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1 // 1 //
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18 // * This code implementation is the result 18 // * This code implementation is the result of the scientific and *
19 // * technical work of the GEANT4 collaboratio 19 // * technical work of the GEANT4 collaboration. *
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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 PDBatom.cc 36 /// \file PDBatom.cc
37 /// \brief Implementation of the PDBatom class 37 /// \brief Implementation of the PDBatom class
38 38
39 #include "PDBatom.hh" 39 #include "PDBatom.hh"
40 40
41 //....oooOO0OOooo........oooOO0OOooo........oo 41 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
42 42
43 Atom::Atom(int s, const std::string& n, const << 43 Atom::Atom(int s, const std::string& n,
44 double yInit, double zInit, double << 44 const std::string& rN,int numInRes,int rS,
45 { << 45 double xInit,double yInit,double zInit,
46 fSerial = s; << 46 double radius,
47 fName = n; //!< Atom name << 47 double o, double tF, const std::string& e)
48 fResName = rN; //!< Residue name << 48 {
49 fNumInRes = numInRes; << 49 fSerial=s;
50 fResSeq = rS; //!< Residue sequence number << 50 fName=n;//!< Atom name
51 fX = xInit; << 51 fResName=rN;//!< Residue name
52 fY = yInit; << 52 fNumInRes=numInRes;
53 fZ = zInit; << 53 fResSeq=rS;//!< Residue sequence number
54 fVdwRadius = radius; << 54 fX=xInit;
55 fOccupancy = o; //!< occupancy << 55 fY=yInit;
56 fTempFactor = tF; << 56 fZ=zInit;
57 fElement = e; << 57 fVdwRadius=radius;
58 fpNext = 0; << 58 fOccupancy=o;//!< occupancy
>> 59 fTempFactor=tF;
>> 60 fElement=e;
>> 61 fpNext=0;
59 } 62 }
60 63
61 //....oooOO0OOooo........oooOO0OOooo........oo 64 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
62 65
63 Atom* Atom::GetNext() << 66 Atom *Atom::GetNext()
64 { 67 {
65 return fpNext; 68 return fpNext;
66 } 69 }
67 70
68 //....oooOO0OOooo........oooOO0OOooo........oo 71 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
69 72
70 double Atom::GetX() 73 double Atom::GetX()
71 { 74 {
72 return fX; 75 return fX;
73 } 76 }
74 77
75 //....oooOO0OOooo........oooOO0OOooo........oo 78 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
76 79
77 double Atom::GetY() 80 double Atom::GetY()
78 { 81 {
79 return fY; 82 return fY;
80 } 83 }
81 84
82 //....oooOO0OOooo........oooOO0OOooo........oo 85 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
83 86
84 double Atom::GetZ() 87 double Atom::GetZ()
85 { 88 {
86 return fZ; 89 return fZ;
87 } 90 }
88 91
89 //....oooOO0OOooo........oooOO0OOooo........oo 92 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
90 93
91 int Atom::GetID() 94 int Atom::GetID()
92 { 95 {
93 return fSerial; 96 return fSerial;
94 } 97 }
95 98
96 //....oooOO0OOooo........oooOO0OOooo........oo 99 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
97 100
98 const std::string& Atom::GetName() 101 const std::string& Atom::GetName()
99 { 102 {
100 return fName; 103 return fName;
101 } 104 }
102 105
103 //....oooOO0OOooo........oooOO0OOooo........oo 106 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
104 107
105 const std::string& Atom::GetElementName() 108 const std::string& Atom::GetElementName()
106 { 109 {
107 return fElement; 110 return fElement;
108 } 111 }
109 112
110 //....oooOO0OOooo........oooOO0OOooo........oo 113 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
111 114
112 double Atom::GetVanDerWaalsRadius() 115 double Atom::GetVanDerWaalsRadius()
113 { 116 {
114 return fVdwRadius; 117 return fVdwRadius;
115 } 118 }
116 119
117 //....oooOO0OOooo........oooOO0OOooo........oo 120 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
118 121
119 void Atom::SetNext(Atom* AtomNext) << 122 void Atom::SetNext(Atom *AtomNext)
120 { 123 {
121 fpNext = AtomNext; << 124 fpNext=AtomNext;
122 } 125 }
123 126