#ifndef __AATOM_HH__
#define __AATOM_HH__

//--- C/C++ includes ---
#include <string>
#include <math.h>

//--- SkyMol includes ---
#include "calc.hh"

class AGroup;
class APoint;

class AAtom : public CoordType
{
public:

  //--- Constructors ---
  virtual AAtom *newAtom(double _x,double _y,double _z,
			 const char *name) = 0;

  //--- Destructors ---
  virtual ~AAtom() { ; }

  //---- Manipulations with to coordinates ---
  virtual double getX()         = 0;
  virtual double getY()         = 0;
  virtual double getZ()         = 0;
  virtual void   setX(double x) = 0;
  virtual void   setY(double y) = 0;
  virtual void   setZ(double z) = 0;
  virtual double getActualX()   = 0;
  virtual double getActualY()   = 0;
  virtual double getActualZ()   = 0;

  //--- Access to the next atom ---
  virtual AAtom *getNext()           = 0;
  virtual bool  setNext(AAtom *atom) = 0; // Not recommended for use

  //--- Atom serial number in a molecule ---
  virtual int  getSerialNum() = 0;

  //--- Atom conformation ---
  virtual char getConformation() = 0;

  //--- Access chemichal identification ---
  virtual bool isHydrogen()   = 0;
  virtual bool isCarbon()     = 0;
  virtual bool isNitrogen()   = 0;
  virtual bool isOxygen()     = 0;
  virtual bool isPhosphorus() = 0;
  virtual bool isSulphur()    = 0;

  //--- Selection status ---
  virtual bool isSelected()     = 0;
  virtual void setSelected()    = 0;
  virtual void setNotSelected() = 0;

  //--- Temporary selection status use it in your program ---
  virtual bool isTmpSel()     = 0;
  virtual void setTmpSel()    = 0;
  virtual void setNotTmpSel() = 0;

  //--- Group to which the atom belongs to ---
  virtual AGroup *getGroup() = 0;
  
  //--- Access position in a residue ---
  virtual bool isNBackbone()       = 0;
  virtual bool isAlphaCarbon()     = 0;
  virtual bool isCBackbone()       = 0;
  virtual bool isOBackbone()       = 0;
  virtual bool isAminoBackbone()   = 0;
  virtual bool isBetaCarbon()      = 0;
  virtual bool isSugarPhosphate()  = 0;
  virtual bool isNucleicBackbone() = 0;
  virtual bool isCysteineSulphur() = 0;
  virtual bool isHetero()          = 0;

  //--- Charges on atoms ---
  virtual short getCharge()             = 0;
  virtual short setCharge(short charge) = 0;

  //--- Alignment flag ---
  virtual bool isAligned()     = 0;
  virtual void setAligned()    = 0;
  virtual void setNotAligned() = 0;

  //--- Names ---
  virtual std::string getName()         = 0; // 4-letter name
  virtual std::string getChemicalName() = 0; // 2-letter name

  //--- Calculations ---
  virtual double originalDistTo(AAtom *atom)      = 0;
  virtual double actualDistTo(AAtom *atom)        = 0;
  virtual double angleWith(AAtom* atom1,
			   AAtom* atom2)          = 0;
  virtual double dihedralAngleWith(AAtom *atom_j,
				   AAtom *atom_k,
				   AAtom *atom_l) = 0;

  //--- Extracting colors ---
  virtual void setColor(int col_) = 0;
  virtual int  getColor()         = 0;

  //--- You may assosiate some data structure with an atom ---
  virtual void* assignData(void *) = 0;
  virtual void* getAssignedData()  = 0;

  //--- T bonded atoms ---
  virtual APoint *getTBonded()                = 0;
  virtual bool testTBonded(AAtom *atom)       = 0;
  virtual bool replaceTBonded(APoint *points) = 0;

  //--- CA bonded atoms ---
  virtual APoint *getCABonded()          = 0;
  virtual bool testCABonded(AAtom *atom) = 0;

  //--- Integer property ---
  virtual void setIntProperty(int prop) = 0;
  virtual int  getIntProperty()         = 0;

  //--- Temperature factor for atom ---
  virtual short getTemperature()           = 0;
  virtual void  setTemperature(short temp) = 0;
};

#endif