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25 //
26 //
27 /// \file PhysGeoImport.hh
28 /// \brief Definition of the PhysGeoImport class
29
30 #ifndef GEOIMPORT_HH
31 #define GEOIMPORT_HH
32
33 #include <map>
34 #include <fstream>
35 #include <algorithm>
36 #include <array>
37 #include "G4String.hh"
38 #include "G4ThreeVector.hh"
39 #include "G4Orb.hh"
40 #include "G4Ellipsoid.hh"
41 #include "G4EllipticalTube.hh"
42 #include "G4VSolid.hh"
43 #include "G4Box.hh"
44 #include "G4SystemOfUnits.hh"
45 #include "G4SubtractionSolid.hh"
46 #include "G4LogicalVolume.hh"
47 #include "G4PVPlacement.hh"
48 #include "G4NistManager.hh"
49 #include "G4VisAttributes.hh"
50 #include "G4IntersectionSolid.hh"
51
52 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
53
54 struct Molecule
55 {
56 Molecule(G4String name, G4int copyNumber, G4ThreeVector position,
57 G4double radius, G4double waterRadius, G4String material, G4int strand)
58 {
59 fName = name;
60 fMaterial = material;
61 fCopyNumber = copyNumber;
62 fPosition = position;
63 fRadius = radius;
64 fRadiusWater = waterRadius;
65 fStrand = strand;
66 }
67
68 G4String fName{""};
69 G4String fMaterial{""};
70
71 G4int fCopyNumber{-1};
72 G4int fStrand{-1};
73
74 G4ThreeVector fPosition;
75
76 G4double fRadius{0.};
77 G4double fRadiusWater{0.};
78
79 // To sort the molecules in function of their z coordinate
80 G4bool operator<(const Molecule& str) const
81 {
82 return (fPosition.z() < str.fPosition.z() );
83 }
84 };
85
86 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
87
88 struct Voxel
89 {
90 enum VoxelType
91 {
92 Straight,
93 Left,
94 Right,
95 Up,
96 Down,
97 Straight2,
98 Left2,
99 Right2,
100 Up2,
101 Down2,
102 Other
103 };
104
105 Voxel(G4int copyNumber, G4int chromoNum, G4int domainNum,
106 VoxelType type, const G4ThreeVector& pos, G4RotationMatrix* rot)
107 {
108 fCopyNumber = copyNumber;
109 fChromoNum = chromoNum;
110 fDomainNum = domainNum;
111 fType = type;
112 fPos = pos;
113 fpRot = rot;
114 }
115
116 G4int fCopyNumber{0};
117 G4int fChromoNum{0};
118 G4int fDomainNum{0};
119 G4ThreeVector fPos;
120 G4RotationMatrix* fpRot{nullptr};
121 VoxelType fType{VoxelType::Other};
122 };
123
124 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
125
126 enum ChromatinType{
127 fUnspecified = 0,
128 fHeterochromatin = 1,
129 fEuchromatin = 2,
130 };
131
132 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
133
134 class PhysGeoImport
135 {
136 public:
137 PhysGeoImport();
138 PhysGeoImport(G4bool isVisu);
139 ~PhysGeoImport() = default;
140
141 void SetFactor(G4double factor){fFactor=factor;}
142
143 G4double GetFactor() const {return fFactor;}
144
145 G4String GetGeoName() const {return fGeoName;}
146
147 // This method will trigger the parse of the file and the build of the geometry
148 G4LogicalVolume* CreateLogicVolume(const G4String& fileName, G4String& voxelName);
149
150 G4LogicalVolume* CreateNucleusLogicVolume(const G4String& fileName);
151
152 std::vector<Voxel>* CreateVoxelsData(const G4String& fileName);
153 std::map<G4String, G4int> GetVoxelNbHistoneMap() {return fVoxelNbHistoneMap;}
154 std::map<G4String, G4int> GetVoxelNbBpMap() {return fVoxelNbBpMap;}
155 unsigned long long GetTotalNbBpPlacedInGeo() {return fTotalNbBpPlacedInGeo;}
156 unsigned long long GetTotalNbHistonePlacedInGeo() {return fTotalNbHistonePlacedInGeo;}
157 G4double GetNucleusVolume() {return fNucleusVolume;}
158 G4double GetVoxelFullSize() {return fSize;}
159 std::map<G4String, G4double> GetNucleusSizeData() {return fNucleusData;}
160 std::map<ChromatinType, unsigned long long> GetChromatinTypeCountMap() {return fChromatinTypeCount;}
161 private:
162
163 G4bool fIsVisu{false};
164
165 // Factor to scale the geometry
166 G4double fFactor{1.};
167
168 G4double fSize{0.};
169 G4double fNucleusVolume{0.};
170 unsigned long long fTotalNbBpPlacedInGeo = 0;
171 unsigned long long fTotalNbHistonePlacedInGeo = 0;
172 G4String fGeoName="";
173
174 G4String fNucleusName="CellNucleus";
175 G4String fNucleusType="";
176 std::map<G4String, G4double> fNucleusData;
177
178 std::map<G4String, G4double> fRadiusMap;
179 std::map<G4String, G4double> fWaterRadiusMap;
180 std::map<G4String, G4int> fVoxelNbBpMap;
181 std::map<G4String, G4int> fVoxelNbHistoneMap;
182
183 // Vector to contain all the molecule structures listed within the imput file
184 std::vector<Molecule> fMolecules;
185
186 // To check if this is the first voxel of the chromosome
187 std::map<G4int, G4bool> fFirstMap;
188
189 // Materials
190 std::vector<G4Material*> fMaterialVect;
191 G4Material* fpWater{nullptr};
192 G4Material* fTHF{nullptr};
193 G4Material* fPY{nullptr};
194 G4Material* fPU{nullptr};
195 G4Material* fTMP{nullptr};
196 G4Material* fSugarMixt{nullptr};
197 G4Material* fDeoxyribose{nullptr};
198 G4Material* fPhosphate{nullptr};
199 G4Material* fCytosine_PY{nullptr};
200 G4Material* fThymine_PY{nullptr};
201 G4Material* fGuanine_PU{nullptr};
202 G4Material* fAdenine_PU{nullptr};
203 G4Material* fHomogeneous_dna{nullptr};
204 G4Material* fVacuum{nullptr};
205 G4String ParseFile(const G4String& fileName);
206 G4VSolid* CreateCutSolid(G4Orb *solidOrbRef,
207 Molecule &molRef,
208 std::vector<Molecule> &molList,
209 G4bool in);
210 void DefineMaterial();
211
212 std::map<ChromatinType, unsigned long long> fChromatinTypeCount;
213 };
214
215 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
216
217 #endif // GEOIMPORT_HH
218