mmcif::Atom::compound() revision

.gitignore

@@ -13,3 +13,4 @@ msvc/
 Testing/
 Testing/
 rsrc/feature-request.txt
 rsrc/feature-request.txt
 test/1cbs.cif
 test/1cbs.cif
+test/test-create_sugar_2.cif

CMakeLists.txt

@@ -25,7 +25,7 @@
 cmake_minimum_required(VERSION 3.16)
 cmake_minimum_required(VERSION 3.16)
 
 
 # set the project name
 # set the project name
-project(cifpp VERSION 4.0.0 LANGUAGES CXX)
+project(cifpp VERSION 4.1.0 LANGUAGES CXX)
 
 
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 
 

changelog

+Version 4.1.0
+- Some interface changes for mmcif::Atom
+
 Version 4.0.0
 Version 4.0.0
 - getResidue in mmcif::Structure now requires both a
 - getResidue in mmcif::Structure now requires both a
   sequence ID and an auth sequence ID. As a result the code was cleaned
   sequence ID and an auth sequence ID. As a result the code was cleaned

include/cif++/Structure.hpp

@@ -80,7 +80,7 @@ class Atom
 
 
 		void moveTo(const Point &p);
 		void moveTo(const Point &p);
 
 
-		const Compound &comp() const;
+		const Compound *compound() const;
 
 
 		const std::string get_property(const std::string_view name) const;
 		const std::string get_property(const std::string_view name) const;
 		void set_property(const std::string_view name, const std::string &value);
 		void set_property(const std::string_view name, const std::string &value);
@@ -186,7 +186,7 @@ class Atom
 	bool isSymmetryCopy() const { return impl().mSymmetryCopy; }
 	bool isSymmetryCopy() const { return impl().mSymmetryCopy; }
 	std::string symmetry() const { return impl().mSymmetryOperator; }
 	std::string symmetry() const { return impl().mSymmetryOperator; }
 
 
-	const Compound &comp() const { return impl().comp(); }
+	const Compound &compound() const;
 	bool isWater() const { return impl().mCompID == "HOH" or impl().mCompID == "H2O" or impl().mCompID == "WAT"; }
 	bool isWater() const { return impl().mCompID == "HOH" or impl().mCompID == "H2O" or impl().mCompID == "WAT"; }
 	int charge() const;
 	int charge() const;
 
 

src/Structure.cpp

@@ -148,19 +148,10 @@ int Atom::AtomImpl::charge() const
 
 
 	if (not formalCharge.has_value())
 	if (not formalCharge.has_value())
 	{
 	{
-		try
-		{
-			auto &compound = comp();
+		auto c = compound();
 
 
-			if (compound.atoms().size() == 1)
-				formalCharge = compound.atoms().front().charge;
-		}
-		catch (const std::exception &ex)
-		{
-			if (cif::VERBOSE > 0)
-				std::cerr << "Error when trying to get charge of atom: " << ex.what() << std::endl;
-			formalCharge = 0;
-		}
+		if (c != nullptr and c->atoms().size() == 1)
+			formalCharge = c->atoms().front().charge;
 	}
 	}
 
 
 	return formalCharge.value_or(0);
 	return formalCharge.value_or(0);
@@ -188,23 +179,16 @@ void Atom::AtomImpl::moveTo(const Point &p)
 	mLocation = p;
 	mLocation = p;
 }
 }
 
 
-const Compound &Atom::AtomImpl::comp() const
+const Compound *Atom::AtomImpl::compound() const
 {
 {
 	if (mCompound == nullptr)
 	if (mCompound == nullptr)
 	{
 	{
-		std::string compID;
-		cif::tie(compID) = mRow.get("label_comp_id");
+		std::string compID = get_property("label_comp_id");
 
 
 		mCompound = CompoundFactory::instance().create(compID);
 		mCompound = CompoundFactory::instance().create(compID);
-
-		if (cif::VERBOSE > 0 and mCompound == nullptr)
-			std::cerr << "Compound not found: '" << compID << '\'' << std::endl;
 	}
 	}
 
 
-	if (mCompound == nullptr)
-		throw std::runtime_error("no compound");
-
-	return *mCompound;
+	return mCompound;
 }
 }
 
 
 const std::string Atom::AtomImpl::get_property(const std::string_view name) const
 const std::string Atom::AtomImpl::get_property(const std::string_view name) const
@@ -281,6 +265,21 @@ std::string Atom::pdbID() const
 	       get_property<std::string>("pdbx_PDB_ins_code");
 	       get_property<std::string>("pdbx_PDB_ins_code");
 }
 }
 
 
+const Compound &Atom::compound() const
+{
+	auto result = impl().compound();
+
+	if (result == nullptr)
+	{
+		if (cif::VERBOSE > 0)
+			std::cerr << "Compound not found: '" << get_property<std::string>("label_comp_id") << '\'' << std::endl;
+
+		throw std::runtime_error("no compound");
+	}
+
+	return *result;
+}
+
 int Atom::charge() const
 int Atom::charge() const
 {
 {
 	return impl().charge();
 	return impl().charge();