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 5.0.4 LANGUAGES CXX)
+project(cifpp VERSION 5.0.5 LANGUAGES CXX)
 
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 

changelog

@@ -1,3 +1,6 @@
+Version 5.0.5
+- Fix code to work on 32 bit machines
+
 Version 5.0.4
 - Revert removal of CIFPP_SHARE_DIR export
 

cmake/cifppConfig.cmake.in

@@ -4,7 +4,6 @@ include(CMakeFindDependencyMacro)
 find_dependency(Threads)
 
 find_dependency(ZLIB REQUIRED)
-find_dependency(LibLZMA REQUIRED)
 
 INCLUDE("${CMAKE_CURRENT_LIST_DIR}/cifppTargets.cmake")
 

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);
 		}