File indexing completed on 2025-02-23 09:22:01
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0027 #include "DNAGeometryMessenger.hh"
0028
0029 #include "DNAGeometry.hh"
0030 #include "UtilityFunctions.hh"
0031
0032 #include "G4UIcmdWith3VectorAndUnit.hh"
0033 #include "G4UIcmdWithABool.hh"
0034 #include "G4UIcmdWithADouble.hh"
0035 #include "G4UIcmdWithADoubleAndUnit.hh"
0036 #include "G4UIcmdWithAString.hh"
0037 #include "G4UIcmdWithAnInteger.hh"
0038 #include "G4UIcmdWithoutParameter.hh"
0039 #include "G4UIdirectory.hh"
0040
0041
0042
0043 DNAGeometryMessenger::DNAGeometryMessenger(DNAGeometry* dnaGeometry)
0044 : fpDNAGeometry(dnaGeometry),
0045 fpDNADirectory(new G4UIdirectory("/dnageom/")),
0046 fpNewPlacementVolumeFile(new G4UIcmdWithAString("/dnageom/placementVolume", this)),
0047 fpVoxelPlacementsFile(new G4UIcmdWithAString("/dnageom/definitionFile", this)),
0048 fpVoxelSideLength(new G4UIcmdWith3VectorAndUnit("/dnageom/placementSize", this)),
0049 fpFractalScaling(new G4UIcmdWith3VectorAndUnit("/dnageom/fractalScaling", this)),
0050 fpAnglesAsPi(new G4UIcmdWithABool("/dnageom/setVoxelPlacementAnglesAsMultiplesOfPi", this)),
0051 fpCustomMoleculeSizes(new G4UIcmdWithABool("/dnageom/useCustomMoleculeSizes", this)),
0052 fpAddMoleculeSize(new G4UIcmdWithAString("/dnageom/moleculeSize", this)),
0053 fpCheckDNAOverlaps(new G4UIcmdWithABool("/dnageom/checkOverlaps", this)),
0054 fpVerbosity(new G4UIcmdWithAnInteger("/dnageom/verbose", this)),
0055 fpSmartless(new G4UIcmdWithAnInteger("/dnageom/setSmartVoxels", this)),
0056 fpIntRangeDirect(new G4UIcmdWithADoubleAndUnit("/dnageom/interactionDirectRange", this)),
0057 fpRadicalKillDistance(new G4UIcmdWithADoubleAndUnit("/dnageom/radicalKillDistance", this)),
0058 fpUseHistoneScav(new G4UIcmdWithABool("/dnageom/activateHistoneScavenging", this)),
0059 fpDrawCellVolumes(new G4UIcmdWithABool("/dnageom/drawCellVolumes", this)),
0060 fpTestDirectory(new G4UIdirectory("/dnatests/")),
0061 fpChromosomeTest(new G4UIcmdWithoutParameter("/dnatests/chromosome", this)),
0062 fpBasePairTest(new G4UIcmdWithoutParameter("/dnatests/basepairs", this)),
0063 fpUniqueIDTest(new G4UIcmdWithoutParameter("/dnatests/uniqueid", this))
0064 {
0065
0066 fpDNADirectory->SetGuidance("Commands to control the fractal.");
0067
0068 fpNewPlacementVolumeFile->SetGuidance("Set a placement volume");
0069 fpNewPlacementVolumeFile->SetGuidance("format: name path");
0070 fpNewPlacementVolumeFile->SetParameterName("name path", false);
0071
0072 fpVoxelPlacementsFile->SetGuidance("Path to file that defines placement locations");
0073 fpVoxelPlacementsFile->SetParameterName("path", false);
0074
0075 fpVoxelSideLength->SetGuidance("Side length for each placement (x, y, z)");
0076 fpVoxelSideLength->SetParameterName("xlength", "ylength", "zlength", false);
0077
0078 fpFractalScaling->SetGuidance("Scaling of XYZ in fractal definition file");
0079 fpFractalScaling->SetParameterName("xlength", "ylength", "zlength", false);
0080
0081 fpAnglesAsPi->SetGuidance("Take the angles in the voxel placement file as multiples of pi");
0082 fpAnglesAsPi->SetGuidance("E.g. set to true if the angle 0.5 should mean 90 degrees");
0083 fpAnglesAsPi->SetParameterName("true/false angles as pi", false);
0084 fpAnglesAsPi->SetDefaultValue(false);
0085
0086 fpAnglesAsPi->SetGuidance("Enable custom molecule sizes");
0087 fpAnglesAsPi->SetGuidance("These can now be set via /dnageom/moleculeSize");
0088 fpAnglesAsPi->SetParameterName("true/false custom sizes", false);
0089 fpAnglesAsPi->SetDefaultValue(false);
0090
0091 fpAddMoleculeSize->SetGuidance("Set a molecule size in angstrom.");
0092 fpAddMoleculeSize->SetGuidance("format: molecule_name x y z");
0093 fpAddMoleculeSize->SetGuidance("E.G.: PHOSPHATE 3 4 5");
0094 fpAddMoleculeSize->SetGuidance("Note: molecule names are case insensitive");
0095 fpAddMoleculeSize->SetParameterName("name x y z units", false);
0096
0097
0098 fpCheckDNAOverlaps->SetGuidance("Check overlaps in DNA geometry region");
0099 fpCheckDNAOverlaps->SetParameterName("true/false check overlaps", false);
0100
0101 fpVerbosity->SetGuidance("Verbosity for DNA geometry");
0102 fpVerbosity->SetParameterName("int verbose level", false);
0103
0104 fpSmartless->SetGuidance("Optimisation value (int) for smart voxels");
0105 fpSmartless->SetGuidance("The G4 default is 2");
0106 fpSmartless->SetParameterName("Optimasation value", false);
0107
0108 fpIntRangeDirect->SetGuidance("Critical range to start recording SSBs from direct effects");
0109 fpIntRangeDirect->SetParameterName("Range", false);
0110
0111 fpRadicalKillDistance->SetGuidance("Distance from base pairs at which to kill radicals");
0112 fpRadicalKillDistance->SetParameterName("Range", false);
0113
0114 fpUseHistoneScav->SetGuidance("Activate Histone scavenging function with default radius");
0115 fpUseHistoneScav->SetGuidance("Radius can be controlled with /dnageom/histoneScavengingRadius");
0116 fpUseHistoneScav->SetParameterName("true/false, set histone scavenging on", false);
0117
0118 fpDrawCellVolumes->SetGuidance(
0119 "Draw cell/chromosome volumes rather than DNA (makes DNA invisible)");
0120 fpDrawCellVolumes->SetParameterName("true/false draw cell volumes", false);
0121
0122
0123 fpTestDirectory->SetGuidance("Tests of the DNA geometry");
0124
0125 fpChromosomeTest->SetGuidance("Test Chromosome Placement classes");
0126
0127 fpBasePairTest->SetGuidance("Test Base Pair indices are correct");
0128
0129 fpUniqueIDTest->SetGuidance("Test Unique ID Algorithm");
0130 }
0131
0132
0133
0134 void DNAGeometryMessenger::SetNewValue(G4UIcommand* command, G4String newValue)
0135 {
0136
0137 if (command == fpNewPlacementVolumeFile.get()) {
0138 std::vector<G4String> cmd = utility::Split(newValue, ' ');
0139
0140 if (!(cmd.size() == 2 || cmd.size() == 3)) {
0141 G4cout << "Invalid input. Command takes 2 string parameters only" << G4endl
0142 << "separated by a space, or three parameters" << G4endl
0143 << "where the last is a boolean." << G4endl;
0144 }
0145 else {
0146 G4String vname = (G4String)cmd[0];
0147 G4String path = (G4String)cmd[1];
0148 G4bool twist = false;
0149 if (cmd.size() == 3) {
0150 if ((G4String)cmd[2] == "true") {
0151 twist = true;
0152 }
0153 else if ((G4String)cmd[2] != "false") {
0154 G4ExceptionDescription errmsg;
0155 errmsg << "Invalid input. Third value must be a boolean"
0156 << "written as true or false." << G4endl;
0157 G4Exception("DNAGeometryMessenger::SetNewValue", "DNAGeometry001", FatalException,
0158 errmsg);
0159 }
0160 }
0161
0162 if (utility::Path_exists(path)) {
0163 fpDNAGeometry->AddVoxelFile(vname, path, twist);
0164 }
0165 else {
0166 G4ExceptionDescription errmsg;
0167 errmsg << path << " has wrong path or does not exist :";
0168 G4Exception("DNAGeometryMessenger::SetNewValue", "DNAGeometry002", FatalException, errmsg);
0169 }
0170 }
0171 }
0172 else if (command == fpVoxelPlacementsFile.get()) {
0173 G4String path = newValue;
0174 if (utility::Path_exists(path)) {
0175 fpDNAGeometry->SetFractalFilename(path);
0176 }
0177 else {
0178 G4ExceptionDescription errmsg;
0179 errmsg << "The fractal file path has wrong path or does not exist : " << path << G4endl;
0180 G4Exception("DNAGeometryMessenger::SetNewValue", "DNAGeometry003", FatalException, errmsg);
0181 }
0182 }
0183 else if (command == fpVoxelSideLength.get()) {
0184 fpDNAGeometry->SetVoxelSideLength(G4UIcmdWith3VectorAndUnit::GetNew3VectorValue(newValue));
0185 }
0186 else if (command == fpFractalScaling.get()) {
0187 fpDNAGeometry->SetFractalScaling(G4UIcmdWith3VectorAndUnit::GetNew3VectorValue(newValue));
0188 }
0189 else if (command == fpAnglesAsPi.get()) {
0190 fpDNAGeometry->SetFractalAnglesAsPi(G4UIcmdWithABool::GetNewBoolValue(newValue));
0191 }
0192 else if (command == fpCustomMoleculeSizes.get()) {
0193 fpDNAGeometry->EnableCustomMoleculeSizes(G4UIcmdWithABool::GetNewBoolValue(newValue));
0194 }
0195 else if (command == fpAddMoleculeSize.get()) {
0196 std::vector<G4String> cmd = utility::Split(newValue, ' ');
0197
0198 if (cmd.size() == 4) {
0199 G4cout << "Invalid input. Command takes 4 parameters only" << G4endl
0200 << "separated by a space, e.g. phosphate 1 2 3" << G4endl;
0201 }
0202 else {
0203 try {
0204 G4String name = cmd[0];
0205 G4int x_size = std::stod(cmd[1]);
0206 G4int y_size = std::stod(cmd[2]);
0207 G4int z_size = std::stod(cmd[3]);
0208 G4ThreeVector molecule_size = G4ThreeVector(x_size, y_size, z_size);
0209 fpDNAGeometry->AddChangeMoleculeSize(name, molecule_size);
0210 }
0211 catch (const std::invalid_argument& ia) {
0212 G4cerr << "Invalid argument to convert to double: " << ia.what() << G4endl;
0213 }
0214 }
0215 }
0216
0217 else if (command == fpCheckDNAOverlaps.get()) {
0218 fpDNAGeometry->SetOverlaps(G4UIcmdWithABool::GetNewBoolValue(newValue));
0219 }
0220 else if (command == fpVerbosity.get()) {
0221 fpDNAGeometry->SetVerbosity(G4UIcmdWithAnInteger::GetNewIntValue(newValue));
0222 }
0223 else if (command == fpSmartless.get()) {
0224 fpDNAGeometry->SetSmartless(G4UIcmdWithAnInteger::GetNewIntValue(newValue));
0225 }
0226 else if (command == fpIntRangeDirect.get()) {
0227 fpDNAGeometry->SetDirectInteractionRange(
0228 G4UIcmdWithADoubleAndUnit::GetNewDoubleValue(newValue));
0229 }
0230 else if (command == fpRadicalKillDistance.get()) {
0231 fpDNAGeometry->SetRadicalKillDistance(G4UIcmdWithADoubleAndUnit::GetNewDoubleValue(newValue));
0232 }
0233 else if (command == fpUseHistoneScav.get()) {
0234 fpDNAGeometry->SetHistoneScav(G4UIcmdWithABool::GetNewBoolValue(newValue));
0235 }
0236 else if (command == fpDrawCellVolumes.get()) {
0237 fpDNAGeometry->SetDrawCellVolumes(G4UIcmdWithABool::GetNewBoolValue(newValue));
0238 }
0239 else if (command == fpChromosomeTest.get()) {
0240 fpDNAGeometry->ChromosomeTest();
0241 }
0242 else if (command == fpBasePairTest.get()) {
0243 fpDNAGeometry->BasePairIndexTest();
0244 }
0245 else if (command == fpUniqueIDTest.get()) {
0246 fpDNAGeometry->UniqueIDTest();
0247 }
0248 }
0249
0250
