| Geant4 Cross Reference |
1 // 1
2 // *******************************************
3 // * License and Disclaimer
4 // *
5 // * The Geant4 software is copyright of th
6 // * the Geant4 Collaboration. It is provided
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9 // * include a list of copyright holders.
10 // *
11 // * Neither the authors of this software syst
12 // * institutes,nor the agencies providing fin
13 // * work make any representation or warran
14 // * regarding this software system or assum
15 // * use. Please see the license in the file
16 // * for the full disclaimer and the limitatio
17 // *
18 // * This code implementation is the result
19 // * technical work of the GEANT4 collaboratio
20 // * By using, copying, modifying or distri
21 // * any work based on the software) you ag
22 // * use in resulting scientific publicati
23 // * acceptance of all terms of the Geant4 Sof
24 // *******************************************
25 //
26 //
27 #include "DNAGeometryMessenger.hh"
28
29 #include "DNAGeometry.hh"
30 #include "UtilityFunctions.hh"
31
32 #include "G4UIcmdWith3VectorAndUnit.hh"
33 #include "G4UIcmdWithABool.hh"
34 #include "G4UIcmdWithADouble.hh"
35 #include "G4UIcmdWithADoubleAndUnit.hh"
36 #include "G4UIcmdWithAString.hh"
37 #include "G4UIcmdWithAnInteger.hh"
38 #include "G4UIcmdWithoutParameter.hh"
39 #include "G4UIdirectory.hh"
40
41 //....oooOO0OOooo........oooOO0OOooo........oo
42
43 DNAGeometryMessenger::DNAGeometryMessenger(DNA
44 : fpDNAGeometry(dnaGeometry),
45 fpDNADirectory(new G4UIdirectory("/dnageom
46 fpNewPlacementVolumeFile(new G4UIcmdWithAS
47 fpVoxelPlacementsFile(new G4UIcmdWithAStri
48 fpVoxelSideLength(new G4UIcmdWith3VectorAn
49 fpFractalScaling(new G4UIcmdWith3VectorAnd
50 fpAnglesAsPi(new G4UIcmdWithABool("/dnageo
51 fpCustomMoleculeSizes(new G4UIcmdWithABool
52 fpAddMoleculeSize(new G4UIcmdWithAString("
53 fpCheckDNAOverlaps(new G4UIcmdWithABool("/
54 fpVerbosity(new G4UIcmdWithAnInteger("/dna
55 fpSmartless(new G4UIcmdWithAnInteger("/dna
56 fpIntRangeDirect(new G4UIcmdWithADoubleAnd
57 fpRadicalKillDistance(new G4UIcmdWithADoub
58 fpUseHistoneScav(new G4UIcmdWithABool("/dn
59 fpDrawCellVolumes(new G4UIcmdWithABool("/d
60 fpTestDirectory(new G4UIdirectory("/dnates
61 fpChromosomeTest(new G4UIcmdWithoutParamet
62 fpBasePairTest(new G4UIcmdWithoutParameter
63 fpUniqueIDTest(new G4UIcmdWithoutParameter
64 {
65 // Fractals
66 fpDNADirectory->SetGuidance("Commands to con
67
68 fpNewPlacementVolumeFile->SetGuidance("Set a
69 fpNewPlacementVolumeFile->SetGuidance("forma
70 fpNewPlacementVolumeFile->SetParameterName("
71
72 fpVoxelPlacementsFile->SetGuidance("Path to
73 fpVoxelPlacementsFile->SetParameterName("pat
74
75 fpVoxelSideLength->SetGuidance("Side length
76 fpVoxelSideLength->SetParameterName("xlength
77
78 fpFractalScaling->SetGuidance("Scaling of XY
79 fpFractalScaling->SetParameterName("xlength"
80
81 fpAnglesAsPi->SetGuidance("Take the angles i
82 fpAnglesAsPi->SetGuidance("E.g. set to true
83 fpAnglesAsPi->SetParameterName("true/false a
84 fpAnglesAsPi->SetDefaultValue(false);
85
86 fpCustomMoleculeSizes->SetGuidance("Enable c
87 fpCustomMoleculeSizes->SetGuidance("These ca
88 fpCustomMoleculeSizes->SetParameterName("tru
89 fpCustomMoleculeSizes->SetDefaultValue(false
90
91 fpAddMoleculeSize->SetGuidance("Set a molecu
92 fpAddMoleculeSize->SetGuidance("format: mole
93 fpAddMoleculeSize->SetGuidance("E.G.: PHOSPH
94 fpAddMoleculeSize->SetGuidance("Note: molecu
95 fpAddMoleculeSize->SetParameterName("name x
96
97 // control
98 fpCheckDNAOverlaps->SetGuidance("Check overl
99 fpCheckDNAOverlaps->SetParameterName("true/f
100
101 fpVerbosity->SetGuidance("Verbosity for DNA
102 fpVerbosity->SetParameterName("int verbose l
103
104 fpSmartless->SetGuidance("Optimisation value
105 fpSmartless->SetGuidance("The G4 default is
106 fpSmartless->SetParameterName("Optimasation
107
108 fpIntRangeDirect->SetGuidance("Critical rang
109 fpIntRangeDirect->SetParameterName("Range",
110
111 fpRadicalKillDistance->SetGuidance("Distance
112 fpRadicalKillDistance->SetParameterName("Ran
113
114 fpUseHistoneScav->SetGuidance("Activate Hist
115 fpUseHistoneScav->SetGuidance("Radius can be
116 fpUseHistoneScav->SetParameterName("true/fal
117
118 fpDrawCellVolumes->SetGuidance(
119 "Draw cell/chromosome volumes rather than
120 fpDrawCellVolumes->SetParameterName("true/fa
121
122 // Tests
123 fpTestDirectory->SetGuidance("Tests of the D
124
125 fpChromosomeTest->SetGuidance("Test Chromoso
126
127 fpBasePairTest->SetGuidance("Test Base Pair
128
129 fpUniqueIDTest->SetGuidance("Test Unique ID
130 }
131
132 //....oooOO0OOooo........oooOO0OOooo........oo
133
134 void DNAGeometryMessenger::SetNewValue(G4UIcom
135 {
136 // Fractals
137 if (command == fpNewPlacementVolumeFile.get(
138 std::vector<G4String> cmd = utility::Split
139 // input validation
140 if (!(cmd.size() == 2 || cmd.size() == 3))
141 G4cout << "Invalid input. Command takes
142 << "separated by a space, or thre
143 << "where the last is a boolean."
144 }
145 else {
146 G4String vname = (G4String)cmd[0];
147 G4String path = (G4String)cmd[1];
148 G4bool twist = false;
149 if (cmd.size() == 3) {
150 if ((G4String)cmd[2] == "true") {
151 twist = true;
152 }
153 else if ((G4String)cmd[2] != "false")
154 G4ExceptionDescription errmsg;
155 errmsg << "Invalid input. Third valu
156 << "written as true or false.
157 G4Exception("DNAGeometryMessenger::S
158 errmsg);
159 }
160 }
161
162 if (utility::Path_exists(path)) {
163 fpDNAGeometry->AddVoxelFile(vname, pat
164 }
165 else {
166 G4ExceptionDescription errmsg;
167 errmsg << path << " has wrong path or
168 G4Exception("DNAGeometryMessenger::Set
169 }
170 }
171 }
172 else if (command == fpVoxelPlacementsFile.ge
173 G4String path = newValue;
174 if (utility::Path_exists(path)) {
175 fpDNAGeometry->SetFractalFilename(path);
176 }
177 else {
178 G4ExceptionDescription errmsg;
179 errmsg << "The fractal file path has wro
180 G4Exception("DNAGeometryMessenger::SetNe
181 }
182 }
183 else if (command == fpVoxelSideLength.get())
184 fpDNAGeometry->SetVoxelSideLength(G4UIcmdW
185 }
186 else if (command == fpFractalScaling.get())
187 fpDNAGeometry->SetFractalScaling(G4UIcmdWi
188 }
189 else if (command == fpAnglesAsPi.get()) {
190 fpDNAGeometry->SetFractalAnglesAsPi(G4UIcm
191 }
192 else if (command == fpCustomMoleculeSizes.ge
193 fpDNAGeometry->EnableCustomMoleculeSizes(G
194 }
195 else if (command == fpAddMoleculeSize.get())
196 std::vector<G4String> cmd = utility::Split
197 // input validation
198 if (cmd.size() == 4) {
199 G4cout << "Invalid input. Command takes
200 << "separated by a space, e.g. ph
201 }
202 else {
203 try {
204 G4String name = cmd[0];
205 G4int x_size = std::stod(cmd[1]);
206 G4int y_size = std::stod(cmd[2]);
207 G4int z_size = std::stod(cmd[3]);
208 G4ThreeVector molecule_size = G4ThreeV
209 fpDNAGeometry->AddChangeMoleculeSize(n
210 }
211 catch (const std::invalid_argument& ia)
212 G4cerr << "Invalid argument to convert
213 }
214 }
215 }
216 // control
217 else if (command == fpCheckDNAOverlaps.get()
218 fpDNAGeometry->SetOverlaps(G4UIcmdWithABoo
219 }
220 else if (command == fpVerbosity.get()) {
221 fpDNAGeometry->SetVerbosity(G4UIcmdWithAnI
222 }
223 else if (command == fpSmartless.get()) {
224 fpDNAGeometry->SetSmartless(G4UIcmdWithAnI
225 }
226 else if (command == fpIntRangeDirect.get())
227 fpDNAGeometry->SetDirectInteractionRange(
228 G4UIcmdWithADoubleAndUnit::GetNewDoubleV
229 }
230 else if (command == fpRadicalKillDistance.ge
231 fpDNAGeometry->SetRadicalKillDistance(G4UI
232 }
233 else if (command == fpUseHistoneScav.get())
234 fpDNAGeometry->SetHistoneScav(G4UIcmdWithA
235 }
236 else if (command == fpDrawCellVolumes.get())
237 fpDNAGeometry->SetDrawCellVolumes(G4UIcmdW
238 }
239 else if (command == fpChromosomeTest.get())
240 fpDNAGeometry->ChromosomeTest();
241 }
242 else if (command == fpBasePairTest.get()) {
243 fpDNAGeometry->BasePairIndexTest();
244 }
245 else if (command == fpUniqueIDTest.get()) {
246 fpDNAGeometry->UniqueIDTest();
247 }
248 }
249
250 //....oooOO0OOooo........oooOO0OOooo........oo
251