Fixes for deuterium...

Fixes for sugar branches

include/cif++/atom_type.hpp

@@ -166,7 +166,7 @@ enum atom_type : uint8_t
 	No = 102, // Nobel­ium
 	Lr = 103, // Lawren­cium
 
-	D = 129, // Deuterium
+	D = 119, // Deuterium
 };
 
 // --------------------------------------------------------------------

include/cif++/symmetry.hpp

@@ -81,6 +81,11 @@ struct symop_data
 		return m_packed == rhs.m_packed;
 	}
 
+	bool operator<(const symop_data &rhs) const
+	{
+		return m_packed < rhs.m_packed;
+	}
+
 	std::array<int, 15> data() const
 	{
 		return {

src/atom_type.cpp

@@ -1077,9 +1077,13 @@ bool atom_type_traits::is_metal(const std::string& symbol)
 
 auto atom_type_traits::wksf(int charge) const -> const SFData&
 {
+	auto type = m_info->type;
+	if (type == D)
+		type = H;
+
 	for (auto& sf: data::kWKSFData)
 	{
-		if (sf.symbol == m_info->type and sf.charge == charge)
+		if (sf.symbol == type and sf.charge == charge)
 			return sf.sf;
 	}
 
@@ -1092,7 +1096,7 @@ auto atom_type_traits::wksf(int charge) const -> const SFData&
 
 		for (auto& sf: data::kWKSFData)
 		{
-			if (sf.symbol == m_info->type and sf.charge == 0)
+			if (sf.symbol == type and sf.charge == 0)
 				return sf.sf;
 		}
 	}
@@ -1102,9 +1106,13 @@ auto atom_type_traits::wksf(int charge) const -> const SFData&
 	
 auto atom_type_traits::elsf() const -> const SFData&
 {
+	auto type = m_info->type;
+	if (type == D)
+		type = H;
+
 	for (auto& sf: data::kELSFData)
 	{
-		if (sf.symbol == m_info->type)
+		if (sf.symbol == type)
 			return sf.sf;
 	}
 

src/model.cpp

@@ -1118,8 +1118,8 @@ branch::branch(structure &structure, const std::string &asym_id)
 		for (const auto &[num1, num2, atom1, atom2] : branch_link.find<size_t, size_t, std::string, std::string>(
 				 "entity_id"_key == entity_id, "entity_branch_list_num_1", "entity_branch_list_num_2", "atom_id_1", "atom_id_2"))
 		{
-			if (not iequals(atom1, "c1"))
-				throw std::runtime_error("invalid pdbx_entity_branch_link");
+			// if (not iequals(atom1, "c1"))
+			// 	throw std::runtime_error("invalid pdbx_entity_branch_link");
 
 			auto &s1 = at(num1 - 1);
 			auto &s2 = at(num2 - 1);
@@ -1143,8 +1143,8 @@ void branch::link_atoms()
 	for (const auto &[num1, num2, atom1, atom2] : branch_link.find<size_t, size_t, std::string, std::string>(
 			 "entity_id"_key == entity_id, "entity_branch_list_num_1", "entity_branch_list_num_2", "atom_id_1", "atom_id_2"))
 	{
-		if (not iequals(atom1, "c1"))
-			throw std::runtime_error("invalid pdbx_entity_branch_link");
+		// if (not iequals(atom1, "c1"))
+		// 	throw std::runtime_error("invalid pdbx_entity_branch_link");
 
 		auto &s1 = at(num1 - 1);
 		auto &s2 = at(num2 - 1);
@@ -1279,7 +1279,7 @@ void structure::load_atoms_for_model(StructureOpenOptions options)
 		if (model_nr and *model_nr != m_model_nr)
 			continue;
 
-		if ((options bitand StructureOpenOptions::SkipHydrogen) and type_symbol == "H")
+		if ((options bitand StructureOpenOptions::SkipHydrogen) and (type_symbol == "H" or type_symbol == "D"))
 			continue;
 
 		emplace_atom(std::make_shared<atom::atom_impl>(m_db, id));