pdb4dna/include/PDBbarycenter.hh

0001 //
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0025 //
0026 // This example is provided by the Geant4-DNA collaboration
0027 // Any report or published results obtained using the Geant4-DNA software
0028 // shall cite the following Geant4-DNA collaboration publication:
0029 // Med. Phys. 37 (2010) 4692-4708
0030 // Delage et al. PDB4DNA: implementation of DNA geometry from the Protein Data
0031 //                  Bank (PDB) description for Geant4-DNA Monte-Carlo
0032 //                  simulations (submitted to Comput. Phys. Commun.)
0033 // The Geant4-DNA web site is available at http://geant4-dna.org
0034 //
0035 // --------------------------------------------------------------
0036 // Authors: E. Delage
0037 // november 2013
0038 // --------------------------------------------------------------
0039 //
0040 //
0041 /// \file PDBbarycenter.hh
0042 /// \brief Definition of the Barycenter class
0043
0044 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0045
0046 #ifndef BARY_H
0047 #  define BARY_H
0048
0049 //! Molecule Class
0050 /*!
0051  * This Class define Molecule model ...
0052  */
0053 class Barycenter
0054 {
0055   public:
0056     //! First constructor
0057     Barycenter();
0058     //! Second constructor
0059     Barycenter(int bNum, double x, double y, double z,  // Nucleotide bar. coordinates
0060                double Bx, double By, double Bz,  // Base bar. coordinates
0061                double Sx, double Sy, double Sz,  // Sugar bar. coordinates
0062                double Px, double Py, double Pz);  // Phosphate bar. coordinates
0063     //! Destructor
0064     ~Barycenter() {};
0065
0066     //! Get the next Barycenter
0067     Barycenter* GetNext();
0068     //! Get the first
0069     // Residue *GetFirst();
0070     //! Get number Barycenter
0071     int GetID();
0072     //! Set the next Barycenter
0073     void SetNext(Barycenter*);
0074     //! Set the distance between atom i and nucleotide barycenter
0075     void SetDistance(int i, double);
0076     //! Get the distance between atom i and nucleotide barycenter
0077     double GetDistance(int i);
0078     //! Set the distance between the farther atom and nucleotide barycenter
0079     void SetRadius(double);
0080     //! Get the distance between the farther atom and nucleotide barycenter
0081     double GetRadius();
0082
0083     int fBaryNum;  //!< Barycenter number
0084     double fDistanceTab[33];  //!< distance table [0..32] (11 hydrogens!)
0085     double fRadius;
0086
0087     double fCenterX;  //!< "X coordinate" of this nucelotide Barycenter
0088     double fCenterY;  //!< "Y coordinate" of this nucelotide Barycenter
0089     double fCenterZ;  //!< "Z coordinate" of this nucelotide Barycenter
0090
0091     double fCenterBaseX;  //!< "X coordinate" of this Base Barycenter
0092     double fCenterBaseY;  //!< "Y coordinate" of this Base Barycenter
0093     double fCenterBaseZ;  //!< "Z coordinate" of this Base Barycenter
0094
0095     double fCenterSugarX;  //!< "X coordinate" of this Sugar Barycenter
0096     double fCenterSugarY;  //!< "Y coordinate" of this Sugar Barycenter
0097     double fCenterSugarZ;  //!< "Z coordinate" of this Sugar Barycenter
0098
0099     double fCenterPhosphateX;  //!< "X coordinate" of this Phosphate Barycenter
0100     double fCenterPhosphateY;  //!< "Y coordinate" of this Phosphate Barycenter
0101     double fCenterPhosphateZ;  //!< "Z coordinate" of this Phosphate Barycenter
0102
0103   private:
0104     Barycenter* fpNext;  //!< Header of the next Molecule (usage before vector)
0105 };
0106 #endif
0107
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