peptideCapProcessor.h

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

#ifndef BALL_STRUCTURE_PEPTIDECAPPROCESSOR_H
#define BALL_STRUCTURE_PEPTIDECAPPROCESSOR_H

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

#ifndef BALL_CONCEPT_COMPOSITE_H
# include <BALL/CONCEPT/composite.h>
#endif

#ifndef BALL_MATHS_VECTOR3_H
# include <BALL/MATHS/vector3.h>
#endif

#ifndef BALL_KERNEL_RESIDUE_H
# include <BALL/KERNEL/residue.h>
#endif

#ifndef BALL_STRUCTURE_ATOMBIJECTION_H
# include <BALL/STRUCTURE/atomBijection.h>
#endif

namespace BALL
{
  
  class BALL_EXPORT PeptideCapProcessor 
    : public UnaryProcessor<Composite>
  {
    public:


        PeptideCapProcessor();


        virtual Processor::Result operator() (Composite& composite);

    protected:

      //function to compute the distance of the cap atoms and the last residue
      float computeDistance(std::vector<Atom*>& a, std::vector<Atom*>& b);

      //function to optimize cap position by rotation
      void optimizeCapPosition(Protein* p, bool start);
  };

} //namespace BALL

#endif // BALL_STRUCTURE_PEPTIDECAPPROCESSOR_H

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