reconstructFragmentProcessor.h

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

#ifndef BALL_STRUCTURE_RECONSTRUCFRAGMENTPROCESSOR_H
#define BALL_STRUCTURE_RECONSTRUCFRAGMENTPROCESSOR_H

#include <list>

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

#ifndef BALL_DATATYPE_TRIPLE_H
# include <BALL/DATATYPE/triple.h>
#endif

#ifndef BALL_MATHS_MATRIX44_H
# include <BALL/MATHS/matrix44.h>
#endif

#ifndef BALL_KERNEL_FRAGMENT_H
# include <BALL/KERNEL/fragment.h>
#endif

namespace BALL 
{
  class FragmentDB;

  class BALL_EXPORT ReconstructFragmentProcessor 
    : public UnaryProcessor<Fragment> 
  { 
    
    public:


    ReconstructFragmentProcessor();

    ReconstructFragmentProcessor(const FragmentDB& db);

    ReconstructFragmentProcessor(const ReconstructFragmentProcessor& db);

    virtual ~ReconstructFragmentProcessor();



    virtual bool start();
    
    virtual bool finish();
    
    virtual Processor::Result operator() (Fragment&);


    
    list<Atom*>& getInsertedAtoms();

    Size getNumberOfInsertedAtoms() const;

    void setFragmentDB(const FragmentDB& fragment_db);

    const FragmentDB* getFragmentDB() const;


    // ???? This should be replaced by the corresponding method in StructureMapper
    // We don't need two implementations with the same code.
    static Matrix4x4 mapThreeVectors
      (const Vector3& w1, const Vector3& w2, const Vector3& w3,
       const Vector3& v1, const Vector3& v2, const Vector3& v3);

    static Triple<bool, const Atom*, const Atom*>
    getTwoReferenceAtoms(const Atom& ref_center_atom, const HashSet<const Atom*>& allowed)
      ;

    static list<Atom*> reconstructFragment(Fragment& frag, const Fragment& tplate);

    protected:
    
    /*_ @name Protected attributes
    */
    //_@{

    /*_ Pointer to the fragment DB 
    */  
    const FragmentDB* fragment_db_;
    
    /*_ List of atoms inserted during the last application of the processor.
    */
    list<Atom*> inserted_atoms_;
    //_@}
  };
  
} // namespace BALL

#endif // BALL_STRUCTURE_RECONSTRUCFRAGMENTPROCESSOR_H