Clear pdbx_nonpoly_scheme before filling it in reconstruction

CMakeLists.txt

@@ -34,7 +34,7 @@ endif()
 # set the project name
 project(
     libcifpp
-    VERSION 10.0.2
+    VERSION 10.0.3
     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 +1,11 @@
+Version 10.0.3
+- Clear pdbx_nonpoly_scheme before filling it in reconstruction
+
 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++/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

@@ -749,16 +749,38 @@ 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
+					try
+					{
+						v.cast_to_int();
+					}
+					catch (...)
+					{
+						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 +912,13 @@ 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 +1474,12 @@ 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 +1606,18 @@ 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 +1829,12 @@ 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 +2204,7 @@ 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/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/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/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

@@ -1340,6 +1340,8 @@ 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))

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");