Fix equals in condition_impl, columns might be unknown

include/cif++/condition.hpp

@@ -215,7 +215,8 @@ namespace detail
 				if (m_single_hit.has_value() or ri->m_single_hit.has_value())
 				if (m_single_hit.has_value() or ri->m_single_hit.has_value())
 					return m_single_hit == ri->m_single_hit;
 					return m_single_hit == ri->m_single_hit;
 				else
 				else
-					return m_item_ix == ri->m_item_ix and m_value == ri->m_value;
+					// watch out, both m_item_ix might be the same while tags might be diffent (in case they both do not exist in the category)
+					return m_item_ix == ri->m_item_ix and m_value == ri->m_value and m_item_tag == ri->m_item_tag;
 			}
 			}
 			return this == rhs;
 			return this == rhs;
 		}
 		}
@@ -272,7 +273,8 @@ namespace detail
 				if (m_single_hit.has_value() or ri->m_single_hit.has_value())
 				if (m_single_hit.has_value() or ri->m_single_hit.has_value())
 					return m_single_hit == ri->m_single_hit;
 					return m_single_hit == ri->m_single_hit;
 				else
 				else
-					return m_item_ix == ri->m_item_ix and m_value == ri->m_value;
+					// watch out, both m_item_ix might be the same while tags might be diffent (in case they both do not exist in the category)
+					return m_item_ix == ri->m_item_ix and m_value == ri->m_value and m_item_tag == ri->m_item_tag;
 			}
 			}
 			return this == rhs;
 			return this == rhs;
 		}
 		}

include/cif++/model.hpp

@@ -408,6 +408,8 @@ class residue
 	{
 	{
 	}
 	}
 
 
+	residue(const structure &structure, const std::vector<atom> &atoms);
+
 	residue(const residue &rhs) = delete;
 	residue(const residue &rhs) = delete;
 	residue &operator=(const residue &rhs) = delete;
 	residue &operator=(const residue &rhs) = delete;
 
 
@@ -763,6 +765,9 @@ class structure
 	/// \brief Return the atom closest to point \a p with atom type \a type in a residue of type \a res_type
 	/// \brief Return the atom closest to point \a p with atom type \a type in a residue of type \a res_type
 	atom get_atom_by_position_and_type(point p, std::string_view type, std::string_view res_type) const;
 	atom get_atom_by_position_and_type(point p, std::string_view type, std::string_view res_type) const;
 
 
+	/// \brief Create a non-poly residue based on atoms already present in this structure.
+	residue &create_residue(const std::vector<atom> &atoms);
+
 	/// \brief Get a non-poly residue for an asym with id \a asymID
 	/// \brief Get a non-poly residue for an asym with id \a asymID
 	residue &get_residue(const std::string &asymID)
 	residue &get_residue(const std::string &asymID)
 	{
 	{
@@ -898,7 +903,7 @@ class structure
 	void load_atoms_for_model(StructureOpenOptions options);
 	void load_atoms_for_model(StructureOpenOptions options);
 
 
 	template <typename... Args>
 	template <typename... Args>
-	atom &emplace_atom(Args... args)
+	atom &emplace_atom(Args&... args)
 	{
 	{
 		return emplace_atom(atom{ std::forward<Args>(args)... });
 		return emplace_atom(atom{ std::forward<Args>(args)... });
 	}
 	}

src/condition.cpp

@@ -63,7 +63,7 @@ namespace detail
 
 
 	condition_impl *key_equals_condition_impl::prepare(const category &c)
 	condition_impl *key_equals_condition_impl::prepare(const category &c)
 	{
 	{
-		m_item_ix = get_column_ix(c, m_item_tag);
+		m_item_ix = c.get_column_ix(m_item_tag);
 		m_icase = is_column_type_uchar(c, m_item_tag);
 		m_icase = is_column_type_uchar(c, m_item_tag);
 
 
 		if (c.get_cat_validator() != nullptr and
 		if (c.get_cat_validator() != nullptr and

src/model.cpp

@@ -305,6 +305,25 @@ std::ostream &operator<<(std::ostream &os, const atom &atom)
 // --------------------------------------------------------------------
 // --------------------------------------------------------------------
 // residue
 // residue
 
 
+residue::residue(const structure &structure, const std::vector<atom> &atoms)
+	: m_structure(&structure)
+{
+	if (atoms.empty())
+		throw std::runtime_error("Empty list of atoms");
+	
+	auto &a = atoms.front();
+
+	m_compound_id = a.get_label_comp_id();
+	m_asym_id = a.get_label_asym_id();
+	m_seq_id = a.get_label_seq_id();
+	m_auth_asym_id = a.get_auth_asym_id();
+	m_auth_seq_id = a.get_auth_seq_id();
+	m_pdb_ins_code = a.get_pdb_ins_code();
+
+	for (auto atom : atoms)
+		m_atoms.push_back(atom);
+}
+
 // residue::residue(residue &&rhs)
 // residue::residue(residue &&rhs)
 // 	: m_structure(rhs.m_structure)
 // 	: m_structure(rhs.m_structure)
 // 	, m_compound_id(std::move(rhs.m_compound_id))
 // 	, m_compound_id(std::move(rhs.m_compound_id))
@@ -1514,6 +1533,11 @@ polymer &structure::get_polymer_by_asym_id(const std::string &asym_id)
 	throw std::runtime_error("polymer with asym id " + asym_id + " not found");
 	throw std::runtime_error("polymer with asym id " + asym_id + " not found");
 }
 }
 
 
+residue &structure::create_residue(const std::vector<atom> &atoms)
+{
+	return m_non_polymers.emplace_back(*this, atoms);
+}
+
 residue &structure::get_residue(const std::string &asym_id, int seqID, const std::string &authSeqID)
 residue &structure::get_residue(const std::string &asym_id, int seqID, const std::string &authSeqID)
 {
 {
 	if (seqID == 0)
 	if (seqID == 0)