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 2.0.2 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-		option(RECREATE_SYMOP_DATA "Recreate SymOp data table in case it is out of date" ON)
+		option(CIFPP_RECREATE_SYMOP_DATA "Recreate SymOp data table in case it is out of date" ON)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::
@@ -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 +1,13 @@
+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:

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();
 }
 
 // --------------------------------------------------------------------

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)