Merge branch 'develop' of github.com:PDB-REDO/libcifpp into develop

include/cif++/Structure.hpp

@@ -511,7 +511,7 @@ class Branch : public std::vector<Sugar>
 
 	std::string name() const;
 	float weight() const;
-	std::string asymID() const	{ return mAsymID; }
+	std::string asymID() const { return mAsymID; }
 
 	Structure &structure() { return *mStructure; }
 	const Structure &structure() const { return *mStructure; }
@@ -601,12 +601,12 @@ class Structure
 
 	const Polymer &getPolymerByAsymID(const std::string &asymID) const
 	{
-		return const_cast<Structure*>(this)->getPolymerByAsymID(asymID);
+		return const_cast<Structure *>(this)->getPolymerByAsymID(asymID);
 	}
 
 	const std::list<Branch> &branches() const { return mBranches; }
 	std::list<Branch> &branches() { return mBranches; }
-	
+
 	Branch &getBranchByAsymID(const std::string &asymID);
 	const Branch &getBranchByAsymID(const std::string &asymID) const;
 
@@ -624,13 +624,25 @@ class Structure
 	/// \brief Return the atom closest to point \a p with atom type \a type in a residue of type \a res_type
 	Atom getAtomByPositionAndType(Point p, std::string_view type, std::string_view res_type) const;
 
+	/// \brief Get a non-poly residue for an asym with id \a asymID
+	Residue &getResidue(const std::string &asymID)
+	{
+		return getResidue(asymID, 0, "");
+	}
+
+	/// \brief Get a non-poly residue for an asym with id \a asymID
+	const Residue &getResidue(const std::string &asymID) const
+	{
+		return getResidue(asymID, 0, "");
+	}
+
 	/// \brief Get a residue for an asym with id \a asymID seq id \a seqID and authSeqID \a authSeqID
 	Residue &getResidue(const std::string &asymID, int seqID, const std::string &authSeqID);
 
 	/// \brief Get a the single residue for an asym with id \a asymID seq id \a seqID and authSeqID \a authSeqID
 	const Residue &getResidue(const std::string &asymID, int seqID, const std::string &authSeqID) const
 	{
-		return const_cast<Structure*>(this)->getResidue(asymID, seqID, authSeqID);
+		return const_cast<Structure *>(this)->getResidue(asymID, seqID, authSeqID);
 	}
 
 	/// \brief Get a residue for an asym with id \a asymID, compound id \a compID, seq id \a seqID and authSeqID \a authSeqID
@@ -639,16 +651,7 @@ class Structure
 	/// \brief Get a residue for an asym with id \a asymID, compound id \a compID, seq id \a seqID and authSeqID \a authSeqID
 	const Residue &getResidue(const std::string &asymID, const std::string &compID, int seqID, const std::string &authSeqID) const
 	{
-		return const_cast<Structure*>(this)->getResidue(asymID, compID, seqID, authSeqID);
-	}
-
-	/// \brief Get a the single residue for an asym with id \a asymID
-	Residue &getResidue(const std::string &asymID);
-
-	/// \brief Get a the single residue for an asym with id \a asymID
-	const Residue &getResidue(const std::string &asymID) const
-	{
-		return const_cast<Structure*>(this)->getResidue(asymID);
+		return const_cast<Structure *>(this)->getResidue(asymID, compID, seqID, authSeqID);
 	}
 
 	/// \brief Get a the residue for atom \a atom
@@ -665,8 +668,8 @@ class Structure
 
 	// Actions
 	void removeAtom(Atom &a);
-	void swapAtoms(Atom &a1, Atom &a2); // swap the labels for these atoms
-	void moveAtom(Atom &a, Point p);    // move atom to a new location
+	void swapAtoms(Atom a1, Atom a2); // swap the labels for these atoms
+	void moveAtom(Atom a, Point p);  // move atom to a new location
 	void changeResidue(Residue &res, const std::string &newCompound,
 		const std::vector<std::tuple<std::string, std::string>> &remappedAtoms);
 
@@ -692,10 +695,10 @@ class Structure
 	std::string createNonpoly(const std::string &entity_id, std::vector<std::vector<cif::Item>> &atom_info);
 
 	/// \brief Create a new (sugar) branch with one first NAG containing atoms \a nag_atoms
-	Branch& createBranch(std::vector<std::vector<cif::Item>> &nag_atoms);
+	Branch &createBranch(std::vector<std::vector<cif::Item>> &nag_atoms);
 
 	/// \brief Extend an existing (sugar) branch identified by \a asymID with one sugar containing atoms \a atoms
-	Branch& extendBranch(const std::string &asym_id, std::vector<std::vector<cif::Item>> &atoms);
+	Branch &extendBranch(const std::string &asym_id, std::vector<std::vector<cif::Item>> &atoms);
 
 	/// \brief Remove a residue, can be monomer or nonpoly
 	///

src/Structure.cpp

@@ -1625,26 +1625,13 @@ Polymer &Structure::getPolymerByAsymID(const std::string &asymID)
 	throw std::runtime_error("Polymer with asym id " + asymID + " not found");
 }
 
-Residue &Structure::getResidue(const std::string &asymID)
-{
-	for (auto &res : mNonPolymers)
-	{
-		if (res.asymID() != asymID)
-			continue;
-
-		return res;
-	}
-
-	throw std::out_of_range("Could not find residue " + asymID);
-}
-
 Residue &Structure::getResidue(const std::string &asymID, int seqID, const std::string &authSeqID)
 {
 	if (seqID == 0)
 	{
 		for (auto &res : mNonPolymers)
 		{
-			if (res.asymID() == asymID and res.authSeqID() == authSeqID)
+			if (res.asymID() == asymID and (authSeqID.empty() or res.authSeqID() == authSeqID))
 				return res;
 		}
 	}
@@ -1835,11 +1822,7 @@ void Structure::removeAtom(Atom &a)
 	assert(L <= R);
 }
 
-// void Structure::removeResidue(const std::string &asym_id, int seq_id)
-// {
-// }
-
-void Structure::swapAtoms(Atom &a1, Atom &a2)
+void Structure::swapAtoms(Atom a1, Atom a2)
 {
 	cif::Datablock &db = datablock();
 	auto &atomSites = db["atom_site"];
@@ -1867,7 +1850,7 @@ void Structure::swapAtoms(Atom &a1, Atom &a2)
 	l3.swap(l4);
 }
 
-void Structure::moveAtom(Atom &a, Point p)
+void Structure::moveAtom(Atom a, Point p)
 {
 	a.location(p);
 }

test/structure-test.cpp

@@ -321,4 +321,26 @@ BOOST_AUTO_TEST_CASE(atom_numbers_1)
 	}
 
 	BOOST_ASSERT(ai == atoms.end());
-}
\ No newline at end of file
+}
+// --------------------------------------------------------------------
+
+BOOST_AUTO_TEST_CASE(test_load_1)
+{
+	using namespace cif::literals;
+
+	const std::filesystem::path example(gTestDir / ".." / "examples" / "1cbs.cif.gz");
+	mmcif::File file(example.string());
+
+	auto &db = file.data();
+
+	mmcif::Structure s(file);
+
+	BOOST_CHECK(s.polymers().size() == 1);
+
+	auto &pdbx_poly_seq_scheme = db["pdbx_poly_seq_scheme"];
+
+	for (auto &poly : s.polymers())
+	{
+		BOOST_CHECK_EQUAL(poly.size(), pdbx_poly_seq_scheme.find("asym_id"_key == poly.asymID()).size());
+	}
+}