Fix uncompressing concatenated gzip files

Use the same Linux paths, as the cron implementations available on
the Hurd as usually the same as Linux.

CMakeLists.txt

@@ -25,7 +25,7 @@
 cmake_minimum_required(VERSION 3.16)
 
 # set the project name
-project(cifpp VERSION 5.1.0 LANGUAGES CXX)
+project(cifpp VERSION 5.1.1 LANGUAGES CXX)
 
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 
@@ -98,33 +98,33 @@ if(BUILD_FOR_CCP4)
 	endif()
 endif()
 
+if(WIN32)
+    if(${CMAKE_SYSTEM_VERSION} GREATER_EQUAL 10) # Windows 10
+        add_definitions(-D _WIN32_WINNT=0x0A00)
+    elseif(${CMAKE_SYSTEM_VERSION} EQUAL 6.3) # Windows 8.1
+        add_definitions(-D _WIN32_WINNT=0x0603)
+    elseif(${CMAKE_SYSTEM_VERSION} EQUAL 6.2) # Windows 8
+        add_definitions(-D _WIN32_WINNT=0x0602)
+    elseif(${CMAKE_SYSTEM_VERSION} EQUAL 6.1) # Windows 7
+        add_definitions(-D _WIN32_WINNT=0x0601)
+    elseif(${CMAKE_SYSTEM_VERSION} EQUAL 6.0) # Windows Vista
+        add_definitions(-D _WIN32_WINNT=0x0600)
+    else() # Windows XP (5.1)
+        add_definitions(-D _WIN32_WINNT=0x0501)
+    endif()
+
+	add_definitions(-DNOMINMAX)
+endif()
+
 if(MSVC)
-	# make msvc standards compliant...
-	add_compile_options(/permissive-)
+    # make msvc standards compliant...
+    add_compile_options(/permissive-)
 
-	macro(get_WIN32_WINNT version)
-		if(CMAKE_SYSTEM_VERSION)
-			set(ver ${CMAKE_SYSTEM_VERSION})
-			string(REGEX MATCH "^([0-9]+).([0-9])" ver ${ver})
-			string(REGEX MATCH "^([0-9]+)" verMajor ${ver})
-
-			# Check for Windows 10, b/c we'll need to convert to hex 'A'.
-			if("${verMajor}" MATCHES "10")
-				set(verMajor "A")
-				string(REGEX REPLACE "^([0-9]+)" ${verMajor} ver ${ver})
-			endif()
-
-			# Remove all remaining '.' characters.
-			string(REPLACE "." "" ver ${ver})
-
-			# Prepend each digit with a zero.
-			string(REGEX REPLACE "([0-9A-Z])" "0\\1" ver ${ver})
-			set(${version} "0x${ver}")
-		endif()
-	endmacro()
-
-	get_WIN32_WINNT(ver)
-	add_definitions(-D_WIN32_WINNT=${ver})
+	if(BUILD_SHARED_LIBS)
+		set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>DLL")
+	else()
+		set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
+	endif()
 endif()
 
 # Libraries
@@ -292,7 +292,7 @@ target_include_directories(cifpp
 	"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
 )
 
-target_link_libraries(cifpp PUBLIC Threads::Threads ZLIB::ZLIB ${CIFPP_REQUIRED_LIBRARIES})
+target_link_libraries(cifpp PUBLIC Threads::Threads ZLIB::ZLIB Eigen3::Eigen ${CIFPP_REQUIRED_LIBRARIES})
 
 if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
 	target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
@@ -307,18 +307,7 @@ if(CIFPP_DOWNLOAD_CCD)
 			file(MAKE_DIRECTORY ${PROJECT_SOURCE_DIR}/data/)
 		endif()
 
-		find_program(GUNZIP gunzip)
-
-		if(GUNZIP)
-			file(DOWNLOAD ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz ${COMPONENTS_CIF}.gz
-				SHOW_PROGRESS)
-			add_custom_command(OUTPUT ${COMPONENTS_CIF}
-				COMMAND ${GUNZIP} ${COMPONENTS_CIF}.gz
-				WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/data/)
-		else()
-			file(DOWNLOAD ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif ${COMPONENTS_CIF}
-				SHOW_PROGRESS)
-		endif()
+		file(DOWNLOAD https://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif ${COMPONENTS_CIF} SHOW_PROGRESS)
 	endif()
 
 	add_custom_target(COMPONENTS ALL DEPENDS ${COMPONENTS_CIF})
@@ -469,7 +458,7 @@ endif()
 
 # Optionally install the update scripts for CCD and dictionary files
 if(CIFPP_INSTALL_UPDATE_SCRIPT)
-	if(${CMAKE_SYSTEM_NAME} STREQUAL "Linux")
+	if(${CMAKE_SYSTEM_NAME} STREQUAL "Linux" OR ${CMAKE_SYSTEM_NAME} STREQUAL "GNU")
 		set(CIFPP_CRON_DIR "${CIFPP_ETC_DIR}/cron.weekly")
 	elseif(UNIX) # assume all others are like FreeBSD...
 		set(CIFPP_CRON_DIR "${CIFPP_ETC_DIR}/periodic/weekly")

README.md

@@ -30,14 +30,21 @@ int main(int argc, char *argv[])
         exit(1);
     }
 
+    // Take the first datablock in the file
     auto &db = file.front();
+
+    // Use the atom_site category
     auto &atom_site = db["atom_site"];
-    auto n = atom_site.find(cif::key("label_atom_id") == "OXT").size();
+
+    // Count the atoms with atom-id "OXT"
+    auto n = atom_site.count(cif::key("label_atom_id") == "OXT");
 
     std::cout << "File contains " << atom_site.size() << " atoms of which "
               << n << (n == 1 ? " is" : " are") << " OXT" << std::endl
               << "residues with an OXT are:" << std::endl;
 
+    // Loop over all atoms with atom-id "OXT" and print out some info.
+    // That info is extracted using structured binding in C++
     for (const auto &[asym, comp, seqnr] :
             atom_site.find<std::string, std::string, int>(
                 cif::key("label_atom_id") == "OXT",

changelog

@@ -1,3 +1,9 @@
+Version 5.1.1
+- Added missing include <compare> in symmetry.hpp
+- Added empty() to matrix
+- Fix for parsing PDB files with a last line that does not end with
+  a new line character.
+
 Version 5.1
 - New parser, optimised for speed
 - Fix in unique ID generator

cmake/cifppConfig.cmake.in

@@ -4,6 +4,7 @@ include(CMakeFindDependencyMacro)
 find_dependency(Threads)
 
 find_dependency(ZLIB REQUIRED)
+find_dependency(Eigen3 REQUIRED)
 
 if(MSVC)
 	find_dependency(zeep REQUIRED)

include/cif++/gzio.hpp

@@ -246,10 +246,13 @@ class basic_igzip_streambuf : public basic_streambuf<CharT, Traits>
 					zstream.avail_in = static_cast<uInt>(this->m_upstream->sgetn(m_in_buffer.data(), m_in_buffer.size()));
 				}
 
+				if (zstream.avail_in == 0)
+					break;
+
 				int err = ::inflate(&zstream, Z_SYNC_FLUSH);
 				std::streamsize n = kBufferByteSize - zstream.avail_out;
 
-				if (err == Z_STREAM_END or (err == Z_OK and n > 0))
+				if (n > 0)
 				{
 					this->setg(
 						m_out_buffer.data(),
@@ -258,6 +261,9 @@ class basic_igzip_streambuf : public basic_streambuf<CharT, Traits>
 					break;
 				}
 
+				if (err == Z_STREAM_END and zstream.avail_in > 0)
+					err = ::inflateReset2(&zstream, 47);
+
 				if (err < Z_OK)
 					break;
 			}

include/cif++/matrix.hpp

@@ -44,22 +44,24 @@ template <typename M>
 class matrix_expression
 {
   public:
-	constexpr uint32_t dim_m() const { return static_cast<const M &>(*this).dim_m(); }
-	constexpr uint32_t dim_n() const { return static_cast<const M &>(*this).dim_n(); }
+	constexpr size_t dim_m() const { return static_cast<const M &>(*this).dim_m(); }
+	constexpr size_t dim_n() const { return static_cast<const M &>(*this).dim_n(); }
 
-	constexpr auto &operator()(uint32_t i, uint32_t j)
+	constexpr bool empty() const { return dim_m() == 0 or dim_n() == 0; }
+
+	constexpr auto &operator()(size_t i, size_t j)
 	{
 		return static_cast<M &>(*this).operator()(i, j);
 	}
 
-	constexpr auto operator()(uint32_t i, uint32_t j) const
+	constexpr auto operator()(size_t i, size_t j) const
 	{
 		return static_cast<const M &>(*this).operator()(i, j);
 	}
 
-	void swap_row(uint32_t r1, uint32_t r2)
+	void swap_row(size_t r1, size_t r2)
 	{
-		for (uint32_t c = 0; c < dim_m(); ++c)
+		for (size_t c = 0; c < dim_m(); ++c)
 		{
 			auto v = operator()(r1, c);
 			operator()(r1, c) = operator()(r2, c);
@@ -67,9 +69,9 @@ class matrix_expression
 		}
 	}
 
-	void swap_col(uint32_t c1, uint32_t c2)
+	void swap_col(size_t c1, size_t c2)
 	{
-		for (uint32_t r = 0; r < dim_n(); ++r)
+		for (size_t r = 0; r < dim_n(); ++r)
 		{
 			auto &a = operator()(r, c1);
 			auto &b = operator()(r, c2);
@@ -120,9 +122,9 @@ class matrix : public matrix_expression<matrix<F>>
 		, m_n(m.dim_n())
 		, m_data(m_m * m_n)
 	{
-		for (uint32_t i = 0; i < m_m; ++i)
+		for (size_t i = 0; i < m_m; ++i)
 		{
-			for (uint32_t j = 0; j < m_n; ++j)
+			for (size_t j = 0; j < m_n; ++j)
 				operator()(i, j) = m(i, j);
 		}
 	}
@@ -178,9 +180,9 @@ class matrix_fixed : public matrix_expression<matrix_fixed<F, M, N>>
 	matrix_fixed(const M2 &m)
 	{
 		assert(M == m.dim_m() and N == m.dim_n());
-		for (uint32_t i = 0; i < M; ++i)
+		for (size_t i = 0; i < M; ++i)
 		{
-			for (uint32_t j = 0; j < N; ++j)
+			for (size_t j = 0; j < N; ++j)
 				operator()(i, j) = m(i, j);
 		}
 	}
@@ -242,7 +244,7 @@ class symmetric_matrix : public matrix_expression<symmetric_matrix<F>>
   public:
 	using value_type = F;
 
-	symmetric_matrix(uint32_t n, value_type v = 0)
+	symmetric_matrix(size_t n, value_type v = 0)
 		: m_n(n)
 		, m_data((m_n * (m_n + 1)) / 2)
 	{
@@ -255,17 +257,17 @@ class symmetric_matrix : public matrix_expression<symmetric_matrix<F>>
 	symmetric_matrix &operator=(symmetric_matrix &&m) = default;
 	symmetric_matrix &operator=(const symmetric_matrix &m) = default;
 
-	constexpr uint32_t dim_m() const { return m_n; }
-	constexpr uint32_t dim_n() const { return m_n; }
+	constexpr size_t dim_m() const { return m_n; }
+	constexpr size_t dim_n() const { return m_n; }
 
-	constexpr value_type operator()(uint32_t i, uint32_t j) const
+	constexpr value_type operator()(size_t i, size_t j) const
 	{
 		return i < j
 		           ? m_data[(j * (j + 1)) / 2 + i]
 		           : m_data[(i * (i + 1)) / 2 + j];
 	}
 
-	constexpr value_type &operator()(uint32_t i, uint32_t j)
+	constexpr value_type &operator()(size_t i, size_t j)
 	{
 		if (i > j)
 			std::swap(i, j);
@@ -274,7 +276,7 @@ class symmetric_matrix : public matrix_expression<symmetric_matrix<F>>
 	}
 
   private:
-	uint32_t m_n;
+	size_t m_n;
 	std::vector<value_type> m_data;
 };
 
@@ -296,17 +298,17 @@ class symmetric_matrix_fixed : public matrix_expression<symmetric_matrix_fixed<F
 	symmetric_matrix_fixed &operator=(symmetric_matrix_fixed &&m) = default;
 	symmetric_matrix_fixed &operator=(const symmetric_matrix_fixed &m) = default;
 
-	constexpr uint32_t dim_m() const { return M; }
-	constexpr uint32_t dim_n() const { return M; }
+	constexpr size_t dim_m() const { return M; }
+	constexpr size_t dim_n() const { return M; }
 
-	constexpr value_type operator()(uint32_t i, uint32_t j) const
+	constexpr value_type operator()(size_t i, size_t j) const
 	{
 		return i < j
 		           ? m_data[(j * (j + 1)) / 2 + i]
 		           : m_data[(i * (i + 1)) / 2 + j];
 	}
 
-	constexpr value_type &operator()(uint32_t i, uint32_t j)
+	constexpr value_type &operator()(size_t i, size_t j)
 	{
 		if (i > j)
 			std::swap(i, j);
@@ -332,21 +334,21 @@ class identity_matrix : public matrix_expression<identity_matrix<F>>
   public:
 	using value_type = F;
 
-	identity_matrix(uint32_t n)
+	identity_matrix(size_t n)
 		: m_n(n)
 	{
 	}
 
-	constexpr uint32_t dim_m() const { return m_n; }
-	constexpr uint32_t dim_n() const { return m_n; }
+	constexpr size_t dim_m() const { return m_n; }
+	constexpr size_t dim_n() const { return m_n; }
 
-	constexpr value_type operator()(uint32_t i, uint32_t j) const
+	constexpr value_type operator()(size_t i, size_t j) const
 	{
-		return i == j ? 1 : 0;
+		return static_cast<value_type>(i == j ? 1 : 0);
 	}
 
   private:
-	uint32_t m_n;
+	size_t m_n;
 };
 
 // --------------------------------------------------------------------
@@ -364,10 +366,10 @@ class matrix_subtraction : public matrix_expression<matrix_subtraction<M1, M2>>
 		assert(m_m1.dim_n() == m_m2.dim_n());
 	}
 
-	constexpr uint32_t dim_m() const { return m_m1.dim_m(); }
-	constexpr uint32_t dim_n() const { return m_m1.dim_n(); }
+	constexpr size_t dim_m() const { return m_m1.dim_m(); }
+	constexpr size_t dim_n() const { return m_m1.dim_n(); }
 
-	constexpr auto operator()(uint32_t i, uint32_t j) const
+	constexpr auto operator()(size_t i, size_t j) const
 	{
 		return m_m1(i, j) - m_m2(i, j);
 	}
@@ -394,16 +396,16 @@ class matrix_matrix_multiplication : public matrix_expression<matrix_matrix_mult
 		assert(m1.dim_m() == m2.dim_n());
 	}
 
-	constexpr uint32_t dim_m() const { return m_m1.dim_m(); }
-	constexpr uint32_t dim_n() const { return m_m1.dim_n(); }
+	constexpr size_t dim_m() const { return m_m1.dim_m(); }
+	constexpr size_t dim_n() const { return m_m1.dim_n(); }
 
-	constexpr auto operator()(uint32_t i, uint32_t j) const
+	constexpr auto operator()(size_t i, size_t j) const
 	{
 		using value_type = decltype(m_m1(0, 0));
 
 		value_type result = {};
 
-		for (uint32_t k = 0; k < m_m1.dim_m(); ++k)
+		for (size_t k = 0; k < m_m1.dim_m(); ++k)
 			result += m_m1(i, k) * m_m2(k, j);
 
 		return result;
@@ -426,10 +428,10 @@ class matrix_scalar_multiplication : public matrix_expression<matrix_scalar_mult
 	{
 	}
 
-	constexpr uint32_t dim_m() const { return m_m.dim_m(); }
-	constexpr uint32_t dim_n() const { return m_m.dim_n(); }
+	constexpr size_t dim_m() const { return m_m.dim_m(); }
+	constexpr size_t dim_n() const { return m_m.dim_n(); }
 
-	constexpr auto operator()(uint32_t i, uint32_t j) const
+	constexpr auto operator()(size_t i, size_t j) const
 	{
 		return m_m(i, j) * m_v;
 	}
@@ -498,10 +500,10 @@ class matrix_cofactors : public matrix_expression<matrix_cofactors<M>>
 	{
 	}
 
-	constexpr uint32_t dim_m() const { return m_m.dim_m(); }
-	constexpr uint32_t dim_n() const { return m_m.dim_n(); }
+	constexpr size_t dim_m() const { return m_m.dim_m(); }
+	constexpr size_t dim_n() const { return m_m.dim_n(); }
 
-	constexpr auto operator()(uint32_t i, uint32_t j) const
+	constexpr auto operator()(size_t i, size_t j) const
 	{
 		const size_t ixs[4][3] = {
 			{ 1, 2, 3 },

include/cif++/point.hpp

@@ -31,6 +31,7 @@
 #include <array>
 #include <cmath>
 #include <complex>
+#include <cstdint>
 #include <functional>
 #include <valarray>
 

include/cif++/symmetry.hpp

@@ -34,6 +34,10 @@
 #include <cstdint>
 #include <string>
 
+#if defined(__cpp_impl_three_way_comparison)
+#include <compare>
+#endif
+
 /// \file cif++/symmetry.hpp
 /// This file contains code to do symmetry operations based on the
 /// operations as specified in the International Tables.
@@ -180,7 +184,7 @@ class datablock;
 class cell;
 class spacegroup;
 class rtop;
-class sym_op;
+struct sym_op;
 
 
 /// @brief A class that encapsulates the symmetry operations as used in PDB files, i.e. a rotational number and a translation vector

include/cif++/utilities.hpp

@@ -34,7 +34,7 @@
 #define STDOUT_FILENO 1
 #endif
 
-#if _MSC_VER
+#if _WIN32
 #include <io.h>
 #define isatty _isatty
 #else

src/category.cpp

@@ -670,9 +670,13 @@ void category::set_validator(const validator *v, datablock &db)
 
 			if (missing.empty())
 				m_index = new category_index(this);
-			else if (VERBOSE > 0)
-				std::cerr << "Cannot construct index since the key field" << (missing.size() > 1 ? "s" : "") << " "
-							<< cif::join(missing, ", ") + " in " + m_name + " " + (missing.size() == 1 ? "is" : "are") << " missing" << std::endl;
+			else
+			{
+				std::ostringstream msg;
+				msg << "Cannot construct index since the key field" << (missing.size() > 1 ? "s" : "") << " "
+							<< cif::join(missing, ", ") << " in " << m_name << " " << (missing.size() == 1 ? "is" : "are") << " missing" << std::endl;
+				throw std::runtime_error(msg.str());
+			}
 		}
 	}
 	else
@@ -1708,8 +1712,7 @@ void category::reorder_by_index()
 
 namespace detail
 {
-
-	size_t write_value(std::ostream &os, std::string_view value, size_t offset, size_t width)
+	size_t write_value(std::ostream &os, std::string_view value, size_t offset, size_t width, bool right_aligned)
 	{
 		if (value.find('\n') != std::string::npos or width == 0 or value.length() > 132) // write as text field
 		{
@@ -1733,17 +1736,33 @@ namespace detail
 		}
 		else if (sac_parser::is_unquoted_string(value))
 		{
+			if (right_aligned)
+			{
+				if (value.length() < width)
+				{
+					os << std::string(width - value.length() - 1, ' ');
+					offset += width;
+				}
+				else
+					offset += value.length() + 1;
+			}
+
 			os << value;
 
-			if (value.length() < width)
-			{
-				os << std::string(width - value.length(), ' ');
-				offset += width;
-			}
+			if (right_aligned)
+				os << ' ';
 			else
 			{
-				os << ' ';
-				offset += value.length() + 1;
+				if (value.length() < width)
+				{
+					os << std::string(width - value.length(), ' ');
+					offset += width;
+				}
+				else
+				{
+					os << ' ';
+					offset += value.length() + 1;
+				}
 			}
 		}
 		else
@@ -1837,6 +1856,19 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
 	// If the first Row has a next, we need a loop_
 	bool needLoop = (m_head->m_next != nullptr);
 
+	std::vector<bool> right_aligned(m_columns.size(), false);
+
+	if (m_cat_validator != nullptr)
+	{
+		for (auto cix : order)
+		{
+			auto &col = m_columns[cix];
+			right_aligned[cix] = col.m_validator != nullptr and
+				col.m_validator->m_type != nullptr and
+				col.m_validator->m_type->m_primitive_type == cif::DDL_PrimitiveType::Numb;
+		}
+	}
+
 	if (needLoop)
 	{
 		os << "loop_" << '\n';
@@ -1905,7 +1937,7 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
 					offset = 0;
 				}
 
-				offset = detail::write_value(os, s, offset, w);
+				offset = detail::write_value(os, s, offset, w, right_aligned[cix]);
 
 				if (offset > 132)
 				{
@@ -1933,6 +1965,30 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
 
 		l += 3;
 
+		size_t width = 1;
+
+		for (auto cix : order)
+		{
+			if (not right_aligned[cix])
+				continue;
+
+			std::string_view s;
+			auto iv = m_head->get(cix);
+			if (iv != nullptr)
+				s = iv->text();
+
+			if (s.empty())
+				s = "?";
+
+			size_t l2 = s.length();
+
+			if (not sac_parser::is_unquoted_string(s))
+				l2 += 2;
+
+			if (width < l2)
+				width = l2;
+		}
+
 		for (uint16_t cix : order)
 		{
 			auto &col = m_columns[cix];
@@ -1957,7 +2013,7 @@ void category::write(std::ostream &os, const std::vector<uint16_t> &order, bool
 				offset = 0;
 			}
 
-			if (detail::write_value(os, s, offset, 1) != 0)
+			if (detail::write_value(os, s, offset, width, s.empty() or right_aligned[cix]) != 0)
 				os << '\n';
 		}
 	}

src/compound.cpp

@@ -313,7 +313,7 @@ class compound_factory_impl : public std::enable_shared_from_this<compound_facto
 		{
 			for (auto cmp : impl->m_compounds)
 			{
-				if (cmp->id() == id)
+				if (iequals(cmp->id(), id))
 				{
 					result = cmp;
 					break;
@@ -582,12 +582,12 @@ CCP4_compound_factory_impl::CCP4_compound_factory_impl(const fs::path &clibd_mon
 
 	auto &chemComps = m_file["comp_list"]["chem_comp"];
 
-	for (const auto &[group, threeLetterCode] : chemComps.rows<std::string, std::string>("group", "three_letter_code"))
+	for (const auto &[group, comp_id] : chemComps.rows<std::string, std::string>("group", "id"))
 	{
 		if (std::regex_match(group, peptideRx))
-			m_known_peptides.insert(threeLetterCode);
+			m_known_peptides.insert(comp_id);
 		else if (cif::iequals(group, "DNA") or cif::iequals(group, "RNA"))
-			m_known_bases.insert(threeLetterCode);
+			m_known_bases.insert(comp_id);
 	}
 }
 
@@ -597,7 +597,7 @@ compound *CCP4_compound_factory_impl::create(const std::string &id)
 
 	auto &cat = m_file["comp_list"]["chem_comp"];
 
-	auto rs = cat.find(cif::key("three_letter_code") == id);
+	auto rs = cat.find(cif::key("id") == id);
 
 	if (rs.size() == 1)
 	{

src/pdb/pdb2cif.cpp

@@ -1170,6 +1170,8 @@ void PDBFileParser::PreParseInput(std::istream &is)
 		std::string value;
 		if (lookahead.length() > 6)
 			value = cif::trim_right_copy(lookahead.substr(6));
+		
+		lookahead.clear();
 
 		uint32_t curLineNr = lineNr;
 		getline(is, lookahead);

src/point.cpp

@@ -61,7 +61,7 @@ quaternion_type<T> normalize(quaternion_type<T> q)
 
 quaternion construct_from_angle_axis(float angle, point axis)
 {
-	angle = (angle * kPI / 180) / 2;
+	angle = static_cast<float>((angle * kPI / 180) / 2);
 	auto s = std::sin(angle);
 	auto c = std::cos(angle);
 
@@ -119,7 +119,7 @@ point center_points(std::vector<point> &Points)
 }
 
 quaternion construct_for_dihedral_angle(point p1, point p2, point p3, point p4,
-	float angle, float esd)
+	float angle, float /*esd*/)
 {
 	p1 -= p3;
 	p2 -= p3;

src/symmetry.cpp

@@ -70,12 +70,12 @@ void cell::init()
 
 	m_orthogonal = identity_matrix(3);
 
-	m_orthogonal(0, 0) = m_a;
-	m_orthogonal(0, 1) = m_b * std::cos(gamma);
-	m_orthogonal(0, 2) = m_c * std::cos(beta);
-	m_orthogonal(1, 1) = m_b * std::sin(gamma);
-	m_orthogonal(1, 2) = -m_c * std::sin(beta) * std::cos(alpha_star);
-	m_orthogonal(2, 2) = m_c * std::sin(beta) * std::sin(alpha_star);
+	m_orthogonal(0, 0) = static_cast<float>(m_a);
+	m_orthogonal(0, 1) = static_cast<float>(m_b * std::cos(gamma));
+	m_orthogonal(0, 2) = static_cast<float>(m_c * std::cos(beta));
+	m_orthogonal(1, 1) = static_cast<float>(m_b * std::sin(gamma));
+	m_orthogonal(1, 2) = static_cast<float>(-m_c * std::sin(beta) * std::cos(alpha_star));
+	m_orthogonal(2, 2) = static_cast<float>(m_c * std::sin(beta) * std::sin(alpha_star));
 
 	m_fractional = inverse(m_orthogonal);
 }
@@ -90,7 +90,7 @@ sym_op::sym_op(std::string_view s)
 	int rnri = 256;	// default to unexisting number
 	auto r = std::from_chars(b, e, rnri);
 	
-	m_nr = rnri;
+	m_nr = static_cast<uint8_t>(rnri);
 	m_ta = r.ptr[1] - '0';
 	m_tb = r.ptr[2] - '0';
 	m_tc = r.ptr[3] - '0';
@@ -121,21 +121,21 @@ transformation::transformation(const symop_data &data)
 {
 	const auto &d = data.data();
 
-	m_rotation(0, 0) = d[0];
-	m_rotation(0, 1) = d[1];
-	m_rotation(0, 2) = d[2];
-	m_rotation(1, 0) = d[3];
-	m_rotation(1, 1) = d[4];
-	m_rotation(1, 2) = d[5];
-	m_rotation(2, 0) = d[6];
-	m_rotation(2, 1) = d[7];
-	m_rotation(2, 2) = d[8];
+	m_rotation(0, 0) = static_cast<float>(d[0]);
+	m_rotation(0, 1) = static_cast<float>(d[1]);
+	m_rotation(0, 2) = static_cast<float>(d[2]);
+	m_rotation(1, 0) = static_cast<float>(d[3]);
+	m_rotation(1, 1) = static_cast<float>(d[4]);
+	m_rotation(1, 2) = static_cast<float>(d[5]);
+	m_rotation(2, 0) = static_cast<float>(d[6]);
+	m_rotation(2, 1) = static_cast<float>(d[7]);
+	m_rotation(2, 2) = static_cast<float>(d[8]);
 
 	try_create_quaternion();
 
-	m_translation.m_x = d[9] == 0 ? 0 : 1.0 * d[9] / d[10];
-	m_translation.m_y = d[11] == 0 ? 0 : 1.0 * d[11] / d[12];
-	m_translation.m_z = d[13] == 0 ? 0 : 1.0 * d[13] / d[14];
+	m_translation.m_x = static_cast<float>(d[9] == 0 ? 0 : 1.0 * d[9] / d[10]);
+	m_translation.m_y = static_cast<float>(d[11] == 0 ? 0 : 1.0 * d[11] / d[12]);
+	m_translation.m_z = static_cast<float>(d[13] == 0 ? 0 : 1.0 * d[13] / d[14]);
 }
 
 transformation::transformation(const matrix3x3<float> &r, const cif::point &t)
@@ -461,7 +461,7 @@ std::tuple<float,point,sym_op> crystal::closest_symmetry_copy(point a, point b)
 
 	for (size_t i = 0; i < m_spacegroup.size(); ++i)
 	{
-		sym_op s(i + 1);
+		sym_op s(static_cast<uint8_t>(i + 1));
 		auto &t = m_spacegroup[i];
 
 		auto fsb = t(fb);

src/text.cpp

@@ -239,7 +239,7 @@ std::string cif_id_for_number(int number)
 	do
 	{
 		int r = number % 26;
-		result += 'A' + r;
+		result += static_cast<char>('A' + r);
 
 		number = (number - r) / 26 - 1;
 	}

src/utilities.cpp

@@ -43,7 +43,7 @@
 #include <sstream>
 #include <thread>
 
-#if not defined(_MSC_VER)
+#if not defined(_WIN32)
 #include <sys/ioctl.h>
 #include <termios.h>
 #endif
@@ -68,7 +68,7 @@ std::string get_version_nr()
 
 // --------------------------------------------------------------------
 
-#ifdef _MSC_VER
+#ifdef _WIN32
 }
 #include <Windows.h>
 #include <libloaderapi.h>
@@ -204,7 +204,7 @@ void progress_bar_impl::run()
 			std::lock_guard lock(m_mutex);
 
 			if (not printedAny and isatty(STDOUT_FILENO))
-				std::cout << "\e[?25l";
+				std::cout << "\x1b[?25l";
 
 			print_progress();
 
@@ -220,7 +220,7 @@ void progress_bar_impl::run()
 	{
 		print_done();
 		if (isatty(STDOUT_FILENO))
-			std::cout << "\e[?25h";
+			std::cout << "\x1b[?25h";
 	}
 }
 
@@ -411,11 +411,19 @@ struct rsrc_imp
 };
 } // namespace mrsrc
 
-#if _MSC_VER
+#if _WIN32
 
-extern "C" CIFPP_EXPORT const mrsrc::rsrc_imp *gResourceIndexDefault[1] = {};
-extern "C" CIFPP_EXPORT const char *gResourceDataDefault[1] = {};
-extern "C" CIFPP_EXPORT const char *gResourceNameDefault[1] = {};
+#if __MINGW32__
+
+extern "C" __attribute__((weak, alias("gResourceIndexDefault"))) const mrsrc::rsrc_imp gResourceIndex[];
+extern "C" __attribute__((weak, alias("gResourceDataDefault"))) const char gResourceData[];
+extern "C" __attribute__((weak, alias("gResourceNameDefault"))) const char gResourceName[];
+
+#else
+
+extern "C" const mrsrc::rsrc_imp *gResourceIndexDefault[1] = {};
+extern "C" const char *gResourceDataDefault[1] = {};
+extern "C" const char *gResourceNameDefault[1] = {};
 
 extern "C" const mrsrc::rsrc_imp gResourceIndex[];
 extern "C" const char gResourceData[];
@@ -425,6 +433,8 @@ extern "C" const char gResourceName[];
 #pragma comment(linker, "/alternatename:gResourceData=gResourceDataDefault")
 #pragma comment(linker, "/alternatename:gResourceName=gResourceNameDefault")
 
+#endif
+
 #else
 extern const __attribute__((weak)) mrsrc::rsrc_imp gResourceIndex[];
 extern const __attribute__((weak)) char gResourceData[];

test/REA_v2.cif

@@ -0,0 +1,187 @@
+data_REA_v2
+# 
+_chem_comp.id                                    REA_v2 
+_chem_comp.name                                  "RETINOIC ACID" 
+_chem_comp.type                                  NON-POLYMER 
+_chem_comp.pdbx_type                             HETAIN 
+_chem_comp.formula                               "C20 H28 O2" 
+_chem_comp.mon_nstd_parent_comp_id               ? 
+_chem_comp.pdbx_synonyms                         ? 
+_chem_comp.pdbx_formal_charge                    0 
+_chem_comp.pdbx_initial_date                     1999-07-08 
+_chem_comp.pdbx_modified_date                    2016-10-18 
+_chem_comp.pdbx_ambiguous_flag                   N 
+_chem_comp.pdbx_release_status                   REL 
+_chem_comp.pdbx_replaced_by                      ? 
+_chem_comp.pdbx_replaces                         3KV 
+_chem_comp.formula_weight                        300.435 
+_chem_comp.one_letter_code                       ? 
+_chem_comp.pdbx_model_coordinates_details        ? 
+_chem_comp.pdbx_model_coordinates_missing_flag   N 
+_chem_comp.pdbx_ideal_coordinates_details        Corina 
+_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
+_chem_comp.pdbx_model_coordinates_db_code        1CBS 
+_chem_comp.pdbx_subcomponent_list                ? 
+_chem_comp.pdbx_processing_site                  RCSB 
+# 
+loop_
+_chem_comp_atom.comp_id 
+_chem_comp_atom.atom_id 
+_chem_comp_atom.alt_atom_id 
+_chem_comp_atom.type_symbol 
+_chem_comp_atom.charge 
+_chem_comp_atom.pdbx_align 
+_chem_comp_atom.pdbx_aromatic_flag 
+_chem_comp_atom.pdbx_leaving_atom_flag 
+_chem_comp_atom.pdbx_stereo_config 
+_chem_comp_atom.model_Cartn_x 
+_chem_comp_atom.model_Cartn_y 
+_chem_comp_atom.model_Cartn_z 
+_chem_comp_atom.pdbx_model_Cartn_x_ideal 
+_chem_comp_atom.pdbx_model_Cartn_y_ideal 
+_chem_comp_atom.pdbx_model_Cartn_z_ideal 
+_chem_comp_atom.pdbx_component_atom_id 
+_chem_comp_atom.pdbx_component_comp_id 
+_chem_comp_atom.pdbx_ordinal 
+REA_v2 C1   C1   C 0 1 N N N 21.972 29.831 16.739 -4.684 0.932  -0.497 C1   REA_v2 1  
+REA_v2 C2   C2   C 0 1 N N N 20.921 30.524 15.841 -5.837 0.190  -1.176 C2   REA_v2 2  
+REA_v2 C3   C3   C 0 1 N N N 20.245 29.635 14.848 -6.441 -0.798 -0.171 C3   REA_v2 3  
+REA_v2 C4   C4   C 0 1 N N N 19.555 28.479 15.488 -5.418 -1.903 0.100  C4   REA_v2 4  
+REA_v2 C5   C5   C 0 1 N N N 20.389 27.812 16.587 -4.082 -1.301 0.429  C5   REA_v2 5  
+REA_v2 C6   C6   C 0 1 N N N 21.425 28.446 17.218 -3.756 -0.048 0.161  C6   REA_v2 6  
+REA_v2 C7   C7   C 0 1 N N N 22.242 27.851 18.297 -2.457 0.396  0.516  C7   REA_v2 7  
+REA_v2 C8   C8   C 0 1 N N N 21.868 26.977 19.240 -1.363 -0.229 0.007  C8   REA_v2 8  
+REA_v2 C9   C9   C 0 1 N N N 22.705 26.434 20.286 -0.076 0.257  0.298  C9   REA_v2 9  
+REA_v2 C10  C10  C 0 1 N N N 22.159 25.536 21.131 1.022  -0.370 -0.213 C10  REA_v2 10 
+REA_v2 C11  C11  C 0 1 N N N 22.875 24.924 22.234 2.306  0.115  0.077  C11  REA_v2 11 
+REA_v2 C12  C12  C 0 1 N N N 22.237 24.026 22.990 3.405  -0.513 -0.435 C12  REA_v2 12 
+REA_v2 C13  C13  C 0 1 N N N 22.856 23.377 24.125 4.689  -0.028 -0.144 C13  REA_v2 13 
+REA_v2 C14  C14  C 0 1 N N N 22.135 22.473 24.834 5.787  -0.655 -0.656 C14  REA_v2 14 
+REA_v2 C15  C15  C 0 1 N N N 22.563 21.710 26.016 7.077  -0.265 -0.244 C15  REA_v2 15 
+REA_v2 C16  C16  C 0 1 N N N 22.238 30.737 17.948 -5.246 1.886  0.559  C16  REA_v2 16 
+REA_v2 C17  C17  C 0 1 N N N 23.292 29.620 15.948 -3.911 1.737  -1.544 C17  REA_v2 17 
+REA_v2 C18  C18  C 0 1 N N N 19.791 26.449 16.947 -3.056 -2.175 1.103  C18  REA_v2 18 
+REA_v2 C19  C19  C 0 1 N N N 24.181 26.841 20.385 0.090  1.471  1.175  C19  REA_v2 19 
+REA_v2 C20  C20  C 0 1 N N N 24.303 23.747 24.489 4.855  1.186  0.733  C20  REA_v2 20 
+REA_v2 O1   O1   O 0 1 N N N 23.640 21.075 25.978 7.210  0.553  0.648  O1   REA_v2 21 
+REA_v2 O2   O2   O 0 1 N N N 21.840 21.712 27.037 8.166  -0.798 -0.840 O2   REA_v2 22 
+REA_v2 H21  H21  H 0 1 N N N 20.147 30.955 16.494 -6.598 0.905  -1.490 H21  REA_v2 23 
+REA_v2 H22  H22  H 0 1 N N N 21.425 31.330 15.288 -5.462 -0.353 -2.044 H22  REA_v2 24 
+REA_v2 H31  H31  H 0 1 N N N 19.501 30.227 14.295 -6.673 -0.278 0.759  H31  REA_v2 25 
+REA_v2 H32  H32  H 0 1 N N N 21.001 29.250 14.148 -7.349 -1.234 -0.586 H32  REA_v2 26 
+REA_v2 H41  H41  H 0 1 N N N 18.613 28.835 15.931 -5.756 -2.511 0.938  H41  REA_v2 27 
+REA_v2 H42  H42  H 0 1 N N N 19.335 27.730 14.713 -5.322 -2.531 -0.786 H42  REA_v2 28 
+REA_v2 H7   H7   H 0 1 N N N 23.276 28.162 18.329 -2.337 1.230  1.191  H7   REA_v2 29 
+REA_v2 H8   H8   H 0 1 N N N 20.840 26.645 19.217 -1.482 -1.100 -0.622 H8   REA_v2 30 
+REA_v2 H10  H10  H 0 1 N N N 21.127 25.256 20.977 0.903  -1.241 -0.842 H10  REA_v2 31 
+REA_v2 H11  H11  H 0 1 N N N 23.902 25.189 22.440 2.425  0.985  0.706  H11  REA_v2 32 
+REA_v2 H12  H12  H 0 1 N N N 21.216 23.774 22.743 3.286  -1.383 -1.063 H12  REA_v2 33 
+REA_v2 H14  H14  H 0 1 N N N 21.127 22.292 24.490 5.667  -1.451 -1.376 H14  REA_v2 34 
+REA_v2 H161 H161 H 0 0 N N N 22.984 30.265 18.604 -5.802 1.316  1.303  H161 REA_v2 35 
+REA_v2 H162 H162 H 0 0 N N N 22.618 31.709 17.601 -4.426 2.415  1.044  H162 REA_v2 36 
+REA_v2 H163 H163 H 0 0 N N N 21.302 30.887 18.506 -5.911 2.605  0.081  H163 REA_v2 37 
+REA_v2 H171 H171 H 0 0 N N N 24.033 29.127 16.595 -4.598 2.394  -2.077 H171 REA_v2 38 
+REA_v2 H172 H172 H 0 0 N N N 23.095 28.989 15.069 -3.146 2.335  -1.050 H172 REA_v2 39 
+REA_v2 H173 H173 H 0 0 N N N 23.683 30.595 15.620 -3.439 1.054  -2.251 H173 REA_v2 40 
+REA_v2 H181 H181 H 0 0 N N N 20.397 25.979 17.736 -3.448 -3.187 1.201  H181 REA_v2 41 
+REA_v2 H182 H182 H 0 0 N N N 18.761 26.584 17.308 -2.145 -2.194 0.503  H182 REA_v2 42 
+REA_v2 H183 H183 H 0 0 N N N 19.786 25.804 16.056 -2.831 -1.775 2.092  H183 REA_v2 43 
+REA_v2 H191 H191 H 0 0 N N N 24.647 26.327 21.238 0.171  1.159  2.216  H191 REA_v2 44 
+REA_v2 H192 H192 H 0 0 N N N 24.702 26.559 19.458 0.993  2.008  0.885  H192 REA_v2 45 
+REA_v2 H193 H193 H 0 0 N N N 24.252 27.929 20.529 -0.774 2.125  1.058  H193 REA_v2 46 
+REA_v2 H201 H201 H 0 0 N N N 24.620 23.168 25.369 5.026  0.871  1.762  H201 REA_v2 47 
+REA_v2 H202 H202 H 0 0 N N N 24.965 23.516 23.641 5.707  1.771  0.386  H202 REA_v2 48 
+REA_v2 H203 H203 H 0 0 N N N 24.360 24.822 24.717 3.952  1.795  0.685  H203 REA_v2 49 
+REA_v2 HO2  HO2  H 0 1 N N N 22.244 21.180 27.713 9.006  -0.469 -0.490 HO2  REA_v2 50 
+# 
+loop_
+_chem_comp_bond.comp_id 
+_chem_comp_bond.atom_id_1 
+_chem_comp_bond.atom_id_2 
+_chem_comp_bond.value_order 
+_chem_comp_bond.pdbx_aromatic_flag 
+_chem_comp_bond.pdbx_stereo_config 
+_chem_comp_bond.pdbx_ordinal 
+REA_v2 C1  C2   SING N N 1  
+REA_v2 C1  C6   SING N N 2  
+REA_v2 C1  C16  SING N N 3  
+REA_v2 C1  C17  SING N N 4  
+REA_v2 C2  C3   SING N N 5  
+REA_v2 C2  H21  SING N N 6  
+REA_v2 C2  H22  SING N N 7  
+REA_v2 C3  C4   SING N N 8  
+REA_v2 C3  H31  SING N N 9  
+REA_v2 C3  H32  SING N N 10 
+REA_v2 C4  C5   SING N N 11 
+REA_v2 C4  H41  SING N N 12 
+REA_v2 C4  H42  SING N N 13 
+REA_v2 C5  C6   DOUB N N 14 
+REA_v2 C5  C18  SING N N 15 
+REA_v2 C6  C7   SING N N 16 
+REA_v2 C7  C8   DOUB N E 17 
+REA_v2 C7  H7   SING N N 18 
+REA_v2 C8  C9   SING N N 19 
+REA_v2 C8  H8   SING N N 20 
+REA_v2 C9  C10  DOUB N E 21 
+REA_v2 C9  C19  SING N N 22 
+REA_v2 C10 C11  SING N N 23 
+REA_v2 C10 H10  SING N N 24 
+REA_v2 C11 C12  DOUB N E 25 
+REA_v2 C11 H11  SING N N 26 
+REA_v2 C12 C13  SING N N 27 
+REA_v2 C12 H12  SING N N 28 
+REA_v2 C13 C14  DOUB N E 29 
+REA_v2 C13 C20  SING N N 30 
+REA_v2 C14 C15  SING N N 31 
+REA_v2 C14 H14  SING N N 32 
+REA_v2 C15 O1   DOUB N N 33 
+REA_v2 C15 O2   SING N N 34 
+REA_v2 C16 H161 SING N N 35 
+REA_v2 C16 H162 SING N N 36 
+REA_v2 C16 H163 SING N N 37 
+REA_v2 C17 H171 SING N N 38 
+REA_v2 C17 H172 SING N N 39 
+REA_v2 C17 H173 SING N N 40 
+REA_v2 C18 H181 SING N N 41 
+REA_v2 C18 H182 SING N N 42 
+REA_v2 C18 H183 SING N N 43 
+REA_v2 C19 H191 SING N N 44 
+REA_v2 C19 H192 SING N N 45 
+REA_v2 C19 H193 SING N N 46 
+REA_v2 C20 H201 SING N N 47 
+REA_v2 C20 H202 SING N N 48 
+REA_v2 C20 H203 SING N N 49 
+REA_v2 O2  HO2  SING N N 50 
+# 
+loop_
+_pdbx_chem_comp_descriptor.comp_id 
+_pdbx_chem_comp_descriptor.type 
+_pdbx_chem_comp_descriptor.program 
+_pdbx_chem_comp_descriptor.program_version 
+_pdbx_chem_comp_descriptor.descriptor 
+REA_v2 SMILES           ACDLabs              12.01 "C1(CCCC(=C1\C=C\C(=C\C=C\C(=C\C(=O)O)C)C)C)(C)C"                                                                                                     
+REA_v2 InChI            InChI                1.03  "InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8+,16-14+" 
+REA_v2 InChIKey         InChI                1.03  SHGAZHPCJJPHSC-YCNIQYBTSA-N                                                                                                                           
+REA_v2 SMILES_CANONICAL CACTVS               3.385 "CC1=C(\C=C\C(C)=C\C=C\C(C)=C\C(O)=O)C(C)(C)CCC1"                                                                                                     
+REA_v2 SMILES           CACTVS               3.385 "CC1=C(C=CC(C)=CC=CC(C)=CC(O)=O)C(C)(C)CCC1"                                                                                                          
+REA_v2 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=C(C(CCC1)(C)C)/C=C/C(=C/C=C/C(=C/C(=O)O)/C)/C"                                                                                                   
+REA_v2 SMILES           "OpenEye OEToolkits" 1.7.6 "CC1=C(C(CCC1)(C)C)C=CC(=CC=CC(=CC(=O)O)C)C"                                                                                                          
+# 
+loop_
+_pdbx_chem_comp_identifier.comp_id 
+_pdbx_chem_comp_identifier.type 
+_pdbx_chem_comp_identifier.program 
+_pdbx_chem_comp_identifier.program_version 
+_pdbx_chem_comp_identifier.identifier 
+REA_v2 "SYSTEMATIC NAME" ACDLabs              12.01 "retinoic acid"                                                                             
+REA_v2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexen-1-yl)nona-2,4,6,8-tetraenoic acid" 
+# 
+loop_
+_pdbx_chem_comp_audit.comp_id 
+_pdbx_chem_comp_audit.action_type 
+_pdbx_chem_comp_audit.date 
+_pdbx_chem_comp_audit.processing_site 
+REA_v2 "CREA_v2te component"   1999-07-08 RCSB 
+REA_v2 "Modify descriptor"  2011-06-04 RCSB 
+REA_v2 "Other modification" 2016-10-18 RCSB 
+# 

test/unit-v2-test.cpp

@@ -3150,4 +3150,60 @@ _test.value
 
 	v = test.find1<std::optional<float>>("id"_key == 4, "value");
 	BOOST_CHECK(v.has_value() == false);
-}
+}
+
+// --------------------------------------------------------------------
+
+BOOST_AUTO_TEST_CASE(compound_test_1)
+{
+	cif::compound_factory::instance().push_dictionary(gTestDir / "REA_v2.cif");
+	auto compound = cif::compound_factory::instance().create("REA_v2");
+	BOOST_ASSERT(compound != nullptr);
+	BOOST_CHECK(compound->id() == "REA_v2");
+}
+
+// --------------------------------------------------------------------
+
+BOOST_AUTO_TEST_CASE(pdb_parser_test_1)
+{
+	char k1CBS[] = R"(HEADER    RETINOIC-ACID TRANSPORT                 28-SEP-94   1CBS
+TITLE     CRYSTAL STRUCTURE OF CELLULAR RETINOIC-ACID-BINDING
+TITLE    2 PROTEINS I AND II IN COMPLEX WITH ALL-TRANS-RETINOIC ACID
+TITLE    3 AND A SYNTHETIC RETINOID
+COMPND    MOL_ID: 1;
+COMPND   2 MOLECULE: CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II;
+COMPND   3 CHAIN: A;
+COMPND   4 ENGINEERED: YES
+SOURCE    MOL_ID: 1;
+SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
+SOURCE   3 ORGANISM_COMMON: HUMAN;
+SOURCE   4 ORGANISM_TAXID: 9606;
+SOURCE   5 CELL_LINE: BL21;
+SOURCE   6 GENE: HUMAN CRABP-II;
+SOURCE   7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
+SOURCE   8 EXPRESSION_SYSTEM_TAXID: 469008;
+SOURCE   9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3);
+SOURCE  10 EXPRESSION_SYSTEM_PLASMID: PET-3A
+KEYWDS    RETINOIC-ACID TRANSPORT
+EXPDTA    X-RAY DIFFRACTION
+AUTHOR    G.J.KLEYWEGT,T.BERGFORS,T.A.JONES
+ATOM      1  N   PRO A   1      16.979  13.301  44.555  1.00 30.05           N
+ATOM      2  CA  PRO A   1      18.150  13.525  43.680  1.00 28.82           C
+ATOM      3  C   PRO A   1      18.656  14.966  43.784  1.00 26.59           C
+ATOM      4  O   PRO A   1      17.890  15.889  44.078  1.00 26.84           O
+ATOM      5  CB  PRO A   1      17.678  13.270  42.255  1.00 29.24           C
+ATOM      6  CG  PRO A   1      16.248  13.734  42.347  1.00 29.29           C
+ATOM      7  CD  PRO A   1      15.762  13.216  43.724  1.00 30.71           C)";
+
+	struct membuf : public std::streambuf
+	{
+		membuf(char *text, size_t length)
+		{
+			this->setg(text, text, text + length);
+		}
+	} buffer(k1CBS, sizeof(k1CBS) - 1);
+
+	std::istream is(&buffer);
+
+	auto f = cif::pdb::read(is);
+}