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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 /// \file PDBbarycenter.cc 36 /// \file PDBbarycenter.cc
37 /// \brief Implementation of the PDBbarycenter 37 /// \brief Implementation of the PDBbarycenter class
38 38
39 #include "PDBbarycenter.hh" 39 #include "PDBbarycenter.hh"
40 40
41 //....oooOO0OOooo........oooOO0OOooo........oo 41 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
42 42
43 Barycenter::Barycenter() << 43 Barycenter::Barycenter():fBaryNum(0),fRadius(0),
44 : fBaryNum(0), << 44 fCenterX(0),fCenterY(0),fCenterZ(0),
45 fRadius(0), << 45 fCenterBaseX(0),fCenterBaseY(0),fCenterBaseZ(0),
46 fCenterX(0), << 46 fCenterSugarX(0),fCenterSugarY(0),fCenterSugarZ(0),
47 fCenterY(0), << 47 fCenterPhosphateX(0),fCenterPhosphateY(0),fCenterPhosphateZ(0),
48 fCenterZ(0), << 48 fpNext(0)
49 fCenterBaseX(0), << 49 {
50 fCenterBaseY(0), << 50 for ( int i = 0; i < 33; ++i )
51 fCenterBaseZ(0), << 51 {
52 fCenterSugarX(0), << 52 fDistanceTab[i] = 0.; //initialization
53 fCenterSugarY(0), <<
54 fCenterSugarZ(0), <<
55 fCenterPhosphateX(0), <<
56 fCenterPhosphateY(0), <<
57 fCenterPhosphateZ(0), <<
58 fpNext(0) <<
59 { <<
60 for (int i = 0; i < 33; ++i) { <<
61 fDistanceTab[i] = 0.; // initialization <<
62 } 53 }
63 } 54 }
64 55
65 //....oooOO0OOooo........oooOO0OOooo........oo 56 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
66 57
67 Barycenter::Barycenter(int bNum, double x, dou << 58 Barycenter::Barycenter(int bNum,double x,double y,double z,
68 double Bz, // Base bar << 59 double Bx,double By, double Bz, //Base barycenter coordinates
69 double Sx, double Sy, d << 60 double Sx,double Sy, double Sz, //Sugar barycenter coordinates
70 double Px, double Py, d << 61 double Px,double Py, double Pz)//Phosphate barycenter coordinates
71 { << 62 {
72 fBaryNum = bNum; //!< Barycenter number << 63 fBaryNum=bNum;//!<Barycenter number
73 fRadius = 0; << 64 fRadius=0;
74 fCenterX = x; << 65 fCenterX=x;
75 fCenterY = y; << 66 fCenterY=y;
76 fCenterZ = z; << 67 fCenterZ=z;
77 for (int i = 0; i < 33; ++i) { << 68 for ( int i = 0; i < 33; ++i )
78 fDistanceTab[i] = 0.; // initialization << 69 {
>> 70 fDistanceTab[i] = 0.; //initialization
79 } 71 }
80 fCenterBaseX = Bx; //!< "X coordinate" of t << 72 fCenterBaseX=Bx; //!< "X coordinate" of this Base Barycenter
81 fCenterBaseY = By; //!< "Y coordinate" of t << 73 fCenterBaseY=By; //!< "Y coordinate" of this Base Barycenter
82 fCenterBaseZ = Bz; //!< "Z coordinate" of t << 74 fCenterBaseZ=Bz; //!< "Z coordinate" of this Base Barycenter
83 fCenterSugarX = Sx; //!< "X coordinate" of << 75 fCenterSugarX=Sx; //!< "X coordinate" of this Sugar Barycenter
84 fCenterSugarY = Sy; //!< "Y coordinate" of << 76 fCenterSugarY=Sy; //!< "Y coordinate" of this Sugar Barycenter
85 fCenterSugarZ = Sz; //!< "Z coordinate" of << 77 fCenterSugarZ=Sz; //!< "Z coordinate" of this Sugar Barycenter
86 fCenterPhosphateX = Px; //!< "X coordinate" << 78 fCenterPhosphateX=Px; //!< "X coordinate" of this Phosphate Barycenter
87 fCenterPhosphateY = Py; //!< "Y coordinate" << 79 fCenterPhosphateY=Py; //!< "Y coordinate" of this Phosphate Barycenter
88 fCenterPhosphateZ = Pz; //!< "Z coordinate" << 80 fCenterPhosphateZ=Pz; //!< "Z coordinate" of this Phosphate Barycenter
89 fpNext = 0; << 81 fpNext=0;
90 } 82 }
91 83
92 //....oooOO0OOooo........oooOO0OOooo........oo 84 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
93 85
94 Barycenter* Barycenter::GetNext() << 86 Barycenter *Barycenter::GetNext()
95 { 87 {
96 return fpNext; 88 return fpNext;
97 } 89 }
98 90
99 int Barycenter::GetID() 91 int Barycenter::GetID()
100 { 92 {
101 return fBaryNum; 93 return fBaryNum;
102 } 94 }
103 95
104 //....oooOO0OOooo........oooOO0OOooo........oo 96 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
105 97
106 void Barycenter::SetNext(Barycenter* barycente << 98 void Barycenter::SetNext(Barycenter *barycenterNext)
107 { 99 {
108 fpNext = barycenterNext; << 100 fpNext=barycenterNext;
109 } 101 }
110 102
111 //....oooOO0OOooo........oooOO0OOooo........oo 103 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
112 104
113 void Barycenter::SetDistance(int i, double dis 105 void Barycenter::SetDistance(int i, double dist)
114 { 106 {
115 fDistanceTab[i] = dist; << 107 fDistanceTab[i]=dist;
116 } 108 }
117 109
118 //....oooOO0OOooo........oooOO0OOooo........oo 110 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
119 111
120 double Barycenter::GetDistance(int i) 112 double Barycenter::GetDistance(int i)
121 { 113 {
122 return fDistanceTab[i]; 114 return fDistanceTab[i];
123 } 115 }
124 116
125 //....oooOO0OOooo........oooOO0OOooo........oo 117 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
126 118
127 void Barycenter::SetRadius(double rds) 119 void Barycenter::SetRadius(double rds)
128 { 120 {
129 fRadius = rds; << 121 fRadius=rds;
130 } 122 }
131 123
132 //....oooOO0OOooo........oooOO0OOooo........oo 124 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
133 125
134 double Barycenter::GetRadius() 126 double Barycenter::GetRadius()
135 { 127 {
136 return fRadius; 128 return fRadius;
137 } 129 }
>> 130
138 131