Merge branch 'develop' of github.com:PDB-REDO/libcifpp into develop

CMakeLists.txt

@@ -25,7 +25,7 @@
 cmake_minimum_required(VERSION 3.16)
 
 # set the project name
-project(cifpp VERSION 1.1.1 LANGUAGES CXX)
+project(cifpp VERSION 2.0.0 LANGUAGES CXX)
 
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 
@@ -34,6 +34,7 @@ enable_testing()
 include(GNUInstallDirs)
 include(CheckFunctionExists)
 include(CheckIncludeFiles)
+include(FindFilesystem)
 include(CheckLibraryExists)
 include(CMakePackageConfigHelpers)
 include(Dart)
@@ -43,6 +44,8 @@ set(CXX_EXTENSIONS OFF)
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
+find_package(Filesystem REQUIRED)
+
 if(CMAKE_COMPILER_IS_GNUCC)
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter")
 endif()
@@ -81,12 +84,14 @@ endif()
 
 # When CCP4 is sourced in the environment, we can recreate the symmetry operations table
 if(EXISTS "${CCP4}")
-	option(RECREATE_SYMOP_DATA "Recreate SymOp data table in case it is out of date" ON)
-
 	if(RECREATE_SYMOP_DATA AND NOT EXISTS "${CLIBD}/syminfo.lib")
-		message(FATAL_ERROR "Symop data table recreation requested, but file syminfo.lib was not found in ${CLIBD}")
+		message(WARNING "Symop data table recreation requested, but file syminfo.lib was not found in ${CLIBD}")
+		set(RECREATE_SYMOP_DATA OFF)
+	else()
+		option(RECREATE_SYMOP_DATA "Recreate SymOp data table in case it is out of date" ON)
 	endif()
 else()
+	set(RECREATE_SYMOP_DATA OFF)
 	message("Not trying to recreate SymOpTable_data.hpp since CCP4 is not defined")
 endif()
 
@@ -166,8 +171,6 @@ set(THREADS_PREFER_PTHREAD_FLAG)
 find_package(Threads)
 
 set (Boost_DETAILED_FAILURE_MSG ON)
-# set (Boost_DEBUG ON)
-# set (Boost_VERBOSE ON)
 find_package(Boost 1.70.0 REQUIRED COMPONENTS system iostreams regex date_time program_options)
 
 # find_package(ZLIB)
@@ -364,11 +367,11 @@ install(FILES
 	COMPONENT Devel
 )
 
-set(cifpp_MAJOR_VERSION 1)
+set(cifpp_MAJOR_VERSION ${CMAKE_PROJECT_VERSION_MAJOR})
 set_target_properties(cifpp PROPERTIES
 	VERSION ${PROJECT_VERSION}
-	SOVERSION 1
-	INTERFACE_cifpp_MAJOR_VERSION 1)
+	SOVERSION ${cifpp_MAJOR_VERSION}
+	INTERFACE_cifpp_MAJOR_VERSION ${cifpp_MAJOR_VERSION})
 
 set_property(TARGET cifpp APPEND PROPERTY
   COMPATIBLE_INTERFACE_STRING cifpp_MAJOR_VERSION

cmake/FindFilesystem.cmake

+# Simplistic reimplementation of https://github.com/vector-of-bool/CMakeCM/blob/master/modules/FindFilesystem.cmake
+
+if(TARGET std::filesystem)
+	return()
+endif()
+
+cmake_minimum_required(VERSION 3.10)
+
+include(CMakePushCheckState)
+include(CheckIncludeFileCXX)
+include(CheckCXXSourceCompiles)
+
+cmake_push_check_state()
+
+set(CMAKE_CXX_STANDARD 17)
+
+check_include_file_cxx("filesystem" _CXX_FILESYSTEM_HAVE_HEADER)
+mark_as_advanced(_CXX_FILESYSTEM_HAVE_HEADER)
+
+set(code [[
+#include <cstdlib>
+#include <filesystem>
+
+int main() {
+	auto cwd = std::filesystem::current_path();
+	return EXIT_SUCCESS;
+}
+]])
+
+# Check a simple filesystem program without any linker flags
+check_cxx_source_compiles("${code}" CXX_FILESYSTEM_NO_LINK_NEEDED)
+
+set(_found ${CXX_FILESYSTEM_NO_LINK_NEEDED})
+
+if(NOT CXX_FILESYSTEM_NO_LINK_NEEDED)
+	set(prev_libraries ${CMAKE_REQUIRED_LIBRARIES})
+	# Add the libstdc++ flag
+	set(CMAKE_REQUIRED_LIBRARIES ${prev_libraries} -lstdc++fs)
+	check_cxx_source_compiles("${code}" CXX_FILESYSTEM_STDCPPFS_NEEDED)
+	set(_found ${CXX_FILESYSTEM_STDCPPFS_NEEDED})
+	if(NOT CXX_FILESYSTEM_STDCPPFS_NEEDED)
+		# Try the libc++ flag
+		set(CMAKE_REQUIRED_LIBRARIES ${prev_libraries} -lc++fs)
+		check_cxx_source_compiles("${code}" CXX_FILESYSTEM_CPPFS_NEEDED)
+		set(_found ${CXX_FILESYSTEM_CPPFS_NEEDED})
+	endif()
+endif()
+
+if(_found)
+	add_library(std::filesystem INTERFACE IMPORTED)
+	set_property(TARGET std::filesystem APPEND PROPERTY INTERFACE_COMPILE_FEATURES cxx_std_17)
+
+	if(CXX_FILESYSTEM_NO_LINK_NEEDED)
+		# Nothing to add...
+	elseif(CXX_FILESYSTEM_STDCPPFS_NEEDED)
+		set_property(TARGET std::filesystem APPEND PROPERTY INTERFACE_LINK_LIBRARIES -lstdc++fs)
+	elseif(CXX_FILESYSTEM_CPPFS_NEEDED)
+		set_property(TARGET std::filesystem APPEND PROPERTY INTERFACE_LINK_LIBRARIES -lc++fs)
+	endif()
+endif()
+
+cmake_pop_check_state()
+
+set(Filesystem_FOUND ${_found} CACHE BOOL "TRUE if we can run a program using std::filesystem" FORCE)
+
+if(Filesystem_FIND_REQUIRED AND NOT Filesystem_FOUND)
+    message(FATAL_ERROR "Cannot run simple program using std::filesystem")
+endif()

include/cif++/Cif++.hpp

@@ -2354,8 +2354,6 @@ conditional_iterator_proxy<CategoryType, Ts...>::conditional_iterator_proxy(Cate
 {
 	static_assert(sizeof...(Ts) == sizeof...(Ns), "Number of column names should be equal to number of requested value types");
 
-	size_t N = sizeof...(Ns);
-
 	mCondition.prepare(cat);
 
 	while (mCBegin != mCEnd and not mCondition(*mCat, mCBegin.row()))

src/Structure.cpp

@@ -1053,7 +1053,7 @@ Atom Residue::atomByID(const std::string &atomID) const
 		}
 	}
 
-	if (not result and cif::VERBOSE)
+	if (not result and cif::VERBOSE > 1)
 		std::cerr << "Atom with atom_id " << atomID << " not found in residue " << mAsymID << ':' << mSeqID << std::endl;
 
 	return result;
@@ -2216,7 +2216,7 @@ std::string Structure::insertCompound(const std::string &compoundID, bool isEnti
 		catch(const std::exception& ex)
 		{
 			auto &entity = db["entity"];
-			entity_id = std::to_string(entity.size() + 1);
+			entity_id = entity.getUniqueID("");
 
 			entity.emplace({
 				{"id", entity_id},
@@ -2474,9 +2474,11 @@ std::string Structure::createNonpoly(const std::string &entity_id, const std::ve
 
 	for (auto& atom: atoms)
 	{
-		atom_site.emplace({
+		auto atom_id = atom_site.getUniqueID("");
+
+		auto &&[row, inserted ] = atom_site.emplace({
 			{ "group_PDB",			atom.property<std::string>("group_PDB") },
-			{ "id",					atom_site.getUniqueID("") },
+			{ "id",					atom_id },
 			{ "type_symbol",		atom.property<std::string>("type_symbol") },
 			{ "label_atom_id",		atom.property<std::string>("label_atom_id") },
 			{ "label_alt_id",		atom.property<std::string>("label_alt_id") },
@@ -2497,8 +2499,12 @@ std::string Structure::createNonpoly(const std::string &entity_id, const std::ve
 			{ "auth_atom_id",		atom.property<std::string>("label_atom_id") },
 			{ "pdbx_PDB_model_num",	1 }
 		});
+
+		mAtoms.emplace_back(new AtomImpl(db, atom_id, row));
 	}
 
+	mNonPolymers.emplace_back(*this, comp_id, asym_id);
+
 	return asym_id;
 }
 

src/revision.hpp.in

 const char kRevision[] = R"(
-libzeep-version: @PROJECT_VERSION@
+lib@PROJECT_NAME@-version: @PROJECT_VERSION@
 @BUILD_VERSION_STRING@
 Date: @BUILD_DATE_TIME@
 )";

tools/update-dictionary-script.in

@@ -45,3 +45,9 @@ fetch_dictionary () {
 
 fetch_dictionary "@CIFPP_CACHE_DIR@/mmcif_pdbx_v50.dic" "https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz"
 fetch_dictionary "@CIFPP_CACHE_DIR@/components.cif" "ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz"
+
+# notify subscribers
+
+if [ -d /etc/libcifpp/cache-update.d ] && [ -x /bin/run-parts ]; then
+	run-parts --arg "@CIFPP_CACHE_DIR@" -- /etc/libcifpp/cache-update.d
+fi