non-throwing remove_residue

add chem_comp for sugars

include/cif++/model.hpp

@@ -842,10 +842,7 @@ class structure
 	///
 	///
 	/// \param asym_id     The asym ID
 	/// \param asym_id     The asym ID
 	/// \param seq_id      The sequence ID
 	/// \param seq_id      The sequence ID
-	void remove_residue(const std::string &asym_id, int seq_id, const std::string &auth_seq_id)
-	{
-		remove_residue(get_residue(asym_id, seq_id, auth_seq_id));
-	}
+	void remove_residue(const std::string &asym_id, int seq_id, const std::string &auth_seq_id);
 
 
 	/// \brief Create a new non-polymer entity, returns new ID
 	/// \brief Create a new non-polymer entity, returns new ID
 	/// \param mon_id	The mon_id for the new nonpoly, must be an existing and known compound from CCD
 	/// \param mon_id	The mon_id for the new nonpoly, must be an existing and known compound from CCD

src/model.cpp

@@ -1222,6 +1222,22 @@ sugar &branch::construct_sugar(const std::string &compound_id)
 {
 {
 	auto &db = m_structure->get_datablock();
 	auto &db = m_structure->get_datablock();
 
 
+	auto compound = compound_factory::instance().create(compound_id);
+	if (compound == nullptr)
+		throw std::runtime_error("Trying to insert unknown compound " + compound_id + " (not found in CCD)");
+
+	auto &chemComp = db["chem_comp"];
+	auto r = chemComp.find(key("id") == compound_id);
+	if (r.empty())
+	{
+		chemComp.emplace({
+			{"id", compound_id},
+			{"name", compound->name()},
+			{"formula", compound->formula()},
+			{"formula_weight", compound->formula_weight()},
+			{"type", compound->type()}});
+	}
+
 	sugar &result = emplace_back(*this, compound_id, m_asym_id, size() + 1);
 	sugar &result = emplace_back(*this, compound_id, m_asym_id, size() + 1);
 
 
 	db["pdbx_branch_scheme"].emplace({
 	db["pdbx_branch_scheme"].emplace({
@@ -2017,6 +2033,51 @@ void structure::change_residue(residue &res, const std::string &newCompound,
 	}
 	}
 }
 }
 
 
+void structure::remove_residue(const std::string &asym_id, int seq_id, const std::string &auth_seq_id)
+{
+	if (seq_id == 0)
+	{
+		for (auto &res : m_non_polymers)
+		{
+			if (res.get_asym_id() == asym_id and (auth_seq_id.empty() or res.get_auth_seq_id() == auth_seq_id))
+			{
+				remove_residue(res);
+				return;
+			}
+		}
+	}
+
+	for (auto &poly : m_polymers)
+	{
+		if (poly.get_asym_id() != asym_id)
+			continue;
+
+		for (auto &res : poly)
+		{
+			if (res.get_seq_id() == seq_id)
+			{
+				remove_residue(res);
+				return;
+			}
+		}
+	}
+
+	for (auto &branch : m_branches)
+	{
+		if (branch.get_asym_id() != asym_id)
+			continue;
+
+		for (auto &sugar : branch)
+		{
+			if (sugar.get_asym_id() == asym_id and sugar.get_auth_seq_id() == auth_seq_id)
+			{
+				remove_residue(sugar);
+				return;
+			}
+		}
+	}
+}
+
 void structure::remove_residue(residue &res)
 void structure::remove_residue(residue &res)
 {
 {
 	using namespace literals;
 	using namespace literals;