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/// \file PDBatom.hh
/// \brief Definition of the PDBatom class

// This example is provided by the Geant4-DNA collaboration
// Any report or published results obtained using the Geant4-DNA software
// shall cite the following Geant4-DNA collaboration publication:
// Med. Phys. 37 (2010) 4692-4708
// Delage et al. PDB4DNA: implementation of DNA geometry from the Protein Data
//                  Bank (PDB) description for Geant4-DNA Monte-Carlo
//                  simulations (submitted to Comput. Phys. Commun.)
// The Geant4-DNA web site is available at http://geant4-dna.org
//
// --------------------------------------------------------------
// Authors: E. Delage
// november 2013
// --------------------------------------------------------------
//
//

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#ifndef ATOM_H
#  define ATOM_H

#  include <string>

//! Atom Class
/*!
 * This Class define Atom model ...
 */
class Atom
{
  public:
    //! constructor with initialization
    Atom(int serial, const std::string& name, const std::string& resName, int numInRes, int resSeq,
         double xInit, double yInit, double zInit, double radius, double occupancy,
         double tempFactor, const std::string& element);

    //! Empty destructor
    ~Atom() {};

    //! Returns the next Atom
    Atom* GetNext();
    //! Return the X position for the Atom
    double GetX();
    //! Return the Y position for the Atom
    double GetY();
    //! Return the Z position for the Atom
    double GetZ();
    //! Return the Atom's ID
    int GetID();
    //! Return name of the atom
    const std::string& GetName();
    //! Return name of the element
    const std::string& GetElementName();
    //! Return name of the atom
    double GetVanDerWaalsRadius();
    //! Set the next atom
    void SetNext(Atom*);

    int fSerial;  //!< its serial number
    int fNumInRes;  //!< its number in residue sequence
    std::string fName;  //!< Atom name
    std::string fResName;  //!< Residue name
    int fResSeq;  //!< Residue sequence number
    double fX;  //!< X orthogonal coordinates in Angstroms
    double fY;  //!< Y orthogonal coordinates in Angstroms
    double fZ;  //!< Z orthogonal coordinates in Angstroms
    double fVdwRadius;  // Vand der Waals Radius in Angstrom
    double fOccupancy;  //!< Occupancy for the Atom
    std::string fElement;  //!< Element symbol extracted from 'atom name'
    double fTempFactor;  //!< Temperature factor for the Atom

  private:
    Atom* fpNext;  //!< Pointer to the next Atom
};
#endif

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