| Geant4 Cross Reference |
1 //
2 // ********************************************************************
3 // * License and Disclaimer *
4 // * *
5 // * The Geant4 software is copyright of the Copyright Holders of *
6 // * the Geant4 Collaboration. It is provided under the terms and *
7 // * conditions of the Geant4 Software License, included in the file *
8 // * LICENSE and available at http://cern.ch/geant4/license . These *
9 // * include a list of copyright holders. *
10 // * *
11 // * Neither the authors of this software system, nor their employing *
12 // * institutes,nor the agencies providing financial support for this *
13 // * work make any representation or warranty, express or implied, *
14 // * regarding this software system or assume any liability for its *
15 // * use. Please see the license in the file LICENSE and URL above *
16 // * for the full disclaimer and the limitation of liability. *
17 // * *
18 // * This code implementation is the result of the scientific and *
19 // * technical work of the GEANT4 collaboration. *
20 // * By using, copying, modifying or distributing the software (or *
21 // * any work based on the software) you agree to acknowledge its *
22 // * use in resulting scientific publications, and indicate your *
23 // * acceptance of all terms of the Geant4 Software license. *
24 // ********************************************************************
25 //
26 //
27 /// \file DNAHit.cc
28 /// \brief Hit class for a hit interacting with a DNA molecule
29
30 #include "DNAHit.hh"
31
32 #include <utility>
33
34 G4ThreadLocal G4Allocator<DNAHit>* MolecularDNAHitAllocator = nullptr;
35
36 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
37
38 DNAHit::DNAHit(const molecule& mol, G4int placement_idx, // ORG
39 G4int chain, G4int strand, // ORG
40 int64_t bp, const G4ThreeVector& pos,
41 const G4ThreeVector& localpos, // dousatsu
42 const G4double& energy, const G4double& d, const G4String& chromo,
43 const G4MolecularConfiguration* radical)
44 : fMoleculeEnum(mol),
45 fPlacementIdx(placement_idx),
46 fChainIdx(chain),
47 fStrandIdx(strand),
48 fBasePairIdx(bp),
49 fPosition(pos),
50 fLocalPosition(localpos),
51 fEnergy(energy),
52 fDistance(d),
53 fChromosome(chromo),
54 fRadical(radical)
55 {
56 // Computed quantities
57 if (fStrandIdx == 0) {
58 if ((fMoleculeEnum == SUGAR) || (fMoleculeEnum == PHOSPHATE)) {
59 fStrand1Rad = fRadical;
60 fStrand1Energy = fEnergy;
61 }
62 else if ((fMoleculeEnum == CYTOSINE) || (fMoleculeEnum == GUANINE) || (fMoleculeEnum == ADENINE)
63 || (fMoleculeEnum == THYMINE))
64 {
65 fBase1Rad = fRadical;
66 fBP1Energy = fEnergy;
67 }
68 else {
69 G4Exception("DNAHit", "ERR_UNKNOWN_MOLECULE", JustWarning,
70 "Chemical Reaction with unknown molecule");
71 }
72 }
73 else if (fStrandIdx == 1) {
74 if ((fMoleculeEnum == SUGAR) || (fMoleculeEnum == PHOSPHATE)) {
75 fStrand2Rad = fRadical;
76 fStrand2Energy = fEnergy;
77 }
78 else if ((fMoleculeEnum == CYTOSINE) || (fMoleculeEnum == GUANINE) || (fMoleculeEnum == ADENINE)
79 || (fMoleculeEnum == THYMINE))
80 {
81 fBase2Rad = fRadical;
82 fBP2Energy = fEnergy;
83 }
84 else {
85 G4Exception("DNAHit", "ERR_UNKNOWN_MOLECULE", JustWarning, "Hit with unknown molecule");
86 }
87 }
88 }
89
90 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
91
92 // This method is used to combine the computed quantities of two hits.
93 // It keeps the settable parameters of the current hit, but the computed
94 // parameters come from both, letting the hit reflect what happened on each
95 // base pair.
96 void DNAHit::AddHit(const DNAHit& right)
97 {
98 this->fStrand1Energy += right.GetStrand1Energy();
99 this->fStrand2Energy += right.GetStrand2Energy();
100 this->fBP1Energy += right.GetBP1Energy();
101 this->fBP2Energy += right.GetBP2Energy();
102 if (right.GetStrand1Rad() != nullptr) {
103 this->fStrand1Rad = right.GetStrand1Rad();
104 }
105 if (right.GetBase1Rad() != nullptr) {
106 this->fBase1Rad = right.GetBase1Rad();
107 }
108 if (right.GetStrand2Rad() != nullptr) {
109 this->fStrand2Rad = right.GetStrand2Rad();
110 }
111 if (right.GetBase2Rad() != nullptr) {
112 this->fBase2Rad = right.GetBase2Rad();
113 }
114 }
115
116 DNAHit::DNAHit(const DNAHit& right)
117 {
118 this->SetPlacementIdx(right.GetPlacementIdx());
119 this->SetMolecule(right.GetMolecule());
120 this->SetChainIdx(right.GetChainIdx());
121 this->SetStrandIdx(right.GetStrandIdx());
122 this->SetBasePairIdx(right.GetBasePairIdx());
123 this->SetPosition(right.GetPosition());
124 this->SetLocalPosition(right.GetLocalPosition());
125 this->SetEnergy(right.GetEnergy());
126 this->SetDistance(right.GetDistance());
127 this->SetChromosome(right.GetChromosome());
128 this->SetRadical(right.GetRadical());
129
130 // Computed Quantities, no setters.
131 this->fStrand1Energy = right.GetStrand1Energy();
132 this->fStrand2Energy = right.GetStrand2Energy();
133 this->fBP1Energy = right.GetBP1Energy();
134 this->fBP2Energy = right.GetBP2Energy();
135 this->fStrand1Rad = right.GetStrand1Rad();
136 this->fBase1Rad = right.GetBase1Rad();
137 this->fStrand2Rad = right.GetStrand2Rad();
138 this->fBase2Rad = right.GetBase2Rad();
139 }
140
141 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
142
143 const DNAHit& DNAHit::operator=(const DNAHit& right)
144 {
145 this->SetMolecule(right.GetMolecule());
146 this->SetPlacementIdx(right.GetPlacementIdx());
147 this->SetChainIdx(right.GetChainIdx());
148 this->SetStrandIdx(right.GetStrandIdx());
149 this->SetBasePairIdx(right.GetBasePairIdx());
150 this->SetPosition(right.GetPosition());
151 this->SetLocalPosition(right.GetLocalPosition());
152 this->SetEnergy(right.GetEnergy());
153 this->SetDistance(right.GetDistance());
154 this->SetChromosome(right.GetChromosome());
155 this->SetRadical(right.GetRadical());
156
157 this->fStrand1Energy = right.GetStrand1Energy();
158 this->fStrand2Energy = right.GetStrand2Energy();
159 this->fBP1Energy = right.GetBP1Energy();
160 this->fBP2Energy = right.GetBP2Energy();
161 this->fStrand1Rad = right.GetStrand1Rad();
162 this->fBase1Rad = right.GetBase1Rad();
163 this->fStrand2Rad = right.GetStrand2Rad();
164 this->fBase2Rad = right.GetBase2Rad();
165 return *this;
166 }
167
168 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
169
170 G4int DNAHit::operator==(const DNAHit& right) const
171 {
172 return (this == &right) ? 1 : 0;
173 }
174 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
175