/*
 * atom.hpp
 *
 *  Created on: Aug 3, 2009
 *      Author: heber
 */

#ifndef ATOM_HPP_
#define ATOM_HPP_

using namespace std;

/*********************************************** includes ***********************************/

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <iostream>
#include <list>
#include <vector>

#include "atom_atominfo.hpp"
#include "atom_bondedparticle.hpp"
#include "atom_graphnode.hpp"
#include "atom_particleinfo.hpp"
#include "atom_trajectoryparticle.hpp"
#include "tesselation.hpp"

/****************************************** forward declarations *****************************/

class Vector;

/********************************************** declarations *******************************/

/** Single atom.
 * Class incorporates position, type
 */
class atom : public TesselPoint, public TrajectoryParticle, public GraphNode, public BondedParticle, public virtual ParticleInfo, public virtual AtomInfo {
  public:
    atom *previous; //!< previous atom in molecule list
    atom *next;     //!< next atom in molecule list
    atom *father;   //!< In many-body bond order fragmentations points to originating atom
    int *sort;      //!< sort criteria

  atom();
  atom(class atom *pointer);
  virtual ~atom();

  bool OutputIndexed(ofstream * const out, const int ElementNo, const int AtomNo, const char *comment = NULL) const;
  bool OutputArrayIndexed(ofstream * const out, const int *ElementNo, int *AtomNo, const char *comment = NULL) const;
  bool OutputXYZLine(ofstream *out) const;
  bool OutputTrajectory(ofstream * const out, const int *ElementNo, int *AtomNo, const int step) const;
  bool OutputTrajectoryXYZ(ofstream * const out, const int step) const;
  void OutputMPQCLine(ofstream * const out, const Vector *center, int *AtomNo) const;

  void InitComponentNr();

  void EqualsFather ( const atom *ptr, const atom **res ) const;
  void CorrectFather();
  atom *GetTrueFather();
  bool Compare(const atom &ptr) const;

  double DistanceToVector(const Vector &origin) const;
  double DistanceSquaredToVector(const Vector &origin) const;
  bool IsInParallelepiped(const Vector offset, const double *parallelepiped) const;

  private:
};

#endif /* ATOM_HPP_ */