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File indexing completed on 2025-10-13 08:25:11 

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_chromosomes.C
0011 // ROOT6.x should be installed
0012 //
0013 
0014 //***************************************//
0015 // Please define the parameters below    //
0016 // ifile, r3, Nbp (as shown in terminal) //
0017 //***************************************//
0018 
0019 {
0020 //*******************************************************************************//
0021 // If you need to add multiple root outputs, by multithreading, use this command:
0022 system ("hadd -O -f molecular-dna.root molecular-dna_t*.root");
0023 
0024 // Define these parameters of the simulation
0025 char ifile[256] = "molecular-dna.root";  // input filepath
0026 Double_t r3 = 10575e-9 * 3450e-9 * 10575e-9;  // a * b * c   // Chromosome size, as defined in the mac file, but in meters. If sphere, a=b=c
0027 Double_t Nbp = 6383.848410; // Mbp // Length of the DNA chain in Mbp
0028 Double_t mass = 997 * 4 * 3.141592 * r3 / 3 ;  // waterDensity * 4/3 * pi * r3 in kg
0029 ///////////////////////////////////////////////////////////////////////////////////
0030 //*******************************************************************************//
0031 
0032 typedef std::pair <int64_t, int64_t> ipair;
0033 bool greaterPair(const ipair &l, const ipair &r);
0034 bool smallerPair(const ipair &l, const ipair &r);
0035 
0036 void BinLogX(TH1 *h);
0037 
0038 gROOT->Reset();
0039 gStyle->SetPalette(1);
0040 gROOT->SetStyle("Plain");
0041 gStyle->SetOptStat(00000);
0042 
0043 // Initialize output histograms
0044 TCanvas *cfragment = new TCanvas("cfragment","DNA Fragments Distribution", 900, 120, 600,400);
0045 cfragment->SetLogx();
0046 cfragment->SetLogy();
0047 TH1F *h1fragments = new TH1F("h1fragments","h1fragments",40,0,5);
0048 BinLogX(h1fragments);
0049 
0050 TCanvas *c1 = new TCanvas("c1", "Molecular DNA - Damage Quantification", 60, 120, 800, 800);
0051 c1->SetBorderSize(0);
0052 c1->SetFillColor(0);
0053 c1->SetFillStyle(4000);
0054 gPad->SetLeftMargin(0.13);
0055 
0056 TPad* pad1 = new TPad("pad1","Species", 0, 0.51, 0.49, 1);
0057 pad1->SetBorderSize(0);
0058 pad1->SetFillColor(0);
0059 pad1->SetFillStyle(4000);
0060 pad1->SetLeftMargin(0.15);
0061 pad1->SetRightMargin(0.01);
0062 pad1->SetBottomMargin(0.2);
0063 
0064 TPad* pad2 = new TPad("pad2","Damage Yield", 0.51, 0.5, 1, 1);
0065 pad2->SetBorderSize(0);
0066 pad2->SetFillColor(0);
0067 pad2->SetFillStyle(4000);
0068 pad2->SetLeftMargin(0.15);
0069 pad2->SetRightMargin(0.05);
0070 pad2->SetBottomMargin(0.2);
0071 
0072 TPad* pad3 = new TPad("pad3","Breaks Yield SSB", 0, 0, 0.49, 0.49);
0073 pad3->SetBorderSize(0);
0074 pad3->SetFillColor(0);
0075 pad3->SetFillStyle(4000);
0076 pad3->SetLeftMargin(0.15);
0077 pad3->SetRightMargin(0.01);
0078 //pad3->SetTopMargin(0.2);
0079 pad3->SetBottomMargin(0.2);
0080 
0081 TPad* pad4 = new TPad("pad4","Breaks Yield DSB", 0.51, 0, 1, 0.49);
0082 pad4->SetBorderSize(0);
0083 pad4->SetFillColor(0);
0084 pad4->SetFillStyle(4000);
0085 pad4->SetLeftMargin(0.15);
0086 pad4->SetRightMargin(0.05);
0087 //pad3->SetTopMargin(0.2);
0088 pad4->SetBottomMargin(0.2);
0089 
0090 pad1->Draw();
0091 pad2->Draw();
0092 pad3->Draw();
0093 pad4->Draw();
0094 
0095 // Open root file
0096 TFile *f = TFile::Open(ifile);
0097 
0098 // Initialize Variables
0099 Int_t EB, ES, OHB, OHS, HB, HS, FL;
0100 Int_t total_EB, total_ES, total_OHB, total_OHS, total_HB, total_HS, total_FL;
0101 Float_t total_EB2, total_ES2, total_OHB2, total_OHS2, total_HB2, total_HS2, total_FL2;
0102 Float_t SD_EB, SD_ES, SD_OHB, SD_OHS, SD_HB, SD_HS;
0103 Float_t SD_SSB, SD_SSBp, SD_SSB2p, SD_sSSB, SD_SSBd, SD_SSBi, SD_SSBm;
0104 Float_t SD_DSB, SD_DSBp, SD_DSBpp, SD_sDSB, SD_DSBd, SD_DSBi, SD_DSBm, SD_DSBh;
0105 
0106 Int_t SSB, SSBp, SSB2p;
0107 Int_t total_SSB, total_SSBp, total_SSB2p;
0108 Float_t total_SSB2, total_SSBp2, total_SSB2p2;
0109 Int_t DSB, DSBp, DSBpp;
0110 Int_t total_DSB, total_DSBp, total_DSBpp;
0111 Float_t total_DSB2, total_DSBp2, total_DSBpp2;
0112 
0113 Int_t SSBd, SSBi, SSBm;
0114 Int_t total_sSSB, total_SSBd, total_SSBi, total_SSBm;
0115 Float_t total_sSSB2, total_SSBd2, total_SSBi2, total_SSBm2;
0116 Int_t DSBd, DSBi, DSBm, DSBh;
0117 Int_t total_sDSB, total_DSBd, total_DSBi, total_DSBm, total_DSBh;
0118 Float_t total_sDSB2, total_DSBd2, total_DSBi2, total_DSBm2, total_DSBh2;
0119 
0120 Double_t dose = 0;
0121 Double_t SD_dose = 0;
0122 
0123 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;
0124 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;
0125 
0126 Double_t SSB_yield = 0; Double_t SSBp_yield = 0; Double_t SSB2p_yield = 0;
0127 Double_t SD_SSB_yield = 0; Double_t SD_SSBp_yield = 0; Double_t SD_SSB2p_yield = 0;
0128 Double_t DSB_yield = 0; Double_t DSBp_yield = 0; Double_t DSBpp_yield = 0;
0129 Double_t SD_DSB_yield = 0; Double_t SD_DSBp_yield = 0; Double_t SD_DSBpp_yield = 0;
0130 
0131 Double_t sSSB_yield = 0; Double_t SSBi_yield = 0; Double_t SSBd_yield = 0; Double_t SSBm_yield = 0;
0132 Double_t SD_sSSB_yield = 0; Double_t SD_SSBi_yield = 0; Double_t SD_SSBd_yield = 0; Double_t SD_SSBm_yield = 0;
0133 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;
0134 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;
0135 
0136 total_EB  = 0; total_ES = 0; total_OHB = 0; total_OHS = 0; total_HB = 0; total_HS = 0;
0137 
0138 total_SSB  = 0; total_SSBp = 0; total_SSB2p = 0;
0139 total_SSB2  = 0; total_SSBp2 = 0; total_SSB2p2 = 0;
0140 total_DSB  = 0; total_DSBp = 0; total_DSBpp = 0;
0141 total_DSB2  = 0; total_DSBp2 = 0; total_DSBpp2 = 0;
0142 
0143 total_sSSB = 0; total_SSBd = 0; total_SSBi = 0; total_SSBm = 0;
0144 total_sSSB2 = 0; total_SSBd2 = 0; total_SSBi2 = 0; total_SSBm2 = 0;
0145 total_sDSB = 0; total_DSBd = 0; total_DSBi = 0; total_DSBm = 0; total_DSBh = 0;
0146 total_sDSB2 = 0; total_DSBd2 = 0; total_DSBi2 = 0; total_DSBm2 = 0;  total_DSBh2 = 0;
0147 
0148 Double_t eVtoJ = 1.60218e-19;
0149 Double_t EnergyDeposited_eV = 0;
0150 Double_t acc_edep = 0;
0151 Double_t acc_edep2 = 0;
0152 
0153 Double_t Energy;
0154 Double_t BPID;
0155 Char_t Primary;
0156 char *primaryName = new char[32];
0157 char *type= new char[256];
0158 
0159 // Read trees and leaves from root file, and give values to variables
0160 TTree* tree = (TTree*) f->Get("tuples/primary_source");
0161 Float_t number = (Float_t) tree->GetEntries();
0162 
0163 if (number<2) {
0164   std::cout << "Not enough entries in the \"primary_source\" TTree (" << (long)number << " entries)\n";
0165   gApplication->Terminate(0);
0166 }
0167 
0168 vector<pair<int,int64_t>> DSBBPID;
0169 
0170 // For reading species production
0171 tree = (TTree*) f->Get("tuples/damage");
0172 tree->SetBranchAddress("Primary",           &Primary);
0173 tree->SetBranchAddress("Energy",            &Energy);
0174 tree->SetBranchAddress("EaqBaseHits",       &EB);
0175 tree->SetBranchAddress("EaqStrandHits",     &ES);
0176 tree->SetBranchAddress("OHBaseHits",        &OHB);
0177 tree->SetBranchAddress("OHStrandHits",      &OHS);
0178 tree->SetBranchAddress("HBaseHits",         &HB);
0179 tree->SetBranchAddress("HStrandHits",       &HS);
0180 tree->SetBranchAddress("TypeClassification", type);
0181 tree->SetBranchAddress("BasePair",          &BPID);
0182 
0183 
0184 Long64_t nentries = tree->GetEntries();
0185 for(int i = 0;i<nentries;i++){
0186   tree->GetEntry(i);
0187 
0188   total_EB   += EB;
0189   total_EB2  += pow(EB,2);
0190   total_ES   += ES;
0191   total_ES2  += pow(ES,2);
0192   total_OHB  += OHB;
0193   total_OHB2 += pow(OHB,2);
0194   total_OHS  += OHS;
0195   total_OHS2 += pow(OHS,2);
0196   total_HB   += HB;
0197   total_HB2  += pow(HB,2);
0198   total_HS   += HS;
0199   total_HS2  += pow(HS,2);
0200 
0201   if((string)type=="DSB"||(string)type=="DSB+"||(string)type=="DSB++"){
0202     //cout << "DSB:"<<type<<endl;
0203     DSBBPID.push_back(make_pair(i,(int64_t)BPID));
0204     }
0205 
0206   }
0207 
0208 // Find the number of fragments that have been produced, but first test if there are enough breaks.
0209 // If no more than 2 DSBs exist in the DSBBPID vector ( DSBBPID.size() is 0 or 1 ),
0210 // the subtraction DSBBPID.size() - 1 makes the loop condition evaluate to ie < -1 (in unsigned terms,
0211 // this becomes a large number, which is incorrect) and leads to undefined behavior (crash).
0212 if (DSBBPID.size() < 2) {
0213     std::cerr << "Not enough damage to create fragments distribution." << std::endl;
0214     //return;
0215 }
0216 if (DSBBPID.size() >= 2) {
0217   // Sort DSBs from the one with lower ID value to the one with higher ID value
0218   sort(DSBBPID.begin(),  DSBBPID.end(), smallerPair);
0219   for(int ie = 0;ie<DSBBPID.size()-1;ie++){
0220     int64_t dsbfragment = DSBBPID[ie+1].second-DSBBPID[ie].second;
0221 
0222     double val       = (double)dsbfragment/1000.;
0223     double meanw     = h1fragments->GetBinCenter(h1fragments->FindBin(val));
0224     double binw      = h1fragments->GetBinWidth (h1fragments->FindBin(val));
0225     h1fragments->Fill(val,1./binw/1000);//bp-1
0226     //cout <<"val:"<<val<<endl;
0227     }
0228 }
0229 
0230 // Calculate the SEM
0231 SD_EB  = sqrt(abs(((total_EB2  / number) - pow(total_EB  / number,2)))/(number -1));
0232 SD_ES  = sqrt(abs(((total_ES2  / number) - pow(total_ES  / number,2)))/(number -1));
0233 SD_OHB = sqrt(abs(((total_OHB2 / number) - pow(total_OHB / number,2)))/(number -1));
0234 SD_OHS = sqrt(abs(((total_OHS2 / number) - pow(total_OHS / number,2)))/(number -1));
0235 SD_HB  = sqrt(abs(((total_HB2  / number) - pow(total_HB  / number,2)))/(number -1));
0236 SD_HS  = sqrt(abs(((total_HS2  / number) - pow(total_HS  / number,2)))/(number -1));
0237 
0238 // Read damage classification SSB, SSB+, 2SSB, DSB, DSB+, DSB++
0239 // As they have been defined in: Nikjoo, H., O’Neill, O., Goodhead, T., & Terrissol, M. 1997,
0240 // Computational modelling of low-energy electron-induced DNA damage by early physical
0241 // and chemical events, International Journal of Radiation Biology, 71, 467.
0242 tree = (TTree *) f->Get("tuples/classification");
0243 tree->SetBranchAddress("Primary",&Primary);
0244 tree->SetBranchAddress("Energy", &Energy);
0245 tree->SetBranchAddress("SSB",    &SSB);
0246 tree->SetBranchAddress("SSBp",   &SSBp);
0247 tree->SetBranchAddress("2SSB",   &SSB2p);
0248 tree->SetBranchAddress("DSB",    &DSB);
0249 tree->SetBranchAddress("DSBp",   &DSBp);
0250 tree->SetBranchAddress("DSBpp",  &DSBpp);
0251 
0252 
0253 Long64_t nentriesC = tree->GetEntries();
0254 for(int i = 0;i<nentriesC;i++){
0255   tree->GetEntry(i);
0256 
0257   total_SSBp   += SSBp;
0258   total_SSBp2  += pow(SSBp,2);
0259   total_SSB2p  += SSB2p;
0260   total_SSB2p2 += pow(SSB2p,2);
0261   total_SSB    += SSB;
0262   total_SSB2   += pow(SSB,2);
0263 
0264   total_DSBp   += DSBp;
0265   total_DSBp2  += pow(DSBp,2);
0266   total_DSBpp  += DSBpp;
0267   total_DSBpp2 += pow(DSBpp,2);
0268   total_DSB    += DSB;
0269   total_DSB2   += pow(DSB,2);
0270 
0271   }
0272 
0273 // Calculate the SEM
0274 SD_SSB   = sqrt(abs(((total_SSB2   / number) - pow(total_SSB   / number,2)))/(number -1));
0275 SD_SSBp  = sqrt(abs(((total_SSBp2  / number) - pow(total_SSBp  / number,2)))/(number -1));
0276 SD_SSB2p = sqrt(abs(((total_SSB2p2 / number) - pow(total_SSB2p / number,2)))/(number -1));
0277 
0278 SD_DSB   = sqrt(abs(((total_DSB2   / number) - pow(total_DSB   / number,2)))/(number -1));
0279 SD_DSBp  = sqrt(abs(((total_DSBp2  / number) - pow(total_DSBp  / number,2)))/(number -1));
0280 SD_DSBpp = sqrt(abs(((total_DSBpp2 / number) - pow(total_DSBpp / number,2)))/(number -1));
0281 
0282 // Read damage classification SSBd, SSBi, SSBm, DSBd, DSBi, DSBm, DSBh
0283 // As they have been defined in: Nikjoo, H., O’Neill, O., Goodhead, T., & Terrissol, M. 1997,
0284 // Computational modelling of low-energy electron-induced DNA damage by early physical
0285 // and chemical events, International Journal of Radiation Biology, 71, 467.
0286 tree = (TTree *) f->Get("tuples/source");
0287 tree->SetBranchAddress("Primary",primaryName);
0288 tree->SetBranchAddress("Energy", &Energy);
0289 tree->SetBranchAddress("SSBd",   &SSBd);
0290 tree->SetBranchAddress("SSBi",   &SSBi);
0291 tree->SetBranchAddress("SSBm",   &SSBm);
0292 tree->SetBranchAddress("DSBd",   &DSBd);
0293 tree->SetBranchAddress("DSBi",   &DSBi);
0294 tree->SetBranchAddress("DSBm",   &DSBm);
0295 tree->SetBranchAddress("DSBh",   &DSBh);
0296 
0297 Long64_t nentriesS = tree->GetEntries();
0298 for(int i = 0;i<nentriesS;i++){
0299   tree->GetEntry(i);
0300 
0301   total_SSBd += SSBd;
0302   total_SSBd2 += pow((SSBd),2);
0303   total_SSBi += SSBi;
0304   total_SSBi2 += pow((SSBi),2);
0305   total_SSBm += SSBm;
0306   total_SSBm2 += pow((SSBm),2);
0307   total_sSSB += SSBd + SSBi + SSBm;
0308   total_sSSB2 += pow((SSBd+SSBi+SSBm),2);
0309 
0310   total_DSBd  += DSBd;
0311   total_DSBd2 += pow(DSBd,2);
0312   total_DSBi  += DSBi;
0313   total_DSBi2 += pow(DSBi,2);
0314   total_DSBm  += DSBm;
0315   total_DSBm2 += pow(DSBm,2);
0316   total_DSBh  += DSBh;
0317   total_DSBh2 += pow(DSBh,2);
0318   total_sDSB  += DSBd + DSBi + DSBm + DSBh;
0319   total_sDSB2 += pow((DSBd+DSBi+DSBm+DSBh),2);
0320 
0321   }
0322 
0323 // Calculate the SEM
0324 SD_sSSB = sqrt(abs(((total_sSSB2 / number) - pow(total_sSSB / number,2)))/(number -1));
0325 SD_SSBd = sqrt(abs(((total_SSBd2 / number) - pow(total_SSBd / number,2)))/(number -1));
0326 SD_SSBi = sqrt(abs(((total_SSBi2 / number) - pow(total_SSBi / number,2)))/(number -1));
0327 SD_SSBm = sqrt(abs(((total_SSBm2 / number) - pow(total_SSBm / number,2)))/(number -1));
0328 
0329 SD_sDSB = sqrt(abs(((total_sDSB2 / number) - pow(total_sDSB / number,2)))/(number -1));
0330 SD_DSBd = sqrt(abs(((total_DSBd2 / number) - pow(total_DSBd / number,2)))/(number -1));
0331 SD_DSBi = sqrt(abs(((total_DSBi2 / number) - pow(total_DSBi / number,2)))/(number -1));
0332 SD_DSBm = sqrt(abs(((total_DSBm2 / number) - pow(total_DSBm / number,2)))/(number -1));
0333 SD_DSBh = sqrt(abs(((total_DSBh2 / number) - pow(total_DSBh / number,2)))/(number -1));
0334 
0335 
0336 // Measure the Deposited Energy in the whole volume that includes DNA chain (chromosome)
0337 
0338 tree = (TTree *) f->Get("tuples/chromosome_hits");
0339 tree->SetBranchAddress("e_chromosome_kev",&EnergyDeposited_eV);
0340 nentries = tree->GetEntries();
0341 for(int i = 0;i<nentries;i++){
0342   tree->GetEntry(i);
0343   acc_edep += EnergyDeposited_eV *1e3;
0344   acc_edep2 += EnergyDeposited_eV *EnergyDeposited_eV *1e6;
0345 }
0346 tree->SetBranchAddress("e_dna_kev",&EnergyDeposited_eV);
0347 nentries = tree->GetEntries();
0348 for(int i = 0;i<nentries;i++){
0349   tree->GetEntry(i);
0350   acc_edep += EnergyDeposited_eV *1e3;
0351   acc_edep2 += EnergyDeposited_eV *EnergyDeposited_eV *1e6;
0352 }
0353 
0354 // Close the root file to free space
0355 f->Close();
0356 
0357 // Calculate the absorbed dose
0358 dose = acc_edep * eVtoJ / mass;
0359 
0360 // This is a normalization factor to produce the output in Gy-1 Gbp-1, or else.
0361 // Default value is 1 to produce the result in Gy-1 Mbp-1
0362 // It changes Mbp to Gbp. Some other changes may be needed in graphs section (name of axes)
0363 double norm = 1000;
0364 
0365 // Calculate the yields, together with their error
0366 EB_yield  = (Double_t) total_EB  / dose / Nbp;
0367 ES_yield  = (Double_t) total_ES  / dose / Nbp;
0368 OHB_yield = (Double_t) total_OHB / dose / Nbp;
0369 OHS_yield = (Double_t) total_OHS / dose / Nbp;
0370 HB_yield  = (Double_t) total_HB  / dose / Nbp;
0371 HS_yield  = (Double_t) total_HS  / dose / Nbp;
0372 
0373 SD_EB_yield  = SD_EB  / dose / Nbp;
0374 SD_ES_yield  = SD_ES  / dose / Nbp;
0375 SD_OHB_yield = SD_OHB / dose / Nbp;
0376 SD_OHS_yield = SD_OHS / dose / Nbp;
0377 SD_HB_yield  = SD_HB  / dose / Nbp;
0378 SD_HS_yield  = SD_HS  / dose / Nbp;
0379 
0380 
0381 SSB_yield   = (Double_t) norm * total_SSB   / dose / Nbp;
0382 SSBp_yield  = (Double_t) norm * total_SSBp  / dose / Nbp;
0383 SSB2p_yield = (Double_t) norm * total_SSB2p / dose / Nbp;
0384 
0385 DSB_yield   = (Double_t) norm * total_DSB   / dose / Nbp;
0386 DSBp_yield  = (Double_t) norm * total_DSBp  / dose / Nbp;
0387 DSBpp_yield = (Double_t) norm * total_DSBpp / dose / Nbp;
0388 
0389 SD_SSB_yield   = norm * SD_SSB   / dose / Nbp;
0390 SD_SSBp_yield  = norm * SD_SSBp  / dose / Nbp;
0391 SD_SSB2p_yield = norm * SD_SSB2p / dose / Nbp;
0392 
0393 SD_DSB_yield   = norm * SD_DSB   / dose / Nbp;
0394 SD_DSBp_yield  = norm * SD_DSBp  / dose / Nbp;
0395 SD_DSBpp_yield = norm * SD_DSBpp / dose / Nbp;
0396 
0397 
0398 sSSB_yield = (Double_t) norm * total_sSSB / dose / Nbp;
0399 SSBi_yield = (Double_t) norm * total_SSBi / dose / Nbp;
0400 SSBd_yield = (Double_t) norm * total_SSBd / dose / Nbp;
0401 SSBm_yield = (Double_t) norm * total_SSBm / dose / Nbp;
0402 
0403 sDSB_yield = (Double_t) norm * total_sDSB / dose / Nbp;
0404 DSBi_yield = (Double_t) norm * total_DSBi / dose / Nbp;
0405 DSBd_yield = (Double_t) norm * total_DSBd / dose / Nbp;
0406 DSBm_yield = (Double_t) norm * total_DSBm / dose / Nbp;
0407 DSBh_yield = (Double_t) norm * total_DSBh / dose / Nbp;
0408 
0409 SD_sSSB_yield = norm * SD_sSSB / dose / Nbp;
0410 SD_SSBi_yield = norm * SD_SSBi / dose / Nbp;
0411 SD_SSBd_yield = norm * SD_SSBd / dose / Nbp;
0412 SD_SSBm_yield = norm * SD_SSBm / dose / Nbp;
0413 
0414 SD_sDSB_yield = norm * SD_sDSB / dose / Nbp;
0415 SD_DSBi_yield = norm * SD_DSBi / dose / Nbp;
0416 SD_DSBd_yield = norm * SD_DSBd / dose / Nbp;
0417 SD_DSBm_yield = norm * SD_DSBm / dose / Nbp;
0418 SD_DSBh_yield = norm * SD_DSBh / dose / Nbp;
0419 
0420 
0421 // Print output in terminal
0422 
0423 float total_SSB_totalYield = SSB_yield + SSBp_yield + SSB2p_yield;
0424 float total_DSB_totalYield = DSB_yield + DSBp_yield + DSBpp_yield;
0425 
0426 cout<<"\n"                      <<ifile         <<'\n'
0427     <<"\nDose Absorbed (Gy): "  <<dose          <<'\n'
0428     <<"Particle : "             <<primaryName   <<'\t'
0429     <<"Energy (MeV) : "         <<Energy        <<'\t'
0430     <<"Number of Primaries : "  <<number        <<'\n'
0431     <<"  Output Damage : "                      <<'\n'<<'\t'
0432     <<"     Species Hits (Gy-1 Mbp-1) "      <<'\n'<<'\t'
0433     <<"EaqBaseHits   : "     <<EB_yield     <<"   \t"      <<" error %: "   <<100*SD_EB_yield/EB_yield        <<'\n'<<'\t'
0434     <<"EaqStrandHits : "     <<ES_yield     <<"   \t"      <<" error %: "   <<100*SD_ES_yield/ES_yield        <<'\n'<<'\t'
0435     <<"OHBaseHits    : "     <<OHB_yield    <<"   \t"      <<" error %: "   <<100*SD_OHB_yield/OHB_yield      <<'\n'<<'\t'
0436     <<"OHStrandHits  : "     <<OHS_yield    <<"   \t"      <<" error %: "   <<100*SD_OHS_yield/OHS_yield      <<'\n'<<'\t'
0437     <<"HBaseHits     : "     <<HB_yield     <<"   \t"      <<" error %: "   <<100*SD_HB_yield/HB_yield        <<'\n'<<'\t'
0438     <<"HStrandHits   : "     <<HS_yield     <<"   \t"      <<" error %: "   <<100*SD_HS_yield/HS_yield        <<'\n'<<'\n'<<'\t'
0439     <<"     Damage yield (Gy-1 Gbp-1) "      <<'\n'<<'\t'
0440     <<"SSB           : "     <<SSB_yield    <<"   \t"      <<" error %: "   <<100*SD_SSB_yield/SSB_yield      <<'\n'<<'\t'
0441     <<"SSB+          : "     <<SSBp_yield   <<"   \t"      <<" error %: "   <<100*SD_SSBp_yield/SSBp_yield    <<'\n'<<'\t'
0442     <<"2SSB          : "     <<SSB2p_yield  <<"   \t"      <<" error %: "   <<100*SD_SSB2p_yield/SSB2p_yield  <<'\n'<<'\t'
0443     <<"SSB total     : "     <<total_SSB_totalYield        <<'\n'<<'\t'
0444     <<"DSB           : "     <<DSB_yield    <<"   \t"      <<" error %: "   <<100*SD_DSB_yield/DSB_yield     <<'\n'<<'\t'
0445     <<"DSB+          : "     <<DSBp_yield   <<"   \t"      <<" error %: "   <<100*SD_DSBp_yield/DSBp_yield   <<'\n'<<'\t'
0446     <<"DSB++         : "     <<DSBpp_yield  <<"   \t"      <<" error %: "   <<100*SD_DSBpp_yield/DSBpp_yield <<'\n'<<'\t'
0447     <<"DSB total     : "     <<total_DSB_totalYield        <<'\n'<<'\n'<<'\t'
0448     <<"     Breaks yield (Gy-1 Gbp-1) "      <<'\n'<<'\t'
0449     <<"SSB direct    : "     <<SSBd_yield   <<"   \t"      <<" error %: "   <<100*SD_SSBd_yield/SSBd_yield   <<'\n'<<'\t'
0450     <<"SSB indirect  : "     <<SSBi_yield   <<"   \t"      <<" error %: "   <<100*SD_SSBi_yield/SSBi_yield   <<'\n'<<'\t'
0451     <<"SSB mixed     : "     <<SSBm_yield   <<"   \t"      <<" error %: "   <<100*SD_SSBm_yield/SSBi_yield   <<'\n'<<'\t'
0452     <<"SSB total     : "     <<sSSB_yield   <<"   \t"      <<" error %: "   <<100*SD_sSSB_yield/sSSB_yield   <<'\n'<<'\t'
0453     <<"DSB direct    : "     <<DSBd_yield   <<"   \t"      <<" error %: "   <<100*SD_DSBd_yield/DSBd_yield   <<'\n'<<'\t'
0454     <<"DSB indirect  : "     <<DSBi_yield   <<"   \t"      <<" error %: "   <<100*SD_DSBi_yield/DSBi_yield   <<'\n'<<'\t'
0455     <<"DSB mixed     : "     <<DSBm_yield   <<"   \t"      <<" error %: "   <<100*SD_DSBm_yield/DSBm_yield   <<'\n'<<'\t'
0456     <<"DSB hybrid    : "     <<DSBh_yield   <<"   \t"      <<" error %: "   <<100*SD_DSBh_yield/DSBh_yield   <<'\n'<<'\t'
0457     <<"DSB total     : "     <<sDSB_yield   <<"   \t"      <<" error %: "   <<100*SD_sDSB_yield/sDSB_yield   <<'\n'<<'\n'<<'\t'
0458     <<"SSB/DSB       : "     <<sSSB_yield/sDSB_yield       <<'\n'<<'\n';
0459 
0460 
0461 // Plot Histograms
0462 
0463 cfragment->GetCanvas()->cd();
0464 h1fragments->SetStats(false);
0465 h1fragments->SetMarkerSize(0.1);
0466 h1fragments->SetMarkerColor(kRed);
0467 h1fragments->SetLineColor  (kRed);
0468 h1fragments->Scale(1./(Nbp*1e6)); //bp^-1
0469 h1fragments->SetTitle("");
0470 h1fragments->SetYTitle("Number of Fragments (bp^{-2})");
0471 h1fragments->SetXTitle("Fragment Length (kbp)");
0472 h1fragments->SetAxisRange(10,1e4);
0473 h1fragments->SetMaximum(3e-11);
0474 h1fragments->SetMinimum(1e-15);
0475 h1fragments->Draw();
0476 
0477 
0478 c1->GetCanvas()->cd();
0479 pad1->cd();
0480 const Int_t n = 6;
0481 Double_t x[n] = {1,2,3,4,5,6};
0482 Double_t y[n] = {EB_yield,ES_yield,OHB_yield,OHS_yield,HB_yield,HS_yield};
0483 Double_t err_y[n] = {SD_EB_yield,SD_ES_yield,SD_OHB_yield,SD_OHS_yield,SD_HB_yield,SD_HS_yield};
0484 TGraph* gr = new TGraphErrors(n,x,y,0,err_y);
0485 gr->SetTitle("Species");
0486 gr->GetXaxis()->SetBinLabel(9, "EaqBaseHits");
0487 gr->GetXaxis()->SetBinLabel(25,"EaqStrandHits");
0488 gr->GetXaxis()->SetBinLabel(42,"OHBaseHits");
0489 gr->GetXaxis()->SetBinLabel(58,"OHStrandHits");
0490 gr->GetXaxis()->SetBinLabel(75,"HBaseHits");
0491 gr->GetXaxis()->SetBinLabel(92,"HStrandHits");
0492 gr->GetYaxis()->SetTitle("Species Hits (Gy^{-1} Mbp^{-1})");
0493 gr->GetYaxis()->SetTitleOffset(2);
0494 
0495 gr->SetFillColor(49);
0496 gr->Draw("ba");
0497 
0498 
0499 pad2->cd();
0500 Double_t x2[n] = {1,2,3,4,5,6};
0501 Double_t y2[n] = {SSBp_yield,SSB2p_yield,SSB_yield,DSBp_yield,DSBpp_yield,DSB_yield};
0502 Double_t err_y2[n] = {SD_SSBp_yield,SD_SSB2p_yield,SD_SSB_yield,SD_DSBp_yield,SD_DSBpp_yield,SD_DSB_yield};
0503 TGraph* gr2 = new TGraphErrors(n,x2,y2,0,err_y2);
0504 gr2->SetTitle("Damage Yield");
0505 gr2->GetXaxis()->SetBinLabel(9, "SSB+");
0506 gr2->GetXaxis()->SetBinLabel(25,"2SSB");
0507 gr2->GetXaxis()->SetBinLabel(42,"SSB");
0508 gr2->GetXaxis()->SetBinLabel(58,"DSB+");
0509 gr2->GetXaxis()->SetBinLabel(75,"DSB++");
0510 gr2->GetXaxis()->SetBinLabel(92,"DSB");
0511 //gr2->GetYaxis()->SetTitle("Damage yield (Gy^{-1} Mbp^{-1})");
0512 gr2->GetYaxis()->SetTitle("Damage yield (Gy^{-1} Gbp^{-1})");
0513 gr2->GetYaxis()->SetTitleOffset(2);
0514 
0515 gr2->SetFillColor(8);
0516 gr2->Draw("ba");
0517 
0518 
0519 pad3->cd();
0520 const Int_t m = 4;
0521 Double_t x3[m] = {1,2,3,4};
0522 Double_t y3[m] = {SSBd_yield,SSBi_yield,SSBm_yield,sSSB_yield};
0523 Double_t err_y3[m] = {SD_SSBd_yield,SD_SSBi_yield,SD_SSBm_yield,SD_sSSB_yield};
0524 TGraph* gr3 = new TGraphErrors(m,x3,y3,0,err_y3);
0525 gr3->SetTitle("Breaks Yield");
0526 gr3->GetXaxis()->SetBinLabel(8, "SSB direct");
0527 gr3->GetXaxis()->SetBinLabel(35,"SSB indirect");
0528 gr3->GetXaxis()->SetBinLabel(64,"SSB mixed");
0529 gr3->GetXaxis()->SetBinLabel(92,"SSB all");
0530 //gr3->GetYaxis()->SetTitle("Breaks yield (Gy^{-1} Mbp^{-1})");
0531 gr3->GetYaxis()->SetTitle("SSB yield (Gy^{-1} Gbp^{-1})");
0532 gr3->GetYaxis()->SetTitleOffset(2);
0533 
0534 gr3->SetFillColor(7);
0535 gr3->Draw("ba");
0536 
0537 
0538 pad4->cd();
0539 const Int_t k = 5;
0540 Double_t x4[k] = {1,2,3,4,5};
0541 Double_t y4[k] = {DSBd_yield,DSBi_yield,DSBm_yield,DSBh_yield,sDSB_yield};
0542 Double_t err_y4[k] = {SD_DSBd_yield,SD_DSBi_yield,SD_DSBm_yield,SD_DSBh_yield,SD_sDSB_yield};
0543 TGraph* gr4 = new TGraphErrors(k,x4,y4,0,err_y4);
0544 gr4->SetTitle("Breaks Yield");
0545 gr4->GetXaxis()->SetBinLabel(8,"DSB direct");
0546 gr4->GetXaxis()->SetBinLabel(29,"DSB indirect");
0547 gr4->GetXaxis()->SetBinLabel(50,"DSB mixed");
0548 gr4->GetXaxis()->SetBinLabel(71,"DSB hybrid");
0549 gr4->GetXaxis()->SetBinLabel(92,"DSB all");
0550 //gr4->GetYaxis()->SetTitle("Breaks yield (Gy^{-1} Mbp^{-1})");
0551 gr4->GetYaxis()->SetTitle("DSB yield (Gy^{-1} Gbp^{-1})");
0552 gr4->GetYaxis()->SetTitleOffset(2);
0553 
0554 gr4->SetFillColor(4);
0555 gr4->Draw("ba");
0556 
0557 }
0558 
0559 // Some important bools that are needed to run the root macro file
0560 bool greaterPair(const ipair& l, const ipair& r){return l.second > r.second;}
0561 bool smallerPair(const ipair& l, const ipair& r){return l.second < r.second;}
0562 
0563 void BinLogX(TH1 *h) {
0564   TAxis *axis = h->GetXaxis();
0565   int bins = axis->GetNbins();
0566   Axis_t from = axis->GetXmin();
0567   Axis_t to = axis->GetXmax();
0568   Axis_t width = (to - from) / bins;
0569   Axis_t *new_bins = new Axis_t[bins + 1];
0570   for (int i = 0; i <= bins; i++) {
0571     new_bins[i] = TMath::Power(10, from + i * width);
0572   }
0573   axis->Set(bins, new_bins);
0574   delete[] new_bins;
0575 
0576 }
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