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25 // 25 //
26 // This example is provided by the Geant4-DNA 26 // This example is provided by the Geant4-DNA collaboration
27 // Any report or published results obtained us 27 // Any report or published results obtained using the Geant4-DNA software
28 // shall cite the following Geant4-DNA collabo 28 // shall cite the following Geant4-DNA collaboration publication:
29 // Med. Phys. 37 (2010) 4692-4708 29 // Med. Phys. 37 (2010) 4692-4708
30 // Delage et al. PDB4DNA: implementation of DN 30 // Delage et al. PDB4DNA: implementation of DNA geometry from the Protein Data
31 // Bank (PDB) description for 31 // Bank (PDB) description for Geant4-DNA Monte-Carlo
32 // simulations (submitted to 32 // simulations (submitted to Comput. Phys. Commun.)
33 // The Geant4-DNA web site is available at htt 33 // The Geant4-DNA web site is available at http://geant4-dna.org
34 // 34 //
35 // ------------------------------------------- 35 // --------------------------------------------------------------
36 // Authors: E. Delage 36 // Authors: E. Delage
37 // november 2013 37 // november 2013
38 // ------------------------------------------- 38 // --------------------------------------------------------------
39 // 39 //
>> 40 // $Id$
40 // 41 //
41 /// \file PDBbarycenter.hh 42 /// \file PDBbarycenter.hh
42 /// \brief Definition of the Barycenter class 43 /// \brief Definition of the Barycenter class
43 44
44 //....oooOO0OOooo........oooOO0OOooo........oo 45 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
45 46
46 #ifndef BARY_H 47 #ifndef BARY_H
47 # define BARY_H << 48 #define BARY_H
48 49
49 //! Molecule Class 50 //! Molecule Class
50 /*! 51 /*!
51 * This Class define Molecule model ... << 52 * This Class define Molecule model ...
52 */ 53 */
53 class Barycenter 54 class Barycenter
54 { 55 {
55 public: << 56 public:
56 //! First constructor << 57 //! First constructor
57 Barycenter(); << 58 Barycenter();
58 //! Second constructor << 59 //! Second constructor
59 Barycenter(int bNum, double x, double y, d << 60 Barycenter(int bNum,double x,double y, double z,//Nucleotide bar. coordinates
60 double Bx, double By, double Bz << 61 double Bx,double By, double Bz, //Base bar. coordinates
61 double Sx, double Sy, double Sz << 62 double Sx,double Sy, double Sz, //Sugar bar. coordinates
62 double Px, double Py, double Pz << 63 double Px,double Py, double Pz);//Phosphate bar. coordinates
63 //! Destructor << 64 //! Destructor
64 ~Barycenter() {}; << 65 ~Barycenter() {};
65 << 66
66 //! Get the next Barycenter << 67 //! Get the next Barycenter
67 Barycenter* GetNext(); << 68 Barycenter *GetNext();
68 //! Get the first << 69 //! Get the first
69 // Residue *GetFirst(); << 70 //Residue *GetFirst();
70 //! Get number Barycenter << 71 //! Get number Barycenter
71 int GetID(); << 72 int GetID();
72 //! Set the next Barycenter << 73 //! Set the next Barycenter
73 void SetNext(Barycenter*); << 74 void SetNext(Barycenter *);
74 //! Set the distance between atom i and nu << 75 //! Set the distance between atom i and nucleotide barycenter
75 void SetDistance(int i, double); << 76 void SetDistance(int i, double);
76 //! Get the distance between atom i and nu << 77 //! Get the distance between atom i and nucleotide barycenter
77 double GetDistance(int i); << 78 double GetDistance(int i);
78 //! Set the distance between the farther a << 79 //! Set the distance between the farther atom and nucleotide barycenter
79 void SetRadius(double); << 80 void SetRadius(double );
80 //! Get the distance between the farther a << 81 //! Get the distance between the farther atom and nucleotide barycenter
81 double GetRadius(); << 82 double GetRadius();
82 << 83
83 int fBaryNum; //!< Barycenter number << 84 int fBaryNum;//!< Barycenter number
84 double fDistanceTab[33]; //!< distance ta << 85 double fDistanceTab[33];//!< distance table [0..32] (11 hydrogens!)
85 double fRadius; << 86 double fRadius;
86 << 87
87 double fCenterX; //!< "X coordinate" of t << 88 double fCenterX; //!< "X coordinate" of this nucelotide Barycenter
88 double fCenterY; //!< "Y coordinate" of t << 89 double fCenterY; //!< "Y coordinate" of this nucelotide Barycenter
89 double fCenterZ; //!< "Z coordinate" of t << 90 double fCenterZ; //!< "Z coordinate" of this nucelotide Barycenter
90 << 91
91 double fCenterBaseX; //!< "X coordinate" << 92 double fCenterBaseX; //!< "X coordinate" of this Base Barycenter
92 double fCenterBaseY; //!< "Y coordinate" << 93 double fCenterBaseY; //!< "Y coordinate" of this Base Barycenter
93 double fCenterBaseZ; //!< "Z coordinate" << 94 double fCenterBaseZ; //!< "Z coordinate" of this Base Barycenter
94 << 95
95 double fCenterSugarX; //!< "X coordinate" << 96 double fCenterSugarX; //!< "X coordinate" of this Sugar Barycenter
96 double fCenterSugarY; //!< "Y coordinate" << 97 double fCenterSugarY; //!< "Y coordinate" of this Sugar Barycenter
97 double fCenterSugarZ; //!< "Z coordinate" << 98 double fCenterSugarZ; //!< "Z coordinate" of this Sugar Barycenter
98 << 99
99 double fCenterPhosphateX; //!< "X coordin << 100 double fCenterPhosphateX; //!< "X coordinate" of this Phosphate Barycenter
100 double fCenterPhosphateY; //!< "Y coordin << 101 double fCenterPhosphateY; //!< "Y coordinate" of this Phosphate Barycenter
101 double fCenterPhosphateZ; //!< "Z coordin << 102 double fCenterPhosphateZ; //!< "Z coordinate" of this Phosphate Barycenter
102 103
103 private: << 104 private:
104 Barycenter* fpNext; //!< Header of the ne << 105 Barycenter *fpNext; //!< Header of the next Molecule (usage before vector)
105 }; 106 };
106 #endif 107 #endif
107 108
108 //....oooOO0OOooo........oooOO0OOooo........oo 109 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
>> 110
109 111