fix cif::item constructor

fix ordering atoms

include/cif++/item.hpp

@@ -378,7 +378,7 @@ struct item_handle
 	template <typename T>
 	template <typename T>
 	item_handle &operator=(T &&value)
 	item_handle &operator=(T &&value)
 	{
 	{
-		assign_value(item{ "", std::move(value) }.value());
+		assign_value(item{ "", std::forward<T>(value) }.value());
 		return *this;
 		return *this;
 	}
 	}
 
 

src/model.cpp

@@ -2886,7 +2886,7 @@ static int compare_numbers(std::string_view a, std::string_view b)
 	ra = selected_charconv<double>::from_chars(a.data(), a.data() + a.length(), da);
 	ra = selected_charconv<double>::from_chars(a.data(), a.data() + a.length(), da);
 	rb = selected_charconv<double>::from_chars(b.data(), b.data() + b.length(), db);
 	rb = selected_charconv<double>::from_chars(b.data(), b.data() + b.length(), db);
 
 
-	if (not (bool)ra.ec and not (bool)rb.ec)
+	if (not(bool) ra.ec and not(bool) rb.ec)
 	{
 	{
 		auto d = da - db;
 		auto d = da - db;
 		if (std::abs(d) > std::numeric_limits<double>::epsilon())
 		if (std::abs(d) > std::numeric_limits<double>::epsilon())
@@ -2901,7 +2901,7 @@ static int compare_numbers(std::string_view a, std::string_view b)
 		result = 1;
 		result = 1;
 	else
 	else
 		result = -1;
 		result = -1;
-	
+
 	return result;
 	return result;
 }
 }
 
 
@@ -2910,26 +2910,51 @@ void structure::reorder_atoms()
 	auto &atom_site = m_db["atom_site"];
 	auto &atom_site = m_db["atom_site"];
 
 
 	atom_site.sort([](row_handle a, row_handle b)
 	atom_site.sort([](row_handle a, row_handle b)
-	{
-		int d;
+		{
+			int d;
 
 
-		// First by model number
-		d = a.get<int>("pdbx_PDB_model_num") - b.get<int>("pdbx_PDB_model_num");
-		if (d == 0)
-			d = a.get<std::string>("label_asym_id").compare(b.get<std::string>("label_asym_id"));
-		if (d == 0)
-			d = a.get<int>("label_seq_id") - b.get<int>("label_seq_id");
-		if (d == 0)
-			d = compare_numbers(a.get<std::string>("id"), b.get<std::string>("id"));
+			// First by model number
+			d = a.get<int>("pdbx_PDB_model_num") - b.get<int>("pdbx_PDB_model_num");
+			if (d == 0)
+				d = a.get<std::string>("label_asym_id").compare(b.get<std::string>("label_asym_id"));
+			if (d == 0)
+			{
+				auto na = a.get<std::optional<int>>("label_seq_id");
+				auto nb = b.get<std::optional<int>>("label_seq_id");
+
+				if (na.has_value() and nb.has_value())
+					d = *na - *nb;
+				else if (na.has_value())
+					d = 1;
+				else if (nb.has_value())
+					d = -1;
+			}
 
 
-		return d;
-	});
+			if (d == 0)
+			{
+				auto na = a.get<std::optional<int>>("auth_seq_id");
+				auto nb = b.get<std::optional<int>>("auth_seq_id");
+
+				if (na.has_value() and nb.has_value())
+					d = *na - *nb;
+				else if (na.has_value())
+					d = 1;
+				else if (nb.has_value())
+					d = -1;
+			}
+
+			if (d == 0)
+				d = compare_numbers(a.get<std::string>("id"), b.get<std::string>("id"));
+
+			return d;
+			//
+		});
 
 
 	// atom_site.set_validator(nullptr, m_db);
 	// atom_site.set_validator(nullptr, m_db);
 
 
 	// for (int nr = 1; auto r : atom_site)
 	// for (int nr = 1; auto r : atom_site)
 	// 	r["id"] = nr++;
 	// 	r["id"] = nr++;
-	
+
 	// atom_site.set_validator(m_db.get_validator(), m_db);
 	// atom_site.set_validator(m_db.get_validator(), m_db);
 }
 }
 
 

src/pdb/reconstruct.cpp

@@ -590,18 +590,18 @@ void checkAtomAnisotropRecords(datablock &db)
 			row["type_symbol"] = parent["type_symbol"].text();
 			row["type_symbol"] = parent["type_symbol"].text();
 		}
 		}
 
 
-		if (row["pdbx_auth_alt_id"].empty())
+		if (row["pdbx_auth_alt_id"].empty() and not parent["pdbx_auth_alt_id"].empty())
 			row["pdbx_auth_alt_id"] = parent["pdbx_auth_alt_id"].text();
 			row["pdbx_auth_alt_id"] = parent["pdbx_auth_alt_id"].text();
-		if (row["pdbx_label_seq_id"].empty())
+		if (row["pdbx_label_seq_id"].empty() and not parent["pdbx_label_seq_id"].empty())
 			row["pdbx_label_seq_id"] = parent["label_seq_id"].text();
 			row["pdbx_label_seq_id"] = parent["label_seq_id"].text();
-		if (row["pdbx_label_asym_id"].empty())
+		if (row["pdbx_label_asym_id"].empty() and not parent["pdbx_label_asym_id"].empty())
 			row["pdbx_label_asym_id"] = parent["label_asym_id"].text();
 			row["pdbx_label_asym_id"] = parent["label_asym_id"].text();
-		if (row["pdbx_label_atom_id"].empty())
+		if (row["pdbx_label_atom_id"].empty() and not parent["pdbx_label_atom_id"].empty())
 			row["pdbx_label_atom_id"] = parent["label_atom_id"].text();
 			row["pdbx_label_atom_id"] = parent["label_atom_id"].text();
-		if (row["pdbx_label_comp_id"].empty())
+		if (row["pdbx_label_comp_id"].empty() and not parent["pdbx_label_comp_id"].empty())
 			row["pdbx_label_comp_id"] = parent["label_comp_id"].text();
 			row["pdbx_label_comp_id"] = parent["label_comp_id"].text();
-		if (row["pdbx_PDB_model_num"].empty())
-			row["pdbx_PDB_model_num"] = parent["pdbx_PDB_model_num"].text();
+		// if (row["pdbx_PDB_model_num"].empty() and not parent["pdbx_PDB_model_num"].empty())
+		// 	row["pdbx_PDB_model_num"] = parent["pdbx_PDB_model_num"].text();
 	}
 	}
 
 
 	if (not to_be_deleted.empty())
 	if (not to_be_deleted.empty())