#ifndef RMSDTOOLS_H
#define RMSDTOOLS_H

#include "coordinate3D.h"
#include "structureAlignment.h"

#include <math.h>
#include <stdio.h>

class RmsdTools {

 public:
  RmsdTools(StructureAlignment* sa);
  ~RmsdTools();

  int rmsd();
  int rmsdPerResidue(int struct1, int struct2);
  int printRmsd(FILE* outfile);
  int printRmsdPerResidue(FILE* outfile);
  

 private:
  StructureAlignment* alignment;
  float **rmsdScores;
  float  *rmsdPerRes;

};

#endif