All tests pass

.gitignore

@@ -12,4 +12,6 @@ CMakeSettings.json
 msvc/
 Testing/
 rsrc/feature-request.txt
-test/test-create_sugar_2.cif
+test/test-create_sugar_?.cif
+test/oprofile_data/abi
+test/oprofile_data/samples/operf.log

include/cif++/condition.hpp

@@ -358,6 +358,9 @@ namespace detail
 		std::regex mRx;
 	};
 
+	// TODO: Optimize and_condition by having a list of sub items.
+	// That way you can also collapse multiple _is_ conditions in
+	// case they make up an indexed tuple.
 	struct and_condition_impl : public condition_impl
 	{
 		and_condition_impl(condition &&a, condition &&b)

include/cif++/model.hpp

@@ -609,7 +609,10 @@ class sugar : public residue
 
 	size_t get_link_nr() const
 	{
-		return m_link ? std::stoi(m_link.get_auth_seq_id()) : 0;
+		size_t result = 0;
+		if (m_link)
+			result = m_link.get_property_int("auth_seq_id");
+		return result;
 	}
 
   private:

include/cif++/row.hpp

@@ -307,6 +307,11 @@ class row_initializer : public std::vector<item>
 	row_initializer(row_handle rh);
 
 	void set_value(std::string_view name, std::string_view value);
+	void set_value(item &&i)
+	{
+		set_value(i.name(), i.value());
+	}
+
 	void set_value_if_empty(std::string_view name, std::string_view value);
 	void set_value_if_empty(item &&i)
 	{

src/category.cpp

@@ -986,6 +986,11 @@ condition category::get_children_condition(row_handle rh, const category &childC
 
 	condition result;
 
+	iset mandatoryChildFields;
+	auto childCatValidator = m_validator->get_validator_for_category(childCat.name());
+	if (childCatValidator != nullptr)
+		mandatoryChildFields = childCatValidator->m_mandatory_fields;
+
 	for (auto &link : m_validator->get_links_for_parent(m_name))
 	{
 		if (link->m_child_category != childCat.m_name)
@@ -1002,14 +1007,13 @@ condition category::get_children_condition(row_handle rh, const category &childC
 
 			if (parentValue.empty())
 				cond = std::move(cond) and key(childKey) == null;
+			else if (link->m_parent_keys.size() > 1 and not mandatoryChildFields.contains(childKey))
+				cond = std::move(cond) and (key(childKey) == parentValue.text() or key(childKey) == null);
 			else
 				cond = std::move(cond) and key(childKey) == parentValue.text();
 		}
 
-		if (result)
 		result = std::move(result) or std::move(cond);
-		else
-			result = std::move(cond);
 	}
 
 	return result;

src/file.cpp

@@ -48,6 +48,9 @@ bool file::is_valid() const
 	for (auto &d : *this)
 		result = d.is_valid() and result;
 
+	if (result)
+		result = validate_links();
+
 	return result;
 }
 
@@ -203,6 +206,9 @@ void file::save(const std::filesystem::path &p) const
 
 void file::save(std::ostream &os) const
 {
+	if (not is_valid())
+		std::cout << "File is not valid!" << std::endl;
+
 	for (auto &db : *this)
 		db.write(os);
 }

src/model.cpp

@@ -1859,11 +1859,9 @@ void structure::change_residue(residue &res, const std::string &newCompound,
 		// create a copy of the entity first
 		auto &entity = m_db["entity"];
 
-		try
-		{
 		entityID = entity.find1<std::string>("type"_key == "non-polymer" and "pdbx_description"_key == compound->name(), "id");
-		}
-		catch (const std::exception &ex)
+
+		if (entityID.empty())
 		{
 			entityID = entity.get_unique_id("");
 			entity.emplace({{"id", entityID},
@@ -1881,6 +1879,7 @@ void structure::change_residue(residue &res, const std::string &newCompound,
 		for (auto nps : pdbxNonPolyScheme.find("asym_id"_key == asym_id))
 		{
 			nps.assign("mon_id", newCompound, true);
+			nps.assign("pdb_mon_id", newCompound, true);
 			nps.assign("auth_mon_id", newCompound, true);
 			nps.assign("entity_id", entityID, true);
 		}
@@ -2192,13 +2191,13 @@ std::string structure::create_non_poly(const std::string &entity_id, std::vector
 
 		atom.set_value("name", atom_id);
 		atom.set_value("label_asym_id", asym_id);
+		atom.set_value("auth_asym_id", asym_id);
+		atom.set_value("label_entity_id", entity_id);
 
 		atom.set_value_if_empty({"group_PDB", "HETATM"});
 		atom.set_value_if_empty({"label_comp_id", comp_id});
 		atom.set_value_if_empty({"label_seq_id", ""});
-		atom.set_value_if_empty({"label_entity_id", entity_id});
 		atom.set_value_if_empty({"auth_comp_id", comp_id});
-		atom.set_value_if_empty({"auth_asym_id", asym_id});
 		atom.set_value_if_empty({"auth_seq_id", 1});
 		atom.set_value_if_empty({"pdbx_PDB_model_num", 1});
 		atom.set_value_if_empty({"label_alt_id", ""});
@@ -2256,14 +2255,14 @@ branch &structure::create_branch(std::vector<row_initializer> atoms)
 
 		atom.set_value("id", atom_id);
 		atom.set_value("label_asym_id", asym_id);
+		atom.set_value("auth_asym_id", asym_id);
+		atom.set_value("label_entity_id", tmp_entity_id);
+		atom.set_value({ "auth_seq_id", 1 });
 
 		atom.set_value_if_empty({"group_PDB", "HETATM"});
 		atom.set_value_if_empty({"label_comp_id", "NAG"});
 		atom.set_value_if_empty({"label_seq_id", "."});
-		atom.set_value_if_empty({"label_entity_id", tmp_entity_id});
 		atom.set_value_if_empty({"auth_comp_id", "NAG"});
-		atom.set_value_if_empty({"auth_asym_id", asym_id});
-		atom.set_value_if_empty({"auth_seq_id", 1});
 		atom.set_value_if_empty({"pdbx_PDB_model_num", 1});
 		atom.set_value_if_empty({"label_alt_id", ""});
 
@@ -2353,12 +2352,13 @@ branch &structure::extend_branch(const std::string &asym_id, std::vector<row_ini
 
 		atom.set_value("id", atom_id);
 		atom.set_value("label_asym_id", asym_id);
+		atom.set_value("auth_asym_id", asym_id);
+		atom.set_value("label_entity_id", tmp_entity_id);
+		atom.set_value({"auth_seq_id", sugarNum });
 
 		atom.set_value_if_empty({"group_PDB", "HETATM"});
 		atom.set_value_if_empty({"label_comp_id", compoundID});
-		atom.set_value_if_empty({"label_entity_id", tmp_entity_id});
 		atom.set_value_if_empty({"auth_comp_id", compoundID});
-		atom.set_value_if_empty({"auth_asym_id", asym_id});
 		atom.set_value_if_empty({"pdbx_PDB_model_num", 1});
 		atom.set_value_if_empty({"label_alt_id", ""});
 

test/rename-compound-test.cpp

@@ -58,6 +58,11 @@ int main(int argc, char* argv[])
 		structure.cleanup_empty_categories();
 
 		f.save(std::cout);
+
+		if (not f.is_valid())
+			throw std::runtime_error("Invalid");
+
+		f.save(std::cout);
 	}
 	catch (const std::exception& e)
 	{

test/sugar-test.cpp

@@ -135,6 +135,10 @@ BOOST_AUTO_TEST_CASE(create_sugar_1)
 	BOOST_CHECK_EQUAL(branch.size(), 1);
 
 	BOOST_CHECK_EQUAL(branch[0].atoms().size(), nagAtoms.size());
+
+	BOOST_CHECK(file.is_valid());
+
+	file.save(gTestDir / "test-create_sugar_1.cif");
 }
 
 // --------------------------------------------------------------------
@@ -170,12 +174,18 @@ BOOST_AUTO_TEST_CASE(create_sugar_2)
 
 	s.remove_branch(bH);
 
+	file.save(gTestDir / "test-create_sugar_2-0.cif");
+
+	BOOST_CHECK(file.is_valid());
+
 	auto &bN = s.create_branch(ai[0]);
 	s.extend_branch(bN.get_asym_id(), ai[1], 1, "O4");
 
 	BOOST_CHECK_EQUAL(bN.name(), "2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose");
 	BOOST_CHECK_EQUAL(bN.size(), 2);
 
+	BOOST_CHECK(file.is_valid());
+
 	file.save(gTestDir / "test-create_sugar_2.cif");
 
 	BOOST_CHECK_NO_THROW(cif::mm::structure s2(file));
@@ -205,6 +215,8 @@ BOOST_AUTO_TEST_CASE(delete_sugar_1)
 	BOOST_CHECK_EQUAL(bN.name(), "2-acetamido-2-deoxy-beta-D-glucopyranose");
 	BOOST_CHECK_EQUAL(bN.size(), 1);
 
+	BOOST_CHECK(file.is_valid());
+
 	file.save(gTestDir / "test-create_sugar_3.cif");
 
 	BOOST_CHECK_NO_THROW(cif::mm::structure s2(file));

test/unit-v2-test.cpp

@@ -1037,12 +1037,12 @@ _cat_2.desc
 	cat1.erase(cif::key("id") == 10);
 
 	BOOST_CHECK_EQUAL(cat1.size(), 2);
-	BOOST_CHECK_EQUAL(cat2.size(), 3); // TODO: Is this really what we want?
+	BOOST_CHECK_EQUAL(cat2.size(), 2); // TODO: Is this really what we want?
 
 	cat1.erase(cif::key("id") == 20);
 
 	BOOST_CHECK_EQUAL(cat1.size(), 1);
-	BOOST_CHECK_EQUAL(cat2.size(), 2); // TODO: Is this really what we want?
+	BOOST_CHECK_EQUAL(cat2.size(), 1); // TODO: Is this really what we want?
 }
 
 // --------------------------------------------------------------------