atomBijection.h

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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//

#ifndef BALL_STRUCTURE_ATOMBIJECTION_H
#define BALL_STRUCTURE_ATOMBIJECTION_H

#ifndef BALL_COMMON_H
# include <BALL/common.h>
#endif

#ifndef BALL_KERNEL_ATOMCONTAINER_H
# include <BALL/KERNEL/atomContainer.h>
#endif

namespace BALL 
{

  class BALL_EXPORT AtomBijection
    : public std::vector<std::pair<Atom*, Atom*> >
  {
    public:

    typedef std::pair<Atom*, Atom*> AtomPair;
    typedef std::vector<std::pair<Atom*, Atom*> > PairVector;
    

    AtomBijection() {}

    AtomBijection(AtomContainer& A, AtomContainer& B, bool limit_to_selection = false);

    virtual ~AtomBijection() {}


    Size assignTrivial(AtomContainer& A, AtomContainer& B, bool limit_to_selection = false);

    Size assignByName(AtomContainer& A, AtomContainer& B, bool limit_to_selection = false);

    Size assignCAlphaAtoms(AtomContainer& A, AtomContainer& B, bool limit_to_selection = false);


    Size assignBackboneAtoms(AtomContainer& A, AtomContainer& B, bool limit_to_selection = false);

    Size assignAtomsByProperty(AtomContainer& A, AtomContainer& B);


    double calculateRMSD() const;

    using PairVector::size;
    using PairVector::push_back;
    using PairVector::begin;
    using PairVector::end;
    using PairVector::rbegin;
    using PairVector::rend;

  };

} // namespace BALL

#endif // BALL_STRUCTURE_ATOMBIJECTION_H