C1C   C   0  1  Y  N  N   1.395  -22.786  34.659   3.964   1.345  -0.174  C1C   HEM  22  
+HEM  C2C   C2C   C   0  1  Y  N  N   0.854  -24.130  34.500   4.531   2.601  -0.445  C2C   HEM  23  
+HEM  C3C   C3C   C   0  1  Y  N  N   0.689  -24.626  35.757   3.510   3.536  -0.437  C3C   HEM  24  
+HEM  C4C   C4C   C   0  1  Y  N  N   1.139  -23.583  36.674   2.304   2.846  -0.139  C4C   HEM  25  
+HEM  CMC   CMC   C   0  1  N  N  N   0.550  -24.782  33.175   5.991   2.880  -0.697  CMC   HEM  26  
+HEM  CAC   CAC   C   0  1  N  N  N   0.164  -25.943  36.196   3.649   4.981  -0.692  CAC   HEM  27  
+HEM  CBC   CBC   C   0  1  N  N  N   0.498  -27.158  35.750   4.201   5.407  -1.823  CBC   HEM  28  
+HEM  C1D   C1D   C   0  1  N  N  N   1.550  -22.718  38.980  -0.102   2.753   0.298  C1D   HEM  29  
+HEM  C2D   C2D   C   0  1  N  N  N   1.513  -22.879  40.415  -1.382   3.388   0.641  C2D   HEM  30  
+HEM  C3D   C3D   C   0  1  N  N  N   1.951  -21.691  40.929  -2.283   2.389   0.774  C3D   HEM  31  
+HEM  C4D   C4D   C   0  1  N  N  N   2.277  -20.826  39.811  -1.561   1.137   0.511  C4D   HEM  32  
+HEM  CMD   CMD   C   0  1  N  N  N   1.055  -24.094  41.156  -1.639   4.863   0.811  CMD   HEM  33  
+HEM  CAD   CAD   C   0  1  N  N  N   2.048  -21.326  42.352  -3.741   2.532   1.123  CAD   HEM  34  
+HEM  CBD   CBD   C   0  1  N  N  N   0.741  -20.498  42.530  -4.573   2.563  -0.160  CBD   HEM  35  
+HEM  CGD   CGD   C   0  1  N  N  N   0.578  -19.987  43.892  -6.032   2.706   0.189  CGD   HEM  36  
+HEM  O1D   O1D   O   0  1  N  N  N   1.387  -19.103  44.303  -6.372   2.776   1.347  O1D   HEM  37  
+HEM  O2D   O2D   O   0  1  N  N  N  -0.401  -20.468  44.537  -6.954   2.755  -0.785  O2D   HEM  38  
+HEM  NA    NA    N   0  1  Y  N  N   2.863  -18.969  37.554  -0.068  -1.456   0.321  NA    HEM  39  
+HEM  NB    NB    N   0  1  N  N  N   2.439  -19.944  34.911   2.820  -1.386   0.207  NB    HEM  40  
+HEM  NC    NC    N   0  1  Y  N  N   1.537  -22.509  35.976   2.604   1.506  -0.033  NC    HEM  41  
+HEM  ND    ND    N   0  1  N  N  N   2.008  -21.465  38.663  -0.276   1.431   0.298  ND    HEM  42  
+HEM  FE    FE    FE  0  0  N  N  N   2.196  -20.749  36.814   1.010   0.157  -0.060  FE    HEM  43  
+HEM  HHB   HHB   H   0  1  N  N  N   3.587  -16.798  35.072   1.498  -4.508   0.309  HHB   HEM  44  
+HEM  HHC   HHC   H   0  1  N  N  N   1.553  -22.268  32.633   5.786   0.229  -0.153  HHC   HEM  45  
+HEM  HHD   HHD   H   0  1  N  N  N   0.802  -24.613  38.472   1.018   4.543  -0.083  HHD   HEM  46  
+HEM  HMA   HMA   H   0  1  N  N  N   5.316  -15.524  37.249  -1.220  -5.306  -0.847  HMA   HEM  47  
+HEM  HMAA  HMAA  H   0  0  N  N  N   3.749  -15.149  36.455  -0.328  -5.480   0.683  HMAA  HEM  48  
+HEM  HMAB  HMAB  H   0  0  N  N  N   3.998  -14.743  38.187  -2.097  -5.285   0.702  HMAB  HEM  49  
+HEM  HAA   HAA   H   0  1  N  N  N   3.905  -15.575  40.197  -3.662  -3.862   0.782  HAA   HEM  50  
+HEM  HAAA  HAAA  H   0  0  N  N  N   3.268  -16.991  41.102  -4.024  -2.121   0.869  HAAA  HEM  51  
+HEM  HBA   HBA   H   0  1  N  N  N   5.368  -18.237  40.627  -3.825  -1.956  -1.597  HBA   HEM  52  
+HEM  HBAA  HBAA  H   0  0  N  N  N   6.004  -16.819  39.725  -3.464  -3.697  -1.684  HBAA  HEM  53  
+HEM  HMB   HMB   H   0  1  N  N  N   3.319  -17.449  31.336   3.256  -5.336   0.660  HMB   HEM  54  
+HEM  HMBA  HMBA  H   0  0  N  N  N   2.753  -16.442  32.711   4.794  -5.175  -0.222  HMBA  HEM  55  
+HEM  HMBB  HMBB  H   0  0  N  N  N   4.435  -17.072  32.692   4.752  -4.948   1.543  HMBB  HEM  56  
+HEM  HAB   HAB   H   0  1  N  N  N   2.770  -21.100  30.963   6.927  -1.863   1.011  HAB   HEM  57  
+HEM  HBB   HBB   H   0  1  N  N  N   1.719  -19.927  29.245   7.994  -3.600  -0.277  HBB   HEM  58  
+HEM  HBBA  HBBA  H   0  0  N  N  N   1.308  -18.526  30.414   6.360  -3.987  -1.102  HBBA  HEM  59  
+HEM  HMC   HMC   H   0  1  N  N  N   0.153  -25.793  33.346   6.554   1.949  -0.639  HMC   HEM  60  
+HEM  HMCA  HMCA  H   0  0  N  N  N  -0.196  -24.182  32.634   6.110   3.316  -1.689  HMCA  HEM  61  
+HEM  HMCB  HMCB  H   0  0  N  N  N   1.472  -24.846  32.578   6.362   3.578   0.053  HMCB  HEM  62  
+HEM  HAC   HAC   H   0  1  N  N  N  -0.583  -25.916  36.975   3.303   5.694   0.042  HAC   HEM  63  
+HEM  HBC   HBC   H   0  1  N  N  N   0.027  -28.035  36.169   4.614   4.696  -2.523  HBC   HEM  64  
+HEM  HBCA  HBCA  H   0  0  N  N  N   1.239  -27.263  34.971   4.235   6.464  -2.043  HBCA  HEM  65  
+HEM  HMD   HMD   H   0  1  N  N  N   1.142  -23.919  42.238  -0.715   5.415   0.639  HMD   HEM  66  
+HEM  HMDA  HMDA  H   0  0  N  N  N   0.006  -24.304  40.902  -2.394   5.185   0.094  HMDA  HEM  67  
+HEM  HMDB  HMDB  H   0  0  N  N  N   1.680  -24.954  40.872  -1.994   5.055   1.824  HMDB  HEM  68  
+HEM  HAD   HAD   H   0  1  N  N  N   2.055  -22.216  42.999  -4.052   1.687   1.738  HAD   HEM  69  
+HEM  HADA  HADA  H   0  0  N  N  N   2.943  -20.719  42.554  -3.893   3.459   1.677  HADA  HEM  70  
+HEM  HBD   HBD   H   0  1  N  N  N   0.767  -19.646  41.835  -4.262   3.408  -0.775  HBD   HEM  71  
+HEM  HBDA  HBDA  H   0  0  N  N  N  -0.119  -21.141  42.290  -4.421   1.636  -0.714  HBDA  HEM  72  
+HEM  H2A   H2A   H   0  1  N  N  N   6.201  -16.682  43.632  -7.082  -3.510  -2.254  H2A   HEM  73  
+HEM  H2D   H2D   H   0  1  N  N  N  -0.445  -20.063  45.395  -7.877   2.847  -0.512  H2D   HEM  74  
+HEM  HHA   HHA   H   0  1  N  N  N   2.913  -19.150  40.893  -3.246  -0.188   0.567  HHA   HEM  75  
+#   #
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.value_order
+_chem_comp_bond.pdbx_aromatic_flag
+_chem_comp_bond.pdbx_stereo_config
+_chem_comp_bond.pdbx_ordinal
+HEM  CHA  C1A   SING  N  N   1  
+HEM  CHA  C4D   DOUB  N  N   2  
+HEM  CHA  HHA   SING  N  N   3  
+HEM  CHB  C4A   SING  N  N   4  
+HEM  CHB  C1B   DOUB  N  N   5  
+HEM  CHB  HHB   SING  N  N   6  
+HEM  CHC  C4B   SING  N  N   7  
+HEM  CHC  C1C   DOUB  N  N   8  
+HEM  CHC  HHC   SING  N  N   9  
+HEM  CHD  C4C   DOUB  N  N  10  
+HEM  CHD  C1D   SING  N  N  11  
+HEM  CHD  HHD   SING  N  N  12  
+HEM  C1A  C2A   DOUB  Y  N  13  
+HEM  C1A  NA    SING  Y  N  14  
+HEM  C2A  C3A   SING  Y  N  15  
+HEM  C2A  CAA   SING  N  N  16  
+HEM  C3A  C4A   DOUB  Y  N  17  
+HEM  C3A  CMA   SING  N  N  18  
+HEM  C4A  NA    SING  Y  N  19  
+HEM  CMA  HMA   SING  N  N  20  
+HEM  CMA  HMAA  SING  N  N  21  
+HEM  CMA  HMAB  SING  N  N  22  
+HEM  CAA  CBA   SING  N  N  23  
+HEM  CAA  HAA   SING  N  N  24  
+HEM  CAA  HAAA  SING  N  N  25  
+HEM  CBA  CGA   SING  N  N  26  
+HEM  CBA  HBA   SING  N  N  27  
+HEM  CBA  HBAA  SING  N  N  28  
+HEM  CGA  O1A   DOUB  N  N  29  
+HEM  CGA  O2A   SING  N  N  30  
+HEM  C1B  C2B   SING  N  N  31  
+HEM  C1B  NB    SING  N  N  32  
+HEM  C2B  C3B   DOUB  N  N  33  
+HEM  C2B  CMB   SING  N  N  34  
+HEM  C3B  C4B   SING  N  N  35  
+HEM  C3B  CAB   SING  N  N  36  
+HEM  C4B  NB    DOUB  N  N  37  
+HEM  CMB  HMB   SING  N  N  38  
+HEM  CMB  HMBA  SING  N  N  39  
+HEM  CMB  HMBB  SING  N  N  40  
+HEM  CAB  CBB   DOUB  N  N  41  
+HEM  CAB  HAB   SING  N  N  42  
+HEM  CBB  HBB   SING  N  N  43  
+HEM  CBB  HBBA  SING  N  N  44  
+HEM  C1C  C2C   SING  Y  N  45  
+HEM  C1C  NC    SING  Y  N  46  
+HEM  C2C  C3C   DOUB  Y  N  47  
+HEM  C2C  CMC   SING  N  N  48  
+HEM  C3C  C4C   SING  Y  N  49  
+HEM  C3C  CAC   SING  N  N  50  
+HEM  C4C  NC    SING  Y  N  51  
+HEM  CMC  HMC   SING  N  N  52  
+HEM  CMC  HMCA  SING  N  N  53  
+HEM  CMC  HMCB  SING  N  N  54  
+HEM  CAC  CBC   DOUB  N  N  55  
+HEM  CAC  HAC   SING  N  N  56  
+HEM  CBC  HBC   SING  N  N  57  
+HEM  CBC  HBCA  SING  N  N  58  
+HEM  C1D  C2D   SING  N  N  59  
+HEM  C1D  ND    DOUB  N  N  60  
+HEM  C2D  C3D   DOUB  N  N  61  
+HEM  C2D  CMD   SING  N  N  62  
+HEM  C3D  C4D   SING  N  N  63  
+HEM  C3D  CAD   SING  N  N  64  
+HEM  C4D  ND    SING  N  N  65  
+HEM  CMD  HMD   SING  N  N  66  
+HEM  CMD  HMDA  SING  N  N  67  
+HEM  CMD  HMDB  SING  N  N  68  
+HEM  CAD  CBD   SING  N  N  69  
+HEM  CAD  HAD   SING  N  N  70  
+HEM  CAD  HADA  SING  N  N  71  
+HEM  CBD  CGD   SING  N  N  72  
+HEM  CBD  HBD   SING  N  N  73  
+HEM  CBD  HBDA  SING  N  N  74  
+HEM  CGD  O1D   DOUB  N  N  75  
+HEM  CGD  O2D   SING  N  N  76  
+HEM  O2A  H2A   SING  N  N  77  
+HEM  O2D  H2D   SING  N  N  78  
+HEM  FE   NA    SING  N  N  79  
+HEM  FE   NB    SING  N  N  80  
+HEM  FE   NC    SING  N  N  81  
+HEM  FE   ND    SING  N  N  82  
+#   #
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+HEM  SMILES            ACDLabs               12.01  "C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O"  
+HEM  InChI             InChI                 1.03   "InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;"  
+HEM  InChIKey          InChI                 1.03   KABFMIBPWCXCRK-RGGAHWMASA-L  
+HEM  SMILES_CANONICAL  CACTVS                3.385  "CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C"  
+HEM  SMILES            CACTVS                3.385  "CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C"  
+HEM  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O"  
+HEM  SMILES            "OpenEye OEToolkits"  1.7.6  "Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O"  
+#   #
+loop_
+_pdbx_chem_comp_identifier.comp_id
+_pdbx_chem_comp_identifier.type
+_pdbx_chem_comp_identifier.program
+_pdbx_chem_comp_identifier.program_version
+_pdbx_chem_comp_identifier.identifier
+HEM  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.6.1  "3-[(5Z,10Z,14Z,19Z)-18-(2-carboxyethyl)-8,13-bis(ethenyl)-3,7,12,17-tetramethyl-21,23-dihydroporphyrin-2-yl]propanoic acid"  
+HEM  "SYSTEMATIC NAME"  ACDLabs               12.01  "[3,3'-(7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~)dipropanoato(2-)]iron"  
+#   #
+loop_
+_pdbx_chem_comp_audit.comp_id
+_pdbx_chem_comp_audit.action_type
+_pdbx_chem_comp_audit.date
+_pdbx_chem_comp_audit.processing_site
+HEM  "Create component"    1999-07-08  RCSB  
+HEM  "Other modification"  2016-01-20  RCSB  
+HEM  "Modify synonyms"     2020-06-05  PDBE  
+#
+_pdbx_chem_comp_synonyms.ordinal     1
+_pdbx_chem_comp_synonyms.comp_id     HEM
+_pdbx_chem_comp_synonyms.name        HEME
+_pdbx_chem_comp_synonyms.provenance  ?
+_pdbx_chem_comp_synonyms.type        ?
+##
+

test/structure-test.cpp

@@ -24,7 +24,7 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-#define BOOST_TEST_MODULE Structure_Test
+#define BOOST_TEST_ALTERNATIVE_INIT_API
 #include <boost/test/included/unit_test.hpp>
 
 #include <stdexcept>
@@ -52,16 +52,23 @@ cif::File operator""_cf(const char* text, size_t length)
 
 std::filesystem::path gTestDir = std::filesystem::current_path();
 
-BOOST_AUTO_TEST_CASE(init)
+bool init_unit_test()
 {
-	// not a test, just initialize test dir
+    cif::VERBOSE = 1;
 
+	// not a test, just initialize test dir
 	if (boost::unit_test::framework::master_test_suite().argc == 2)
 		gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
 
+	// do this now, avoids the need for installing
+	cif::addFileResource("mmcif_pdbx_v50.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx_v50.dic");
+
 	// initialize CCD location
-	if (std::filesystem::exists(gTestDir / ".."/"data"/"components.cif"))
-		cif::addFileResource("components.cif", gTestDir / ".."/"data"/"components.cif");
+	cif::addFileResource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
+
+	mmcif::CompoundFactory::instance().pushDictionary(gTestDir / "HEM.cif");
+
+	return true;
 }
 
 // --------------------------------------------------------------------

test/unit-test.cpp

@@ -24,7 +24,8 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-#define BOOST_TEST_MODULE LibCifPP_Test
+#define BOOST_TEST_ALTERNATIVE_INIT_API
+// #define BOOST_TEST_MODULE LibCifPP_Test
 #include <boost/test/included/unit_test.hpp>
 
 #include <stdexcept>
@@ -53,23 +54,27 @@ cif::File operator""_cf(const char* text, size_t length)
 
 // --------------------------------------------------------------------
 
-BOOST_AUTO_TEST_CASE(init)
+bool init_unit_test()
 {
-	// not a test, just initialize test dir
+    cif::VERBOSE = 1;
 
+	// not a test, just initialize test dir
 	if (boost::unit_test::framework::master_test_suite().argc == 2)
 		gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
+
+	// do this now, avoids the need for installing
+	cif::addFileResource("mmcif_pdbx_v50.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx_v50.dic");
+
+	// initialize CCD location
+	cif::addFileResource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
+
+	return true;
 }
 
 // --------------------------------------------------------------------
 
 BOOST_AUTO_TEST_CASE(ut1)
 {
-    cif::VERBOSE = 1;
-
-	// do this now, avoids the need for installing
-	cif::addFileResource("mmcif_pdbx_v50.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx_v50.dic");
-
     // using namespace mmcif;
 
     auto f = R"(data_TEST
@@ -1527,8 +1532,6 @@ BOOST_AUTO_TEST_CASE(bondmap_1)
 {
     cif::VERBOSE = 2;
 
-	cif::addFileResource("components.cif", gTestDir / ".." / "data" / "components.cif");
-
 	// sections taken from CCD compounds.cif
 	auto components = R"(
 data_ASN