class AtomBijection
{
%TypeHeaderCode
	#include <BALL/STRUCTURE/atomBijection.h>
%End
	public:
	typedef std::pair<Atom*, Atom*> AtomPair;
	typedef std::vector<std::pair<Atom*, Atom*>> PairVector;

	AtomBijection();
	AtomBijection(AtomContainer& A, AtomContainer& B);

	Size assignTrivial(AtomContainer& A, AtomContainer& B);
	Size assignByName(AtomContainer& A, AtomContainer& B);
	Size assignCAlphaAtoms(AtomContainer& A, AtomContainer& B);
	Size assignBackboneAtoms(AtomContainer& A, AtomContainer& B);
};
