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 5.0.6 LANGUAGES CXX)
+project(cifpp VERSION 5.0.8 LANGUAGES CXX)
 
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 
@@ -89,6 +89,7 @@ if(BUILD_FOR_CCP4)
 		list(APPEND CMAKE_MODULE_PATH "$ENV{CCP4}")
 		list(APPEND CMAKE_PREFIX_PATH "$ENV{CCP4}")
 		set(CMAKE_INSTALL_PREFIX "$ENV{CCP4}")
+		set(CMAKE_INSTALL_FULL_DATADIR "${CMAKE_INSTALL_PREFIX}/share/libcifpp")
 
 		if(WIN32)
 			set(BUILD_SHARED_LIBS ON)
@@ -173,6 +174,12 @@ list(APPEND CIFPP_REQUIRED_LIBRARIES ${STDCPPFS_LIBRARY})
 include(FindAtomic)
 list(APPEND CIFPP_REQUIRED_LIBRARIES ${STDCPPATOMIC_LIBRARY})
 
+if(MSVC)
+	# this dependency can go once MSVC supports std::experimental::is_detected
+	find_package(zeep 5.1.8 REQUIRED)
+	list(APPEND CIFPP_REQUIRED_LIBRARIES zeep::zeep)
+endif()
+
 # Create a revision file, containing the current git version info
 include(VersionString)
 write_version_header(${PROJECT_SOURCE_DIR}/src/ "LibCIFPP")

changelog

+Version 5.0.8
+- implemented find_first, find_min, find_max and count in category
+- find1 now throws an exception if condition does not not exactly match one row
+- Change in writing out PDB files, now looking up the original auth_seq_num
+  via the pdbx_xxx_scheme categories based on the atom_site.auth_seq_num ->
+  pdbx_xxx_scheme.pdb_seq_num relationship.
+
+Version 5.0.7.1
+- Use the implementation from zeep for std::experimental::is_detected
+
+Version 5.0.7
+- Reintroduce exports file. For DLL's
+
 Version 5.0.6
 - Fix file::contains, using iequals
 - Fix is_cis

cmake/cifppConfig.cmake.in

@@ -5,6 +5,10 @@ find_dependency(Threads)
 
 find_dependency(ZLIB REQUIRED)
 
+if(MSVC)
+	find_dependency(zeep REQUIRED)
+endif()
+
 INCLUDE("${CMAKE_CURRENT_LIST_DIR}/cifppTargets.cmake")
 
 set_and_check(CIFPP_SHARE_DIR "@PACKAGE_CIFPP_DATA_DIR@")

include/cif++/condition.hpp

@@ -182,6 +182,33 @@ namespace detail
 		uint16_t m_item_ix = 0;
 	};
 
+	struct key_is_not_empty_condition_impl : public condition_impl
+	{
+		key_is_not_empty_condition_impl(const std::string &item_tag)
+			: m_item_tag(item_tag)
+		{
+		}
+
+		condition_impl *prepare(const category &c) override
+		{
+			m_item_ix = get_column_ix(c, m_item_tag);
+			return this;
+		}
+
+		bool test(row_handle r) const override
+		{
+			return not r[m_item_ix].empty();
+		}
+
+		void str(std::ostream &os) const override
+		{
+			os << m_item_tag << " IS NOT NULL";
+		}
+
+		std::string m_item_tag;
+		uint16_t m_item_ix = 0;
+	};
+
 	struct key_equals_condition_impl : public condition_impl
 	{
 		key_equals_condition_impl(item &&i)
@@ -824,6 +851,11 @@ inline condition operator==(const key &key, const empty_type &)
 	return condition(new detail::key_is_empty_condition_impl(key.m_item_tag));
 }
 
+inline condition operator!=(const key &key, const empty_type &)
+{
+	return condition(new detail::key_is_not_empty_condition_impl(key.m_item_tag));
+}
+
 inline condition operator not(condition &&rhs)
 {
 	return condition(new detail::not_condition_impl(std::move(rhs)));

include/cif++/text.hpp

@@ -39,66 +39,8 @@
 #if __has_include(<experimental/type_traits>)
 #include <experimental/type_traits>
 #else
-#include <type_traits>
-#endif
-
-#if (not defined(__cpp_lib_experimental_detect) or (__cpp_lib_experimental_detect < 201505)) and (not defined(_LIBCPP_VERSION) or _LIBCPP_VERSION < 5000)
-// This code is copied from:
-// https://ld2015.scusa.lsu.edu/cppreference/en/cpp/experimental/is_detected.html
-
-namespace std
-{
-	template< class... >
-	using void_t = void;
-
-	namespace experimental
-	{
-		namespace detail
-		{
-			template <class Default, class AlwaysVoid,
-					template<class...> class Op, class... Args>
-			struct detector
-			{
-				using value_t = false_type;
-				using type = Default;
-			};
-			
-			template <class Default, template<class...> class Op, class... Args>
-			struct detector<Default, void_t<Op<Args...>>, Op, Args...> {
-				// Note that std::void_t is a c++17 feature
-				using value_t = true_type;
-				using type = Op<Args...>;
-			};
-		} // namespace detail
-
-		struct nonesuch
-		{
-			nonesuch() = delete;
-			~nonesuch() = delete;
-			nonesuch(nonesuch const&) = delete;
-			void operator=(nonesuch const&) = delete;
-		};
-
-		template <template<class...> class Op, class... Args>
-		using is_detected = typename detail::detector<nonesuch, void, Op, Args...>::value_t;
-
-		template <template<class...> class Op, class... Args>
-		constexpr inline bool is_detected_v = is_detected<Op,Args...>::value;
-
-		template <template<class...> class Op, class... Args>
-		using detected_t = typename detail::detector<nonesuch, void, Op, Args...>::type;
-
-		template <class Default, template<class...> class Op, class... Args>
-		using detected_or = detail::detector<Default, void, Op, Args...>;
-
-		template <class Expected, template <class...> class Op, class... Args>
-		using is_detected_exact = std::is_same<Expected, detected_t<Op, Args...>>;
-
-		template <class Expected, template<class...> class Op, class... Args>
-		constexpr inline bool is_detected_exact_v = is_detected_exact<Expected, Op, Args...>::value;
-	}
-}
-
+// sub optimal, but replicating the same code is worse
+#include <zeep/type-traits.hpp>
 #endif
 
 namespace cif

src/atom_type.cpp

@@ -1029,6 +1029,9 @@ atom_type_traits::atom_type_traits(const std::string& symbol)
 		}
 	}
 
+	if (symbol == "X")
+		m_info = &data::kKnownAtoms[0];
+	
 	if (m_info == nullptr)
 		throw std::invalid_argument("Not a known element: " + symbol);
 }

src/model.cpp

@@ -1780,7 +1780,7 @@ std::string structure::insert_compound(const std::string &compoundID, bool is_en
 	{
 		auto &pdbxEntityNonpoly = m_db["pdbx_entity_nonpoly"];
 
-		entity_id = pdbxEntityNonpoly.find1<std::string>("comp_id"_key == compoundID, "entity_id");
+		entity_id = pdbxEntityNonpoly.find_first<std::string>("comp_id"_key == compoundID, "entity_id");
 
 		if (entity_id.empty())
 		{
@@ -1954,7 +1954,7 @@ void structure::change_residue(residue &res, const std::string &newCompound,
 		// create a copy of the entity first
 		auto &entity = m_db["entity"];
 
-		entityID = entity.find1<std::string>("type"_key == "non-polymer" and "pdbx_description"_key == compound->name(), "id");
+		entityID = entity.find_first<std::string>("type"_key == "non-polymer" and "pdbx_description"_key == compound->name(), "id");
 
 		if (entityID.empty())
 		{
@@ -2573,7 +2573,7 @@ std::string structure::create_entity_for_branch(branch &branch)
 
 	auto &entity = m_db["entity"];
 
-	std::string entityID = entity.find1<std::string>("type"_key == "branched" and "pdbx_description"_key == entityName, "id");
+	std::string entityID = entity.find_first<std::string>("type"_key == "branched" and "pdbx_description"_key == entityName, "id");
 
 	if (entityID.empty())
 	{

src/pdb/pdb2cif.cpp

@@ -4343,9 +4343,9 @@ void PDBFileParser::ConstructEntities()
 		{ "mon_id", hetID },
 		{ "ndb_seq_num", seqNr },
 		{ "pdb_seq_num", het.seqNum },
-			// { "auth_seq_num", het.seqNum },	// ????
+		{ "auth_seq_num", het.seqNum },	// Yes
 		{ "pdb_mon_id", hetID },
-			// { "auth_mon_id", hetID },
+		{ "auth_mon_id", hetID },
 		{ "pdb_strand_id", std::string{ het.chainID } },
 		{ "pdb_ins_code", iCode } });
 

test/unit-v2-test.cpp

@@ -1774,8 +1774,6 @@ _test.name
 
 BOOST_AUTO_TEST_CASE(c3)
 {
-	cif::VERBOSE = 1;
-
 	auto f = R"(data_TEST
 #
 loop_
@@ -1811,6 +1809,43 @@ _test.name
 	BOOST_CHECK_EQUAL(name, "aap");
 }
 
+BOOST_AUTO_TEST_CASE(c4)
+{
+	auto f = R"(data_TEST
+#
+loop_
+_test.id
+_test.name
+1 aap
+2 noot
+3 mies
+4 .
+5 ?
+    )"_cf;
+
+	auto &db = f.front();
+
+	// query tests
+	BOOST_TEST(db["test"].find_max<int>("id") == 5);
+	BOOST_TEST(db["test"].find_max<int>("id", cif::key("name") != cif::null) == 3);
+
+	BOOST_TEST(db["test"].find_min<int>("id") == 1);
+	BOOST_TEST(db["test"].find_min<int>("id", cif::key("name") == cif::null) == 4);
+
+	// count tests
+	BOOST_TEST(db["test"].count(cif::all()) == 5);
+	BOOST_TEST(db["test"].count(cif::key("name") != cif::null) == 3);
+	BOOST_TEST(db["test"].count(cif::key("name") == cif::null) == 2);
+
+	// find_first tests
+	BOOST_TEST(db["test"].find_first<int>(cif::key("id") == 1, "id") == 1);
+	BOOST_TEST(db["test"].find_first<int>(cif::all(), "id") == 1);
+
+	// find1 tests
+	BOOST_TEST(db["test"].find1<int>(cif::key("id") == 1, "id") == 1);
+	BOOST_CHECK_THROW(db["test"].find1<int>(cif::all(), "id"), cif::multiple_results_error);
+}
+
 // --------------------------------------------------------------------
 // rename test
 

tools/update-libcifpp-data.in

@@ -6,7 +6,7 @@ set -e
 euid=${EUID:-$(id -u)}
 
 if [ "${euid}" -ne 0 ] ; then
-	then echo "Please run as root"
+	echo "Please run as root"
 	exit
 fi