reconstruction fixes

src/datablock.cpp

@@ -282,7 +282,11 @@ void datablock::write(std::ostream &os) const
 		cat_order_t cat_order;
 		cat_order_t cat_order;
 
 
 		for (auto &cat : *this)
 		for (auto &cat : *this)
+		{
+			if (cat.name() == "entry" or cat.name() == "audit_conform")
+				continue;
 			cat_order.emplace_back(cat.name(), -1, false);
 			cat_order.emplace_back(cat.name(), -1, false);
+		}
 
 
 		for (auto i = cat_order.begin(); i != cat_order.end(); ++i)
 		for (auto i = cat_order.begin(); i != cat_order.end(); ++i)
 			calculate_cat_order(cat_order, i, *m_validator);
 			calculate_cat_order(cat_order, i, *m_validator);
@@ -292,25 +296,18 @@ void datablock::write(std::ostream &os) const
 			const auto &[cat_a, count_a, on_stack_a] = a;
 			const auto &[cat_a, count_a, on_stack_a] = a;
 			const auto &[cat_b, count_b, on_stack_b] = b;
 			const auto &[cat_b, count_b, on_stack_b] = b;
 
 
-			int d = 0;
-
-			if (cat_a == "audit_conform")
-				d = -1;
-			else if (cat_b == "audit_conform")
-				d = 1;
-			else if (cat_a == "entry")
-				d = -1;
-			else if (cat_b == "entry")
-				d = 1;
-			else
-			{
-				d = std::get<1>(a) - std::get<1>(b);
-				if (d == 0)
-					d = cat_b.compare(cat_a);
-			}
+			int d = std::get<1>(a) - std::get<1>(b);
+			if (d == 0)
+				d = cat_b.compare(cat_a);
 
 
 			return d < 0; });
 			return d < 0; });
 
 
+		if (auto entry = get("entry"); entry != nullptr)
+			entry->write(os);
+
+		if (auto audit_conform = get("audit_conform"); audit_conform != nullptr)
+			audit_conform->write(os);
+
 		for (auto &&[cat, count, on_stack] : cat_order)
 		for (auto &&[cat, count, on_stack] : cat_order)
 			get(cat)->write(os);
 			get(cat)->write(os);
 	}
 	}
@@ -320,20 +317,13 @@ void datablock::write(std::ostream &os) const
 		// and if it exists, _AND_ we have a Validator, write out the
 		// and if it exists, _AND_ we have a Validator, write out the
 		// audit_conform record.
 		// audit_conform record.
 
 
-		for (auto &cat : *this)
-		{
-			if (cat.name() != "entry")
-				continue;
-
-			cat.write(os);
-
-			break;
-		}
+		if (auto entry = get("entry"); entry != nullptr)
+			entry->write(os);
 
 
 		// If the dictionary declares an audit_conform category, put it in,
 		// If the dictionary declares an audit_conform category, put it in,
 		// but only if it does not exist already!
 		// but only if it does not exist already!
-		if (get("audit_conform"))
-			get("audit_conform")->write(os);
+		if (auto audit_conform = get("audit_conform"); audit_conform != nullptr)
+			audit_conform->write(os);
 
 
 		for (auto &cat : *this)
 		for (auto &cat : *this)
 		{
 		{
@@ -348,7 +338,7 @@ void datablock::write(std::ostream &os, const std::vector<std::string> &item_nam
 	os << "data_" << m_name << '\n'
 	os << "data_" << m_name << '\n'
 	   << "# \n";
 	   << "# \n";
 
 
-	std::vector<std::string> cat_order;
+	std::vector<std::string> cat_order{ "entry", "audit_conform" };
 	for (auto &o : item_name_order)
 	for (auto &o : item_name_order)
 	{
 	{
 		std::string cat_name, item_name;
 		std::string cat_name, item_name;
@@ -360,6 +350,9 @@ void datablock::write(std::ostream &os, const std::vector<std::string> &item_nam
 
 
 	for (auto &c : cat_order)
 	for (auto &c : cat_order)
 	{
 	{
+		if (c == "entry" or c == "audit_conform")
+			continue;
+
 		auto cat = get(c);
 		auto cat = get(c);
 		if (cat == nullptr)
 		if (cat == nullptr)
 			continue;
 			continue;

src/pdb/reconstruct.cpp

@@ -386,12 +386,16 @@ void checkAtomRecords(datablock &db)
 
 
 		auto chem_comp_entry = chem_comp.find_first("id"_key == comp_id);
 		auto chem_comp_entry = chem_comp.find_first("id"_key == comp_id);
 
 
+		std::optional<bool> non_std;
+		if  (cf.is_monomer(comp_id))
+			non_std = cf.is_std_monomer(comp_id);
+
 		if (not chem_comp_entry)
 		if (not chem_comp_entry)
 		{
 		{
 			chem_comp.emplace({ //
 			chem_comp.emplace({ //
 				{ "id", comp_id },
 				{ "id", comp_id },
 				{ "type", compound->type() },
 				{ "type", compound->type() },
-				{ "mon_nstd_flag", cf.is_std_monomer(comp_id) ? "y" : "n" },
+				{ "mon_nstd_flag", non_std },
 				{ "name", compound->name() },
 				{ "name", compound->name() },
 				{ "formula", compound->formula() },
 				{ "formula", compound->formula() },
 				{ "formula_weight", compound->formula_weight() } });
 				{ "formula_weight", compound->formula_weight() } });
@@ -402,8 +406,8 @@ void checkAtomRecords(datablock &db)
 
 
 			if (not chem_comp_entry["type"])
 			if (not chem_comp_entry["type"])
 				items.emplace_back(item{ "type", compound->type() });
 				items.emplace_back(item{ "type", compound->type() });
-			if (not chem_comp_entry["mon_nstd_flag"])
-				items.emplace_back(item{ "mon_nstd_flag", cf.is_std_monomer(comp_id) ? "y" : "n" });
+			if (not chem_comp_entry["mon_nstd_flag"] and non_std.has_value())
+				items.emplace_back(item{ "mon_nstd_flag", non_std });
 			if (not chem_comp_entry["name"])
 			if (not chem_comp_entry["name"])
 				items.emplace_back(item{ "name", compound->name() });
 				items.emplace_back(item{ "name", compound->name() });
 			if (not chem_comp_entry["formula"])
 			if (not chem_comp_entry["formula"])