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25 //
26 //
27 #ifndef MOLECULAR_ANALYSIS_MANAGER_HH
28 #define MOLECULAR_ANALYSIS_MANAGER_HH
29
30 #include "G4AnalysisManager.hh"
31 #include "G4Electron_aq.hh"
32 #include "G4Hydrogen.hh"
33 #include "G4OH.hh"
34 #include "G4RootAnalysisManager.hh"
35 #include "G4ThreeVector.hh"
36 #include "globals.hh"
37
38 #include <map>
39 #include <vector>
40
41 class ChromosomeHit;
42
43 class DNAHit;
44
45 class AnalysisMessenger;
46
47 class DNAGeometry;
48
49 struct BasePairDamageRecord
50 {
51 G4double fStrand1Energy = 0;
52 G4double fStrand2Energy = 0;
53 G4double fBp1Energy = 0;
54 G4double fBp2Energy = 0;
55 G4bool fBp1IndirectDmg = false;
56 G4bool fBp2IndirectDmg = false;
57 G4bool fStrand1IndirectDmg = false;
58 G4bool fStrand2IndirectDmg = false;
59 G4bool fBp1IndirectEvt = false;
60 G4bool fBp2IndirectEvt = false;
61 G4bool fStrand1IndirectEvt = false;
62 G4bool fStrand2IndirectEvt = false;
63 G4bool fbp1DirectDmg = false;
64 G4bool fbp2DirectDmg = false;
65 G4bool fStrand1DirectDmg = false;
66 G4bool fStrand2DirectDmg = false;
67 G4bool fbp1InducedBreak = false;
68 G4bool fbp2InducedBreak = false;
69 };
70
71 // exp
72 enum complexityEnum
73 {
74 SSB,
75 SSBplus,
76 twoSSB,
77 DSB,
78 DSBplus,
79 DSBplusplus,
80 NoneComplexity
81 };
82
83 enum sourceEnum
84 {
85 SSBd,
86 SSBi,
87 SSBm,
88 DSBh,
89 DSBm,
90 DSBd,
91 DSBi,
92 undefined
93 };
94 //
95
96 struct DamageClassification
97 {
98 complexityEnum fComplexity = NoneComplexity;
99 sourceEnum fSource = undefined;
100 G4int fbaseDmg = 0;
101 G4int fStrandDmg = 0;
102 G4int fDirectBreaks = 0;
103 G4int fIndirectBreaks = 0;
104 G4int fInducedBreaks = 0;
105 };
106
107 class DamageRecord
108 {
109 public:
110 DamageRecord(const G4String&, int64_t, G4int, G4int); // dousatsu
111 ~DamageRecord();
112
113 void AddBasePairDamage(BasePairDamageRecord* bp, const G4ThreeVector& pos)
114 {
115 fDamageRecords.push_back(bp);
116 fPositions.push_back(pos);
117 };
118
119 void AddEmptyBPDamage(int64_t ii);
120
121 void AddStrandHit(const G4MoleculeDefinition* mol);
122
123 void AddBaseHit(const G4MoleculeDefinition* mol);
124
125 void PrintRecord(const G4String&, const G4double& dsbDistance = 10);
126
127 DamageClassification* GetClassification(const G4double& dsbDistance = 10);
128
129 inline const G4String& GetName() const { return fName; };
130
131 int64_t GetSize() const { return fDamageRecords.size(); }; // dousatsu
132
133 inline G4int GetOHBaseHits() const { return fOHBase; };
134
135 inline G4int GetEaqBaseHits() const { return fEaqBase; };
136
137 inline G4int GetHBaseHits() const { return fHBase; };
138
139 inline G4int GetOHStrandHits() const { return fOHStrand; };
140
141 inline G4int GetEaqStrandHits() const { return fEaqStrand; };
142
143 inline G4int GetHStrandHits() const { return fHStrand; };
144
145 inline G4int GetPlacementIdx() const { return fStartPlacement; };
146
147 inline G4int GetChainIdx() const { return fChainIdx; };
148
149 inline G4int GetStrandIdx() const { return fStrandIdx; };
150
151 inline int64_t GetStartBPIdx() const { return fStartIndex; }; // dousatsu
152 void AddTestDamage(G4int, G4int, G4int, G4int);
153
154 G4ThreeVector GetMeanPosition() const;
155
156 G4double GetMeanDistance() const;
157
158 G4double GetEnergy() const;
159
160 private:
161 G4String fName;
162 int64_t fStartIndex;
163 G4int fStartPlacement, fChainIdx, fStrandIdx = 0;
164 G4int fOHBase = 0, fOHStrand = 0, fHBase = 0, fHStrand = 0, fEaqBase = 0, fEaqStrand = 0;
165 std::vector<BasePairDamageRecord*> fDamageRecords;
166 std::vector<G4ThreeVector> fPositions;
167
168 const G4MoleculeDefinition* fOH = G4OH::Definition();
169 const G4MoleculeDefinition* fe_aq = G4Electron_aq::Definition();
170 const G4MoleculeDefinition* fH = G4Hydrogen::Definition();
171
172 static const char* fDirectDamageChar;
173 static const char* fIndirectDamageChar;
174 static const char* fHitNoDamageChar;
175 static const char* fNotHitChar;
176 static const char* fBothDamageChar;
177
178 const char* GetChar(const G4bool&, const G4bool&, const G4double&);
179 };
180
181 struct Node
182 {
183 int64_t fkey;
184 DNAHit* fdata;
185 Node* fleft;
186 Node* fright;
187 Node* fparent;
188 };
189
190 // A binary tree is used to order the DNA hit objects
191 // It creates internal copies of all DNA Hits passed to it and then
192 // deletes them
193 class BinaryTree
194 {
195 public:
196 BinaryTree();
197
198 virtual ~BinaryTree();
199
200 void Insert(const DNAHit*);
201
202 DNAHit* Search(int64_t);
203
204 void Destroy_tree();
205
206 // return left-most node
207 DNAHit* First() const;
208
209 // Return next node with higher key
210 DNAHit* Next(const DNAHit*) const;
211
212 private:
213 void Destroy_tree_(Node*);
214
215 void Insert_(DNAHit*, Node*);
216
217 DNAHit* Search_(int64_t, Node*);
218
219 DNAHit* First_(Node*) const;
220
221 DNAHit* Next_(int64_t, Node*) const;
222
223 Node* fRoot;
224 };
225
226 class AnalysisManager
227 {
228 public:
229 AnalysisManager();
230
231 virtual ~AnalysisManager();
232
233 void Initialize();
234
235 void ProcessDNAHitsVector(const std::vector<const DNAHit*>&);
236
237 void ProcessChromosomeHitMap(const std::map<uint32_t, ChromosomeHit*>&);
238
239 void ProcessPrimary(const G4ThreeVector&, const G4double&, const G4double&);
240
241 void ProcessCellEdep(const G4double&); // dousatsu
242 void Close();
243
244 inline void SetSaveStrands(const G4bool strand) { fSaveStrands = strand; };
245
246 inline void SetStrandDirectory(const G4String& dir) { fStrandDirectory = dir; };
247
248 inline void SetFragmentGap(G4int gap) { fFragmentGap = gap; };
249
250 inline void SetDSBDistance(G4int gap) { fDSBDistance = gap; };
251
252 inline void SetChainToSave(G4int i) { fChainToSave = i; };
253
254 inline void SetFileName(const G4String& name) { fFileName = name; };
255
256 void TestClassification();
257
258 private:
259 G4AnalysisManager* fAnalysisManager;
260 G4bool fSaveStrands = false;
261 G4String fStrandDirectory = "./";
262 G4String fFileName = "molecular-dna";
263 G4int fFragmentGap = 100;
264 G4int fDSBDistance = 10;
265 G4int fChainToSave = -1;
266 DNAGeometry* fpDNAGeometry = nullptr;
267 AnalysisMessenger* fpAnalysisMessenger;
268 };
269
270 #endif // MOLECULAR_ANALYSIS_MANAGER_HH
271