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//
// 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
// --------------------------------------------------------------
//
// $Id$
//
/// \file PDBlib.hh
/// \brief Definition of the PDBlib class

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#ifndef PDBlib_h
#define PDBlib_h 1

#include "PDBbarycenter.hh"
#include "PDBmolecule.hh"

//! PDBlib Class
/*!
 * This Class define Molecule model ... 
 */
class PDBlib
{
public:
  //! First constructor
  PDBlib();
  //! Destructor
  ~PDBlib() {};

  //! Load PDB file into memory
  Molecule* Load(const std::string&filename,
                 unsigned short int &isDNA,
                 unsigned short int verbose);

  // All declarations below are 'DNA specific'
  // Just comment those lines if you need to use this code elsewhere.

  //! Compute nucleotide barycenter from memory
  Barycenter* ComputeNucleotideBarycenters(Molecule *moleculeListTemp);

  //! Compute the corresponding bounding volume parameters
  void ComputeBoundingVolumeParams(Molecule *moleculeListTemp,
      double &dX,double &dY,double &dZ,       //Dimensions for bounding volume
      double &tX,double &tY,double &tZ);      //Translation for bounding volume

  //! Compute number of nucleotide per strand
  void ComputeNbNucleotidsPerStrand(Molecule * moleculeListTemp);

  //! Compute if energy is deposited in per atom
  unsigned short int ComputeMatchEdepDNA(Barycenter *,Molecule *,
      double x, double y,double z,
      int &numStrand, int &numNucleotid, int &codeResidue);

private:
  //! return distance between two 3D points
  double DistanceTwo3Dpoints(double xA,double xB,
      double yA,double yB,
      double zA,double zB);

  //! Number of nucleotid per strand
  int fNbNucleotidsPerStrand;
};

#endif

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