Fix cif2pdb, somewhat...

don't use get_item_indices
version bump

.github/workflows/build-documentation.yml

@@ -42,7 +42,7 @@ jobs:
 
     - name: Run Sphinx
       run: |
-        cmake --build ${{ steps.strings.outputs.build-output-dir }} --target Sphinx-libcifpp
+        cmake --build ${{ steps.strings.outputs.build-output-dir }} --target Sphinx-cifpp
         ls -l ${{ steps.strings.outputs.build-output-dir }}
         ls -l ${{ steps.strings.outputs.build-output-dir }}/docs/sphinx
 

CMakeLists.txt

@@ -34,7 +34,7 @@ endif()
 # set the project name
 project(
     libcifpp
-    VERSION 10.0.2
+    VERSION 10.0.4
     LANGUAGES CXX C)
 
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
@@ -138,13 +138,6 @@ if(MSVC)
     # make msvc standards compliant...
     add_compile_options(/permissive- /bigobj)
     add_link_options(/NODEFAULTLIB:library)
-
-    # This is dubious...
-    if(BUILD_SHARED_LIBS)
-        set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>DLL")
-    else()
-        set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
-    endif()
 endif()
 
 # Libraries
@@ -367,8 +360,9 @@ else()
 endif()
 
 if(NOT STD_CHARCONV_COMPILING)
-     target_include_directories(cifpp PRIVATE ${FastFloat_INCLUDE_DIRS})
-	 target_compile_definitions(cifpp PRIVATE USE_FAST_FLOAT)
+    get_target_property(FF_INC_DIR FastFloat::fast_float INTERFACE_INCLUDE_DIRECTORIES)
+    target_include_directories(cifpp PRIVATE ${FF_INC_DIR})
+	target_compile_definitions(cifpp PRIVATE USE_FAST_FLOAT)
 endif()
 
 if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")

changelog

@@ -1,5 +1,18 @@
+Version 10.0.4
+- Fixed find_by_value in the index of a category,
+  avoid swapping columns in the search keys
+
+Version 10.0.3
+- Clear pdbx_nonpoly_scheme before filling it in reconstruction
+- Changed handling of numbers with a preceding plus character,
+  these are now stored as strings to avoid inadvertently
+  mutilating phone numbers.
+
 Version 10.0.2
 - Fixed regression in reconstruction introduced in 10.0.1
+- Fixed symmetry operations
+- Added validation for pdbx_item_enumeration as well as
+  case-sensitive checks for enumerations when needed.
 
 Version 10.0.1
 - Fixed some regressions, like assigning to items.

include/cif++/item.hpp

@@ -331,8 +331,11 @@ class item_value
 			case TEXT:
 			{
 				auto sv = m_data.sv();
+				auto sp = sv.data();
+				if (*sp == '+')
+					++sp;
 				int64_t v;
-				auto &&[ptr, ec] = from_chars(sv.data(), sv.data() + sv.length(), v);
+				auto &&[ptr, ec] = from_chars(sp, sv.data() + sv.length(), v);
 				if (ec != std::errc{})
 					throw std::system_error(std::make_error_code(ec));
 				if (ptr != sv.data() + sv.length())
@@ -361,8 +364,11 @@ class item_value
 			case TEXT:
 			{
 				auto sv = m_data.sv();
+				auto sp = sv.data();
+				if (*sp == '+')
+					++sp;
 				double v;
-				auto &&[ptr, ec] = from_chars(sv.data(), sv.data() + sv.length(), v);
+				auto &&[ptr, ec] = from_chars(sp, sv.data() + sv.length(), v);
 				if (ec != std::errc{})
 					throw std::system_error(std::make_error_code(ec));
 				if (ptr != sv.data() + sv.length())

include/cif++/point.hpp

@@ -902,74 +902,4 @@ quaternion align_points(const std::vector<point> &a, const std::vector<point> &b
 /// \brief The RMSd for the points in \a a and \a b
 double RMSd(const std::vector<point> &a, const std::vector<point> &b);
 
-// --------------------------------------------------------------------
-/**
- * @brief Helper class to generate evenly divided points on a sphere
- *
- * We use a fibonacci sphere to calculate even distribution of the dots
- *
- * @tparam N The number of points on the sphere is 2 * N + 1
- */
-template <int N>
-class spherical_dots
-{
-  public:
-	/// \brief the number of points
-	constexpr static int P = 2 * N * 1;
-
-	/// \brief the *weight* of the fibonacci sphere
-	constexpr static double W = (4 * std::numbers::pi) / P;
-
-	/// \brief the internal storage type
-	using array_type = typename std::array<point, P>;
-
-	/// \brief iterator type
-	using iterator = typename array_type::const_iterator;
-
-	/// \brief singleton instance
-	static spherical_dots &instance()
-	{
-		static spherical_dots sInstance;
-		return sInstance;
-	}
-
-	/// \brief The number of points
-	[[nodiscard]] std::size_t size() const { return P; }
-
-	/// \brief Access a point by index
-	const point operator[](uint32_t inIx) const { return m_points[inIx]; }
-
-	/// \brief iterator pointing to the first point
-	[[nodiscard]] iterator begin() const { return m_points.begin(); }
-
-	/// \brief iterator pointing past the last point
-	[[nodiscard]] iterator end() const { return m_points.end(); }
-
-	/// \brief return the *weight*,
-	[[nodiscard]] double weight() const { return W; }
-
-	spherical_dots()
-	{
-		const double
-			kGoldenRatio = std::numbers::phi;
-
-		auto p = m_points.begin();
-
-		for (int32_t i = -N; i <= N; ++i)
-		{
-			double lat = std::asin((2.0 * i) / P);
-			double lon = std::fmod(i, kGoldenRatio) * 2 * std::numbers::pi / kGoldenRatio;
-
-			p->m_x = std::sin(lon) * std::cos(lat);
-			p->m_y = std::cos(lon) * std::cos(lat);
-			p->m_z = std::sin(lat);
-
-			++p;
-		}
-	}
-
-  private:
-	array_type m_points;
-};
-
 } // namespace cif

include/cif++/validate.hpp

@@ -196,7 +196,7 @@ class validation_exception : public std::runtime_error
   public:
 	// Constructors
 	/// @cond
-	
+
 	validation_exception(validation_error err)
 		: validation_exception(make_error_code(err))
 	{
@@ -337,7 +337,7 @@ struct item_validator
 	std::string m_item_name;           ///< The item name
 	bool m_mandatory;                  ///< Flag indicating this item is mandatory
 	const type_validator *m_type;      ///< The type for this item
-	cif::iset m_enums;                 ///< If filled, the set of allowed values
+	std::set<std::string> m_enums;     ///< If filled, the set of allowed values
 	std::string m_default;             ///< If filled, a default value for this item
 	std::string m_category;            ///< The category this item_validator belongs to
 	std::vector<item_alias> m_aliases; ///< The aliases for this item
@@ -502,15 +502,29 @@ class validator
 	/// @brief Bottleneck function to report an error in validation
 	void report_error(std::error_code ec, bool fatal = true) const;
 
+	/// @brief Bottleneck function to report an error in validation
+	void report_error(validation_error err, std::string value, std::string_view category,
+		std::string_view item, bool fatal = true) const
+	{
+		report_error(make_error_code(err), value, category, item, fatal);
+	}
+
 	/// @brief Bottleneck function to report an error in validation
 	void report_error(validation_error err, std::string_view category,
 		std::string_view item, bool fatal = true) const
 	{
-		report_error(make_error_code(err), category, item, fatal);
+		report_error(make_error_code(err), "", category, item, fatal);
 	}
 
 	/// @brief Bottleneck function to report an error in validation
 	void report_error(std::error_code ec, std::string_view category,
+		std::string_view item, bool fatal = true) const
+	{
+		report_error(ec, "", category, item, fatal);
+	}
+
+	/// @brief Bottleneck function to report an error in validation
+	void report_error(std::error_code ec, std::string value, std::string_view category,
 		std::string_view item, bool fatal = true) const;
 
 	/// @brief Write out the audit_conform data for this validator

src/category.cpp

@@ -118,6 +118,7 @@ class row_comparator
 
 		for (const auto &[k, f] : m_comparator)
 		{
+			assert(cat.get_item_name(k) == ai->name);
 			d = f(ai->value, rhb[k].value());
 
 			if (d != 0)
@@ -363,10 +364,9 @@ row *category_index::find_by_value(const category &cat, const category::key_type
 	// sort the values in k first
 
 	category::key_type k2;
-	for (auto &f : cat.key_item_indices())
+	auto cv = cat.get_cat_validator();
+	for (auto &fld : cv->m_keys)
 	{
-		auto fld = cat.get_item_name(f);
-
 		auto ki = std::ranges::find_if(k, [&fld](auto &i)
 			{ return i.name == fld; });
 		if (ki == k.end())
@@ -749,16 +749,34 @@ void category::set_validator(const validator *v, datablock &db)
 
 		bool number = type->m_primitive_type == DDL_PrimitiveType::Numb;
 		if (number)
-			continue;
-
-		for (auto row = m_head; row != nullptr; row = row->m_next)
 		{
-			if (cix >= row->size() or row->operator[](cix).empty())
-				continue;
+			for (auto row = m_head; row != nullptr; row = row->m_next)
+			{
+				if (cix >= row->size() or row->operator[](cix).empty())
+					continue;
 
-			item_value &v = row->operator[](cix);
-			if (v.is_number())
-				v = v.str();
+				item_value &v = row->operator[](cix);
+				if (not v.is_number())
+				{
+					// Try cast the value to a number and throw in case of failure
+					if (auto sv = v.sv(); sv.find_first_of(".eE") == std::string_view::npos)
+						v.cast_to_int();
+					else
+						v.cast_to_float();
+				}
+			}
+		}
+		else
+		{
+			for (auto row = m_head; row != nullptr; row = row->m_next)
+			{
+				if (cix >= row->size() or row->operator[](cix).empty())
+					continue;
+
+				item_value &v = row->operator[](cix);
+				if (v.is_number())
+					v = v.str();
+			}
 		}
 	}
 
@@ -890,11 +908,13 @@ bool category::is_valid() const
 				seen = true;
 				std::error_code ec;
 
-				iv->validate_value(*ri->get(cix), ec);
+				auto &v = *ri->get(cix);
+
+				iv->validate_value(v, ec);
 
 				if (ec != std::errc{})
 				{
-					m_validator->report_error(ec, m_name, m_items[cix].m_name, false);
+					m_validator->report_error(ec, v.str(), m_name, m_items[cix].m_name, false);
 					continue;
 				}
 			}
@@ -1450,7 +1470,12 @@ void category::update_value(const std::vector<row_handle> &rows, std::string_vie
 
 			std::error_code ec;
 			col.m_validator->validate_value(value, ec);
-			if (ec)
+			if (ec == cif::make_error_code(cif::validation_error::value_is_not_in_enumeration_list))
+			{
+				if (cif::VERBOSE >= 0)
+					m_validator->report_error(ec, m_name, item_name, false);
+			}
+			else if (ec)
 				throw validation_exception(ec, m_name, item_name);
 		}
 	}
@@ -1577,7 +1602,18 @@ void category::update_value(row *row, uint16_t item, item_value value, bool upda
 
 	// check the value
 	if (col.m_validator and validate)
-		col.m_validator->validate_value(value);
+	{
+		std::error_code ec;
+		col.m_validator->validate_value(value, ec);
+		if (ec == cif::make_error_code(cif::validation_error::value_is_not_in_enumeration_list))
+		{
+			if (cif::VERBOSE >= 0)
+				m_validator->report_error(ec, m_name, m_items[item].m_name, false);
+		}
+		else if (ec)
+			throw validation_exception(ec, m_name, m_items[item].m_name);
+
+	}
 
 	// If the item is part of the Key for this category, remove it from the index
 	// before updating
@@ -1789,6 +1825,12 @@ category::iterator category::insert_impl(const_iterator pos, row *n)
 						}
 						else if (ec == cif::make_error_code(cif::validation_error::value_is_not_a_char_string))
 							v->cast_to_string();
+						else if (ec == cif::make_error_code(cif::validation_error::value_is_not_in_enumeration_list))
+						{
+							if (cif::VERBOSE >= 0)
+								m_validator->report_error(ec, m_name, m_items[ix].m_name, false);
+							continue;
+						}
 						else
 							throw std::system_error(ec, "Attempt to insert invalid value");
 
@@ -2158,7 +2200,7 @@ void category::write_cif(std::ostream &os, const std::vector<uint16_t> &order, b
 					offset = 0;
 				}
 
-				offset = detail::write_value(os, s, offset, w, /* right_aligned[cix] */ iv->is_number());
+				offset = detail::write_value(os, s, offset, w, right_aligned[cix]/*  iv->is_number() */);
 
 				if (offset > 132)
 				{

src/compound.cpp

@@ -799,8 +799,8 @@ void compound_factory::report_missing_compound(std::string_view compound_id)
 		std::clog << "\n"
 				  << cif::coloured("Configuration error:", white, red) << "\n\n"
 				  << "The attempt to retrieve compound information for " << std::quoted(compound_id) << " failed.\n\n"
-				  << "This information is searched for in a CCD file called components.cif or\n"
-				  << "components.cif.gz which should be located in one of the following directories:\n\n";
+				  << "This information is searched for in a CCD file called components.cif\n"
+				  << "which should be located in one of the following directories:\n\n";
 
 		cif::list_data_directories(std::clog);
 

src/condition.cpp

@@ -129,9 +129,9 @@ namespace detail
 			m_item_ix = *ix;
 			m_icase = is_item_type_uchar(c, m_item_name);
 
-			if (c.get_cat_validator() != nullptr and
-				c.key_item_indices().contains(m_item_ix) and
-				c.key_item_indices().size() == 1)
+			if (auto cv = c.get_cat_validator();
+				cv != nullptr and cv->m_keys.size() == 1 and
+				cv->m_keys.front() == m_item_name)
 			{
 				m_single_hit = c[{ { m_item_name, m_value } }];
 			}

src/dictionary_parser.cpp

@@ -25,6 +25,8 @@
  */
 
 #include "cif++/cif++.hpp"
+#include "cif++/text.hpp"
+#include "cif++/validate.hpp"
 
 #include <cstddef>
 #include <exception>
@@ -103,7 +105,19 @@ class dictionary_parser : public parser
 				error("Undefined category '" + iv.first);
 
 			for (auto &v : iv.second)
+			{
+				// enums, make lower case if needed
+				auto tv = v.m_type;
+				if (tv and tv->m_primitive_type == DDL_PrimitiveType::UChar)
+				{
+					std::set<std::string> es;
+					for (auto &e : v.m_enums)
+						es.emplace(cif::to_lower_copy(e));
+					std::swap(es, v.m_enums);
+				}
+
 				const_cast<category_validator *>(cv)->add_item_validator(std::move(v));
+			}
 		}
 
 		// check all item validators for having a typeValidator
@@ -275,9 +289,11 @@ class dictionary_parser : public parser
 			if (typeCode.has_value())
 				tv = m_validator.get_validator_for_type(*typeCode);
 
-			iset ess;
+			std::set<std::string> ess;
 			for (auto e : dict["item_enumeration"])
 				ess.insert(e["value"].get<std::string>());
+			for (auto e : dict["pdbx_item_enumeration"])
+				ess.insert(e["value"].get<std::string>());
 
 			std::string defaultValue;
 			if (auto &cat = dict["item_default"]; not cat.empty())

src/item.cpp

@@ -239,7 +239,12 @@ void item_value::cast_to_int()
 		{
 			auto s = sv();
 			int64_t v;
-			auto [ptr, ec] = cif::from_chars(s.data(), s.data() + s.size(), v);
+
+			auto sp = s.data();
+			if (*sp == '+')
+				++sp;
+
+			auto [ptr, ec] = cif::from_chars(sp, s.data() + s.size(), v);
 			if (ec != std::errc{})
 				throw std::system_error(std::make_error_code(ec), "attempt to cast value to integer failed");
 			if (ptr != s.data() + s.size())

src/model.cpp

@@ -2178,8 +2178,8 @@ std::string structure::create_non_poly(const std::string &entity_id, const std::
 			{ "label_comp_id", comp_id },
 			{ "label_asym_id", asym_id },
 			{ "label_entity_id", entity_id },
-			{ "label_seq_id", nullptr },
-			{ "pdbx_PDB_ins_code", "" },
+			{ "label_seq_id", cif::item_value_type::INAPPLICABLE },
+			{ "pdbx_PDB_ins_code", cif::item_value_type::MISSING },
 			{ "Cartn_x", atom.get_property_value("Cartn_x") },
 			{ "Cartn_y", atom.get_property_value("Cartn_y") },
 			{ "Cartn_z", atom.get_property_value("Cartn_z") },
@@ -2190,7 +2190,7 @@ std::string structure::create_non_poly(const std::string &entity_id, const std::
 			{ "auth_comp_id", comp_id },
 			{ "auth_asym_id", asym_id },
 			{ "auth_atom_id", atom.get_property_value("label_atom_id") },
-			{ "pdbx_PDB_model_num", 1 } });
+			{ "pdbx_PDB_model_num", m_model_nr } });
 
 		auto &newAtom = emplace_atom(std::make_shared<atom::atom_impl>(m_db, atom_id));
 		res.add_atom(newAtom);
@@ -2208,7 +2208,7 @@ std::string structure::create_non_poly(const std::string &entity_id, const std::
 		{ "pdb_mon_id", comp_id },
 		{ "auth_mon_id", comp_id },
 		{ "pdb_strand_id", asym_id },
-		{ "pdb_ins_code", nullptr },
+		{ "pdb_ins_code", cif::item_value_type::MISSING },
 	});
 
 	return asym_id;
@@ -2244,12 +2244,14 @@ std::string structure::create_non_poly(const std::string &entity_id, std::vector
 
 		atom.set_value_if_empty({ "group_PDB", "HETATM" });
 		atom.set_value_if_empty({ "label_comp_id", comp_id });
-		atom.set_value_if_empty({ "label_seq_id", nullptr });
+		atom.set_value_if_empty({ "label_seq_id", cif::item_value_type::INAPPLICABLE });
 		atom.set_value_if_empty({ "auth_comp_id", comp_id });
 		atom.set_value_if_empty({ "auth_seq_id", "1" });
-		atom.set_value_if_empty({ "pdbx_PDB_model_num", 1 });
-		atom.set_value_if_empty({ "label_alt_id", "" });
+		atom.set_value_if_empty({ "pdbx_PDB_model_num", m_model_nr });
+		atom.set_value_if_empty({ "label_alt_id", cif::item_value_type::INAPPLICABLE });
 		atom.set_value_if_empty({ "occupancy", { 1.0, 2 } });
+		atom.set_value_if_empty({ "pdbx_formal_charge", cif::item_value_type::MISSING });
+		atom.set_value_if_empty({ "pdbx_tls_group_id", cif::item_value_type::MISSING });
 
 		auto row = atom_site.emplace(atom.begin(), atom.end());
 
@@ -2299,7 +2301,7 @@ std::string structure::create_non_poly(const std::string &compound_id, bool skip
 			{ "Cartn_x", ax },
 			{ "Cartn_y", ay },
 			{ "Cartn_z", az },
-			{ "B_iso_or_equiv", 30.00 } });
+			{ "B_iso_or_equiv", { 30.00, 2 } } });
 	}
 
 	return create_non_poly(create_non_poly_entity(compound_id), atoms);

src/parser.cpp

@@ -25,6 +25,7 @@
  */
 
 #include "cif++/cif++.hpp"
+#include "cif++/utilities.hpp"
 
 #include <cassert>
 #include <cctype>
@@ -635,15 +636,28 @@ sac_parser::CIFToken sac_parser::get_next_token()
 
 	if (result == CIFToken::VALUE_NUMERIC_INTEGER)
 	{
+		// Avoid interpreting phone numbers as integers, TODO: check if this is an issue
 		auto [ptr, ec] = from_chars(m_token_buffer.data(), m_token_buffer.data() + m_token_buffer.size(), m_token_value_int);
 		if (ec != std::errc{})
-			error("Invalid integer value: " + std::make_error_code(ec).message());
+		{
+			if (cif::VERBOSE > 0)
+				std::clog << "Invalid integer value: " << std::make_error_code(ec).message() << '\n';
+
+			result = CIFToken::VALUE_CHARSTRING;
+			m_token_value = std::string_view(m_token_buffer.data(), m_token_buffer.size());
+		}
 	}
 	else if (result == CIFToken::VALUE_NUMERIC_FLOAT)
 	{
 		auto [ptr, ec] = from_chars(m_token_buffer.data(), m_token_buffer.data() + m_token_buffer.size(), m_token_value_float);
 		if (ec != std::errc{})
-			error("Invalid integer value: " + std::make_error_code(ec).message());
+		{
+			if (cif::VERBOSE > 0)
+				std::clog << "Invalid floating point value: " << std::make_error_code(ec).message() << '\n';
+
+			result = CIFToken::VALUE_CHARSTRING;
+			m_token_value = std::string_view(m_token_buffer.data(), m_token_buffer.size());
+		}
 	}
 
 	return result;

src/pdb/cif2pdb.cpp

@@ -1811,13 +1811,10 @@ void WriteRemark3Phenix(std::ostream &pdbFile, const datablock &db)
 void WriteRemark3XPlor(std::ostream &pdbFile, const datablock &db)
 {
 	auto refine = db["refine"].front();
-	auto ls_shell = db["refine_ls_shell"].front();
 	auto hist = db["refine_hist"].front();
 	auto reflns = db["reflns"].front();
 	auto analyze = db["refine_analyze"].front();
 	auto &ls_restr = db["refine_ls_restr"];
-	auto ls_restr_ncs = db["refine_ls_restr_ncs"].front();
-	auto pdbx_xplor_file = db["pdbx_xplor_file"].front();
 
 	pdbFile << RM3("") << '\n'
 			<< RM3(" DATA USED IN REFINEMENT.") << '\n'
@@ -1837,7 +1834,11 @@ void WriteRemark3XPlor(std::ostream &pdbFile, const datablock &db)
 			<< RM3("  FREE R VALUE                     : ", 7, 3) << Ff(refine, "ls_R_factor_R_free") << '\n'
 			<< RM3("  FREE R VALUE TEST SET SIZE   (%) : ", 7, 3) << Ff(refine, "ls_percent_reflns_R_free") << '\n'
 			<< RM3("  FREE R VALUE TEST SET COUNT      : ", 12, 6) << Fi(refine, "ls_number_reflns_R_free") << '\n'
-			<< RM3("  ESTIMATED ERROR OF FREE R VALUE  : ", 7, 3) << Ff(refine, "ls_R_factor_R_free_error") << '\n'
+			<< RM3("  ESTIMATED ERROR OF FREE R VALUE  : ", 7, 3) << Ff(refine, "ls_R_factor_R_free_error") << '\n';
+	if (not db["refine_ls_shell"].empty())
+	{
+		auto ls_shell = db["refine_ls_shell"].front();
+		pdbFile
 
 			<< RM3("") << '\n'
 			<< RM3(" FIT IN THE HIGHEST RESOLUTION BIN.") << '\n'
@@ -1850,60 +1851,68 @@ void WriteRemark3XPlor(std::ostream &pdbFile, const datablock &db)
 			<< RM3("  BIN FREE R VALUE                    : ", 7, 3) << Ff(ls_shell, "R_factor_R_free") << '\n'
 			<< RM3("  BIN FREE R VALUE TEST SET SIZE  (%) : ", 5, 1) << Ff(ls_shell, "percent_reflns_R_free") << '\n'
 			<< RM3("  BIN FREE R VALUE TEST SET COUNT     : ", 12, 6) << Fi(ls_shell, "number_reflns_R_free") << '\n'
-			<< RM3("  ESTIMATED ERROR OF BIN FREE R VALUE : ", 7, 3) << Ff(ls_shell, "R_factor_R_free_error") << '\n'
+			<< RM3("  ESTIMATED ERROR OF BIN FREE R VALUE : ", 7, 3) << Ff(ls_shell, "R_factor_R_free_error") << '\n';
+	}
 
-			<< RM3("") << '\n'
-			<< RM3(" NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.") << '\n'
-			<< RM3("  PROTEIN ATOMS            : ", 12, 6) << Fi(hist, "pdbx_number_atoms_protein") << '\n'
-			<< RM3("  NUCLEIC ACID ATOMS       : ", 12, 6) << Fi(hist, "pdbx_number_atoms_nucleic_acid") << '\n'
-			<< RM3("  HETEROGEN ATOMS          : ", 12, 6) << Fi(hist, "pdbx_number_atoms_ligand") << '\n'
-			<< RM3("  SOLVENT ATOMS            : ", 12, 6) << Fi(hist, "number_atoms_solvent") << '\n'
+	pdbFile
+		<< RM3("") << '\n'
+		<< RM3(" NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.") << '\n'
+		<< RM3("  PROTEIN ATOMS            : ", 12, 6) << Fi(hist, "pdbx_number_atoms_protein") << '\n'
+		<< RM3("  NUCLEIC ACID ATOMS       : ", 12, 6) << Fi(hist, "pdbx_number_atoms_nucleic_acid") << '\n'
+		<< RM3("  HETEROGEN ATOMS          : ", 12, 6) << Fi(hist, "pdbx_number_atoms_ligand") << '\n'
+		<< RM3("  SOLVENT ATOMS            : ", 12, 6) << Fi(hist, "number_atoms_solvent") << '\n'
 
-			<< RM3("") << '\n'
-			<< RM3(" B VALUES.") << '\n'
-			<< RM3("  FROM WILSON PLOT           (A**2) : ", 7, 2) << Ff(reflns, "B_iso_Wilson_estimate") << '\n'
-			<< RM3("  MEAN B VALUE      (OVERALL, A**2) : ", 7, 2) << Ff(refine, "B_iso_mean") << '\n'
+		<< RM3("") << '\n'
+		<< RM3(" B VALUES.") << '\n'
+		<< RM3("  FROM WILSON PLOT           (A**2) : ", 7, 2) << Ff(reflns, "B_iso_Wilson_estimate") << '\n'
+		<< RM3("  MEAN B VALUE      (OVERALL, A**2) : ", 7, 2) << Ff(refine, "B_iso_mean") << '\n'
 
-			<< RM3("  OVERALL ANISOTROPIC B VALUE.") << '\n'
-			<< RM3("   B11 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[1][1]") << '\n'
-			<< RM3("   B22 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[2][2]") << '\n'
-			<< RM3("   B33 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[3][3]") << '\n'
-			<< RM3("   B12 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[1][2]") << '\n'
-			<< RM3("   B13 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[1][3]") << '\n'
-			<< RM3("   B23 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[2][3]") << '\n'
+		<< RM3("  OVERALL ANISOTROPIC B VALUE.") << '\n'
+		<< RM3("   B11 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[1][1]") << '\n'
+		<< RM3("   B22 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[2][2]") << '\n'
+		<< RM3("   B33 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[3][3]") << '\n'
+		<< RM3("   B12 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[1][2]") << '\n'
+		<< RM3("   B13 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[1][3]") << '\n'
+		<< RM3("   B23 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[2][3]") << '\n'
 
-			<< RM3("") << '\n'
-			<< RM3(" ESTIMATED COORDINATE ERROR.") << '\n'
-			<< RM3("  ESD FROM LUZZATI PLOT        (A) : ", 7, 2) << Ff(analyze, "Luzzati_coordinate_error_obs") << '\n'
-			<< RM3("  ESD FROM SIGMAA              (A) : ", 7, 2) << Ff(analyze, "Luzzati_sigma_a_obs") << '\n'
-			<< RM3("  LOW RESOLUTION CUTOFF        (A) : ", 7, 2) << Ff(analyze, "Luzzati_d_res_low_obs") << '\n'
+		<< RM3("") << '\n'
+		<< RM3(" ESTIMATED COORDINATE ERROR.") << '\n'
+		<< RM3("  ESD FROM LUZZATI PLOT        (A) : ", 7, 2) << Ff(analyze, "Luzzati_coordinate_error_obs") << '\n'
+		<< RM3("  ESD FROM SIGMAA              (A) : ", 7, 2) << Ff(analyze, "Luzzati_sigma_a_obs") << '\n'
+		<< RM3("  LOW RESOLUTION CUTOFF        (A) : ", 7, 2) << Ff(analyze, "Luzzati_d_res_low_obs") << '\n'
 
-			<< RM3("") << '\n'
-			<< RM3(" CROSS-VALIDATED ESTIMATED COORDINATE ERROR.") << '\n'
-			<< RM3("  ESD FROM C-V LUZZATI PLOT    (A) : ", 7, 2) << Ff(analyze, "Luzzati_coordinate_error_free") << '\n'
-			<< RM3("  ESD FROM C-V SIGMAA          (A) : ", 7, 2) << Ff(analyze, "Luzzati_sigma_a_free") << '\n'
+		<< RM3("") << '\n'
+		<< RM3(" CROSS-VALIDATED ESTIMATED COORDINATE ERROR.") << '\n'
+		<< RM3("  ESD FROM C-V LUZZATI PLOT    (A) : ", 7, 2) << Ff(analyze, "Luzzati_coordinate_error_free") << '\n'
+		<< RM3("  ESD FROM C-V SIGMAA          (A) : ", 7, 2) << Ff(analyze, "Luzzati_sigma_a_free") << '\n'
 
-			<< RM3("") << '\n'
-			<< RM3(" RMS DEVIATIONS FROM IDEAL VALUES.") << '\n'
-			<< RM3("  BOND LENGTHS                 (A) : ", 7, 3) << Ff(ls_restr, key("type") == "x_bond_d", "dev_ideal") << '\n'
-			<< RM3("  BOND ANGLES            (DEGREES) : ", 7, 2) << Ff(ls_restr, key("type") == "x_angle_deg", "dev_ideal") << '\n'
-			<< RM3("  DIHEDRAL ANGLES        (DEGREES) : ", 7, 2) << Ff(ls_restr, key("type") == "x_dihedral_angle_d", "dev_ideal") << '\n'
-			<< RM3("  IMPROPER ANGLES        (DEGREES) : ", 7, 2) << Ff(ls_restr, key("type") == "x_improper_angle_d", "dev_ideal") << '\n'
+		<< RM3("") << '\n'
+		<< RM3(" RMS DEVIATIONS FROM IDEAL VALUES.") << '\n'
+		<< RM3("  BOND LENGTHS                 (A) : ", 7, 3) << Ff(ls_restr, key("type") == "x_bond_d", "dev_ideal") << '\n'
+		<< RM3("  BOND ANGLES            (DEGREES) : ", 7, 2) << Ff(ls_restr, key("type") == "x_angle_deg", "dev_ideal") << '\n'
+		<< RM3("  DIHEDRAL ANGLES        (DEGREES) : ", 7, 2) << Ff(ls_restr, key("type") == "x_dihedral_angle_d", "dev_ideal") << '\n'
+		<< RM3("  IMPROPER ANGLES        (DEGREES) : ", 7, 2) << Ff(ls_restr, key("type") == "x_improper_angle_d", "dev_ideal") << '\n'
 
-			<< RM3("") << '\n'
-			<< RM3(" ISOTROPIC THERMAL MODEL : ") << Fs(refine, "pdbx_isotropic_thermal_model") << '\n'
+		<< RM3("") << '\n'
+		<< RM3(" ISOTROPIC THERMAL MODEL : ") << Fs(refine, "pdbx_isotropic_thermal_model") << '\n'
 
-			<< RM3("") << '\n'
-			<< RM3(" ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA") << '\n'
-			<< RM3("  MAIN-CHAIN BOND              (A**2) : ", 6, 2) << Ff(ls_restr, key("type") == "x_mcbond_it", "dev_ideal") << SEP("; ", 6, 2)
-			<< Ff(ls_restr, key("type") == "x_mcbond_it", "dev_ideal_target") << '\n'
-			<< RM3("  MAIN-CHAIN ANGLE             (A**2) : ", 6, 2) << Ff(ls_restr, key("type") == "x_mcangle_it", "dev_ideal") << SEP("; ", 6, 2)
-			<< Ff(ls_restr, key("type") == "x_mcangle_it", "dev_ideal_target") << '\n'
-			<< RM3("  SIDE-CHAIN BOND              (A**2) : ", 6, 2) << Ff(ls_restr, key("type") == "x_scbond_it", "dev_ideal") << SEP("; ", 6, 2)
-			<< Ff(ls_restr, key("type") == "x_scbond_it", "dev_ideal_target") << '\n'
-			<< RM3("  SIDE-CHAIN ANGLE             (A**2) : ", 6, 2) << Ff(ls_restr, key("type") == "x_scangle_it", "dev_ideal") << SEP("; ", 6, 2)
-			<< Ff(ls_restr, key("type") == "x_scangle_it", "dev_ideal_target") << '\n'
-			<< RM3("") << '\n'
+		<< RM3("") << '\n'
+		<< RM3(" ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA") << '\n'
+		<< RM3("  MAIN-CHAIN BOND              (A**2) : ", 6, 2) << Ff(ls_restr, key("type") == "x_mcbond_it", "dev_ideal") << SEP("; ", 6, 2)
+		<< Ff(ls_restr, key("type") == "x_mcbond_it", "dev_ideal_target") << '\n'
+		<< RM3("  MAIN-CHAIN ANGLE             (A**2) : ", 6, 2) << Ff(ls_restr, key("type") == "x_mcangle_it", "dev_ideal") << SEP("; ", 6, 2)
+		<< Ff(ls_restr, key("type") == "x_mcangle_it", "dev_ideal_target") << '\n'
+		<< RM3("  SIDE-CHAIN BOND              (A**2) : ", 6, 2) << Ff(ls_restr, key("type") == "x_scbond_it", "dev_ideal") << SEP("; ", 6, 2)
+		<< Ff(ls_restr, key("type") == "x_scbond_it", "dev_ideal_target") << '\n'
+		<< RM3("  SIDE-CHAIN ANGLE             (A**2) : ", 6, 2) << Ff(ls_restr, key("type") == "x_scangle_it", "dev_ideal") << SEP("; ", 6, 2)
+		<< Ff(ls_restr, key("type") == "x_scangle_it", "dev_ideal_target") << '\n'
+		<< RM3("") << '\n';
+
+	if (not db["refine_ls_restr_ncs"].empty())
+	{
+		auto ls_restr_ncs = db["refine_ls_restr_ncs"].front();
+
+		pdbFile
 			<< RM3(" NCS MODEL : ") << Fs(ls_restr_ncs, "ncs_model_details") << '\n'
 
 			<< RM3("") << '\n'
@@ -1913,7 +1922,14 @@ void WriteRemark3XPlor(std::ostream &pdbFile, const datablock &db)
 			<< RM3("  GROUP  1  POSITIONAL            (A) : ", 4, 2) << Ff(ls_restr_ncs, "rms_dev_position") << SEP("; ", 6, 2)
 			<< Ff(ls_restr_ncs, "weight_position") << SEP("; ", 6, 2) << '\n'
 			<< RM3("  GROUP  1  B-FACTOR           (A**2) : ", 4, 2) << Ff(ls_restr_ncs, "rms_dev_B_iso") << SEP("; ", 6, 2)
-			<< Ff(ls_restr_ncs, "weight_B_iso") << SEP("; ", 6, 2) << '\n'
+			<< Ff(ls_restr_ncs, "weight_B_iso") << SEP("; ", 6, 2) << '\n';
+	}
+
+	if (not db["pdbx_xplor_file"].empty())
+	{
+		auto pdbx_xplor_file = db["pdbx_xplor_file"].front();
+
+		pdbFile
 
 			// TODO: using only files from serial_no 1 here
 			<< RM3("") << '\n'
@@ -1921,6 +1937,7 @@ void WriteRemark3XPlor(std::ostream &pdbFile, const datablock &db)
 			<< RM3(" TOPOLOGY FILE   1   : ") << Fs(pdbx_xplor_file, "topol_file") << '\n'
 
 			<< RM3("") << '\n';
+	}
 }
 
 void WriteRemark3NuclSQ(std::ostream &pdbFile, const datablock &db)
@@ -2258,25 +2275,28 @@ void WriteRemark200(std::ostream &pdbFile, const datablock &db)
 			std::string iis = cifSoftware(db, eDataReduction);
 			std::string dss = cifSoftware(db, eDataScaling);
 
-			auto source = diffrn_source["source"].get<std::string>();
-			std::string synchrotron, type;
-
-			if (source.empty())
-				synchrotron = "NULL";
-			else if (iequals(source, "SYNCHROTRON"))
+			std::string source, synchrotron, type;
+			if (not diffrn_source.empty())
 			{
-				synchrotron = "Y";
-				source = diffrn_source["pdbx_synchrotron_site"].get<std::string>();
+				source = diffrn_source["source"].get<std::string>();
+	
 				if (source.empty())
-					source = "NULL";
-				type = "NULL";
-			}
-			else
-			{
-				synchrotron = "N";
-				type = diffrn_source["type"].get<std::string>();
-				if (type.empty())
+					synchrotron = "NULL";
+				else if (iequals(source, "SYNCHROTRON"))
+				{
+					synchrotron = "Y";
+					source = diffrn_source["pdbx_synchrotron_site"].get<std::string>();
+					if (source.empty())
+						source = "NULL";
 					type = "NULL";
+				}
+				else
+				{
+					synchrotron = "N";
+					type = diffrn_source["type"].get<std::string>();
+					if (type.empty())
+						type = "NULL";
+				}
 			}
 
 			if (source.empty())
@@ -2343,7 +2363,7 @@ void WriteRemark200(std::ostream &pdbFile, const datablock &db)
 
 			for (auto &t : kTail)
 			{
-				auto s = t.r[t.field].get<std::string>();
+				auto s = t.r.empty() ? "" : t.r[t.field].get<std::string>();
 
 				if (s.empty())
 				{
@@ -2384,6 +2404,9 @@ void WriteRemark280(std::ostream &pdbFile, const datablock &db)
 				<< RM("MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): ", 6, 2) << Ff(exptl_crystal, "density_Matthews") << '\n'
 				<< RM("") << '\n';
 
+			if (exptl_crystal_grow.empty())
+				continue;
+
 			std::vector<std::string> conditions;
 			auto add = [&conditions](const std::string c)
 			{
@@ -3341,9 +3364,9 @@ void WriteCrystallographic(std::ostream &pdbFile, const datablock &db)
 	if (r)
 	{
 		auto symmetry = r["space_group_name_H-M"].get<std::string>();
-	
+
 		r = db["cell"].find_first(key("entry_id") == db.name());
-	
+
 		pdbFile << std::format("CRYST1{:9.3f}{:9.3f}{:9.3f}{:7.2f}{:7.2f}{:7.2f} {:<11.11s}{:4}", r["length_a"].get<double>(), r["length_b"].get<double>(), r["length_c"].get<double>(), r["angle_alpha"].get<double>(), r["angle_beta"].get<double>(), r["angle_gamma"].get<double>(), symmetry, r["Z_PDB"].get<int>()) << '\n';
 	}
 }

src/pdb/pdb2cif.cpp

@@ -2193,7 +2193,7 @@ void PDBFileParser::ParseRemarks()
 							if (std::regex_match(line, m, rx))
 							{
 								models[0] = std::stoi(m[1].str());
-								models[1] = stoi(m[2].str());
+								models[1] = std::stoi(m[2].str());
 							}
 							else
 								headerSeen = cif::contains(line, "RES C SSSEQI");

src/pdb/reconstruct.cpp

@@ -25,6 +25,7 @@
  */
 
 #include "cif++/cif++.hpp"
+#include "cif++/validate.hpp"
 
 #include <algorithm>
 #include <cstddef>
@@ -1340,6 +1341,8 @@ void createPdbxNonpolyScheme(datablock &db)
 	auto &pdbx_nonpoly_scheme = db["pdbx_nonpoly_scheme"];
 	auto &atom_site = db["atom_site"];
 
+	pdbx_nonpoly_scheme.clear();
+
 	for (const auto &[entity_id, comp_id] : pdbx_entity_nonpoly.rows<std::string, std::string>("entity_id", "comp_id"))
 	{
 		for (int ndb_nr = 1; auto row : atom_site.find("label_entity_id"_key == entity_id and "label_comp_id"_key == comp_id))
@@ -1660,7 +1663,7 @@ bool reconstruct_pdbx(file &file, const validator &validator)
 				if (not iv)
 				{
 					// Drop this item
-					cat.remove_item(item_name);
+					// cat.remove_item(item_name);
 					continue;
 				}
 
@@ -1689,6 +1692,13 @@ bool reconstruct_pdbx(file &file, const validator &validator)
 								continue;
 						}
 
+						if (ec == cif::make_error_code(cif::validation_error::value_is_not_in_enumeration_list))
+						{
+							if (VERBOSE > 0)
+								std::clog << "Value (" << std::quoted(row[ix].str()) << ") for item " << item_name << " in category " << cat.name() << " is not valid since it is not in the list of allowed values\n";
+							continue;
+						}
+
 						if (VERBOSE > 0)
 							std::clog << "Replacing value (" << std::quoted(row[ix].str()) << ") for item " << item_name << " in category " << cat.name() << " since it does not validate: " << ec.message() << "\n";
 

src/symmetry.cpp

@@ -24,6 +24,7 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
+#include "cif++/symmetry.hpp"
 #include "cif++/cif++.hpp"
 #include "symop_table_data.hpp"
 
@@ -292,12 +293,7 @@ point spacegroup::operator()(const point &pt, const cell &c, sym_op symop) const
 	t.m_translation.m_y += symop.m_tb - 5;
 	t.m_translation.m_z += symop.m_tc - 5;
 
-	auto fpt = fractional(pt, c);
-	auto o = offsetToOriginFractional(fpt);
-
-	auto spt = t(fpt + o) - o;
-
-	return orthogonal(spt, c);
+	return orthogonal(t(fractional(pt, c)), c);
 }
 
 point spacegroup::inverse(const point &pt, const cell &c, sym_op symop) const
@@ -311,13 +307,8 @@ point spacegroup::inverse(const point &pt, const cell &c, sym_op symop) const
 	t.m_translation.m_y += symop.m_tb - 5;
 	t.m_translation.m_z += symop.m_tc - 5;
 
-	auto fpt = fractional(pt, c);
-	auto o = offsetToOriginFractional(fpt);
-
 	auto it = cif::inverse(t);
-	auto spt = it(fpt + o) - o;
-
-	return orthogonal(spt, c);
+	return orthogonal(it(fractional(pt, c)), c);
 }
 
 // --------------------------------------------------------------------
@@ -462,9 +453,9 @@ std::tuple<float, point, sym_op> crystal::closest_symmetry_copy(point a, point b
 
 	a = orthogonal(fa, m_cell);
 
-	for (std::size_t i = 0; i < m_spacegroup.size(); ++i)
+	for (uint8_t i = 0; std::cmp_less(i, m_spacegroup.size()); ++i)
 	{
-		sym_op s(static_cast<uint8_t>(i + 1));
+		sym_op s(i + 1);
 		auto &t = m_spacegroup[i];
 
 		auto fsb = t(fb);

src/validate.cpp

@@ -27,6 +27,7 @@
 #include "cif++/validate.hpp"
 
 #include "cif++/cif++.hpp"
+#include "cif++/text.hpp"
 
 #include <cassert>
 #include <charconv>
@@ -245,8 +246,17 @@ bool item_validator::validate_value(const item_value &value, std::error_code &ec
 						ec = make_error_code(validation_error::value_does_not_match_rx);
 					}
 
-					if (ec == std::errc{} and not m_enums.empty() and m_enums.count(value.str()) == 0)
-						ec = make_error_code(validation_error::value_is_not_in_enumeration_list);
+					if (ec == std::errc{} and not m_enums.empty())
+					{
+						bool valid =
+							m_type->m_primitive_type == DDL_PrimitiveType::UChar ? //
+								m_enums.contains(cif::to_lower_copy(value.sv()))
+																				 : //
+								m_enums.contains(std::string{ value.sv() });
+
+						if (not valid)
+							ec = make_error_code(validation_error::value_is_not_in_enumeration_list);
+					}
 				}
 			}
 		}
@@ -436,8 +446,8 @@ void validator::report_error(std::error_code ec, bool fatal) const
 		std::cerr << ec.message() << '\n';
 }
 
-void validator::report_error(std::error_code ec, std::string_view category,
-	std::string_view item, bool fatal) const
+void validator::report_error(std::error_code ec, std::string value,
+	std::string_view category, std::string_view item, bool fatal) const
 {
 	if (m_strict or fatal)
 	{
@@ -448,10 +458,19 @@ void validator::report_error(std::error_code ec, std::string_view category,
 	}
 
 	if (VERBOSE > 0)
-		std::cerr << ec.message()
-				  << "; category: " << std::quoted(category)
-				  << " item: " << std::quoted(item)
-				  << '\n';
+	{
+		if (value.empty())
+			std::cerr << ec.message()
+					  << "; category: " << std::quoted(category)
+					  << " item: " << std::quoted(item)
+					  << '\n';
+		else
+			std::cerr << ec.message()
+					  << "; value: " << std::quoted(value)
+					  << "; category: " << std::quoted(category)
+					  << " item: " << std::quoted(item)
+					  << '\n';
+	}
 }
 
 void validator::fill_audit_conform(category &audit_conform) const

test/model-test.cpp

@@ -443,8 +443,6 @@ TEST_CASE("test_alternates_1")
 	const std::filesystem::path example(gTestDir / ".." / "examples" / "1cbs.cif.gz");
 	cif::file file(example.string());
 
-	auto &db = file.front();
-
 	cif::mm::structure s(file);
 
 	for (auto atom : s.atoms())

test/reconstruction-test.cpp

@@ -41,10 +41,6 @@ TEST_CASE("reconstruct")
 
 	for (std::filesystem::directory_iterator i(gTestDir / "reconstruct"); i != std::filesystem::directory_iterator{}; ++i)
 	{
-if (i->path().filename().string() != "9d3j_fixDMC.cif")
-		continue;
-
-
 		std::cout << i->path() << '\n';
 
 		if (i->path().extension() == ".pdb")

test/unit-3d-test.cpp

@@ -25,6 +25,7 @@
  */
 
 #include "cif++/cif++.hpp"
+#include "cif++/symmetry.hpp"
 #include "test-main.hpp"
 
 #include <catch2/catch_test_macros.hpp>
@@ -35,7 +36,7 @@
 # pragma warning(disable : 4127) // conditional expression is constant
 #endif
 
-// #include <Eigen/Eigenvalues>
+#include <Eigen/Eigen>
 
 // --------------------------------------------------------------------
 
@@ -229,102 +230,31 @@ TEST_CASE("dh_q_1")
 	}
 }
 
-/* TEST_CASE("m2q_0a")
-{
-    for (std::size_t i = 0; i < cif::kSymopNrTableSize; ++i)
-    {
-        auto d = cif::kSymopNrTable[i].symop().data();
-
-        Eigen::Matrix3f rot;
-        rot << static_cast<float>(d[0]), static_cast<float>(d[1]), static_cast<float>(d[2]), static_cast<float>(d[3]), static_cast<float>(d[4]), static_cast<float>(d[5]), static_cast<float>(d[6]), static_cast<float>(d[7]), static_cast<float>(d[8]);
-
-        // check to see if this matrix contains a true rotation
-        if (rot * rot.transpose() != Eigen::Matrix3f::Identity() or rot.determinant() != 1)
-            continue;
-
-        Eigen::Quaternionf qe(rot);
-
-        auto q = normalize(cif::quaternion{ qe.w(), qe.x(), qe.y(), qe.z() });
-
-        cif::point p1{ 1, 1, 1 };
-        cif::point p2 = p1;
-        p2.rotate(q);
-
-        cif::matrix3x3<float> rot_c({ static_cast<float>(d[0]),
-            static_cast<float>(d[1]),
-            static_cast<float>(d[2]),
-            static_cast<float>(d[3]),
-            static_cast<float>(d[4]),
-            static_cast<float>(d[5]),
-            static_cast<float>(d[6]),
-            static_cast<float>(d[7]),
-            static_cast<float>(d[8]) });
-
-        cif::point p3 = rot_c * p1;
-
-        CHECK_THAT(p2.m_x, Catch::Matchers::WithinRel(p3.m_x, 0.01f));
-        CHECK_THAT(p2.m_y, Catch::Matchers::WithinRel(p3.m_y, 0.01f));
-        CHECK_THAT(p2.m_z, Catch::Matchers::WithinRel(p3.m_z, 0.01f));
-    }
-}
- */
-
-// "TEST_CASE(m2q_1")
+// TEST_CASE("m2q_1")
 // {
 // 	for (std::size_t i = 0; i < cif::kSymopNrTableSize; ++i)
 // 	{
 // 		auto d = cif::kSymopNrTable[i].symop().data();
 
-// 		cif::matrix3x3<float> rot;
-// 		float Qxx = rot(0, 0) = d[0];
-// 		float Qxy = rot(0, 1) = d[1];
-// 		float Qxz = rot(0, 2) = d[2];
-// 		float Qyx = rot(1, 0) = d[3];
-// 		float Qyy = rot(1, 1) = d[4];
-// 		float Qyz = rot(1, 2) = d[5];
-// 		float Qzx = rot(2, 0) = d[6];
-// 		float Qzy = rot(2, 1) = d[7];
-// 		float Qzz = rot(2, 2) = d[8];
+// 		Eigen::Matrix3f rot;
 
-// 		cif::matrix4x4<float> m({
-// 			Qxx - Qyy - Qzz, Qyx + Qxy, Qzx + Qxz, Qzy - Qyz,
-// 			Qyx + Qxy, Qyy - Qxx - Qzz, Qzy + Qyz, Qxz - Qzx,
-// 			Qzx + Qxz, Qzy + Qyz, Qzz - Qxx - Qyy, Qyx - Qxy,
-// 			Qzy - Qyz, Qxz - Qzx, Qyx - Qxy, Qxx + Qyy + Qzz
-// 		});
+// 		rot << d[0], d[1], d[2], d[3], d[4], d[5], d[6], d[7], d[8];
 
-// 		auto &&[ev, em] = cif::eigen(m * (1/3.0f), false);
-
-// 		std::size_t bestJ = 0;
-// 		float bestEV = -1;
-
-// 		for (std::size_t j = 0; j < 4; ++j)
+// 		if (rot * rot.transpose() == Eigen::Matrix3f::Identity() and rot.determinant() == 1)
 // 		{
-// 			if (bestEV < ev[j])
-// 			{
-// 				bestEV = ev[j];
-// 				bestJ = j;
-// 			}
+// 			Eigen::Quaternionf qe(rot);
+// 			auto q = normalize(cif::quaternion{ qe.w(), qe.x(), qe.y(), qe.z() });
+
+// 			cif::point p1{ 1, 1, 1 };
+// 			cif::point p2 = p1;
+// 			p2.rotate(q);
+
+// 			auto p3 = rot * Eigen::Vector3f{ p1.m_x, p1.m_y, p1.m_z };
+
+// 			CHECK_THAT(p2.m_x, Catch::Matchers::WithinRel(p3[0], 0.01f));
+// 			CHECK_THAT(p2.m_y, Catch::Matchers::WithinRel(p3[1], 0.01f));
+// 			CHECK_THAT(p2.m_z, Catch::Matchers::WithinRel(p3[2], 0.01f));
 // 		}
-
-// 		if (std::abs(bestEV - 1) > 0.01)
-// 			continue; // not a rotation matrix
-
-// 		auto q = normalize(cif::quaternion{
-// 			static_cast<float>(em(bestJ, 3)),
-// 			static_cast<float>(em(bestJ, 0)),
-// 			static_cast<float>(em(bestJ, 1)),
-// 			static_cast<float>(em(bestJ, 2)) });
-
-// 		cif::point p1{ 1, 1, 1 };
-// 		cif::point p2 = p1;
-// 		p2.rotate(q);
-
-// 		cif::point p3 = rot * p1;
-
-// 		REQUIRE(p2.m_x == p3.m_x);
-// 		REQUIRE(p2.m_y == p3.m_y);
-// 		REQUIRE(p2.m_z == p3.m_z);
 // 	}
 // }
 
@@ -394,35 +324,6 @@ TEST_CASE("symm_4")
 
 // --------------------------------------------------------------------
 
-TEST_CASE("symm_4wvp_1")
-{
-	using namespace cif::literals;
-
-	cif::file f(gTestDir / "4wvp.cif.gz");
-	f.front().set_validator(cif::validator_factory::instance().get("mmcif_pdbx.dic"));
-
-	auto &db = f.front();
-	cif::mm::structure s(db);
-
-	cif::crystal c(db);
-
-	cif::point p{ -78.722f, 98.528f, 11.994f };
-	auto a = s.get_residue("A", 10, "").get_atom_by_atom_id("O");
-
-	auto sp1 = c.symmetry_copy(a.get_location(), "2_565"_symop);
-	CHECK_THAT(sp1.m_x, Catch::Matchers::WithinAbs(p.m_x, 0.5f));
-	CHECK_THAT(sp1.m_y, Catch::Matchers::WithinAbs(p.m_y, 0.5f));
-	CHECK_THAT(sp1.m_z, Catch::Matchers::WithinAbs(p.m_z, 0.5f));
-
-	const auto &[d, sp2, so] = c.closest_symmetry_copy(p, a.get_location());
-
-	REQUIRE(d < 1);
-
-	CHECK_THAT(sp2.m_x, Catch::Matchers::WithinAbs(p.m_x, 0.5f));
-	CHECK_THAT(sp2.m_y, Catch::Matchers::WithinAbs(p.m_y, 0.5f));
-	CHECK_THAT(sp2.m_z, Catch::Matchers::WithinAbs(p.m_z, 0.5f));
-}
-
 TEST_CASE("symm_2bi3_1")
 {
 	cif::file f(gTestDir / "2bi3.cif.gz");
@@ -538,6 +439,96 @@ TEST_CASE("symm_3bwh_1")
 	}
 }
 
+TEST_CASE("symm_476d")
+{
+	cif::file f(gTestDir / "476d.cif.gz");
+	f.front().set_validator(cif::validator_factory::instance().get("mmcif_pdbx.dic"));
+
+	auto &db = f.front();
+	cif::mm::structure s(db);
+
+	cif::crystal c(db);
+
+	auto struct_conn = db["struct_conn"];
+	for (const auto &[asym1, seqid1, authseqid1, atomid1, symm1,
+			 asym2, seqid2, authseqid2, atomid2, symm2,
+			 dist] : struct_conn.find<std::string, int, std::string, std::string, std::string,
+			 std::string, int, std::string, std::string, std::string,
+			 float>(
+			 cif::key("ptnr1_symmetry") != "1_555" or cif::key("ptnr2_symmetry") != "1_555",
+			 "ptnr1_label_asym_id", "ptnr1_label_seq_id", "ptnr1_auth_seq_id", "ptnr1_label_atom_id", "ptnr1_symmetry",
+			 "ptnr2_label_asym_id", "ptnr2_label_seq_id", "ptnr2_auth_seq_id", "ptnr2_label_atom_id", "ptnr2_symmetry",
+			 "pdbx_dist_value"))
+	{
+		auto &r1 = s.get_residue(asym1, seqid1, authseqid1);
+		auto &r2 = s.get_residue(asym2, seqid2, authseqid2);
+
+		auto a1 = r1.get_atom_by_atom_id(atomid1);
+		auto a2 = r2.get_atom_by_atom_id(atomid2);
+
+		auto p1 = a1.get_location();
+		auto p2 = a2.get_location();
+
+		cif::sym_op so1(symm1);
+		cif::sym_op so2(symm2);
+
+		auto sa1 = c.symmetry_copy(p1, so1);
+		auto sa2 = c.symmetry_copy(p2, so2);
+
+		CHECK_THAT(cif::distance(sa1, sa2), Catch::Matchers::WithinAbs(dist, 0.01f));
+	}
+}
+
+TEST_CASE("symm-P_32_2_1_a")
+{
+	cif::cell c{ 80, 80, 120, 90, 90, 120 };
+	cif::spacegroup sg{ 154 };
+
+	cif::crystal crystal{ c, sg };
+
+	cif::point a{ 1, 90, 1 };
+	cif::point p1{ 2, 2, 2 };
+
+	auto d = distance(a, p1);
+
+	auto [d2, p, so] = crystal.closest_symmetry_copy(a, p1);
+
+	std::cout << "d: " << d2 << " p: " << p << " so: " << so.string() << '\n';
+
+	auto p2 = crystal.symmetry_copy(p1, so);
+	auto d3 = distance(p2, a);
+
+	CHECK_THAT(cif::distance(p2, p), Catch::Matchers::WithinAbs(0.f, 0.01f));
+	CHECK_THAT(d3, Catch::Matchers::WithinAbs(d2, 0.01f));
+
+	CHECK(d2 <= d);
+}
+
+TEST_CASE("symm-P_32_2_1")
+{
+	cif::cell c{ 82.162, 82.162, 135.202, 90, 90, 120 };
+	cif::spacegroup sg{ 154 };
+
+	cif::crystal crystal{ c, sg };
+
+	cif::point a{ 1.73727,89.1813,11.1388 };
+	cif::point p1{ -8.98574, 50.3861, -11.6447 };
+
+	auto d = distance(a, p1);
+
+	auto [d2, p, so] = crystal.closest_symmetry_copy(a, p1);
+
+	std::cout << "d: " << d2 << " p: " << p << " so: " << so.string() << '\n';
+
+	auto p2 = crystal.symmetry_copy(p1, so);
+	auto d3 = distance(p2, a);
+
+	CHECK_THAT(cif::distance(p2, p), Catch::Matchers::WithinAbs(0.f, 0.01f));
+	CHECK_THAT(d3, Catch::Matchers::WithinAbs(d2, 0.01f));
+
+	CHECK(d2 <= d);
+}
+
 TEST_CASE("volume_3bwh_1")
 {
 	cif::file f(gTestDir / "1juh.cif.gz");

test/unit-v2-test.cpp

@@ -3664,5 +3664,63 @@ HETATM 2 O O . HOH A 1 . ? 10.518 -1.781 0 1 37.22 ? O HOH 2 D 1
 )");
 }
 
+// --------------------------------------------------------------------
 
+TEST_CASE("number-test-1")
+{
+	auto data = R"(data_test
+_pdbx_contact_author.id      1
+_pdbx_contact_author.name_mi +98765432109
+)"_cf;
 
+	auto &db = data.front();
+	db.load_dictionary("mmcif_pdbx.dic");
+
+	auto r = db["pdbx_contact_author"].front();
+	CHECK(r["name_mi"].str() == "+98765432109");
+	CHECK(r["name_mi"].get<int64_t>() == 98765432109);
+	CHECK(r["name_mi"].get<double>() == 98765432109.0);
+}
+
+TEST_CASE("number-test-2")
+{
+	auto data = R"(data_test
+_pdbx_contact_author.id      1
+_pdbx_contact_author.name_mi '+98765432109'
+)"_cf;
+
+	auto &db = data.front();
+	db.load_dictionary("mmcif_pdbx.dic");
+
+	auto r = db["pdbx_contact_author"].front();
+	CHECK(r["name_mi"].str() == "+98765432109");
+	CHECK(r["name_mi"].get<int64_t>() == 98765432109);
+	CHECK(r["name_mi"].get<double>() == 98765432109.0);
+}// --------------------------------------------------------------------
+
+TEST_CASE("q-1")
+{
+	auto data = R"(data_test
+_test.s
+;1234567890
+1234567890
+;
+	)"_cf;
+
+	auto r = data.front()["test"].find(cif::key("s") == "1234567890\n1234567890");
+	CHECK(r.size() == 1);
+}
+
+TEST_CASE("large-int-1")
+{
+	auto data = R"(data_test
+_entry.id     82E4475FF8B27F36
+)"_cf;
+
+	auto &db = data.front();
+	db.load_dictionary("mmcif_pdbx.dic");
+
+	auto r = db["entry"].front();
+
+	CHECK(r["id"].get<std::string>() == "82E4475FF8B27F36");
+}