| Geant4 Cross Reference |
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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........oooOO0OOooo........oooOO0OOooo......
42
43 DNAGeometryMessenger::DNAGeometryMessenger(DNAGeometry* dnaGeometry)
44 : fpDNAGeometry(dnaGeometry),
45 fpDNADirectory(new G4UIdirectory("/dnageom/")),
46 fpNewPlacementVolumeFile(new G4UIcmdWithAString("/dnageom/placementVolume", this)),
47 fpVoxelPlacementsFile(new G4UIcmdWithAString("/dnageom/definitionFile", this)),
48 fpVoxelSideLength(new G4UIcmdWith3VectorAndUnit("/dnageom/placementSize", this)),
49 fpFractalScaling(new G4UIcmdWith3VectorAndUnit("/dnageom/fractalScaling", this)),
50 fpAnglesAsPi(new G4UIcmdWithABool("/dnageom/setVoxelPlacementAnglesAsMultiplesOfPi", this)),
51 fpCustomMoleculeSizes(new G4UIcmdWithABool("/dnageom/useCustomMoleculeSizes", this)),
52 fpAddMoleculeSize(new G4UIcmdWithAString("/dnageom/moleculeSize", this)),
53 fpCheckDNAOverlaps(new G4UIcmdWithABool("/dnageom/checkOverlaps", this)),
54 fpVerbosity(new G4UIcmdWithAnInteger("/dnageom/verbose", this)),
55 fpSmartless(new G4UIcmdWithAnInteger("/dnageom/setSmartVoxels", this)),
56 fpIntRangeDirect(new G4UIcmdWithADoubleAndUnit("/dnageom/interactionDirectRange", this)),
57 fpRadicalKillDistance(new G4UIcmdWithADoubleAndUnit("/dnageom/radicalKillDistance", this)),
58 fpUseHistoneScav(new G4UIcmdWithABool("/dnageom/activateHistoneScavenging", this)),
59 fpDrawCellVolumes(new G4UIcmdWithABool("/dnageom/drawCellVolumes", this)),
60 fpTestDirectory(new G4UIdirectory("/dnatests/")),
61 fpChromosomeTest(new G4UIcmdWithoutParameter("/dnatests/chromosome", this)),
62 fpBasePairTest(new G4UIcmdWithoutParameter("/dnatests/basepairs", this)),
63 fpUniqueIDTest(new G4UIcmdWithoutParameter("/dnatests/uniqueid", this))
64 {
65 // Fractals
66 fpDNADirectory->SetGuidance("Commands to control the fractal.");
67
68 fpNewPlacementVolumeFile->SetGuidance("Set a placement volume");
69 fpNewPlacementVolumeFile->SetGuidance("format: name path");
70 fpNewPlacementVolumeFile->SetParameterName("name path", false);
71
72 fpVoxelPlacementsFile->SetGuidance("Path to file that defines placement locations");
73 fpVoxelPlacementsFile->SetParameterName("path", false);
74
75 fpVoxelSideLength->SetGuidance("Side length for each placement (x, y, z)");
76 fpVoxelSideLength->SetParameterName("xlength", "ylength", "zlength", false);
77
78 fpFractalScaling->SetGuidance("Scaling of XYZ in fractal definition file");
79 fpFractalScaling->SetParameterName("xlength", "ylength", "zlength", false);
80
81 fpAnglesAsPi->SetGuidance("Take the angles in the voxel placement file as multiples of pi");
82 fpAnglesAsPi->SetGuidance("E.g. set to true if the angle 0.5 should mean 90 degrees");
83 fpAnglesAsPi->SetParameterName("true/false angles as pi", false);
84 fpAnglesAsPi->SetDefaultValue(false);
85
86 fpCustomMoleculeSizes->SetGuidance("Enable custom molecule sizes");
87 fpCustomMoleculeSizes->SetGuidance("These can now be set via /dnageom/moleculeSize");
88 fpCustomMoleculeSizes->SetParameterName("true/false custom sizes", false);
89 fpCustomMoleculeSizes->SetDefaultValue(false);
90
91 fpAddMoleculeSize->SetGuidance("Set a molecule size in angstrom.");
92 fpAddMoleculeSize->SetGuidance("format: molecule_name x y z");
93 fpAddMoleculeSize->SetGuidance("E.G.: PHOSPHATE 3 4 5");
94 fpAddMoleculeSize->SetGuidance("Note: molecule names are case insensitive");
95 fpAddMoleculeSize->SetParameterName("name x y z units", false);
96
97 // control
98 fpCheckDNAOverlaps->SetGuidance("Check overlaps in DNA geometry region");
99 fpCheckDNAOverlaps->SetParameterName("true/false check overlaps", false);
100
101 fpVerbosity->SetGuidance("Verbosity for DNA geometry");
102 fpVerbosity->SetParameterName("int verbose level", false);
103
104 fpSmartless->SetGuidance("Optimisation value (int) for smart voxels");
105 fpSmartless->SetGuidance("The G4 default is 2");
106 fpSmartless->SetParameterName("Optimasation value", false);
107
108 fpIntRangeDirect->SetGuidance("Critical range to start recording SSBs from direct effects");
109 fpIntRangeDirect->SetParameterName("Range", false);
110
111 fpRadicalKillDistance->SetGuidance("Distance from base pairs at which to kill radicals");
112 fpRadicalKillDistance->SetParameterName("Range", false);
113
114 fpUseHistoneScav->SetGuidance("Activate Histone scavenging function with default radius");
115 fpUseHistoneScav->SetGuidance("Radius can be controlled with /dnageom/histoneScavengingRadius");
116 fpUseHistoneScav->SetParameterName("true/false, set histone scavenging on", false);
117
118 fpDrawCellVolumes->SetGuidance(
119 "Draw cell/chromosome volumes rather than DNA (makes DNA invisible)");
120 fpDrawCellVolumes->SetParameterName("true/false draw cell volumes", false);
121
122 // Tests
123 fpTestDirectory->SetGuidance("Tests of the DNA geometry");
124
125 fpChromosomeTest->SetGuidance("Test Chromosome Placement classes");
126
127 fpBasePairTest->SetGuidance("Test Base Pair indices are correct");
128
129 fpUniqueIDTest->SetGuidance("Test Unique ID Algorithm");
130 }
131
132 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
133
134 void DNAGeometryMessenger::SetNewValue(G4UIcommand* command, G4String newValue)
135 {
136 // Fractals
137 if (command == fpNewPlacementVolumeFile.get()) {
138 std::vector<G4String> cmd = utility::Split(newValue, ' ');
139 // input validation
140 if (!(cmd.size() == 2 || cmd.size() == 3)) {
141 G4cout << "Invalid input. Command takes 2 string parameters only" << G4endl
142 << "separated by a space, or three parameters" << G4endl
143 << "where the last is a boolean." << G4endl;
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 value must be a boolean"
156 << "written as true or false." << G4endl;
157 G4Exception("DNAGeometryMessenger::SetNewValue", "DNAGeometry001", FatalException,
158 errmsg);
159 }
160 }
161
162 if (utility::Path_exists(path)) {
163 fpDNAGeometry->AddVoxelFile(vname, path, twist);
164 }
165 else {
166 G4ExceptionDescription errmsg;
167 errmsg << path << " has wrong path or does not exist :";
168 G4Exception("DNAGeometryMessenger::SetNewValue", "DNAGeometry002", FatalException, errmsg);
169 }
170 }
171 }
172 else if (command == fpVoxelPlacementsFile.get()) {
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 wrong path or does not exist : " << path << G4endl;
180 G4Exception("DNAGeometryMessenger::SetNewValue", "DNAGeometry003", FatalException, errmsg);
181 }
182 }
183 else if (command == fpVoxelSideLength.get()) {
184 fpDNAGeometry->SetVoxelSideLength(G4UIcmdWith3VectorAndUnit::GetNew3VectorValue(newValue));
185 }
186 else if (command == fpFractalScaling.get()) {
187 fpDNAGeometry->SetFractalScaling(G4UIcmdWith3VectorAndUnit::GetNew3VectorValue(newValue));
188 }
189 else if (command == fpAnglesAsPi.get()) {
190 fpDNAGeometry->SetFractalAnglesAsPi(G4UIcmdWithABool::GetNewBoolValue(newValue));
191 }
192 else if (command == fpCustomMoleculeSizes.get()) {
193 fpDNAGeometry->EnableCustomMoleculeSizes(G4UIcmdWithABool::GetNewBoolValue(newValue));
194 }
195 else if (command == fpAddMoleculeSize.get()) {
196 std::vector<G4String> cmd = utility::Split(newValue, ' ');
197 // input validation
198 if (cmd.size() == 4) {
199 G4cout << "Invalid input. Command takes 4 parameters only" << G4endl
200 << "separated by a space, e.g. phosphate 1 2 3" << G4endl;
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 = G4ThreeVector(x_size, y_size, z_size);
209 fpDNAGeometry->AddChangeMoleculeSize(name, molecule_size);
210 }
211 catch (const std::invalid_argument& ia) {
212 G4cerr << "Invalid argument to convert to double: " << ia.what() << G4endl;
213 }
214 }
215 }
216 // control
217 else if (command == fpCheckDNAOverlaps.get()) {
218 fpDNAGeometry->SetOverlaps(G4UIcmdWithABool::GetNewBoolValue(newValue));
219 }
220 else if (command == fpVerbosity.get()) {
221 fpDNAGeometry->SetVerbosity(G4UIcmdWithAnInteger::GetNewIntValue(newValue));
222 }
223 else if (command == fpSmartless.get()) {
224 fpDNAGeometry->SetSmartless(G4UIcmdWithAnInteger::GetNewIntValue(newValue));
225 }
226 else if (command == fpIntRangeDirect.get()) {
227 fpDNAGeometry->SetDirectInteractionRange(
228 G4UIcmdWithADoubleAndUnit::GetNewDoubleValue(newValue));
229 }
230 else if (command == fpRadicalKillDistance.get()) {
231 fpDNAGeometry->SetRadicalKillDistance(G4UIcmdWithADoubleAndUnit::GetNewDoubleValue(newValue));
232 }
233 else if (command == fpUseHistoneScav.get()) {
234 fpDNAGeometry->SetHistoneScav(G4UIcmdWithABool::GetNewBoolValue(newValue));
235 }
236 else if (command == fpDrawCellVolumes.get()) {
237 fpDNAGeometry->SetDrawCellVolumes(G4UIcmdWithABool::GetNewBoolValue(newValue));
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........oooOO0OOooo........oooOO0OOooo......
251