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File indexing completed on 2025-10-13 08:25:10 

0001 //-------------------------------------------------------------------------------//
0002 // This macrofile was developed by Konstantinos Chatzipapas at LP2iB (ex. CENBG) //
0003 // in collaboration with the whole team of molecularDNA Geant4-DNA example       //
0004 // For any question please contact through:                                      //
0005 // k.chatzipapas@yahoo.com                                                       //
0006 //-------------------------------------------------------------------------------//
0007 //
0008 // This macro requires the molecular-dna.root file generated from molecularDNA example
0009 // To run this file just insert this command to the terminal:
0010 // root .X human_cell_alphas.C
0011 // ROOT6.x should be installed
0012 //
0013 
0014 {
0015 //*******************************************************************************//
0016 // If you need to add multiple root outputs, by multithreading, use this command:
0017 system ("hadd -O -f molecular-dna.root molecular-dna_t*.root");
0018 
0019 // Define these parameters of the simulation
0020 char ifile[256] = "molecular-dna.root";  // input filepath to be replaced
0021 
0022 //for HTB
0023 Double_t r3 = 8550e-9 * 2500e-9 * 6425e-9; // a * b * c
0024 Double_t Nbp = 6454.227202; // Mbp // Length of the DNA chain in Mbp
0025 
0026 // for MCF
0027 //Double_t r3 = 7005e-9 * 2500e-9 * 5300e-9; // a * b * c
0028 //Double_t Nbp = 6424.831996; // Mbp // Length of the DNA chain in Mbp // for MCF
0029 
0030 Double_t mass = 997 * 4 * 3.141592 * r3 / 3 ;  // density * 4/3 * pi * r3
0031 ///////////////////////////////////////////////////////////////////////////////////
0032 //*******************************************************************************//
0033 
0034 typedef std::pair <int64_t, int64_t> ipair;
0035 bool greaterPair(const ipair &l, const ipair &r);
0036 bool smallerPair(const ipair &l, const ipair &r);
0037 
0038 void BinLogX(TH1 *h);
0039 
0040 gROOT->Reset();
0041 gStyle->SetPalette(1);
0042 gROOT->SetStyle("Plain");
0043 gStyle->SetOptStat(00000);
0044 
0045 // Initialize output histograms
0046 TCanvas *cfragment = new TCanvas("cfragment","DNA Fragments Distribution", 900, 120, 600,400);
0047 cfragment->SetLogx();
0048 cfragment->SetLogy();
0049 TH1F *h1fragments = new TH1F("h1fragments","h1fragments",40,0,5);
0050 BinLogX(h1fragments);
0051 
0052 TCanvas *c1 = new TCanvas("c1", "Molecular DNA - Damage Quantification", 60, 120, 800, 800);
0053 c1->SetBorderSize(0);
0054 c1->SetFillColor(0);
0055 c1->SetFillStyle(4000);
0056 gPad->SetLeftMargin(0.13);
0057 
0058 TPad* pad1 = new TPad("pad1","Species", 0, 0.51, 0.49, 1);
0059 pad1->SetBorderSize(0);
0060 pad1->SetFillColor(0);
0061 pad1->SetFillStyle(4000);
0062 pad1->SetLeftMargin(0.15);
0063 pad1->SetRightMargin(0.01);
0064 pad1->SetBottomMargin(0.2);
0065 
0066 TPad* pad2 = new TPad("pad2","Damage Yield", 0.51, 0.5, 1, 1);
0067 pad2->SetBorderSize(0);
0068 pad2->SetFillColor(0);
0069 pad2->SetFillStyle(4000);
0070 pad2->SetLeftMargin(0.15);
0071 pad2->SetRightMargin(0.05);
0072 pad2->SetBottomMargin(0.2);
0073 
0074 TPad* pad3 = new TPad("pad3","Breaks Yield SSB", 0, 0, 0.49, 0.49);
0075 pad3->SetBorderSize(0);
0076 pad3->SetFillColor(0);
0077 pad3->SetFillStyle(4000);
0078 pad3->SetLeftMargin(0.15);
0079 pad3->SetRightMargin(0.01);
0080 //pad3->SetTopMargin(0.2);
0081 pad3->SetBottomMargin(0.2);
0082 
0083 TPad* pad4 = new TPad("pad4","Breaks Yield DSB", 0.51, 0, 1, 0.49);
0084 pad4->SetBorderSize(0);
0085 pad4->SetFillColor(0);
0086 pad4->SetFillStyle(4000);
0087 pad4->SetLeftMargin(0.15);
0088 pad4->SetRightMargin(0.05);
0089 //pad3->SetTopMargin(0.2);
0090 pad4->SetBottomMargin(0.2);
0091 
0092 pad1->Draw();
0093 pad2->Draw();
0094 pad3->Draw();
0095 pad4->Draw();
0096 
0097 // Open root file
0098 TFile *f = TFile::Open(ifile);
0099 
0100 // Initialize Variables
0101 Int_t EB, ES, OHB, OHS, HB, HS, FL;
0102 Int_t total_EB, total_ES, total_OHB, total_OHS, total_HB, total_HS, total_FL;
0103 Float_t total_EB2, total_ES2, total_OHB2, total_OHS2, total_HB2, total_HS2, total_FL2;
0104 Float_t SD_EB, SD_ES, SD_OHB, SD_OHS, SD_HB, SD_HS;
0105 Float_t SD_SSB, SD_SSBp, SD_SSB2p, SD_sSSB, SD_SSBd, SD_SSBi, SD_SSBm;
0106 Float_t SD_DSB, SD_DSBp, SD_DSBpp, SD_sDSB, SD_DSBd, SD_DSBi, SD_DSBm, SD_DSBh;
0107 
0108 Int_t SSB, SSBp, SSB2p;
0109 Int_t total_SSB, total_SSBp, total_SSB2p;
0110 Float_t total_SSB2, total_SSBp2, total_SSB2p2;
0111 Int_t DSB, DSBp, DSBpp;
0112 Int_t total_DSB, total_DSBp, total_DSBpp;
0113 Float_t total_DSB2, total_DSBp2, total_DSBpp2;
0114 
0115 Int_t SSBd, SSBi, SSBm;
0116 Int_t total_sSSB, total_SSBd, total_SSBi, total_SSBm;
0117 Float_t total_sSSB2, total_SSBd2, total_SSBi2, total_SSBm2;
0118 Int_t DSBd, DSBi, DSBm, DSBh;
0119 Int_t total_sDSB, total_DSBd, total_DSBi, total_DSBm, total_DSBh;
0120 Float_t total_sDSB2, total_DSBd2, total_DSBi2, total_DSBm2, total_DSBh2;
0121 
0122 Double_t dose = 0;
0123 Double_t SD_dose = 0;
0124 
0125 Double_t EB_yield = 0; Double_t ES_yield = 0; Double_t OHB_yield = 0; Double_t OHS_yield = 0; Double_t HB_yield = 0; Double_t HS_yield = 0;
0126 Double_t SD_EB_yield = 0; Double_t SD_ES_yield = 0; Double_t SD_OHB_yield = 0; Double_t SD_OHS_yield = 0; Double_t SD_HB_yield = 0; Double_t SD_HS_yield = 0;
0127 
0128 Double_t SSB_yield = 0; Double_t SSBp_yield = 0; Double_t SSB2p_yield = 0;
0129 Double_t SD_SSB_yield = 0; Double_t SD_SSBp_yield = 0; Double_t SD_SSB2p_yield = 0;
0130 Double_t DSB_yield = 0; Double_t DSBp_yield = 0; Double_t DSBpp_yield = 0;
0131 Double_t SD_DSB_yield = 0; Double_t SD_DSBp_yield = 0; Double_t SD_DSBpp_yield = 0;
0132 
0133 Double_t sSSB_yield = 0; Double_t SSBi_yield = 0; Double_t SSBd_yield = 0; Double_t SSBm_yield = 0;
0134 Double_t SD_sSSB_yield = 0; Double_t SD_SSBi_yield = 0; Double_t SD_SSBd_yield = 0; Double_t SD_SSBm_yield = 0;
0135 Double_t sDSB_yield = 0; Double_t DSBi_yield = 0; Double_t DSBd_yield = 0; Double_t DSBm_yield = 0; Double_t DSBh_yield = 0;
0136 Double_t SD_sDSB_yield = 0; Double_t SD_DSBi_yield = 0; Double_t SD_DSBd_yield = 0; Double_t SD_DSBm_yield = 0; Double_t SD_DSBh_yield = 0;
0137 
0138 total_EB  = 0; total_ES = 0; total_OHB = 0; total_OHS = 0; total_HB = 0; total_HS = 0;
0139 
0140 total_SSB  = 0; total_SSBp = 0; total_SSB2p = 0;
0141 total_SSB2  = 0; total_SSBp2 = 0; total_SSB2p2 = 0;
0142 total_DSB  = 0; total_DSBp = 0; total_DSBpp = 0;
0143 total_DSB2  = 0; total_DSBp2 = 0; total_DSBpp2 = 0;
0144 
0145 total_sSSB = 0; total_SSBd = 0; total_SSBi = 0; total_SSBm = 0;
0146 total_sSSB2 = 0; total_SSBd2 = 0; total_SSBi2 = 0; total_SSBm2 = 0;
0147 total_sDSB = 0; total_DSBd = 0; total_DSBi = 0; total_DSBm = 0; total_DSBh = 0;
0148 total_sDSB2 = 0; total_DSBd2 = 0; total_DSBi2 = 0; total_DSBm2 = 0;  total_DSBh2 = 0;
0149 
0150 Double_t eVtoJ = 1.60218e-19;
0151 Double_t EnergyDeposited_eV = 0;
0152 Double_t acc_edep = 0;
0153 Double_t acc_edep2 = 0;
0154 
0155 Double_t Energy;
0156 Double_t BPID;
0157 Char_t Primary;
0158 char *primaryName = new char[32];
0159 char *type= new char[256];
0160 
0161 // Read trees and leaves from root file, and give values to variables
0162 TTree* tree = (TTree*) f->Get("tuples/primary_source");
0163 Float_t number = (Float_t) tree->GetEntries();
0164 
0165 if (number<2) {
0166   std::cout << "Not enough entries in the \"primary_source\" TTree (" << (long)number << " entries)\n";
0167   gApplication->Terminate(0);
0168 }
0169 
0170 vector<pair<int,int64_t>> DSBBPID;
0171 
0172 // For reading species production
0173 tree = (TTree*) f->Get("tuples/damage");
0174 tree->SetBranchAddress("Primary",           &Primary);
0175 tree->SetBranchAddress("Energy",            &Energy);
0176 tree->SetBranchAddress("EaqBaseHits",       &EB);
0177 tree->SetBranchAddress("EaqStrandHits",     &ES);
0178 tree->SetBranchAddress("OHBaseHits",        &OHB);
0179 tree->SetBranchAddress("OHStrandHits",      &OHS);
0180 tree->SetBranchAddress("HBaseHits",         &HB);
0181 tree->SetBranchAddress("HStrandHits",       &HS);
0182 tree->SetBranchAddress("TypeClassification", type);
0183 tree->SetBranchAddress("BasePair",          &BPID);
0184 
0185 
0186 Long64_t nentries = tree->GetEntries();
0187 for(int i = 0;i<nentries;i++){
0188   tree->GetEntry(i);
0189 
0190   total_EB   += EB;
0191   total_EB2  += pow(EB,2);
0192   total_ES   += ES;
0193   total_ES2  += pow(ES,2);
0194   total_OHB  += OHB;
0195   total_OHB2 += pow(OHB,2);
0196   total_OHS  += OHS;
0197   total_OHS2 += pow(OHS,2);
0198   total_HB   += HB;
0199   total_HB2  += pow(HB,2);
0200   total_HS   += HS;
0201   total_HS2  += pow(HS,2);
0202 
0203   if((string)type=="DSB"||(string)type=="DSB+"||(string)type=="DSB++"){
0204     //cout << "DSB:"<<type<<endl;
0205     DSBBPID.push_back(make_pair(i,(int64_t)BPID));
0206     }
0207 
0208   }
0209 
0210 // Find the number of fragments that have been produced, but first test if there are enough breaks.
0211 // If no more than 2 DSBs exist in the DSBBPID vector ( DSBBPID.size() is 0 or 1 ),
0212 // the subtraction DSBBPID.size() - 1 makes the loop condition evaluate to ie < -1 (in unsigned terms,
0213 // this becomes a large number, which is incorrect) and leads to undefined behavior (crash).
0214 if (DSBBPID.size() < 2) {
0215     std::cerr << "Not enough damage to create fragments distribution." << std::endl;
0216     //return;
0217 }
0218 if (DSBBPID.size() >= 2) {
0219   // Sort DSBs from the one with lower ID value to the one with higher ID value
0220   sort(DSBBPID.begin(),  DSBBPID.end(), smallerPair);
0221   for(int ie = 0;ie<DSBBPID.size()-1;ie++){
0222     int64_t dsbfragment = DSBBPID[ie+1].second-DSBBPID[ie].second;
0223 
0224     double val       = (double)dsbfragment/1000.;
0225     double meanw     = h1fragments->GetBinCenter(h1fragments->FindBin(val));
0226     double binw      = h1fragments->GetBinWidth (h1fragments->FindBin(val));
0227     h1fragments->Fill(val,1./binw/1000);//bp-1
0228     //cout <<"val:"<<val<<endl;
0229     }
0230 }
0231 
0232 // Calculate the SEM
0233 SD_EB  = sqrt(abs(((total_EB2  / number) - pow(total_EB  / number,2)))/(number -1));
0234 SD_ES  = sqrt(abs(((total_ES2  / number) - pow(total_ES  / number,2)))/(number -1));
0235 SD_OHB = sqrt(abs(((total_OHB2 / number) - pow(total_OHB / number,2)))/(number -1));
0236 SD_OHS = sqrt(abs(((total_OHS2 / number) - pow(total_OHS / number,2)))/(number -1));
0237 SD_HB  = sqrt(abs(((total_HB2  / number) - pow(total_HB  / number,2)))/(number -1));
0238 SD_HS  = sqrt(abs(((total_HS2  / number) - pow(total_HS  / number,2)))/(number -1));
0239 
0240 // Read damage classification SSB, SSB+, 2SSB, DSB, DSB+, DSB++
0241 // As they have been defined in: Nikjoo, H., O’Neill, O., Goodhead, T., & Terrissol, M. 1997,
0242 // Computational modelling of low-energy electron-induced DNA damage by early physical
0243 // and chemical events, International Journal of Radiation Biology, 71, 467.
0244 tree = (TTree *) f->Get("tuples/classification");
0245 tree->SetBranchAddress("Primary",&Primary);
0246 tree->SetBranchAddress("Energy", &Energy);
0247 tree->SetBranchAddress("SSB",    &SSB);
0248 tree->SetBranchAddress("SSBp",   &SSBp);
0249 // Check
0250 //tree->SetBranchAddress("SSB2",   &SSB2p);
0251 tree->SetBranchAddress("2SSB",   &SSB2p);
0252 //
0253 tree->SetBranchAddress("DSB",    &DSB);
0254 tree->SetBranchAddress("DSBp",   &DSBp);
0255 tree->SetBranchAddress("DSBpp",  &DSBpp);
0256 
0257 
0258 Long64_t nentriesC = tree->GetEntries();
0259 for(int i = 0;i<nentriesC;i++){
0260   tree->GetEntry(i);
0261 
0262   total_SSBp   += SSBp;
0263   total_SSBp2  += pow(SSBp,2);
0264   total_SSB2p  += SSB2p;
0265   total_SSB2p2 += pow(SSB2p,2);
0266   total_SSB    += SSB;
0267   total_SSB2   += pow(SSB,2);
0268 
0269   total_DSBp   += DSBp;
0270   total_DSBp2  += pow(DSBp,2);
0271   total_DSBpp  += DSBpp;
0272   total_DSBpp2 += pow(DSBpp,2);
0273   total_DSB    += DSB;
0274   total_DSB2   += pow(DSB,2);
0275 
0276   }
0277 
0278 // Calculate the SEM
0279 SD_SSB   = sqrt(abs(((total_SSB2   / number) - pow(total_SSB   / number,2)))/(number -1));
0280 SD_SSBp  = sqrt(abs(((total_SSBp2  / number) - pow(total_SSBp  / number,2)))/(number -1));
0281 SD_SSB2p = sqrt(abs(((total_SSB2p2 / number) - pow(total_SSB2p / number,2)))/(number -1));
0282 
0283 SD_DSB   = sqrt(abs(((total_DSB2   / number) - pow(total_DSB   / number,2)))/(number -1));
0284 SD_DSBp  = sqrt(abs(((total_DSBp2  / number) - pow(total_DSBp  / number,2)))/(number -1));
0285 SD_DSBpp = sqrt(abs(((total_DSBpp2 / number) - pow(total_DSBpp / number,2)))/(number -1));
0286 
0287 // Read damage classification SSBd, SSBi, SSBm, DSBd, DSBi, DSBm, DSBh
0288 // As they have been defined in: Nikjoo, H., O’Neill, O., Goodhead, T., & Terrissol, M. 1997,
0289 // Computational modelling of low-energy electron-induced DNA damage by early physical
0290 // and chemical events, International Journal of Radiation Biology, 71, 467.
0291 tree = (TTree *) f->Get("tuples/source");
0292 tree->SetBranchAddress("Primary",primaryName);
0293 tree->SetBranchAddress("Energy", &Energy);
0294 tree->SetBranchAddress("SSBd",   &SSBd);
0295 tree->SetBranchAddress("SSBi",   &SSBi);
0296 tree->SetBranchAddress("SSBm",   &SSBm);
0297 tree->SetBranchAddress("DSBd",   &DSBd);
0298 tree->SetBranchAddress("DSBi",   &DSBi);
0299 tree->SetBranchAddress("DSBm",   &DSBm);
0300 tree->SetBranchAddress("DSBh",   &DSBh);
0301 
0302 Long64_t nentriesS = tree->GetEntries();
0303 for(int i = 0;i<nentriesS;i++){
0304   tree->GetEntry(i);
0305 
0306   total_SSBd += SSBd;
0307   total_SSBd2 += pow((SSBd),2);
0308   total_SSBi += SSBi;
0309   total_SSBi2 += pow((SSBi),2);
0310   total_SSBm += SSBm;
0311   total_SSBm2 += pow((SSBm),2);
0312   total_sSSB += SSBd + SSBi + SSBm;
0313   total_sSSB2 += pow((SSBd+SSBi+SSBm),2);
0314 
0315   total_DSBd  += DSBd;
0316   total_DSBd2 += pow(DSBd,2);
0317   total_DSBi  += DSBi;
0318   total_DSBi2 += pow(DSBi,2);
0319   total_DSBm  += DSBm;
0320   total_DSBm2 += pow(DSBm,2);
0321   total_DSBh  += DSBh;
0322   total_DSBh2 += pow(DSBh,2);
0323   total_sDSB  += DSBd + DSBi + DSBm + DSBh;
0324   total_sDSB2 += pow((DSBd+DSBi+DSBm+DSBh),2);
0325 
0326   }
0327 
0328 // Calculate the SEM
0329 SD_sSSB = sqrt(abs(((total_sSSB2 / number) - pow(total_sSSB / number,2)))/(number -1));
0330 SD_SSBd = sqrt(abs(((total_SSBd2 / number) - pow(total_SSBd / number,2)))/(number -1));
0331 SD_SSBi = sqrt(abs(((total_SSBi2 / number) - pow(total_SSBi / number,2)))/(number -1));
0332 SD_SSBm = sqrt(abs(((total_SSBm2 / number) - pow(total_SSBm / number,2)))/(number -1));
0333 
0334 SD_sDSB = sqrt(abs(((total_sDSB2 / number) - pow(total_sDSB / number,2)))/(number -1));
0335 SD_DSBd = sqrt(abs(((total_DSBd2 / number) - pow(total_DSBd / number,2)))/(number -1));
0336 SD_DSBi = sqrt(abs(((total_DSBi2 / number) - pow(total_DSBi / number,2)))/(number -1));
0337 SD_DSBm = sqrt(abs(((total_DSBm2 / number) - pow(total_DSBm / number,2)))/(number -1));
0338 SD_DSBh = sqrt(abs(((total_DSBh2 / number) - pow(total_DSBh / number,2)))/(number -1));
0339 
0340 
0341 // Measure the Deposited Energy in the whole volume that includes DNA chain
0342 
0343 tree = (TTree *) f->Get("tuples/chromosome_hits");
0344 tree->SetBranchAddress("e_chromosome_kev",&EnergyDeposited_eV);
0345 nentries = tree->GetEntries();
0346 for(int i = 0;i<nentries;i++){
0347   tree->GetEntry(i);
0348   acc_edep += EnergyDeposited_eV *1e3;
0349   acc_edep2 += EnergyDeposited_eV *EnergyDeposited_eV *1e6;
0350 }
0351 tree->SetBranchAddress("e_dna_kev",&EnergyDeposited_eV);
0352 nentries = tree->GetEntries();
0353 for(int i = 0;i<nentries;i++){
0354   tree->GetEntry(i);
0355   acc_edep += EnergyDeposited_eV *1e3;
0356   acc_edep2 += EnergyDeposited_eV *EnergyDeposited_eV *1e6;
0357 }
0358 
0359 // Close the root file to free space
0360 f->Close();
0361 
0362 // Calculate the absorbed dose
0363 dose = acc_edep * eVtoJ / mass;
0364 cout << acc_edep << "\n";
0365 
0366 // This is a normalization factor to produce the output in Gy-1 Gbp-1, or else.
0367 // Default value is 1 to produce the result in Gy-1 Mbp-1
0368 // It changes Mbp to Gbp. Some other changes may be needed in graphs section (name of axes)
0369 double norm = 1000;
0370 
0371 // Calculate the yields, together with their error
0372 EB_yield  = (Double_t) total_EB  / dose / Nbp;
0373 ES_yield  = (Double_t) total_ES  / dose / Nbp;
0374 OHB_yield = (Double_t) total_OHB / dose / Nbp;
0375 OHS_yield = (Double_t) total_OHS / dose / Nbp;
0376 HB_yield  = (Double_t) total_HB  / dose / Nbp;
0377 HS_yield  = (Double_t) total_HS  / dose / Nbp;
0378 
0379 SD_EB_yield  = SD_EB  / dose / Nbp;
0380 SD_ES_yield  = SD_ES  / dose / Nbp;
0381 SD_OHB_yield = SD_OHB / dose / Nbp;
0382 SD_OHS_yield = SD_OHS / dose / Nbp;
0383 SD_HB_yield  = SD_HB  / dose / Nbp;
0384 SD_HS_yield  = SD_HS  / dose / Nbp;
0385 
0386 
0387 SSB_yield   = (Double_t) norm * total_SSB   / dose / Nbp;
0388 SSBp_yield  = (Double_t) norm * total_SSBp  / dose / Nbp;
0389 SSB2p_yield = (Double_t) norm * total_SSB2p / dose / Nbp;
0390 
0391 DSB_yield   = (Double_t) norm * total_DSB   / dose / Nbp;
0392 DSBp_yield  = (Double_t) norm * total_DSBp  / dose / Nbp;
0393 DSBpp_yield = (Double_t) norm * total_DSBpp / dose / Nbp;
0394 
0395 SD_SSB_yield   = norm * SD_SSB   / dose / Nbp;
0396 SD_SSBp_yield  = norm * SD_SSBp  / dose / Nbp;
0397 SD_SSB2p_yield = norm * SD_SSB2p / dose / Nbp;
0398 
0399 SD_DSB_yield   = norm * SD_DSB   / dose / Nbp;
0400 SD_DSBp_yield  = norm * SD_DSBp  / dose / Nbp;
0401 SD_DSBpp_yield = norm * SD_DSBpp / dose / Nbp;
0402 
0403 
0404 sSSB_yield = (Double_t) norm * total_sSSB / dose / Nbp;
0405 SSBi_yield = (Double_t) norm * total_SSBi / dose / Nbp;
0406 SSBd_yield = (Double_t) norm * total_SSBd / dose / Nbp;
0407 SSBm_yield = (Double_t) norm * total_SSBm / dose / Nbp;
0408 
0409 sDSB_yield = (Double_t) norm * total_sDSB / dose / Nbp;
0410 DSBi_yield = (Double_t) norm * total_DSBi / dose / Nbp;
0411 DSBd_yield = (Double_t) norm * total_DSBd / dose / Nbp;
0412 DSBm_yield = (Double_t) norm * total_DSBm / dose / Nbp;
0413 DSBh_yield = (Double_t) norm * total_DSBh / dose / Nbp;
0414 
0415 SD_sSSB_yield = norm * SD_sSSB / dose / Nbp;
0416 SD_SSBi_yield = norm * SD_SSBi / dose / Nbp;
0417 SD_SSBd_yield = norm * SD_SSBd / dose / Nbp;
0418 SD_SSBm_yield = norm * SD_SSBm / dose / Nbp;
0419 
0420 SD_sDSB_yield = norm * SD_sDSB / dose / Nbp;
0421 SD_DSBi_yield = norm * SD_DSBi / dose / Nbp;
0422 SD_DSBd_yield = norm * SD_DSBd / dose / Nbp;
0423 SD_DSBm_yield = norm * SD_DSBm / dose / Nbp;
0424 SD_DSBh_yield = norm * SD_DSBh / dose / Nbp;
0425 
0426 
0427 // Print output in terminal
0428 
0429 float total_SSB_totalYield = SSB_yield + SSBp_yield + SSB2p_yield;
0430 float total_DSB_totalYield = DSB_yield + DSBp_yield + DSBpp_yield;
0431 
0432 cout<<"\n"                      <<ifile         <<'\n'
0433     <<"\nDose Absorbed (Gy): "  <<dose          <<'\n'
0434     <<"Particle : "             <<primaryName   <<'\t'
0435     <<"Energy (MeV) : "         <<Energy        <<'\t'
0436     <<"Number of Primaries : "  <<number        <<'\n'
0437     <<"  Output Damage : "                      <<'\n'<<'\t'
0438     <<"     Species Hits (Gy-1 Mbp-1) "      <<'\n'<<'\t'
0439     <<"EaqBaseHits   : "     <<EB_yield     <<"   \t"      <<" error %: "   <<100*SD_EB_yield/EB_yield        <<'\n'<<'\t'
0440     <<"EaqStrandHits : "     <<ES_yield     <<"   \t"      <<" error %: "   <<100*SD_ES_yield/ES_yield        <<'\n'<<'\t'
0441     <<"OHBaseHits    : "     <<OHB_yield    <<"   \t"      <<" error %: "   <<100*SD_OHB_yield/OHB_yield      <<'\n'<<'\t'
0442     <<"OHStrandHits  : "     <<OHS_yield    <<"   \t"      <<" error %: "   <<100*SD_OHS_yield/OHS_yield      <<'\n'<<'\t'
0443     <<"HBaseHits     : "     <<HB_yield     <<"   \t"      <<" error %: "   <<100*SD_HB_yield/HB_yield        <<'\n'<<'\t'
0444     <<"HStrandHits   : "     <<HS_yield     <<"   \t"      <<" error %: "   <<100*SD_HS_yield/HS_yield        <<'\n'<<'\n'<<'\t'
0445     <<"     Damage yield (Gy-1 Gbp-1) "      <<'\n'<<'\t'
0446     <<"SSB           : "     <<SSB_yield    <<"   \t"      <<" error %: "   <<100*SD_SSB_yield/SSB_yield      <<'\n'<<'\t'
0447     <<"SSB+          : "     <<SSBp_yield   <<"   \t"      <<" error %: "   <<100*SD_SSBp_yield/SSBp_yield    <<'\n'<<'\t'
0448     <<"2SSB          : "     <<SSB2p_yield  <<"   \t"      <<" error %: "   <<100*SD_SSB2p_yield/SSB2p_yield  <<'\n'<<'\t'
0449     <<"SSB total     : "     <<total_SSB_totalYield        <<'\n'<<'\t'
0450     <<"DSB           : "     <<DSB_yield    <<"   \t"      <<" error %: "   <<100*SD_DSB_yield/DSB_yield     <<'\n'<<'\t'
0451     <<"DSB+          : "     <<DSBp_yield   <<"   \t"      <<" error %: "   <<100*SD_DSBp_yield/DSBp_yield   <<'\n'<<'\t'
0452     <<"DSB++         : "     <<DSBpp_yield  <<"   \t"      <<" error %: "   <<100*SD_DSBpp_yield/DSBpp_yield <<'\n'<<'\t'
0453     <<"DSB total     : "     <<total_DSB_totalYield        <<'\n'<<'\n'<<'\t'
0454     <<"     Breaks yield (Gy-1 Gbp-1) "      <<'\n'<<'\t'
0455     <<"SSB direct    : "     <<SSBd_yield   <<"   \t"      <<" error %: "   <<100*SD_SSBd_yield/SSBd_yield   <<'\n'<<'\t'
0456     <<"SSB indirect  : "     <<SSBi_yield   <<"   \t"      <<" error %: "   <<100*SD_SSBi_yield/SSBi_yield   <<'\n'<<'\t'
0457     <<"SSB mixed     : "     <<SSBm_yield   <<"   \t"      <<" error %: "   <<100*SD_SSBm_yield/SSBi_yield   <<'\n'<<'\t'
0458     <<"SSB total     : "     <<sSSB_yield   <<"   \t"      <<" error %: "   <<100*SD_sSSB_yield/sSSB_yield   <<'\n'<<'\t'
0459     <<"DSB direct    : "     <<DSBd_yield   <<"   \t"      <<" error %: "   <<100*SD_DSBd_yield/DSBd_yield   <<'\n'<<'\t'
0460     <<"DSB indirect  : "     <<DSBi_yield   <<"   \t"      <<" error %: "   <<100*SD_DSBi_yield/DSBi_yield   <<'\n'<<'\t'
0461     <<"DSB mixed     : "     <<DSBm_yield   <<"   \t"      <<" error %: "   <<100*SD_DSBm_yield/DSBm_yield   <<'\n'<<'\t'
0462     <<"DSB hybrid    : "     <<DSBh_yield   <<"   \t"      <<" error %: "   <<100*SD_DSBh_yield/DSBh_yield   <<'\n'<<'\t'
0463     <<"DSB total     : "     <<sDSB_yield   <<"   \t"      <<" error %: "   <<100*SD_sDSB_yield/sDSB_yield   <<'\n'<<'\n'<<'\t'
0464     <<"SSB/DSB       : "     <<sSSB_yield/sDSB_yield       <<'\n'<<'\n';
0465 
0466 
0467 // Plot Histograms
0468 
0469 cfragment->GetCanvas()->cd();
0470 h1fragments->SetStats(false);
0471 h1fragments->SetMarkerSize(0.1);
0472 h1fragments->SetMarkerColor(kRed);
0473 h1fragments->SetLineColor  (kRed);
0474 h1fragments->Scale(1./(Nbp*1e6)); //bp^-1
0475 h1fragments->SetTitle("");
0476 h1fragments->SetYTitle("Number of Fragments (bp^{-2})");
0477 h1fragments->SetXTitle("Fragment Length (kbp)");
0478 h1fragments->SetAxisRange(10,1e4);
0479 h1fragments->SetMaximum(3e-11);
0480 h1fragments->SetMinimum(1e-15);
0481 h1fragments->Draw();
0482 
0483 
0484 c1->GetCanvas()->cd();
0485 pad1->cd();
0486 const Int_t n = 6;
0487 Double_t x[n] = {1,2,3,4,5,6};
0488 Double_t y[n] = {EB_yield,ES_yield,OHB_yield,OHS_yield,HB_yield,HS_yield};
0489 Double_t err_y[n] = {SD_EB_yield,SD_ES_yield,SD_OHB_yield,SD_OHS_yield,SD_HB_yield,SD_HS_yield};
0490 TGraph* gr = new TGraphErrors(n,x,y,0,err_y);
0491 gr->SetTitle("Species");
0492 gr->GetXaxis()->SetBinLabel(9, "EaqBaseHits");
0493 gr->GetXaxis()->SetBinLabel(25,"EaqStrandHits");
0494 gr->GetXaxis()->SetBinLabel(42,"OHBaseHits");
0495 gr->GetXaxis()->SetBinLabel(58,"OHStrandHits");
0496 gr->GetXaxis()->SetBinLabel(75,"HBaseHits");
0497 gr->GetXaxis()->SetBinLabel(92,"HStrandHits");
0498 gr->GetYaxis()->SetTitle("Species Hits (Gy^{-1} Mbp^{-1})");
0499 gr->GetYaxis()->SetTitleOffset(2);
0500 
0501 gr->SetFillColor(49);
0502 gr->Draw("ba");
0503 
0504 
0505 pad2->cd();
0506 Double_t x2[n] = {1,2,3,4,5,6};
0507 Double_t y2[n] = {SSBp_yield,SSB2p_yield,SSB_yield,DSBp_yield,DSBpp_yield,DSB_yield};
0508 Double_t err_y2[n] = {SD_SSBp_yield,SD_SSB2p_yield,SD_SSB_yield,SD_DSBp_yield,SD_DSBpp_yield,SD_DSB_yield};
0509 TGraph* gr2 = new TGraphErrors(n,x2,y2,0,err_y2);
0510 gr2->SetTitle("Damage Yield");
0511 gr2->GetXaxis()->SetBinLabel(9, "SSB+");
0512 gr2->GetXaxis()->SetBinLabel(25,"2SSB");
0513 gr2->GetXaxis()->SetBinLabel(42,"SSB");
0514 gr2->GetXaxis()->SetBinLabel(58,"DSB+");
0515 gr2->GetXaxis()->SetBinLabel(75,"DSB++");
0516 gr2->GetXaxis()->SetBinLabel(92,"DSB");
0517 //gr2->GetYaxis()->SetTitle("Damage yield (Gy^{-1} Mbp^{-1})");
0518 gr2->GetYaxis()->SetTitle("Damage yield (Gy^{-1} Gbp^{-1})");
0519 gr2->GetYaxis()->SetTitleOffset(2);
0520 
0521 gr2->SetFillColor(8);
0522 gr2->Draw("ba");
0523 
0524 
0525 pad3->cd();
0526 const Int_t m = 4;
0527 Double_t x3[m] = {1,2,3,4};
0528 Double_t y3[m] = {SSBd_yield,SSBi_yield,SSBm_yield,sSSB_yield};
0529 Double_t err_y3[m] = {SD_SSBd_yield,SD_SSBi_yield,SD_SSBm_yield,SD_sSSB_yield};
0530 TGraph* gr3 = new TGraphErrors(m,x3,y3,0,err_y3);
0531 gr3->SetTitle("Breaks Yield");
0532 gr3->GetXaxis()->SetBinLabel(8, "SSB direct");
0533 gr3->GetXaxis()->SetBinLabel(35,"SSB indirect");
0534 gr3->GetXaxis()->SetBinLabel(64,"SSB mixed");
0535 gr3->GetXaxis()->SetBinLabel(92,"SSB all");
0536 //gr3->GetYaxis()->SetTitle("Breaks yield (Gy^{-1} Mbp^{-1})");
0537 gr3->GetYaxis()->SetTitle("SSB yield (Gy^{-1} Gbp^{-1})");
0538 gr3->GetYaxis()->SetTitleOffset(2);
0539 
0540 gr3->SetFillColor(7);
0541 gr3->Draw("ba");
0542 
0543 
0544 pad4->cd();
0545 const Int_t k = 5;
0546 Double_t x4[k] = {1,2,3,4,5};
0547 Double_t y4[k] = {DSBd_yield,DSBi_yield,DSBm_yield,DSBh_yield,sDSB_yield};
0548 Double_t err_y4[k] = {SD_DSBd_yield,SD_DSBi_yield,SD_DSBm_yield,SD_DSBh_yield,SD_sDSB_yield};
0549 TGraph* gr4 = new TGraphErrors(k,x4,y4,0,err_y4);
0550 gr4->SetTitle("Breaks Yield");
0551 gr4->GetXaxis()->SetBinLabel(8,"DSB direct");
0552 gr4->GetXaxis()->SetBinLabel(29,"DSB indirect");
0553 gr4->GetXaxis()->SetBinLabel(50,"DSB mixed");
0554 gr4->GetXaxis()->SetBinLabel(71,"DSB hybrid");
0555 gr4->GetXaxis()->SetBinLabel(92,"DSB all");
0556 //gr4->GetYaxis()->SetTitle("Breaks yield (Gy^{-1} Mbp^{-1})");
0557 gr4->GetYaxis()->SetTitle("DSB yield (Gy^{-1} Gbp^{-1})");
0558 gr4->GetYaxis()->SetTitleOffset(2);
0559 
0560 gr4->SetFillColor(4);
0561 gr4->Draw("ba");
0562 
0563 }
0564 
0565 // Some important bools that are needed to run the root macro file
0566 bool greaterPair(const ipair& l, const ipair& r){return l.second > r.second;}
0567 bool smallerPair(const ipair& l, const ipair& r){return l.second < r.second;}
0568 
0569 void BinLogX(TH1 *h) {
0570   TAxis *axis = h->GetXaxis();
0571   int bins = axis->GetNbins();
0572   Axis_t from = axis->GetXmin();
0573   Axis_t to = axis->GetXmax();
0574   Axis_t width = (to - from) / bins;
0575   Axis_t *new_bins = new Axis_t[bins + 1];
0576   for (int i = 0; i <= bins; i++) {
0577     new_bins[i] = TMath::Power(10, from + i * width);
0578   }
0579   axis->Set(bins, new_bins);
0580   delete[] new_bins;
0581 
0582 }
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