Change logic for testing std::filesystem and libatomic

CMakeLists.txt

@@ -37,7 +37,6 @@ include(CheckIncludeFiles)
 include(CheckLibraryExists)
 include(CMakePackageConfigHelpers)
 include(Dart)
-include(FindFilesystem)
 include(GenerateExportHeader)
 
 set(CXX_EXTENSIONS OFF)
@@ -178,8 +177,16 @@ find_package(Boost 1.70.0 REQUIRED COMPONENTS system iostreams regex program_opt
 if(NOT MSVC AND Boost_USE_STATIC_LIBS)
 	find_package(ZLIB REQUIRED)
 	find_package(BZip2 REQUIRED)
+
+	list(APPEND CIFPP_REQUIRED_LIBRARIES ${ZLIB_LIBRARIES} ${BZip2_LIBRARIES})
 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
 
 include(GetGitRevisionDescription)
@@ -203,7 +210,7 @@ if(CIFPP_RECREATE_SYMOP_DATA)
 
 	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()
@@ -274,7 +281,7 @@ 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 Threads::Threads ${Boost_LIBRARIES} ${CIFPP_REQUIRED_LIBRARIES})
 
 if (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
     target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
@@ -431,7 +438,7 @@ if(CIFPP_BUILD_TESTS)
 			${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 ${Boost_LIBRARIES} ${CIFPP_REQUIRED_LIBRARIES})
 	
 		if(MSVC)
 			# Specify unwind semantics so that MSVC knowns how to handle exceptions

cmake/FindAtomic.cmake

+# Simplistic
+
+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) {
+  struct Test { int val; };
+  std::atomic<Test> s;
+  (void)s.is_lock_free();
+  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/FindFilesystem.cmake

@@ -59,8 +59,10 @@ if(_found)
 		# Nothing to add...
 	elseif(CXX_FILESYSTEM_STDCPPFS_NEEDED)
 		set_target_properties(std::filesystem PROPERTIES IMPORTED_LIBNAME stdc++fs)
+		set(STDCPPFS_LIBRARY stdc++fs)
 	elseif(CXX_FILESYSTEM_CPPFS_NEEDED)
 		set_target_properties(std::filesystem PROPERTIES IMPORTED_LIBNAME c++fs)
+		set(STDCPPFS_LIBRARY c++fs)
 	endif()
 endif()
 

include/cif++/Structure.hpp

@@ -481,6 +481,12 @@ class Structure
 	/// \brief Get a the single residue for an asym with id \a asymID
 	Residue &getResidue(const std::string &asymID);
 
+	/// \brief Get a the residue for atom \a atom
+	Residue &getResidue(const mmcif::Atom &atom);
+
+	/// \brief Get a the residue for atom \a atom
+	const Residue &getResidue(const mmcif::Atom &atom) const;
+
 	// map between auth and label locations
 
 	std::tuple<std::string, int, std::string> MapAuthToLabel(const std::string &asymID,

src/Structure.cpp

@@ -2098,6 +2098,16 @@ Residue &Structure::getResidue(const std::string &asymID)
 	return const_cast<Residue&>(const_cast<Structure const&>(*this).getResidue(asymID));
 }
 
+Residue &Structure::getResidue(const mmcif::Atom &atom)
+{
+	return getResidue(atom.labelAsymID(), atom.labelCompID(), atom.labelSeqID());
+}
+
+const Residue &Structure::getResidue(const mmcif::Atom &atom) const
+{
+	return getResidue(atom.labelAsymID(), atom.labelCompID(), atom.labelSeqID());
+}
+
 File &Structure::getFile() const
 {
 	return mFile;