Fix for 32bit, version bump

faster aniso_row retrieval
report missing header line for pdb

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "gxrio"]
-	path = gxrio
-	url = https://github.com/mhekkel/gxrio.git

CMakeLists.txt

@@ -25,7 +25,7 @@
 cmake_minimum_required(VERSION 3.16)
 
 # set the project name
-project(cifpp VERSION 5.0.2 LANGUAGES CXX)
+project(cifpp VERSION 5.0.5 LANGUAGES CXX)
 
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 
@@ -299,19 +299,17 @@ if(CIFPP_DOWNLOAD_CCD)
 	add_custom_target(COMPONENTS ALL DEPENDS ${COMPONENTS_CIF})
 endif()
 
-if(UNIX)
-	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()
-
-set(INCLUDE_INSTALL_DIR ${CMAKE_INSTALL_INCLUDEDIR})
-set(LIBRARY_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR})
-set(SHARE_INSTALL_DIR ${CMAKE_INSTALL_DATADIR}/libcifpp)
-
-set(CIFPP_DATA_DIR "${CMAKE_INSTALL_PREFIX}/${SHARE_INSTALL_DIR}" CACHE STRING "The directory containing the provided data files")
-
+# Installation directories
+set(CIFPP_DATA_DIR "${CMAKE_INSTALL_FULL_DATADIR}/libcifpp")
 target_compile_definitions(cifpp PUBLIC DATA_DIR="${CIFPP_DATA_DIR}")
 
+if(UNIX)
+	set(CIFPP_CACHE_DIR "${CMAKE_INSTALL_FULL_LOCALSTATEDIR}/cache/libcifpp")
+	target_compile_definitions(cifpp PUBLIC CACHE_DIR="${CIFPP_CACHE_DIR}")
+
+	set(CIFPP_ETC_DIR "${CMAKE_INSTALL_FULL_SYSCONFDIR}")
+endif()
+
 # Install rules
 install(TARGETS cifpp
 	EXPORT cifppTargets
@@ -359,7 +357,7 @@ configure_package_config_file(
 	${CONFIG_TEMPLATE_FILE}
 	${CMAKE_CURRENT_BINARY_DIR}/cifpp/cifppConfig.cmake
 	INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/cifpp
-	PATH_VARS INCLUDE_INSTALL_DIR LIBRARY_INSTALL_DIR SHARE_INSTALL_DIR
+	PATH_VARS CIFPP_DATA_DIR
 )
 
 install(FILES
@@ -429,11 +427,15 @@ if(ENABLE_TESTING)
 	endforeach()
 endif()
 
-message("Will install in ${CMAKE_INSTALL_PREFIX}")
-
 # Optionally install the update scripts for CCD and dictionary files
 if(CIFPP_INSTALL_UPDATE_SCRIPT)
-	set(CIFPP_CRON_DIR "$ENV{DESTDIR}/etc/cron.weekly")
+	if(${CMAKE_SYSTEM_NAME} STREQUAL "Linux")
+		set(CIFPP_CRON_DIR "${CIFPP_ETC_DIR}/cron.weekly")
+	elseif(UNIX)	# assume all others are like FreeBSD... 
+		set(CIFPP_CRON_DIR "${CIFPP_ETC_DIR}/periodic/weekly")
+	else()
+		message(FATAL_ERROR "Don't know where to install the update script")
+	endif()
 
 	configure_file(${PROJECT_SOURCE_DIR}/tools/update-libcifpp-data.in update-libcifpp-data @ONLY)
 	install(
@@ -443,15 +445,15 @@ if(CIFPP_INSTALL_UPDATE_SCRIPT)
 	)
 
 	install(DIRECTORY DESTINATION ${CIFPP_CACHE_DIR})
-	install(DIRECTORY DESTINATION "$ENV{DESTDIR}/etc/libcifpp/cache-update.d")
+	install(DIRECTORY DESTINATION "${CIFPP_ETC_DIR}/libcifpp/cache-update.d")
 
 	# a config to, to make it complete
-	if(NOT EXISTS "$ENV{DESTDIR}/etc/libcifpp.conf")
+	if(NOT EXISTS "${CIFPP_ETC_DIR}/libcifpp.conf")
 		file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf [[# Uncomment the next line to enable automatic updates
 # update=true
 ]])
-		install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf DESTINATION "$ENV{DESTDIR}/etc")
-		install(CODE "message(\"A configuration file has been written to $ENV{DESTDIR}/etc/libcifpp.conf, please edit this file to enable automatic updates\")")
+		install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf DESTINATION "${CIFPP_ETC_DIR}")
+		install(CODE "message(\"A configuration file has been written to ${CIFPP_ETC_DIR}/libcifpp.conf, please edit this file to enable automatic updates\")")
 	endif()
 
 	target_compile_definitions(cifpp PUBLIC CACHE_DIR="${CIFPP_CACHE_DIR}")
@@ -462,7 +464,7 @@ set(CPACK_SOURCE_TGZ ON)
 set(CPACK_SOURCE_TBZ2 OFF)
 set(CPACK_SOURCE_TXZ OFF)
 set(CPACK_SOURCE_TZ OFF)
-set(CPACK_SOURCE_IGNORE_FILES "/data/components.cif;/build;/.vscode;/.git;/regex")
+set(CPACK_SOURCE_IGNORE_FILES "/data/components.cif;/build;/.vscode;/.git")
 set(CPACK_PACKAGE_FILE_NAME "${PROJECT_NAME}-${PROJECT_VERSION}")
 set(CPACK_SOURCE_PACKAGE_FILE_NAME ${CPACK_PACKAGE_FILE_NAME})
 include(CPack)

changelog

@@ -1,3 +1,12 @@
+Version 5.0.5
+- Fix code to work on 32 bit machines
+
+Version 5.0.4
+- Revert removal of CIFPP_SHARE_DIR export
+
+Version 5.0.3
+- Fix installation of libcifpp into the correct locations
+
 Version 5.0.2
 - Fix export of CISPEP records in PDB format
 - Better support for exporting package_source

cmake/cifppConfig.cmake.in

@@ -4,12 +4,9 @@ include(CMakeFindDependencyMacro)
 find_dependency(Threads)
 
 find_dependency(ZLIB REQUIRED)
-find_dependency(LibLZMA REQUIRED)
 
 INCLUDE("${CMAKE_CURRENT_LIST_DIR}/cifppTargets.cmake")
 
-set_and_check(CIFPP_INCLUDE_DIR "@PACKAGE_INCLUDE_INSTALL_DIR@")
-set_and_check(CIFPP_LIBRARY_DIR "@PACKAGE_LIBRARY_INSTALL_DIR@")
-set_and_check(CIFPP_SHARE_DIR "@PACKAGE_SHARE_INSTALL_DIR@")
+set_and_check(CIFPP_SHARE_DIR "@PACKAGE_CIFPP_DATA_DIR@")
 
 check_required_components(cifpp)

include/cif++.hpp

@@ -38,3 +38,4 @@
 #include <cif++/model.hpp>
 
 #include <cif++/pdb/io.hpp>
+#include <cif++/gzio.hpp>

include/cif++/gzio.hpp

@@ -26,8 +26,8 @@
 /// whether to use a compressions/decompression algorithm is
 /// based on the extension of the \a filename argument.
 
-// This is a stripped down version of the gzio library from
-// https://github.com/mhekkel/gzio.git
+// This is a stripped down version of the gxrio library from
+// https://github.com/mhekkel/gxrio.git
 // Most notably, the lzma support has been removed since getting
 // that to work in Windows proved to be too much work.
 
@@ -128,15 +128,15 @@ class basic_igzip_streambuf : public basic_streambuf<CharT, Traits>
 		std::swap(m_zstream, rhs.m_zstream);
 		std::swap(m_gzheader, rhs.m_gzheader);
 
-		auto p = std::copy(rhs.gptr(), rhs.egptr(), m_out_buffer.begin());
-		this->setg(m_out_buffer.data(), m_out_buffer.data() + m_out_buffer.size(), p);
+		auto p = std::copy(rhs.gptr(), rhs.egptr(), m_out_buffer.data());
+		this->setg(m_out_buffer.data(), m_out_buffer.data(), p);
 
 		if (m_zstream and m_zstream->avail_in > 0)
 		{
 			auto next_in_offset = m_zstream->next_in - rhs.m_in_buffer.data();
-			std::copy(rhs.m_in_buffer.begin() + next_in_offset,
-				rhs.m_in_buffer.begin() + next_in_offset + m_zstream->avail_in,
-				m_in_buffer.begin());
+			std::copy(rhs.m_in_buffer.data() + next_in_offset,
+				rhs.m_in_buffer.data() + next_in_offset + m_zstream->avail_in,
+				m_in_buffer.data());
 			m_zstream->next_in = m_in_buffer.data();
 		}
 	}
@@ -151,15 +151,15 @@ class basic_igzip_streambuf : public basic_streambuf<CharT, Traits>
 		std::swap(m_zstream, rhs.m_zstream);
 		std::swap(m_gzheader, rhs.m_gzheader);
 
-		auto p = std::copy(rhs.gptr(), rhs.egptr(), m_out_buffer.begin());
-		this->setg(m_out_buffer.data(), m_out_buffer.data() + m_out_buffer.size(), p);
+		auto p = std::copy(rhs.gptr(), rhs.egptr(), m_out_buffer.data());
+		this->setg(m_out_buffer.data(), m_out_buffer.data(), p);
 
 		if (m_zstream and m_zstream->avail_in > 0)
 		{
 			auto next_in_offset = m_zstream->next_in - reinterpret_cast<unsigned char *>(rhs.m_in_buffer.data());
-			std::copy(rhs.m_in_buffer.begin() + next_in_offset,
-				rhs.m_in_buffer.begin() + next_in_offset + m_zstream->avail_in,
-				m_in_buffer.begin());
+			std::copy(rhs.m_in_buffer.data() + next_in_offset,
+				rhs.m_in_buffer.data() + next_in_offset + m_zstream->avail_in,
+				m_in_buffer.data());
 			m_zstream->next_in = reinterpret_cast<unsigned char *>(m_in_buffer.data());
 		}
 

include/cif++/item.hpp

@@ -194,6 +194,7 @@ struct item_value
 	/// \brief constructor
 	item_value(std::string_view text)
 		: m_length(text.length())
+		, m_storage(0)
 	{
 		if (m_length >= kBufferSize)
 		{
@@ -210,7 +211,7 @@ struct item_value
 
 	item_value(item_value &&rhs)
 		: m_length(std::exchange(rhs.m_length, 0))
-		, m_data(std::exchange(rhs.m_data, nullptr))
+		, m_storage(std::exchange(rhs.m_storage, 0))
 	{
 	}
 
@@ -219,7 +220,7 @@ struct item_value
 		if (this != &rhs)
 		{
 			m_length = std::exchange(rhs.m_length, m_length);
-			m_data = std::exchange(rhs.m_data, m_data);
+			m_storage = std::exchange(rhs.m_storage, m_storage);
 		}
 		return *this;
 	}
@@ -228,7 +229,7 @@ struct item_value
 	{
 		if (m_length >= kBufferSize)
 			delete[] m_data;
-		m_data = nullptr;
+		m_storage = 0;
 		m_length = 0;
 	}
 
@@ -245,6 +246,7 @@ struct item_value
 	{
 		char m_local_data[8];
 		char *m_data;
+		uint64_t m_storage;
 	};
 
 	static constexpr size_t kBufferSize = sizeof(m_local_data);
@@ -257,8 +259,7 @@ struct item_value
 	}
 };
 
-// static_assert(sizeof(item_value) == 24, "sizeof(item_value) should be 24 bytes");
-static_assert(sizeof(item_value) == 16, "sizeof(item_value) should be 16 bytes");
+static_assert(sizeof(item_value) == sizeof(void*) + 8, "sizeof(item_value) should be correct");
 
 // --------------------------------------------------------------------
 // Transient object to access stored data

include/cif++/model.hpp

@@ -101,13 +101,13 @@ class atom
 		row_handle row_aniso()
 		{
 			auto cat = m_db.get("atom_site_anisotrop");
-			return cat ? cat->find1(key("id") == m_id) : row_handle{};
+			return cat ? cat->operator[]({ {"id", m_id} }) : row_handle{};
 		}
 
 		const row_handle row_aniso() const
 		{
 			auto cat = m_db.get("atom_site_anisotrop");
-			return cat ? cat->find1(key("id") == m_id) : row_handle{};
+			return cat ? cat->operator[]({ {"id", m_id} }) : row_handle{};
 		}
 
 		const datablock &m_db;

libcifpp.pc.in

@@ -8,6 +8,6 @@ Name: libcifpp
 Description: C++ library for the manipulation of mmCIF files.
 Version: @PACKAGE_VERSION@
 
-Requires.private: zlib, liblzma
+Requires.private: zlib
 Libs: -L${libdir} -lcifpp
 Cflags: -I${includedir} -pthread

src/pdb/pdb2cif.cpp

@@ -6211,7 +6211,16 @@ file read(std::istream &is)
 		if (ch == 'h' or ch == 'H')
 			ReadPDBFile(is, result);
 		else
-			result.load(is);
+		{
+			try
+			{
+				result.load(is);
+			}
+			catch (const std::exception &ex)
+			{
+				std::throw_with_nested(std::runtime_error("Since the file did not start with a valid PDB HEADER line mmCIF was assumed, but that failed."));
+			}
+		}
 	}
 
 	// Must be a PDB like file, right?

src/pdb/tls.cpp

@@ -320,7 +320,7 @@ struct tls_selection_not : public tls_selection
 		for (auto &r : residues)
 			r.selected = not r.selected;
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "NOT" << std::endl;
 			dump_selection(residues, indentLevel);
@@ -339,7 +339,7 @@ struct tls_selection_all : public tls_selection
 		for (auto &r : residues)
 			r.selected = true;
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "ALL" << std::endl;
 			dump_selection(residues, indentLevel);
@@ -361,7 +361,7 @@ struct tls_selection_chain : public tls_selection_all
 		for (auto &r : residues)
 			r.selected = allChains or r.chainID == m_chain;
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "CHAIN " << m_chain << std::endl;
 			dump_selection(residues, indentLevel);
@@ -384,7 +384,7 @@ struct tls_selection_res_id : public tls_selection_all
 		for (auto &r : residues)
 			r.selected = r.seqNr == m_seq_nr and r.iCode == m_icode;
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "ResID " << m_seq_nr << (m_icode ? std::string{ m_icode } : "") << std::endl;
 			dump_selection(residues, indentLevel);
@@ -411,7 +411,7 @@ struct tls_selection_range_seq : public tls_selection_all
 						  (r.seqNr <= m_last or m_last == kResidueNrWildcard));
 		}
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Range " << m_first << ':' << m_last << std::endl;
 			dump_selection(residues, indentLevel);
@@ -461,7 +461,7 @@ struct tls_selection_range_id : public tls_selection_all
 			}
 		}
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Through " << m_first << ':' << m_last << std::endl;
 			dump_selection(residues, indentLevel);
@@ -502,7 +502,7 @@ struct tls_selection_union : public tls_selection
 		for (auto ai = a.begin(), bi = b.begin(), ri = residues.begin(); ri != residues.end(); ++ai, ++bi, ++ri)
 			ri->selected = ai->selected or bi->selected;
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Union" << std::endl;
 			dump_selection(residues, indentLevel);
@@ -543,7 +543,7 @@ struct tls_selection_intersection : public tls_selection
 		for (auto ai = a.begin(), bi = b.begin(), ri = residues.begin(); ri != residues.end(); ++ai, ++bi, ++ri)
 			ri->selected = ai->selected and bi->selected;
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Intersection" << std::endl;
 			dump_selection(residues, indentLevel);
@@ -567,7 +567,7 @@ struct tls_selection_by_name : public tls_selection_all
 		for (auto &r : residues)
 			r.selected = r.name == m_name;
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Name " << m_name << std::endl;
 			dump_selection(residues, indentLevel);
@@ -595,7 +595,7 @@ struct tls_selection_by_element : public tls_selection_all
 		for (auto &r : residues)
 			r.selected = iequals(r.name, m_element);
 
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Element " << m_element << std::endl;
 			dump_selection(residues, indentLevel);
@@ -1404,7 +1404,7 @@ std::tuple<std::string, int> TLSSelectionParserImplBuster::ParseAtom()
 			match(':');
 			std::string atom = m_value_s;
 
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Warning: ignoring atom ID '" << atom << "' in TLS selection" << std::endl;
 
 			match(bt_IDENT);
@@ -1958,14 +1958,14 @@ std::unique_ptr<tls_selection> parse_tls_selection_details(const std::string &pr
 
 		if (not result)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to old BUSTER" << std::endl;
 			result = busterOld.Parse(selection);
 		}
 
 		if (not result)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to PHENIX" << std::endl;
 			result = phenix.Parse(selection);
 		}
@@ -1976,35 +1976,35 @@ std::unique_ptr<tls_selection> parse_tls_selection_details(const std::string &pr
 
 		if (not result)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to BUSTER" << std::endl;
 			result = buster.Parse(selection);
 		}
 
 		if (not result)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to old BUSTER" << std::endl;
 			result = busterOld.Parse(selection);
 		}
 	}
 	else
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "No known program specified, trying PHENIX" << std::endl;
 
 		result = phenix.Parse(selection);
 
 		if (not result)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to BUSTER" << std::endl;
 			result = buster.Parse(selection);
 		}
 
 		if (not result)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to old BUSTER" << std::endl;
 			result = busterOld.Parse(selection);
 		}

tools/update-libcifpp-data.in

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/sh
 
 set -e
 
@@ -7,8 +7,8 @@ if [ "$EUID" -ne 0 ]
 	exit
 fi
 
-if [ -f /etc/libcifpp.conf ] ; then
-	. /etc/libcifpp.conf
+if [ -f "@CIFPP_ETC_DIR@/libcifpp.conf" ] ; then
+	. "@CIFPP_ETC_DIR@/libcifpp.conf"
 fi
 
 # check to see if we're supposed to run at all
@@ -17,7 +17,7 @@ if [ "$update" != "true" ] ; then
 fi
 
 # if cache directory doesn't exist, exit. 
-if ! [ -d @CIFPP_CACHE_DIR@ ]; then
+if ! [ -d "@CIFPP_CACHE_DIR@" ]; then
 	exit
 fi
 
@@ -46,10 +46,10 @@ fetch_dictionary () {
 fetch_dictionary "@CIFPP_CACHE_DIR@/mmcif_pdbx.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
+# notify subscribers, will fail on FreeBSD
 
-if [ -d /etc/libcifpp/cache-update.d ] && [ -x /bin/run-parts ]; then
-	run-parts --arg "@CIFPP_CACHE_DIR@" -- /etc/libcifpp/cache-update.d
+if [ -d "@CIFPP_ETC_DIR@/libcifpp/cache-update.d" ] && [ -x /bin/run-parts ]; then
+	run-parts --arg "@CIFPP_CACHE_DIR@" -- "@CIFPP_ETC_DIR@/libcifpp/cache-update.d"
 fi
 
-wget -O/var/cache/libcifpp/mmcif_ma.dic "https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic"
+wget -O"@CIFPP_CACHE_DIR@/mmcif_ma.dic" "https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic"