//__________________________________________________________________________
void Plot_JpsiV2_a2_newError()
{
gROOT->Macro("/Users/eusmartass/Software/utilities/setStyle.C+");
gStyle->SetOptFit(0);
// options
bool bDoDebug = false;
bool bSavePlots = true;
const int nptbins = 3;
double pts[nptbins+1] = {6.5, 8.0, 10.0, 40.0};
int pt_start = 0;
int pt_end = 3;
int nPads = pt_end - pt_start;
const int nsignals = 3;
const char* signals[nsignals] = {"NSig","NPr","Pr"};
const char* legend[nsignals] = {"Inclusive J/#psi","Non-prompt J/#psi", "Prompt J/#psi"};
int signal_start = 0;
int signal_end = 3;
const int nrapbins = 2;
double raps[nrapbins] = {0.0, 2.4};
const int ncentbins = 1;
int cts[ncentbins+1] = {10, 60};
int vcts1 = cts[0];
int vcts2 = cts[1];
// phi bins
const int nphibins = 4;
float dPhiLimits[nphibins+1] = {0.0, TMath::PiOver2()/4, 2*TMath::PiOver2()/4, 3*TMath::PiOver2()/4, 4*TMath::PiOver2()/4};
double dPhiBinCenters[nphibins];
double dPhiBinCentersErr[nphibins];
for(int ibin=0; ibin<nphibins; ibin++)
{
dPhiBinCenters[ibin] = dPhiLimits[ibin]+dPhiBinWidth/2;
dPhiBinCentersErr[ibin] = 0.0;
cout<<"bin limits"<< dPhiLimits[ibin] << "\t"<< dPhiLimits[ibin+1]<<"\t"<<dPhiBinCenters[ibin]<<endl;
}
// inclusive
double gYieldP_6580_nsig[nphibins] = {0.7144,
0.6189,
0.6412,
0.5720}; // yield of etHFp for 0 - 10 %
double gYieldP_8010_nsig[nphibins] = {0.7267,
0.6793,
0.6196,
0.5209}; // yield of etHFp for 10 - 20 %
double gYieldP_1040_nsig[nphibins] = {0.6255,
0.6932,
0.5899,
0.6379}; // yield of etHFp for 20 - 30 %
double gYieldM_6580_nsig[nphibins] = {0.7359,
0.6641,
0.5687,
0.5779}; // yield of etHFm for 0 - 10 %
double gYieldM_8010_nsig[nphibins] = {0.7465,
0.6629,
0.5406,
0.5964}; // yield of etHFm for 10 - 20 %
double gYieldM_1040_nsig[nphibins] = {0.7645,
0.5795,
0.6301,
0.5723}; // yield of etHFm for 20 - 30 %
double gYieldP_6580_nsig_err[nphibins] = {0.0478,
0.0439,
0.0434,
0.0419}; // error of etHFp for 0 - 10 %
double gYieldP_8010_nsig_err[nphibins] = {0.0459,
0.0446,
0.0422,
0.0383}; // error of etHFp for 10 - 20 %
double gYieldP_1040_nsig_err[nphibins] = {0.0399,
0.0420,
0.0388,
0.0403}; // error of etHFp for 20 - 30 %
double gYieldM_6580_nsig_err[nphibins] = {0.0477,
0.0450,
0.0418,
0.0417}; // error of etHFm for 0 - 10 %
double gYieldM_8010_nsig_err[nphibins] = {0.0475,
0.0444,
0.0405,
0.0423}; // error of etHFm for 10 - 20 %
double gYieldM_1040_nsig_err[nphibins] = {0.0449,
0.0395,
0.0410,
0.0395}; // error of etHFm for 20 - 30 %
// ------------ prompt
double gYieldP_6580_pr[nphibins] = {0.7368,
0.6344,
0.6293,
0.5461}; // yield of etHFp for 0 - 10 %
double gYieldP_8010_pr[nphibins] = {0.7525,
0.6752,
0.6059,
0.5129}; // yield of etHFp for 10 - 20 %
double gYieldP_1040_pr[nphibins] = {0.6117,
0.7130,
0.5835,
0.6383}; // yield of etHFp for 20 - 30 %
double gYieldM_6580_pr[nphibins] = {0.7580,
0.6799,
0.5575,
0.5510}; // yield of etHFm for 0 - 10 %
double gYieldM_8010_pr[nphibins] = {0.7726,
0.6586,
0.5284,
0.5869}; // yield of etHFm for 10 - 20 %
double gYieldM_1040_pr[nphibins] = {0.7497,
0.5977,
0.6249,
0.5741}; // yield of etHFm for 20 - 30 %
//--------
double gYieldP_6580_pr_err[nphibins] = {0.0668,
0.0499,
0.0483,
0.0684}; // error of etHFp for 0 - 10 %
double gYieldP_8010_pr_err[nphibins] = {0.0538,
0.0518,
0.0490,
0.0493}; // error of etHFp for 10 - 20 %
double gYieldP_1040_pr_err[nphibins] = {0.0435,
0.0483,
0.0430,
0.0452}; // error of etHFp for 20 - 30 %
double gYieldM_6580_pr_err[nphibins] = {0.0698,
0.0525,
0.0699,
0.0452}; // error of etHFm for 0 - 10 %
double gYieldM_8010_pr_err[nphibins] = {0.0553,
0.0506,
0.0449,
0.0482}; // error of etHFm for 10 - 20 %
double gYieldM_1040_pr_err[nphibins] = {0.0539,
0.0486,
0.0470,
0.0449}; // error of etHFm for 20 - 30 %
// --------- non-prompt
double gYieldP_6580_npr[nphibins] = {0.6187,
0.5526,
0.6921,
0.6830}; // yield of etHFp for 0 - 10 %
double gYieldP_8010_npr[nphibins] = {0.6399,
0.6930,
0.6656,
0.5479}; // yield of etHFp for 10 - 20 %
double gYieldP_1040_npr[nphibins] = {0.6593,
0.6444,
0.6057,
0.6371}; // yield of etHFp for 20 - 30 %
double gYieldM_6580_npr[nphibins] = {0.6404,
0.5959,
0.6169,
0.6933}; // yield of etHFm for 0 - 10 %
double gYieldM_8010_npr[nphibins] = {0.6585,
0.6775,
0.5819,
0.6285}; // yield of etHFm for 10 - 20 %
double gYieldM_1040_npr[nphibins] = {0.8006,
0.5353,
0.6428,
0.5678}; // yield of etHFm for 20 - 30 %
//-------------
double gYieldP_6580_npr_err[nphibins] = {0.1014,
0.0900,
0.1008,
0.1174}; // error of etHFp for 0 - 10 %
double gYieldP_8010_npr_err[nphibins] = {0.0893,
0.0926,
0.0888,
0.0831}; // error of etHFp for 10 - 20 %
double gYieldP_1040_npr_err[nphibins] = {0.0629,
0.0654,
0.0603,
0.0624}; // error of etHFp for 20 - 30 %
double gYieldM_6580_npr_err[nphibins] = {0.1052,
0.0967,
0.1060,
0.1033}; // error of etHFm for 0 - 10 %
double gYieldM_8010_npr_err[nphibins] = {0.0919,
0.0906,
0.0792,
0.0901}; // error of etHFm for 10 - 20 %
double gYieldM_1040_npr_err[nphibins] = {0.0761,
0.0599,
0.0647,
0.0587}; // error of etHFm for 20 - 30 %
const int nhf = 2;
TGraphErrors *g[nsignals][nptbins][nhf];
double pr[nsignals][nptbins][nhf], ep[nsignals][nptbins][nhf], chi[nsignals][nptbins][nhf], ndf[nsignals][nptbins][nhf];
double gYieldPlus[nptbins];
double gYieldMinus[nptbins];
double gYieldPlus_err[nptbins];
double gYieldMinus_err[nptbins];
for(int iSignal = signal_start; iSignal<signal_end; iSignal++)
{
const char* chosenSignal = signals[iSignal];
for(int ipt = pt_start; ipt < pt_end; ipt++)
{
TGraphErrors *pgTempP;
TGraphErrors *pgTempM;
switch (ipt) {
case 0:
if (iSignal == 0)
{
assignArray(gYieldP_6580_nsig,gYieldPlus);
assignArray(gYieldM_6580_nsig,gYieldMinus);
assignArray(gYieldP_6580_nsig_err,gYieldPlus_err);
assignArray(gYieldM_6580_nsig_err,gYieldMinus_err);
}
else
if (iSignal == 1)
{
assignArray(gYieldP_6580_npr,gYieldPlus);
assignArray(gYieldM_6580_npr,gYieldMinus);
assignArray(gYieldP_6580_npr_err,gYieldPlus_err);
assignArray(gYieldM_6580_npr_err,gYieldMinus_err);
}
else
{
assignArray(gYieldP_6580_pr,gYieldPlus);
assignArray(gYieldM_6580_pr,gYieldMinus);
assignArray(gYieldP_6580_pr_err,gYieldPlus_err);
assignArray(gYieldM_6580_pr_err,gYieldMinus_err);
}
break;
case 1:
if (iSignal == 0)
{
assignArray(gYieldP_8010_nsig,gYieldPlus);
assignArray(gYieldM_8010_nsig,gYieldMinus);
assignArray(gYieldP_8010_nsig_err,gYieldPlus_err);
assignArray(gYieldM_8010_nsig_err,gYieldMinus_err);
}
else
if (iSignal == 1)
{
assignArray(gYieldP_8010_npr,gYieldPlus);
assignArray(gYieldM_8010_npr,gYieldMinus);
assignArray(gYieldP_8010_npr_err,gYieldPlus_err);
assignArray(gYieldM_8010_npr_err,gYieldMinus_err);
}
else
{
assignArray(gYieldP_8010_pr,gYieldPlus);
assignArray(gYieldM_8010_pr,gYieldMinus);
assignArray(gYieldP_8010_pr_err,gYieldPlus_err);
assignArray(gYieldM_8010_pr_err,gYieldMinus_err);
}
break;
case 2:
if (iSignal == 0)
{
assignArray(gYieldP_1040_nsig,gYieldPlus);
assignArray(gYieldM_1040_nsig,gYieldMinus);
assignArray(gYieldP_1040_nsig_err,gYieldPlus_err);
assignArray(gYieldM_1040_nsig_err,gYieldMinus_err);
}
else
if (iSignal == 1)
{
assignArray(gYieldP_1040_npr,gYieldPlus);
assignArray(gYieldM_1040_npr,gYieldMinus);
assignArray(gYieldP_1040_npr_err,gYieldPlus_err);
assignArray(gYieldM_1040_npr_err,gYieldMinus_err);
}
else
{
assignArray(gYieldP_1040_pr,gYieldPlus);
assignArray(gYieldM_1040_pr,gYieldMinus);
assignArray(gYieldP_1040_pr_err,gYieldPlus_err);
assignArray(gYieldM_1040_pr_err,gYieldMinus_err);
}
break;
default:
cout<< "Wrong pt, please pick something else!"<<endl;
}//ipt switch
pgTempP = new TGraphErrors(nphibins, dPhiBinCenters, gYieldPlus, dPhiBinCentersErr, gYieldPlus_err);
pgTempM = new TGraphErrors(nphibins, dPhiBinCenters, gYieldMinus, dPhiBinCentersErr, gYieldMinus_err);
g[iSignal][ipt][0] = pgTempP;
g[iSignal][ipt][1] = pgTempM;
double cp[4] = {0.0, 0.0, 0.0, 0.0};
double cm[4] = {0.0, 0.0, 0.0, 0.0};
GetV2(g[iSignal][ipt][0], cp);
GetV2(g[iSignal][ipt][1], cm);
pr[iSignal][ipt][0] = cp[0];
ep[iSignal][ipt][0] = cp[1];
chi[iSignal][ipt][0] = cp[2];
ndf[iSignal][ipt][0] = cp[3];
pr[iSignal][ipt][1] = cm[0];
ep[iSignal][ipt][1] = cm[1];
chi[iSignal][ipt][1] = cm[2];
ndf[iSignal][ipt][1] = cm[3];
}//pt loop
// #### Drawing:
TLatex *lt1 = new TLatex();
lt1->SetNDC();
lt1->SetTextSize(0.05);
// frawing:
TCanvas *pc1 = new TCanvas("pc1",Form("pcV2_intPt"),0,0,850,350);
TH1F *pp = new TH1F("pp", Form(";| #phi_{J/#psi} - #Psi_{EP} | (rad);#frac{1}{N_{total J/#psi}} #frac{dN}{d#phi} (rad^{-1})"),4,0,TMath::PiOver2());
pp->GetXaxis()->SetLabelSize(20);
pp->GetXaxis()->SetLabelFont(43);
pp->GetXaxis()->SetTitleSize(18);
pp->GetXaxis()->SetTitleFont(43);
pp->GetXaxis()->SetTitleOffset(1.2);
pp->GetXaxis()->CenterTitle();
pp->GetYaxis()->SetLabelSize(20);
pp->GetYaxis()->SetLabelFont(43);
pp->GetYaxis()->SetTitleSize(19);
pp->GetYaxis()->SetTitleFont(43);
pp->GetYaxis()->SetTitleOffset(1.43);
pp->GetYaxis()->CenterTitle();
makeMultiPanelCanvas(pc1,nPads,1,0.0,0.0,0.2,0.15,0.02);
int ind = 0;
for(int ipt = pt_start; ipt < pt_end; ipt++)
{
if(!g[iSignal][ipt][0]|| !g[iSignal][ipt][1])
{
cout<<"No graph! continued !!!!"<<endl;
continue;
}
double vpts1 = pts[ipt];
double vpts2 = pts[ipt+1];
cout<<"Pt bin: "<<vpts1<<"-"<<vpts2<<endl;
pc1->cd(ind+1);
pp->SetMaximum(1.2);
pp->SetMinimum(0.2);
pp->Draw();
TGraphErrors *pgP = (TGraphErrors *) g[iSignal][ipt][0];
TGraphErrors *pgM = (TGraphErrors *) g[iSignal][ipt][1];
pgP->SetMarkerStyle(20);
pgM->SetMarkerStyle(24);
pgP->Draw("pz");
pgM->Draw("pz");
if(ind==0 )
{
// drapwing v2 value and chi2
lt1->SetTextSize(0.045);
lt1->DrawLatex(0.24,0.23,Form("v_{2}^{etHFp} = %.2f #pm %.2f (#chi^{2} / ndf = %.2f / %.0f)", pr[iSignal][ipt][0], ep[iSignal][ipt][0], chi[iSignal][ipt][0], ndf[iSignal][ipt][0]));
lt1->DrawLatex(0.24,0.18,Form("v_{2}^{etHFm} = %.2f #pm %.2f (#chi^{2} / ndf = %.2f / %.0f)", pr[iSignal][ipt][1], ep[iSignal][ipt][1], chi[iSignal][ipt][1], ndf[iSignal][ipt][1]));
lt1->SetTextSize(0.055);
lt1->DrawLatex(0.24,0.3,Form("%.1f < p_{T} < %.0f GeV/c",vpts1, vpts2)); // pt
}
else
{
lt1->SetTextSize(0.05);
lt1->DrawLatex(0.05,0.23,Form("v_{2}^{etHFp} = %.2f #pm %.2f (#chi^{2} / ndf = %.2f / %.0f)", pr[iSignal][ipt][0], ep[iSignal][ipt][0], chi[iSignal][ipt][0], ndf[iSignal][ipt][0]));
lt1->DrawLatex(0.05,0.18,Form("v_{2}^{etHFm} = %.2f #pm %.2f (#chi^{2} / ndf = %.2f / %.0f)", pr[iSignal][ipt][1], ep[iSignal][ipt][1], chi[iSignal][ipt][1], ndf[iSignal][ipt][1]));
lt1->SetTextSize(0.06);
if(ind == 1) lt1->DrawLatex(0.05,0.3,Form("%.1f < p_{T} < %.0f GeV/c", vpts1, vpts2));
if(ind > 1) lt1->DrawLatex(0.05,0.3,Form("%.1f < p_{T} < %.0f GeV/c", vpts1, vpts2));
if(ind == 2)
{
lt1->SetTextSize(0.06);
lt1->DrawLatex(0.45,0.8,Form("|y| < %.1f",raps[1])); // rapidity
lt1->DrawLatex(0.45,0.73,Form("Cent. %d - %d %%",vcts1, vcts2)); // centrality
}
if(ind==1)
{
TLegend *legCent = new TLegend(0.7,0.8,0.95,0.95);
legCent->SetFillColor(0);
legCent->SetBorderSize(0);
legCent->SetTextSize(0.07);
legCent->AddEntry(pgP,"etHFp","P");
legCent->AddEntry(pgM,"etHFm","P");
legCent->Draw("same");
}
}
ind++;
}//ipt
//_______ stuff to write
pc1->cd(1);
TLatex *tex1 = new TLatex(0.23,0.93,"CMS Preliminary");
tex1->SetNDC();
tex1->SetTextAlign(13);
tex1->SetTextFont(43);
tex1->SetTextSize(23);
tex1->SetLineWidth(1);
tex1->Draw();
TLatex *tex2 = new TLatex(0.23,0.84,"PbPb #sqrt{s_{NN}} = 2.76 TeV");
tex2->SetNDC();
tex2->SetTextAlign(13);
tex2->SetTextFont(43);
tex2->SetTextSize(18);
tex2->SetLineWidth(2);
tex2->Draw();
pc1->cd(1);
TLatex *tex3 = new TLatex(0.23,0.75,"L_{int} = 150 #mub^{-1}");
tex3->SetNDC();
tex3->SetTextAlign(13);
tex3->SetTextFont(43);
tex3->SetTextSize(18);
tex3->SetLineWidth(2);
tex3->Draw();
pc1->cd(3);
lt1->SetTextSize(0.06);
lt1->DrawLatex(0.05,0.89,Form("%s",legend[iSignal])); // what signal is
//_______
if(bSavePlots)
{
pc1->SaveAs(Form("%s_Jpsi_a2_newErr_Nominal.png",chosenSignal));
pc1->SaveAs(Form("%s_Jpsi_a2_newErr_Nominal.pdf",chosenSignal));
}
// pc1->Clear();
cout<<""<<endl;
cout<<"%%%%% Category etHFp: "<<signals[iSignal]<<" %%%%%"<<endl;
cout<<"| pt. | 6.5-8.0 | 8-10 | 10-40 |"<<endl;
cout<<"| v2 |"<<" "<<pr[iSignal][0][0]<<" | "<<pr[iSignal][1][0]<<" | "<<pr[iSignal][2][0]<<" |"<<endl;
cout<<"| err |"<<" "<<ep[iSignal][0][0]<<" | "<<ep[iSignal][1][0]<<" | "<<ep[iSignal][2][0]<<" |"<<endl;
cout<<"%%%%% Category etHFm: "<<signals[iSignal]<<" %%%%%"<<endl;
cout<<"| pt. | 6.5-8.0 | 8-10 | 10-40 |"<<endl;
cout<<"| v2 |"<<" "<<pr[iSignal][0][1]<<" | "<<pr[iSignal][1][1]<<" | "<<pr[iSignal][2][1]<<" |"<<endl;
cout<<"| err |"<<" "<<ep[iSignal][0][1]<<" | "<<ep[iSignal][1][1]<<" | "<<ep[iSignal][2][1]<<" |"<<endl;
}// chose signal
}
virtual StaticArray<T>& operator=(const StaticArray<T>& array) {
assignArray(array);
return *this;
}
int main(int argc, char *argv[])
{
int all; /*Nombre d'atomes dans pdb*/
int atom; /*Nombre de carbone CA*/
int help_flag = 0;
char file_name[500];
char file_eigen[500] = "eigen.dat";
char check_name[500];
char check_eigen[500] = "eigen_t.dat";
int verbose = 0;
int mode = 6;
float vinit = 1; // Valeur de base
float bond_factor = 1; // Facteur pour poid des bond strechcing
float angle_factor = 1; // Facteur pour poid des angles
double K_phi1 = 1; // Facteurs pour angles dièdres
double K_phi3 = 0.5;
float init_templaate = 1;
float kp_factor = 1; // Facteur pour poid des angles dièdres
char inputname[500] ="none";
char matrix_name[500];
int i, j, k, l;
int nconn;
int lig = 0;
int lig_t = 0;
float factor = 1.0;
for (i = 1;i < argc;i++)
{
if (strcmp("-i",argv[i]) == 0) {strcpy(file_name,argv[i+1]);--help_flag;}
if (strcmp("-t",argv[i]) == 0) {strcpy(check_name,argv[i+1]);--help_flag;}
if (strcmp("-init",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);vinit = temp;}
if (strcmp("-kr",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);bond_factor = temp;}
if (strcmp("-kt",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);angle_factor = temp;}
if (strcmp("-kpf",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp); kp_factor = temp;}
if (strcmp("-m",argv[i]) == 0) {strcpy(matrix_name,argv[i+1]);help_flag = 0;}
if (strcmp("-lig",argv[i]) == 0) {lig = 1;}
if (strcmp("-ligt",argv[i]) == 0) {lig_t = 1;}
if (strcmp("-h",argv[i]) == 0) {help_flag = 1;}
if (strcmp("-v",argv[i]) == 0) {verbose = 1;}
}
if (help_flag == 1)
{
printf("****************************\nHelp Section\n-i\tFile Input (PDB)\n-o\tOutput Name Motion\n-ieig\tFile Name Eigen\n-v\tVerbose\n-sp\tSuper Node Mode (CA, N, C)\n-m\tMode\n-nm\tNombre de mode\n-lig\tTient compte duligand (sauf HOH)\n-prox\tAffiche la probabilite que deux CA puissent interagir\n-prev\tAffiche les directions principales du mouvement de chaque CA ponderees par leur ecart-type\n****************************\n");
return(0);
}
//***************************************************
//* *
//*Builds a structure contaning information on the initial pdb structure
//* *
//***************************************************
all = count_atom(file_name);
nconn = count_connect(file_name);
if (verbose == 1) {printf("Connect:%d\n",nconn);}
if (verbose == 1) {printf("Assigning Structure\n\tAll Atom\n");}
// Array with all connects
int **connect_h=(int **)malloc(nconn*sizeof(int *));
for(i=0;i<nconn;i++) { connect_h[i]=(int *)malloc(6*sizeof(int));}
assign_connect(file_name,connect_h);
// Assigns all the atoms
struct pdb_atom strc_all[all];
atom = build_all_strc(file_name,strc_all); // Retourne le nombre de Node
if (atom > 800) {printf("Too much nodes .... To fix, ask [email protected]\n");return(1);}
if (verbose == 1) {printf(" Atom:%d\n",all);}
check_lig(strc_all,connect_h,nconn,all);
// Assigns all Nodes
if (verbose == 1) {printf(" CA Structure\n");}
if (verbose == 1) {printf(" Node:%d\n",atom);}
struct pdb_atom strc_node[atom];
atom = build_cord_CA(strc_all, strc_node,all,lig,connect_h,nconn);
if (verbose == 1) {printf(" Assign Node:%d\n",atom);}
// Free Connect
//for(i=0;i<nconn;i++) {printf("I:%d\n",i);free(connect_h[i]);}
//free(connect_h);
printf("Check 1\n");
//***************************************************
//* *
//*Builds a structure contaning information on the target pdb structure
//* *
//***************************************************
nconn = 0;
int all_t = count_atom(check_name);
nconn = count_connect(check_name);
if (verbose == 1) {printf("Connect:%d\n",nconn);}
if (verbose == 1) {printf("Assigning Structure\n\tAll Atom\n");}
// Array with all connects
int **connect_t=(int **)malloc(nconn*sizeof(int *));
for(i=0;i<nconn;i++) { connect_t[i]=(int *)malloc(6*sizeof(int));}
assign_connect(check_name,connect_t);
// Assigns all the atoms
struct pdb_atom strc_all_t[all_t];
int atom_t = build_all_strc(check_name,strc_all_t); // Retourne le nombre de Node
if (atom_t > 800) {printf("Too much node.... To fix, ask [email protected]\n");return(1);}
if (verbose == 1) {printf(" Atom:%d\n",all_t);}
check_lig(strc_all_t,connect_t,nconn,all_t);
// Assigns all Nodes
if (verbose == 1) {printf(" CA Structure\n");}
if (verbose == 1) {printf(" Node:%d\n",atom_t);}
struct pdb_atom strc_node_t[atom_t];
atom_t = build_cord_CA(strc_all_t, strc_node_t,all_t,lig_t,connect_t,nconn);
if (verbose == 1) {printf(" Assign Node:%d\n",atom_t);}
printf("Check 2\n");
//***************************************************
//* *
//*Aligns both structures *
//* *
//***************************************************
int align[atom];
int score = node_align(strc_node,atom,strc_node_t,atom_t,align);
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_no(strc_node,strc_node_t,atom, align)),score,atom);
if ((float)score/(float)atom < 0.8)
{
printf("Low Score... Will try an homemade alignement !!!\n");
score = node_align_onechain(strc_node,atom,strc_node_t,atom_t,align);
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_no(strc_node,strc_node_t,atom, align)),score,atom);
}
if ((float)score/(float)atom < 0.8)
{
printf("Low Score... Will try an homemade alignement !!!\n");
score = node_align_low(strc_node,atom,strc_node_t,atom_t,align);
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_no(strc_node,strc_node_t,atom, align)),score,atom);
}
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_yes(strc_node,strc_node_t,atom, align,strc_all,all)),score,atom);
printf("Check 4\n");
//***************************************************
//* *
//*Build hessian matrices *
//* *
//***************************************************
double **hessian=(double **)malloc(3*atom*sizeof(double *)); // Matrix of the Hessian 1 2 3 (bond, angle, dihedral)
for(i=0;i<3*atom;i++) { hessian[i]=(double *)malloc(3*atom*sizeof(double));}
for(i=0;i<3*atom;i++)for(j=0;j<(3*atom);j++){hessian[i][j]=0;}
gsl_matrix *hess = gsl_matrix_alloc(3*atom,3*atom);
gsl_matrix_set_all(hess, 0);
gsl_matrix *hess_t = gsl_matrix_alloc(3*atom_t,3*atom_t);
gsl_matrix_set_all(hess_t, 0);
assign_atom_type(strc_all, all);
if (strcmp(inputname,"none") == 0) {} else {assign_lig_type(strc_all, all, inputname);}
gsl_matrix *vcon = gsl_matrix_alloc(all,all);
gsl_matrix *inter_m = gsl_matrix_alloc(8,8);
gsl_matrix *templaate = gsl_matrix_alloc(atom*3, atom*3);
gsl_matrix_set_all(templaate,vinit);
gsl_matrix_set_all(vcon,0);
if (verbose == 1) {printf("Do Vcon !!!\n");}
vcon_file_dom(strc_all,vcon,all);
if (verbose == 1) {printf("Reading Interaction Matrix %s\n",matrix_name);}
load_matrix(inter_m,matrix_name);
//write_matrix("vcon_vince.dat", vcon,all,all);
if (verbose == 1) {printf("Building templaate\n");}
all_interaction(strc_all,all, atom, templaate,lig,vcon,inter_m,strc_node);
gsl_matrix_scale (templaate, init_templaate);
if (verbose == 1) {printf("Building Hessian\n");}
if (verbose == 1) {printf("\tCovalent Bond Potential\n");}
build_1st_matrix(strc_node,hessian,atom,bond_factor);
if (verbose == 1) {printf("\tAngle Potential\n");}
build_2_matrix(strc_node,hessian,atom,angle_factor);
if (verbose == 1) {printf("\tDihedral Potential\n");}
build_3_matrix(strc_node, hessian,atom,K_phi1/2+K_phi3*9/2,kp_factor);
if (verbose == 1) {printf("\tNon Local Interaction Potential\n");}
build_4h_matrix(strc_node,hessian,atom,1.0,templaate);
if (verbose == 1) {printf("\tAssigning Array\n");}
assignArray(hess,hessian,3*atom,3*atom);
gsl_matrix_free(vcon);
gsl_matrix_free(templaate);
double **hessian_t=(double **)malloc(3*atom_t*sizeof(double *)); // Matrix of the Hessian 1 2 3 (bond, angle, dihedral)
for(i=0;i<3*atom_t;i++) { hessian_t[i]=(double *)malloc(3*atom_t*sizeof(double));}
for(i=0;i<3*atom_t;i++)for(j=0;j<(3*atom_t);j++){hessian_t[i][j]=0;}
assign_atom_type(strc_all_t, all_t);
if (strcmp(inputname,"none") == 0) {} else {assign_lig_type(strc_all_t, all_t, inputname);}
gsl_matrix *vcon_t = gsl_matrix_alloc(all_t,all_t);
gsl_matrix *templaate_t = gsl_matrix_alloc(atom_t*3, atom_t*3);
gsl_matrix_set_all(templaate_t,vinit);
gsl_matrix_set_all(vcon_t,0);
if (verbose == 1) {printf("Do Vcon !!!\n");}
vcon_file_dom(strc_all_t,vcon_t,all_t);
//write_matrix("vcon_vince.dat", vcon,all,all);
if (verbose == 1) {printf("Building templaate\n");}
all_interaction(strc_all_t,all_t, atom_t, templaate_t,lig,vcon_t,inter_m,strc_node_t);
gsl_matrix_scale (templaate_t, init_templaate);
if (verbose == 1) {printf("Building Hessian\n");}
if (verbose == 1) {printf("\tCovalent Bond Potential\n");}
build_1st_matrix(strc_node_t,hessian_t,atom_t,bond_factor);
if (verbose == 1) {printf("\tAngle Potential\n");}
build_2_matrix(strc_node_t,hessian_t,atom_t,angle_factor);
if (verbose == 1) {printf("\tDihedral Potential\n");}
build_3_matrix(strc_node_t, hessian_t,atom_t,K_phi1/2+K_phi3*9/2,kp_factor);
if (verbose == 1) {printf("\tNon Local Interaction Potential\n");}
build_4h_matrix(strc_node_t,hessian_t,atom_t,1.0,templaate_t);
if (verbose == 1) {printf("\tAssigning Array\n");}
assignArray(hess_t,hessian_t,3*atom_t,3*atom_t);
gsl_matrix_free(vcon_t);
gsl_matrix_free(templaate_t);
printf("Check 5\n");
//***************************************************
//* *
//*Build mini hessian matrices *
//* *
//***************************************************
gsl_matrix *mini_hess = gsl_matrix_alloc(3*score, 3*score);
gsl_matrix_set_all(mini_hess, 0);
gsl_matrix *mini_hess_t = gsl_matrix_alloc(3*score, 3*score);
gsl_matrix_set_all(mini_hess_t, 0);
int sup_line = 0;
int sup_to_node[score];
for(i = 0; i < atom; i++)
{
if(align[i] == -1) {continue;}
sup_to_node[sup_line] = i;
int sup_col = 0;
for(j = 0; j < atom; j++)
{
if(align[j] == -1) {continue;}
for(k = 0; k < 3; k++)
{
for(l = 0; l < 3; l++)
{
gsl_matrix_set(mini_hess, 3*sup_line + k, 3*sup_col + l, gsl_matrix_get(hess, 3*i + k, 3*j + l));
gsl_matrix_set(mini_hess_t, 3*sup_line + k, 3*sup_col + l, gsl_matrix_get(hess_t, 3*align[i] + k, 3*align[j] + l));
}
}
sup_col ++;
}
sup_line++;
}
gsl_matrix_free(hess);
gsl_matrix_free(hess_t);
printf("Check 6\n");
gsl_vector *mini_eval = gsl_vector_alloc(3*score);
gsl_matrix *mini_evec = gsl_matrix_alloc (3*score,3*score);
gsl_vector *mini_eval_t = gsl_vector_alloc(3*score);
gsl_matrix *mini_evec_t = gsl_matrix_alloc (3*score,3*score);
diagonalyse_matrix(mini_hess,3*score,mini_eval,mini_evec);
diagonalyse_matrix(mini_hess_t,3*score,mini_eval_t,mini_evec_t);
gsl_matrix_set_all(mini_hess, 0);
gsl_matrix_set_all(mini_hess_t, 0);
for(i = 0; i < 3*score; i++)
{
if(gsl_vector_get(mini_eval, i) > 0.0000001)
{
gsl_vector_set(mini_eval, i, 1.0 / gsl_vector_get(mini_eval, i));
for(j = 0; j < 3*score; j++)
{
for(k = 0; k < 3*score; k++)
{
gsl_matrix_set(mini_hess, j, k, gsl_matrix_get(mini_hess, j, k) + gsl_matrix_get(mini_evec, j, i)*gsl_matrix_get(mini_evec, k, i)*gsl_vector_get(mini_eval, i));
}
}
}
}
for(i = 0; i < 3*score; i++)
{
if(gsl_vector_get(mini_eval_t, i) > 0.0000001)
{
gsl_vector_set(mini_eval_t, i, 1.0 / gsl_vector_get(mini_eval_t, i));
for(j = 0; j < 3*score; j++)
{
for(k = 0; k < 3*score; k++)
{
gsl_matrix_set(mini_hess_t, j, k, gsl_matrix_get(mini_hess_t, j, k) + gsl_matrix_get(mini_evec_t, j, i)*gsl_matrix_get(mini_evec_t, k, i)*gsl_vector_get(mini_eval_t, i));
}
}
}
}
printf("Check 7\n");
printf("Dynamic distance : %1.10f\n", cmp_gauss(mini_hess, mini_eval, mini_hess_t, mini_eval_t, 3*score));
gsl_matrix_free(mini_hess);
gsl_matrix_free(mini_evec);
gsl_vector_free(mini_eval);
gsl_matrix_free(mini_hess_t);
gsl_matrix_free(mini_evec_t);
gsl_vector_free(mini_eval_t);
free(connect_h);
return(1);
}
//__________________________________________________________________________
void Plot_JpsiV2_a1_newError()
{
gROOT->Macro("/Users/eusmartass/Software/utilities/setStyle.C+");
gStyle->SetOptFit(0);
// options
bool bDoDebug = false;
bool bSavePlots = true;
const int ncentbins = 4;
int cts[ncentbins+1] = {0, 10, 20, 30, 60};
int centrality_start = 0;
int centrality_end = 4;
int nPads = centrality_end - centrality_start;
const int nsignals = 3;
const char* signals[nsignals] = {"NSig","NPr","Pr"};
const char* legend[nsignals] = {"Inclusive J/#psi","Non-prompt J/#psi","Prompt J/#psi",};
int signal_start = 0;
int signal_end = 3;
const int nrapbins = 2;
double raps[nrapbins] = {0.0, 2.4};
const int nptbins = 2;
double pts[nptbins] = {6.5, 40.0};
int pt_start = 0;
int pt_end = 1;
// phi bins
const int nphibins = 4;
float dPhiLimits[nphibins+1] = {0.0, TMath::PiOver2()/4, 2*TMath::PiOver2()/4, 3*TMath::PiOver2()/4, 4*TMath::PiOver2()/4};
double dPhiBinCenters[nphibins];
double dPhiBinCentersErr[nphibins];
for(int ibin=0; ibin<nphibins; ibin++)
{
dPhiBinCenters[ibin] = dPhiLimits[ibin]+dPhiBinWidth/2;
dPhiBinCentersErr[ibin] = 0.0;
cout<<"bin limits"<< dPhiLimits[ibin] << "\t"<< dPhiLimits[ibin+1]<<"\t"<<dPhiBinCenters[ibin]<<endl;
}
// inclusive
double gYieldP_0010_nsig[nphibins] = {0.6791,
0.6419,
0.6078,
0.6177}; // yield of etHFp for 0 - 10 %
double gYieldP_1020_nsig[nphibins] = {0.6788,
0.6745,
0.6424,
0.5508}; // yield of etHFp for 10 - 20 %
double gYieldP_2030_nsig[nphibins] = {0.7705,
0.5811,
0.6172,
0.5776}; // yield of etHFp for 20 - 30 %
double gYieldP_3060_nsig[nphibins] = {0.6405,
0.6994,
0.5997,
0.6069}; // yield of etHFp for 30 - 60 %
double gYieldM_0010_nsig[nphibins] = {0.6796,
0.6196,
0.6358,
0.6115}; // yield of etHFm for 0 - 10 %
double gYieldM_1020_nsig[nphibins] = {0.7550,
0.6097,
0.5786,
0.6032}; // yield of etHFm for 10 - 20 %
double gYieldM_2030_nsig[nphibins] = {0.7167,
0.6719,
0.5886,
0.5693}; // yield of etHFm for 20 - 30 %
double gYieldM_3060_nsig[nphibins] = {0.7554,
0.6385,
0.5759,
0.5767}; // yield of etHFm for 30 - 60 %
double gYieldP_0010_nsig_err[nphibins] = {0.0409,
0.0404,
0.0389,
0.0382}; // error of etHFp for 0 - 10 %
double gYieldP_1020_nsig_err[nphibins] = {0.0436,
0.0427,
0.0413,
0.0386}; // error of etHFp for 10 - 20 %
double gYieldP_2030_nsig_err[nphibins] = {0.0523,
0.0461,
0.0467,
0.0449}; // error of etHFp for 20 - 30 %
double gYieldP_3060_nsig_err[nphibins] = {0.0396,
0.0409,
0.0378,
0.0379}; // error of etHFp for 30 - 60 %
double gYieldM_0010_nsig_err[nphibins] = {0.0419,
0.0405,
0.0403,
0.0399}; // error of etHFm for 0 - 10 %
double gYieldM_1020_nsig_err[nphibins] = {0.0469,
0.0425,
0.0414,
0.0419}; // error of etHFm for 10 - 20 %
double gYieldM_2030_nsig_err[nphibins] = {0.0504,
0.0485,
0.0454,
0.0448}; // error of etHFm for 20 - 30 %
double gYieldM_3060_nsig_err[nphibins] = {0.0423,
0.0389,
0.0369,
0.0371}; // error of etHFm for 30 - 60 %
// prompt
double gYieldP_0010_pr[nphibins] = {0.6533,
0.6450,
0.6174,
0.6307}; // yield of etHFp for 0 - 10 %
double gYieldP_1020_pr[nphibins] = {0.6567,
0.6927,
0.6500,
0.5471}; // yield of etHFp for 10 - 20 %
double gYieldP_2030_pr[nphibins] = {0.8234,
0.5767,
0.5598,
0.5866}; // yield of etHFp for 20 - 30 %
double gYieldP_3060_pr[nphibins] = {0.6453,
0.7071,
0.6158,
0.5782}; // yield of etHFp for 30 - 60 %
double gYieldM_0010_pr[nphibins] = {0.6538,
0.6226,
0.6458,
0.6244}; // yield of etHFm for 0 - 10 %
double gYieldM_1020_pr[nphibins] = {0.7319,
0.6275,
0.5867,
0.6004}; // yield of etHFm for 10 - 20 %
double gYieldM_2030_pr[nphibins] = {0.7665,
0.6673,
0.5342,
0.5785}; // yield of etHFm for 20 - 30 %
double gYieldM_3060_pr[nphibins] = {0.7607,
0.6453,
0.5912,
0.5492}; // yield of etHFm for 30 - 60 %
double gYieldP_0010_pr_err[nphibins] = {0.0555,
0.0472,
0.0510,
0.0450}; // error of etHFp for 0 - 10 %
double gYieldP_1020_pr_err[nphibins] = {0.0525,
0.0511,
0.0516,
0.0513}; // error of etHFp for 10 - 20 %
double gYieldP_2030_pr_err[nphibins] = {0.0613,
0.0568,
0.0490,
0.0615}; // error of etHFp for 20 - 30 %
double gYieldP_3060_pr_err[nphibins] = {0.0476,
0.0476,
0.0431,
0.0439}; // error of etHFp for 30 - 60 %
double gYieldM_0010_pr_err[nphibins] = {0.0465,
0.0492,
0.0482,
0.0463}; // error of etHFm for 0 - 10 %
double gYieldM_1020_pr_err[nphibins] = {0.0625,
0.0491,
0.0517,
0.0515}; // error of etHFm for 10 - 20 %
double gYieldM_2030_pr_err[nphibins] = {0.0617,
0.0561,
0.0488,
0.0516}; // error of etHFm for 20 - 30 %
double gYieldM_3060_pr_err[nphibins] = {0.0504,
0.0443,
0.0465,
0.0419}; // error of etHFm for 30 - 60 %
// non-prompt
double gYieldP_0010_npr[nphibins] = {0.7498,
0.6333,
0.5816,
0.5818}; // yield of etHFp for 0 - 10 %
double gYieldP_1020_npr[nphibins] = {0.7468,
0.6187,
0.6188,
0.5621}; // yield of etHFp for 10 - 20 %
double gYieldP_2030_npr[nphibins] = {0.5920,
0.5960,
0.8109,
0.5476}; // yield of etHFp for 20 - 30 %
double gYieldP_3060_npr[nphibins] = {0.6239,
0.6727,
0.5437,
0.7062}; // yield of etHFp for 30 - 60 %
double gYieldM_0010_npr[nphibins] = {0.7504,
0.6114,
0.6085,
0.5761}; // yield of etHFm for 0 - 10 %
double gYieldM_1020_npr[nphibins] = {0.8253,
0.5557,
0.5538,
0.6116}; // yield of etHFm for 10 - 20 %
double gYieldM_2030_npr[nphibins] = {0.5493,
0.6875,
0.7714,
0.5383}; // yield of etHFm for 20 - 30 %
double gYieldM_3060_npr[nphibins] = {0.7367,
0.6150,
0.5228,
0.6719}; // yield of etHFm for 30 - 60 %
//------
double gYieldP_0010_npr_err[nphibins] = {0.0839,
0.0726,
0.0722,
0.0676}; // error of etHFp for 0 - 10 %
double gYieldP_1020_npr_err[nphibins] = {0.0873,
0.0797,
0.0819,
0.0832}; // error of etHFp for 10 - 20 %
double gYieldP_2030_npr_err[nphibins] = {0.0908,
0.0926,
0.1024,
0.0964}; // error of etHFp for 20 - 30 %
double gYieldP_3060_npr_err[nphibins] = {0.0776,
0.0845,
0.0717,
0.0832}; // error of etHFp for 30 - 60 %
//-----
double gYieldM_0010_npr_err[nphibins] = {0.0771,
0.0724,
0.0719,
0.0678}; // error of etHFm for 0 - 10 %
double gYieldM_1020_npr_err[nphibins] = {0.0993,
0.0730,
0.0768,
0.0875}; // error of etHFm for 10 - 20 %
double gYieldM_2030_npr_err[nphibins] = {0.0862,
0.1007,
0.0991,
0.0899}; // error of etHFm for 20 - 30 %
double gYieldM_3060_npr_err[nphibins] = {0.0880,
0.0779,
0.0717,
0.0793}; // error of etHFm for 30 - 60 %
const int nhf = 2;
TGraphErrors *g[nsignals][ncentbins][nhf];
double pr[nsignals][ncentbins][nhf], ep[nsignals][ncentbins][nhf], chi[nsignals][ncentbins][nhf], ndf[nsignals][ncentbins][nhf];
double vpts1 = pts[pt_start];
double vpts2 = pts[pt_end];
double gYieldPlus[ncentbins];
double gYieldMinus[ncentbins];
double gYieldPlus_err[ncentbins];
double gYieldMinus_err[ncentbins];
for(int iSignal = signal_start; iSignal<signal_end; iSignal++)
{
const char* chosenSignal = signals[iSignal];
for(int mcent = centrality_start; mcent < centrality_end; mcent++)
{
TGraphErrors *pgTempP;
TGraphErrors *pgTempM;
switch (mcent) {
case 0:
if (iSignal == 0)
{
assignArray(gYieldP_0010_nsig,gYieldPlus);
assignArray(gYieldM_0010_nsig,gYieldMinus);
assignArray(gYieldP_0010_nsig_err,gYieldPlus_err);
assignArray(gYieldM_0010_nsig_err,gYieldMinus_err);
}
else
if (iSignal == 1)
{
assignArray(gYieldP_0010_npr,gYieldPlus);
assignArray(gYieldM_0010_npr,gYieldMinus);
assignArray(gYieldP_0010_npr_err,gYieldPlus_err);
assignArray(gYieldM_0010_npr_err,gYieldMinus_err);
}
else
{
assignArray(gYieldP_0010_pr,gYieldPlus);
assignArray(gYieldM_0010_pr,gYieldMinus);
assignArray(gYieldP_0010_pr_err,gYieldPlus_err);
assignArray(gYieldM_0010_pr_err,gYieldMinus_err);
}
break;
case 1:
if (iSignal == 0)
{
assignArray(gYieldP_1020_nsig,gYieldPlus);
assignArray(gYieldM_1020_nsig,gYieldMinus);
assignArray(gYieldP_1020_nsig_err,gYieldPlus_err);
assignArray(gYieldM_1020_nsig_err,gYieldMinus_err);
}
else
if (iSignal == 1)
{
assignArray(gYieldP_1020_npr,gYieldPlus);
assignArray(gYieldM_1020_npr,gYieldMinus);
assignArray(gYieldP_1020_npr_err,gYieldPlus_err);
assignArray(gYieldM_1020_npr_err,gYieldMinus_err);
}
else
{
assignArray(gYieldP_1020_pr,gYieldPlus);
assignArray(gYieldM_1020_pr,gYieldMinus);
assignArray(gYieldP_1020_pr_err,gYieldPlus_err);
assignArray(gYieldM_1020_pr_err,gYieldMinus_err);
}
break;
case 2:
if (iSignal == 0)
{
assignArray(gYieldP_2030_nsig,gYieldPlus);
assignArray(gYieldM_2030_nsig,gYieldMinus);
assignArray(gYieldP_2030_nsig_err,gYieldPlus_err);
assignArray(gYieldM_2030_nsig_err,gYieldMinus_err);
}
else
if (iSignal == 1)
{
assignArray(gYieldP_2030_npr,gYieldPlus);
assignArray(gYieldM_2030_npr,gYieldMinus);
assignArray(gYieldP_2030_npr_err,gYieldPlus_err);
assignArray(gYieldM_2030_npr_err,gYieldMinus_err);
}
else
{
assignArray(gYieldP_2030_pr,gYieldPlus);
assignArray(gYieldM_2030_pr,gYieldMinus);
assignArray(gYieldP_2030_pr_err,gYieldPlus_err);
assignArray(gYieldM_2030_pr_err,gYieldMinus_err);
}
break;
case 3:
if (iSignal == 0)
{
assignArray(gYieldP_3060_nsig,gYieldPlus);
assignArray(gYieldM_3060_nsig,gYieldMinus);
assignArray(gYieldP_3060_nsig_err,gYieldPlus_err);
assignArray(gYieldM_3060_nsig_err,gYieldMinus_err);
}
else
if (iSignal == 1)
{
assignArray(gYieldP_3060_npr,gYieldPlus);
assignArray(gYieldM_3060_npr,gYieldMinus);
assignArray(gYieldP_3060_npr_err,gYieldPlus_err);
assignArray(gYieldM_3060_npr_err,gYieldMinus_err);
}
else
{
assignArray(gYieldP_3060_pr,gYieldPlus);
assignArray(gYieldM_3060_pr,gYieldMinus);
assignArray(gYieldP_3060_pr_err,gYieldPlus_err);
assignArray(gYieldM_3060_pr_err,gYieldMinus_err);
}
break;
default:
cout<< "Wrong centrality, please pick something else!"<<endl;
}//mcent switch
pgTempP = new TGraphErrors(nphibins, dPhiBinCenters, gYieldPlus, dPhiBinCentersErr, gYieldPlus_err);
pgTempM = new TGraphErrors(nphibins, dPhiBinCenters, gYieldMinus, dPhiBinCentersErr, gYieldMinus_err);
g[iSignal][mcent][0] = pgTempP;
g[iSignal][mcent][1] = pgTempM;
double cp[4] = {0.0, 0.0, 0.0, 0.0};
double cm[4] = {0.0, 0.0, 0.0, 0.0};
GetV2(g[iSignal][mcent][0], cp);
GetV2(g[iSignal][mcent][1], cm);
pr[iSignal][mcent][0] = cp[0];
ep[iSignal][mcent][0] = cp[1];
chi[iSignal][mcent][0] = cp[2];
ndf[iSignal][mcent][0] = cp[3];
pr[iSignal][mcent][1] = cm[0];
ep[iSignal][mcent][1] = cm[1];
chi[iSignal][mcent][1] = cm[2];
ndf[iSignal][mcent][1] = cm[3];
}//centrality loop
// #### Drawing:
TLatex *lt1 = new TLatex();
lt1->SetNDC();
lt1->SetTextSize(0.05);
// frawing:
TCanvas *pc1 = new TCanvas("pc1",Form("pcV2_intPt"),0,0,1200,350);
TH1F *pp = new TH1F("pp", Form(";| #phi_{J/#psi} - #Psi_{EP} | (rad);#frac{1}{N_{total J/#psi}} #frac{dN}{d#phi} (rad^{-1})"),4,0,TMath::PiOver2());
pp->GetXaxis()->SetLabelSize(20);
pp->GetXaxis()->SetLabelFont(43);
pp->GetXaxis()->SetTitleSize(18);
pp->GetXaxis()->SetTitleFont(43);
pp->GetXaxis()->SetTitleOffset(1.2);
pp->GetXaxis()->CenterTitle();
pp->GetYaxis()->SetLabelSize(20);
pp->GetYaxis()->SetLabelFont(43);
pp->GetYaxis()->SetTitleSize(19);
pp->GetYaxis()->SetTitleFont(43);
pp->GetYaxis()->SetTitleOffset(1.43);
pp->GetYaxis()->CenterTitle();
makeMultiPanelCanvas(pc1,nPads,1,0.0,0.0,0.2,0.15,0.02);
int ind = 0;
for(int mcent = centrality_start; mcent < centrality_end; mcent++)
{
if(!g[iSignal][mcent][0]|| !g[iSignal][mcent][1])
{
cout<<"No graph! continued !!!!"<<endl;
continue;
}
int vcts1 = cts[mcent];
int vcts2 = cts[mcent+1];
cout<<"Centrlality bin: "<<vcts1<<"-"<<vcts2<<endl;
pc1->cd(ind+1);
pp->SetMaximum(1.2);
pp->SetMinimum(0.2);
pp->Draw();
TGraphErrors *pgP = (TGraphErrors *) g[iSignal][mcent][0];
TGraphErrors *pgM = (TGraphErrors *) g[iSignal][mcent][1];
pgP->SetMarkerStyle(20);
pgM->SetMarkerStyle(24);
pgP->Draw("pz");
pgM->Draw("pz");
if(ind==0 )
{
// drapwing v2 value and chi2
lt1->SetTextSize(0.045);
lt1->DrawLatex(0.24,0.23,Form("v_{2}^{etHFp} = %.2f #pm %.2f (#chi^{2} / ndf = %.2f / %.0f)", pr[iSignal][mcent][0], ep[iSignal][mcent][0], chi[iSignal][mcent][0], ndf[iSignal][mcent][0]));
lt1->DrawLatex(0.24,0.18,Form("v_{2}^{etHFm} = %.2f #pm %.2f (#chi^{2} / ndf = %.2f / %.0f)", pr[iSignal][mcent][1], ep[iSignal][mcent][1], chi[iSignal][mcent][1], ndf[iSignal][mcent][1]));
lt1->SetTextSize(0.055);
lt1->DrawLatex(0.24,0.3,Form("Cent. %d - %d %%",vcts1, vcts2)); // centrality
}
else
{
lt1->SetTextSize(0.05);
lt1->DrawLatex(0.05,0.23,Form("v_{2}^{etHFp} = %.2f #pm %.2f (#chi^{2} / ndf = %.2f / %.0f)", pr[iSignal][mcent][0], ep[iSignal][mcent][0], chi[iSignal][mcent][0], ndf[iSignal][mcent][0]));
lt1->DrawLatex(0.05,0.18,Form("v_{2}^{etHFm} = %.2f #pm %.2f (#chi^{2} / ndf = %.2f / %.0f)", pr[iSignal][mcent][1], ep[iSignal][mcent][1], chi[iSignal][mcent][1], ndf[iSignal][mcent][1]));
lt1->SetTextSize(0.06);
if(ind == 1) lt1->DrawLatex(0.05,0.3,Form("Cent. %d - %d %%",vcts1, vcts2));
if(ind > 1) lt1->DrawLatex(0.05,0.3,Form("Cent. %d - %d %%",vcts1, vcts2));
if(ind == 3)
{
lt1->SetTextSize(0.06);
lt1->DrawLatex(0.45,0.8,Form("|y| < %.1f",raps[1])); // rapidity
lt1->DrawLatex(0.45,0.73,Form("%.1f < p_{T} < %.0f GeV/c", vpts1, vpts2)); // pt
}
if(ind==1)
{
TLegend *legCent = new TLegend(0.7,0.8,0.95,0.95);
legCent->SetFillColor(0);
legCent->SetBorderSize(0);
legCent->SetTextSize(0.07);
legCent->AddEntry(pgP,"etHFp","P");
legCent->AddEntry(pgM,"etHFm","P");
legCent->Draw("same");
}
}
ind++;
}//mcent
//_______ stuff to write
pc1->cd(1);
TLatex *tex1 = new TLatex(0.23,0.93,"CMS Preliminary");
tex1->SetNDC();
tex1->SetTextAlign(13);
tex1->SetTextFont(43);
tex1->SetTextSize(23);
tex1->SetLineWidth(1);
tex1->Draw();
TLatex *tex2 = new TLatex(0.23,0.84,"PbPb #sqrt{s_{NN}} = 2.76 TeV");
tex2->SetNDC();
tex2->SetTextAlign(13);
tex2->SetTextFont(43);
tex2->SetTextSize(18);
tex2->SetLineWidth(2);
tex2->Draw();
pc1->cd(1);
TLatex *tex3 = new TLatex(0.23,0.75,"L_{int} = 150 #mub^{-1}");
tex3->SetNDC();
tex3->SetTextAlign(13);
tex3->SetTextFont(43);
tex3->SetTextSize(18);
tex3->SetLineWidth(2);
tex3->Draw();
pc1->cd(4);
lt1->SetTextSize(0.06);
lt1->DrawLatex(0.05,0.89,Form("%s",legend[iSignal])); // what signal is
//_______
if(bSavePlots)
{
pc1->SaveAs(Form("%s_Jpsi_a1_newErr_Nominal.png",chosenSignal));
pc1->SaveAs(Form("%s_Jpsi_a1_newErr_Nominal.pdf",chosenSignal));
}
// pc1->Clear();
cout<<""<<endl;
cout<<"%%%%% Category etHFp: "<<signals[iSignal]<<" %%%%%"<<endl;
cout<<"| Cent. | 0 - 10 % | 10 - 20 % | 20 - 30 % | 30 - 60 % |"<<endl;
cout<<"| v2 |"<<" "<<pr[iSignal][0][0]<<" | "<<pr[iSignal][1][0]<<" | "<<pr[iSignal][2][0]<<" | "<<pr[iSignal][3][0]<<" |"<<endl;
cout<<"| err |"<<" "<<ep[iSignal][0][0]<<" | "<<ep[iSignal][1][0]<<" | "<<ep[iSignal][2][0]<<" | "<<ep[iSignal][3][0]<<" |"<<endl;
cout<<"%%%%% Category etHFm: "<<signals[iSignal]<<" %%%%%"<<endl;
cout<<"| Cent. | 0 - 10 % | 10 - 20 % | 20 - 30 % | 30 - 60 % |"<<endl;
cout<<"| v2 |"<<" "<<pr[iSignal][0][1]<<" | "<<pr[iSignal][1][1]<<" | "<<pr[iSignal][2][1]<<" | "<<pr[iSignal][3][1]<<" |"<<endl;
cout<<"| err |"<<" "<<ep[iSignal][0][1]<<" | "<<ep[iSignal][1][1]<<" | "<<ep[iSignal][2][1]<<" | "<<ep[iSignal][3][1]<<" |"<<endl;
}// chose signal
}
int main(int argc, char *argv[])
{
int all; /*Number of atoms in the initial PDB*/
int atom; /*Number of initial CAs*/
int all_t; /*Number of atoms in the target PDB*/
int atom_t; /*Number of target CAs*/
int help_flag = 1;
char file_name[500];
char matrix_name[500];
char check_name[500];
int print_inter = 0;
int print_inter_t = 0;
char out_name[500];
char out_name_t[500];
char out_movie[500];
int print_movie = 0;
int verbose = 0;
float vinit = 1; // Valeur de base
float bond_factor = 1; // Facteur pour poid des bond strechcing
float angle_factor = 1; // Facteur pour poid des angles
double K_phi1 = 1; // Facteurs pour angles dièdres
double K_phi3 = 0.5;
float init_templaate = 1;
float kp_factor = 1; // Facteur pour poid des angles dièdres
char inputname[500] ="none";
double beta = 0.000005;
int morph = 0;
char morph_name[500];
int change_density = 0;
int i,j,k,l;
int lig = 0;
int ligt = 0;
int nconn;
int print_flag = 0;
float ligalign = 0; // Flag/valeur pour aligner seulement les résidus dans un cutoff du ligand, 0, one le fait pas... > 0... le cutoff
for (i = 1;i < argc;i++) {
if (strcmp("-i",argv[i]) == 0) {strcpy(file_name,argv[i+1]);--help_flag;}
if (strcmp("-h",argv[i]) == 0) {help_flag = 1;}
if (strcmp("-v",argv[i]) == 0) {verbose = 1;}
if (strcmp("-lig",argv[i]) == 0) {lig= 1;}
if (strcmp("-ligt",argv[i]) == 0) {ligt= 1;}
if (strcmp("-init",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);vinit = temp;}
if (strcmp("-kr",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);bond_factor = temp;}
if (strcmp("-kt",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);angle_factor = temp;}
if (strcmp("-kpf",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp); kp_factor = temp;}
if (strcmp("-b",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);beta = temp;}
if (strcmp("-t",argv[i]) == 0) {strcpy(check_name,argv[i+1]);help_flag = 0;}
if (strcmp("-m",argv[i]) == 0) {strcpy(matrix_name,argv[i+1]);help_flag = 0;}
if (strcmp("-o",argv[i]) == 0) {strcpy(out_name,argv[i+1]); print_inter = 1;}
if (strcmp("-ot",argv[i]) == 0) {strcpy(out_name_t,argv[i+1]); print_inter_t = 1;}
if (strcmp("-om",argv[i]) == 0) {strcpy(out_movie,argv[i+1]); print_movie = 1;}
if (strcmp("-ligc",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);ligalign = temp;}
if (strcmp("-conf",argv[i]) == 0) {change_density = 1;}
if (strcmp("-morph",argv[i]) == 0) {strcpy(morph_name,argv[i+1]); morph = 1;}
}
if (help_flag == 1)
{
printf("****************************\nHelp Section\n-i\tFile Input (PDB)\n-v\tVerbose\n-w\tWeight Vector\n-t\tInitial Value of template (negative value for random)\n\tIf Load Template, multiply the template\n-lt\tLoad input template\n-sp\tSuper Node Mode (CA, N, C)\n-kt\tPoid de l'angle entre les nodes (1)\n-kr\tPoid de la distance entre les nodes (1)\n-f\tFile to fit\n****************************\n");
return(0);
}
//***************************************************
//* *
//*Builds a structure contaning information on the initial pdb structure
//* *
//***************************************************
all = count_atom(file_name);
nconn = count_connect(file_name);
if (verbose == 1) {printf("Connect:%d\n",nconn);}
if (verbose == 1) {printf("Assigning Structure\n\tAll Atom\n");}
// Array with all connects
int **connect_h=(int **)malloc(nconn*sizeof(int *));
for(i=0;i<nconn;i++) { connect_h[i]=(int *)malloc(6*sizeof(int));}
assign_connect(file_name,connect_h);
// Assigns all the atoms
struct pdb_atom strc_all[all];
atom = build_all_strc(file_name,strc_all); // Retourne le nombre de Node
if (atom > 800) {printf("Too much nodes .... To fix, ask [email protected]\n");return(1);}
if (verbose == 1) {printf(" Atom:%d\n",all);}
check_lig(strc_all,connect_h,nconn,all);
// Assigns all Nodes
if (verbose == 1) {printf(" CA Structure\n");}
if (verbose == 1) {printf(" Node:%d\n",atom);}
struct pdb_atom strc_node[atom];
atom = build_cord_CA(strc_all, strc_node,all,lig,connect_h,nconn);
if (verbose == 1) {printf(" Assign Node:%d\n",atom);}
// Free Connect
//for(i=0;i<nconn;i++) {printf("I:%d\n",i);free(connect_h[i]);}
//free(connect_h);
//***************************************************
//* *
//*Builds a structure contaning information on the target pdb structure
//* *
//***************************************************
nconn = 0;
all_t = count_atom(check_name);
nconn = count_connect(check_name);
if (verbose == 1) {printf("Connect:%d\n",nconn);}
if (verbose == 1) {printf("Assigning Structure\n\tAll Atom\n");}
// Array with all connects
int **connect_t=(int **)malloc(nconn*sizeof(int *));
for(i=0;i<nconn;i++) { connect_t[i]=(int *)malloc(6*sizeof(int));}
assign_connect(check_name,connect_t);
// Assigns all the atoms
struct pdb_atom strc_all_t[all_t];
atom_t = build_all_strc(check_name,strc_all_t); // Retourne le nombre de Node
if (atom_t > 800) {printf("Too much node.... To fix, ask [email protected]\n");return(1);}
if (verbose == 1) {printf(" Atom:%d\n",all_t);}
check_lig(strc_all_t,connect_t,nconn,all_t);
// Assigns all Nodes
if (verbose == 1) {printf(" CA Structure\n");}
if (verbose == 1) {printf(" Node:%d\n",atom_t);}
struct pdb_atom strc_node_t[atom_t];
atom_t = build_cord_CA(strc_all_t, strc_node_t,all_t,ligt,connect_t,nconn);
if (verbose == 1) {printf(" Assign Node:%d\n",atom_t);}
//***************************************************
//* *
//*Aligns both structures
//* *
//***************************************************
int align[atom];
int score = node_align(strc_node,atom,strc_node_t,atom_t,align);
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_no(strc_node,strc_node_t,atom, align)),score,atom);
if ((float)score/(float)atom < 0.8)
{
printf("Low Score... Will try an homemade alignement !!!\n");
score = node_align_onechain(strc_node,atom,strc_node_t,atom_t,align);
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_no(strc_node,strc_node_t,atom, align)),score,atom);
}
if ((float)score/(float)atom < 0.8)
{
printf("Low Score... Will try an homemade alignement !!!\n");
score = node_align_low(strc_node,atom,strc_node_t,atom_t,align);
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_no(strc_node,strc_node_t,atom, align)),score,atom);
}
if (ligalign > 0)
{
score = node_align_lig(strc_node,atom,strc_node_t,atom_t,align,strc_all,all,strc_all_t,all_t,ligalign);
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_no(strc_node,strc_node_t,atom, align)),score,atom);
}
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_yes(strc_node,strc_node_t,atom, align,strc_all,all)),score,atom);
// Build hessians
double **hessian=(double **)malloc(3*atom*sizeof(double *)); // Matrix of the Hessian 1 2 3 (bond, angle, dihedral)
for(i=0;i<3*atom;i++) { hessian[i]=(double *)malloc(3*atom*sizeof(double));}
for(i=0;i<3*atom;i++)for(j=0;j<(3*atom);j++){hessian[i][j]=0;}
gsl_matrix *hess = gsl_matrix_alloc(3*atom,3*atom);
gsl_matrix_set_all(hess, 0);
gsl_matrix *hess_t = gsl_matrix_alloc(3*atom_t,3*atom_t);
gsl_matrix_set_all(hess_t, 0);
assign_atom_type(strc_all, all);
if (strcmp(inputname,"none") == 0) {} else {assign_lig_type(strc_all, all, inputname);}
gsl_matrix *vcon = gsl_matrix_alloc(all,all);
gsl_matrix *inter_m = gsl_matrix_alloc(8,8);
gsl_matrix *templaate = gsl_matrix_alloc(atom*3, atom*3);
gsl_matrix_set_all(templaate,vinit);
gsl_matrix_set_all(vcon,0);
if (verbose == 1) {printf("Do Vcon !!!\n");}
vcon_file_dom(strc_all,vcon,all);
if (verbose == 1) {printf("Reading Interaction Matrix %s\n",matrix_name);}
load_matrix(inter_m,matrix_name);
//write_matrix("vcon_vince.dat", vcon,all,all);
if (verbose == 1) {printf("Building templaate\n");}
all_interaction(strc_all,all, atom, templaate,lig,vcon,inter_m,strc_node);
gsl_matrix_scale (templaate, init_templaate);
if (verbose == 1) {printf("Building Hessian\n");}
if (verbose == 1) {printf("\tCovalent Bond Potential\n");}
build_1st_matrix(strc_node,hessian,atom,bond_factor);
if (verbose == 1) {printf("\tAngle Potential\n");}
build_2_matrix(strc_node,hessian,atom,angle_factor);
if (verbose == 1) {printf("\tDihedral Potential\n");}
build_3_matrix(strc_node, hessian,atom,K_phi1/2+K_phi3*9/2,kp_factor);
if (verbose == 1) {printf("\tNon Local Interaction Potential\n");}
build_4h_matrix(strc_node,hessian,atom,1.0,templaate);
if (verbose == 1) {printf("\tAssigning Array\n");}
assignArray(hess,hessian,3*atom,3*atom);
gsl_matrix_free(vcon);
gsl_matrix_free(templaate);
double **hessian_t=(double **)malloc(3*atom_t*sizeof(double *)); // Matrix of the Hessian 1 2 3 (bond, angle, dihedral)
for(i=0;i<3*atom_t;i++) { hessian_t[i]=(double *)malloc(3*atom_t*sizeof(double));}
for(i=0;i<3*atom_t;i++)for(j=0;j<(3*atom_t);j++){hessian_t[i][j]=0;}
assign_atom_type(strc_all_t, all_t);
if (strcmp(inputname,"none") == 0) {} else {assign_lig_type(strc_all_t, all_t, inputname);}
gsl_matrix *vcon_t = gsl_matrix_alloc(all_t,all_t);
gsl_matrix *templaate_t = gsl_matrix_alloc(atom_t*3, atom_t*3);
gsl_matrix_set_all(templaate_t,vinit);
gsl_matrix_set_all(vcon_t,0);
if (verbose == 1) {printf("Do Vcon !!!\n");}
vcon_file_dom(strc_all_t,vcon_t,all_t);
//write_matrix("vcon_vince.dat", vcon,all,all);
if (verbose == 1) {printf("Building templaate\n");}
all_interaction(strc_all_t,all_t, atom_t, templaate_t,lig,vcon_t,inter_m,strc_node_t);
gsl_matrix_scale (templaate_t, init_templaate);
if (verbose == 1) {printf("Building Hessian\n");}
if (verbose == 1) {printf("\tCovalent Bond Potential\n");}
build_1st_matrix(strc_node_t,hessian_t,atom_t,bond_factor);
if (verbose == 1) {printf("\tAngle Potential\n");}
build_2_matrix(strc_node_t,hessian_t,atom_t,angle_factor);
if (verbose == 1) {printf("\tDihedral Potential\n");}
build_3_matrix(strc_node_t, hessian_t,atom_t,K_phi1/2+K_phi3*9/2,kp_factor);
if (verbose == 1) {printf("\tNon Local Interaction Potential\n");}
build_4h_matrix(strc_node_t,hessian_t,atom_t,1.0,templaate_t);
if (verbose == 1) {printf("\tAssigning Array\n");}
assignArray(hess_t,hessian_t,3*atom_t,3*atom_t);
gsl_matrix_free(vcon_t);
gsl_matrix_free(templaate_t);
printf("Check 1\n");
// Build mini-hessians (calculated mini_hess object is equal to mini_hess + mini_hess_t
gsl_matrix *mini_hess = gsl_matrix_alloc(3*score, 3*score);
gsl_matrix_set_all(mini_hess, 0);
gsl_matrix *mini_hess_i = gsl_matrix_alloc(3*score, 3*score);
gsl_matrix_set_all(mini_hess_i, 0);
gsl_matrix *mini_hess_t = gsl_matrix_alloc(3*score, 3*score);
gsl_matrix_set_all(mini_hess_t, 0);
int sup_line = 0;
int sup_to_node[score];
for(i = 0; i < atom; i++)
{
if(align[i] == -1) {continue;}
sup_to_node[sup_line] = i;
int sup_col = 0;
for(j = 0; j < atom; j++)
{
if(align[j] == -1) {continue;}
for(k = 0; k < 3; k++)
{
for(l = 0; l < 3; l++)
{
gsl_matrix_set(mini_hess_i, 3*sup_line + k, 3*sup_col + l, gsl_matrix_get(hess, 3*i + k, 3*j + l));
gsl_matrix_set(mini_hess, 3*sup_line + k, 3*sup_col + l, gsl_matrix_get(hess, 3*i + k, 3*j + l) + gsl_matrix_get(hess_t, 3*align[i] + k, 3*align[j] + l));
gsl_matrix_set(mini_hess_t, 3*sup_line + k, 3*sup_col + l, gsl_matrix_get(hess_t, 3*align[i] + k, 3*align[j] + l));
}
}
sup_col ++;
}
sup_line++;
}
gsl_matrix_free(hess);
gsl_matrix_free(hess_t);
printf("Check 2\n");
// Invert mini_hess
gsl_vector *eval2 = gsl_vector_alloc(3*score);
gsl_matrix *evec2 = gsl_matrix_alloc (3*score,3*score);
diagonalyse_matrix(mini_hess, 3*score, eval2, evec2);
gsl_matrix_set_all(mini_hess, 0);
for(i = 0; i < 3*score; i++)
{
if(gsl_vector_get(eval2, i) > 0.00001)
{
for(j = 0; j < 3*score; j++)
{
for(k = 0; k < 3*score; k++)
{
gsl_matrix_set(mini_hess, j, k, gsl_matrix_get(mini_hess, j, k) + gsl_matrix_get(evec2, j, i)*gsl_matrix_get(evec2, k, i)/gsl_vector_get(eval2, i));
}
}
}
}
gsl_matrix_free(evec2);
gsl_vector_free(eval2);
printf("Check 3\n");
// Evaluate delta-conf of init to most stable transitionnal conformer and store delta-conf of init to target.
gsl_vector *del_conf = gsl_vector_alloc(3*score);
gsl_vector_set_all(del_conf, 0);
gsl_vector *copy_conf = gsl_vector_alloc(3*score);
for(i = 0; i < score; i++)
{
gsl_vector_set(copy_conf, 3*i, strc_node_t[align[i]].x_cord - strc_node[i].x_cord);
gsl_vector_set(copy_conf, 3*i + 1, strc_node_t[align[i]].y_cord - strc_node[i].y_cord);
gsl_vector_set(copy_conf, 3*i + 2, strc_node_t[align[i]].z_cord - strc_node[i].z_cord);
}
for(i = 0; i < 3*score; i++)
{
for(j = 0; j < 3*score; j++)
{
gsl_vector_set(del_conf, i, gsl_vector_get(del_conf, i) + gsl_matrix_get(mini_hess_t, i, j)*gsl_vector_get(copy_conf, j));
}
}
for(i = 0; i < 3*score; i++)
{
gsl_vector_set(copy_conf, i, gsl_vector_get(del_conf, i));
}
gsl_vector_set_all(del_conf, 0);
for(i = 0; i < 3*score; i++)
{
for(j = 0; j < 3*score; j++)
{
gsl_vector_set(del_conf, i, gsl_vector_get(del_conf, i) + gsl_matrix_get(mini_hess, i, j)*gsl_vector_get(copy_conf, j));
}
}
for(i = 0; i < score; i++)
{
gsl_vector_set(copy_conf, 3*i, strc_node_t[align[i]].x_cord - strc_node[i].x_cord);
gsl_vector_set(copy_conf, 3*i + 1, strc_node_t[align[i]].y_cord - strc_node[i].y_cord);
gsl_vector_set(copy_conf, 3*i + 2, strc_node_t[align[i]].z_cord - strc_node[i].z_cord);
}
printf("Check 4\n");
// Translate all the nodes (and all its atoms) of both structures to delta-conf of most stable conformer.
for(i = 0; i < score; i++)
{
for(j = 0; j < all; j++)
{
if(strc_all[j].node == sup_to_node[i])
{
strc_all[j].x_cord += gsl_vector_get(del_conf, 3*i);
strc_all[j].y_cord += gsl_vector_get(del_conf, 3*i + 1);
strc_all[j].z_cord += gsl_vector_get(del_conf, 3*i + 2);
}
}
for(j = 0; j < all_t; j++)
{
if(strc_all_t[j].node == align[sup_to_node[i]])
{
strc_all_t[j].x_cord += gsl_vector_get(del_conf, 3*i) - gsl_vector_get(copy_conf, 3*i);
strc_all_t[j].y_cord += gsl_vector_get(del_conf, 3*i + 1) - gsl_vector_get(copy_conf, 3*i + 1);
strc_all_t[j].z_cord += gsl_vector_get(del_conf, 3*i + 2) - gsl_vector_get(copy_conf, 3*i + 2);
}
}
}
gsl_matrix_free(mini_hess);
printf("Check 5\n");
int aligned[atom_t];
for(i = 0; i < atom_t; i++)
{
aligned[i] = -1;
}
for(i = 0; i < atom; i++)
{
if(align[i] != -1)
{
aligned[align[i]] = 1;
}
}
// Print transition from init
if(print_inter == 1)
{
FILE *out_file;
out_file = fopen(out_name, "w");
for (i = 0; i < all; i++)
{
if(align[strc_all[i].node] != -1)
{
if (strc_all[i].atom_type == 1) {fprintf(out_file,"ATOM ");}
if (strc_all[i].atom_type == 2) {fprintf(out_file,"HETATM");}
if (strc_all[i].atom_type == 3) {fprintf(out_file,"HETATM");}
fprintf(out_file,"%5.d %s%s %s%4.d%12.3f%8.3f%8.3f 1.00 %2.2f\n",
strc_all[i].atom_number,
strc_all[i].atom_prot_type,
strc_all[i].res_type,
strc_all[i].chain,
strc_all[i].res_number,
strc_all[i].x_cord,
strc_all[i].y_cord,
strc_all[i].z_cord,
strc_all[i].b_factor
);
}
}
fclose(out_file);
}
printf("Check 6\n");
// Print transition from target
if(print_inter_t == 1)
{
FILE *out_file_t;
out_file_t = fopen(out_name_t, "w");
for (i = 0; i < all_t; i++)
{
if(aligned[strc_all_t[i].node] != -1)
{
if (strc_all_t[i].atom_type == 1) {fprintf(out_file_t,"ATOM ");}
if (strc_all_t[i].atom_type == 2) {fprintf(out_file_t,"HETATM");}
if (strc_all_t[i].atom_type == 3) {fprintf(out_file_t,"HETATM");}
fprintf(out_file_t,"%5.d %s%s %s%4.d%12.3f%8.3f%8.3f 1.00 %2.2f\n",
strc_all_t[i].atom_number,
strc_all_t[i].atom_prot_type,
strc_all_t[i].res_type,
strc_all_t[i].chain,
strc_all_t[i].res_number,
strc_all_t[i].x_cord,
strc_all_t[i].y_cord,
strc_all_t[i].z_cord,
strc_all_t[i].b_factor
);
}
}
fclose(out_file_t);
}
printf("Check 7\n");
// Translate all the nodes (and all its atoms) of init structure back to its original conformation.
for(i = 0; i < score; i++)
{
for(j = 0; j < all; j++)
{
if(strc_all[j].node == sup_to_node[i])
{
strc_all[j].x_cord -= gsl_vector_get(del_conf, 3*i);
strc_all[j].y_cord -= gsl_vector_get(del_conf, 3*i + 1);
strc_all[j].z_cord -= gsl_vector_get(del_conf, 3*i + 2);
}
}
}
// Print transition from init to target passing by inter
if(print_movie == 1)
{
FILE *out_file_m;
out_file_m = fopen(out_movie, "w");
for(j = 0; j < 30; j++)
{
fprintf(out_file_m, "Model %1i\n", j + 1);
for (i = 0; i < all; i++)
{
if(align[strc_all[i].node] != -1)
{
if (strc_all[i].atom_type == 1) {fprintf(out_file_m,"ATOM ");}
if (strc_all[i].atom_type == 2) {fprintf(out_file_m,"HETATM");}
if (strc_all[i].atom_type == 3) {fprintf(out_file_m,"HETATM");}
fprintf(out_file_m,"%5.d %s%s %s%4.d%12.3f%8.3f%8.3f 1.00 %2.2f\n",
strc_all[i].atom_number,
strc_all[i].atom_prot_type,
strc_all[i].res_type,
strc_all[i].chain,
strc_all[i].res_number,
strc_all[i].x_cord,
strc_all[i].y_cord,
strc_all[i].z_cord,
strc_all[i].b_factor
);
}
}
fprintf(out_file_m, "TER\nENDMDL\n\n");
for(i = 0; i < score; i++)
{
for(k = 0; k < all; k++)
{
if(strc_all[k].node == sup_to_node[i])
{
strc_all[k].x_cord += gsl_vector_get(del_conf, 3*i)/30.0;
strc_all[k].y_cord += gsl_vector_get(del_conf, 3*i + 1)/30.0;
strc_all[k].z_cord += gsl_vector_get(del_conf, 3*i + 2)/30.0;
}
}
}
}
for(j = 0; j < 31; j++)
{
fprintf(out_file_m, "Model %1i\n", j + 31);
for (i = 0; i < all_t; i++)
{
if(aligned[strc_all_t[i].node] != -1)
{
if (strc_all_t[i].atom_type == 1) {fprintf(out_file_m,"ATOM ");}
if (strc_all_t[i].atom_type == 2) {fprintf(out_file_m,"HETATM");}
if (strc_all_t[i].atom_type == 3) {fprintf(out_file_m,"HETATM");}
fprintf(out_file_m,"%5.d %s%s %s%4.d%12.3f%8.3f%8.3f 1.00 %2.2f\n",
strc_all_t[i].atom_number,
strc_all_t[i].atom_prot_type,
strc_all_t[i].res_type,
strc_all_t[i].chain,
strc_all_t[i].res_number,
strc_all_t[i].x_cord,
strc_all_t[i].y_cord,
strc_all_t[i].z_cord,
strc_all_t[i].b_factor
);
}
}
fprintf(out_file_m, "TER\nENDMDL\n\n");
for(i = 0; i < score; i++)
{
for(k = 0; k < all_t; k++)
{
if(strc_all_t[k].node == align[sup_to_node[i]])
{
strc_all_t[k].x_cord -= (gsl_vector_get(del_conf, 3*i) - gsl_vector_get(copy_conf, 3*i))/30.0;
strc_all_t[k].y_cord -= (gsl_vector_get(del_conf, 3*i + 1) - gsl_vector_get(copy_conf, 3*i + 1))/30.0;
strc_all_t[k].z_cord -= (gsl_vector_get(del_conf, 3*i + 2) - gsl_vector_get(copy_conf, 3*i + 2))/30.0;
}
}
}
}
fclose(out_file_m);
}
printf("Check 8\n");
// Translate all the nodes (and all its atoms) of init structure back to its original conformation if print_movie == 1
if(print_movie == 1)
{
for(i = 0; i < score; i++)
{
for(j = 0; j < all; j++)
{
if(strc_all[j].node == sup_to_node[i])
{
strc_all[j].x_cord -= gsl_vector_get(del_conf, 3*i);
strc_all[j].y_cord -= gsl_vector_get(del_conf, 3*i + 1);
strc_all[j].z_cord -= gsl_vector_get(del_conf, 3*i + 2);
}
}
}
}
printf("Check 8.1\n");
// Print transition from init to target by morphing
if(morph == 1)
{
FILE *out_file_morph;
out_file_morph = fopen(morph_name, "w");
printf("Check 8.2\n");
for(j = 0; j < 60; j++)
{
fprintf(out_file_morph, "Model %1i\n", j + 1);
for (i = 0; i < all; i++)
{
if(align[strc_all[i].node] != -1)
{
if (strc_all[i].atom_type == 1) {fprintf(out_file_morph,"ATOM ");}
if (strc_all[i].atom_type == 2) {fprintf(out_file_morph,"HETATM");}
if (strc_all[i].atom_type == 3) {fprintf(out_file_morph,"HETATM");}
fprintf(out_file_morph,"%5.d %s%s %s%4.d%12.3f%8.3f%8.3f 1.00 %2.2f\n",
strc_all[i].atom_number,
strc_all[i].atom_prot_type,
strc_all[i].res_type,
strc_all[i].chain,
strc_all[i].res_number,
strc_all[i].x_cord,
strc_all[i].y_cord,
strc_all[i].z_cord,
strc_all[i].b_factor
);
}
}
fprintf(out_file_morph, "TER\nENDMDL\n\n");
printf("Check 8.3\n");
for(i = 0; i < score; i++)
{
for(k = 0; k < all; k++)
{
if(strc_all[k].node == sup_to_node[i])
{
strc_all[k].x_cord += gsl_vector_get(copy_conf, 3*i)/60.0;
strc_all[k].y_cord += gsl_vector_get(copy_conf, 3*i + 1)/60.0;
strc_all[k].z_cord += gsl_vector_get(copy_conf, 3*i + 2)/60.0;
}
}
}
printf("Check 8.4\n");
}
fclose(out_file_morph);
}
printf("Check 9\n");
// Evaluate theoretical delta-G
gsl_vector *dummy_conf = gsl_vector_alloc(3*score);
gsl_vector_set_all(dummy_conf, 0);
gsl_vector *dummy_conf_t = gsl_vector_alloc(3*score);
gsl_vector_set_all(dummy_conf_t, 0);
for(i = 0; i < 3*score; i++)
{
for(j = 0; j < 3*score; j++)
{
gsl_vector_set(dummy_conf, i, gsl_vector_get(dummy_conf, i) + gsl_vector_get(del_conf, j)*gsl_matrix_get(mini_hess_i, j, i));
gsl_vector_set(dummy_conf_t, i, gsl_vector_get(dummy_conf_t, i) + (gsl_vector_get(del_conf, j) - gsl_vector_get(copy_conf, j))*gsl_matrix_get(mini_hess_t, j, i));
}
}
double energy_ic = 0.0;
double energy_tc = 0.0;
for(i = 0; i < 3*score; i++)
{
energy_ic += gsl_vector_get(dummy_conf, i)*gsl_vector_get(del_conf, i);
energy_tc += gsl_vector_get(dummy_conf_t, i)*(gsl_vector_get(del_conf, i) - gsl_vector_get(copy_conf, i));
}
gsl_vector_free(dummy_conf_t);
gsl_vector_free(del_conf);
printf("Check 10\n");
if(change_density == 1)
{
gsl_vector_set_all(dummy_conf, 0);
gsl_vector *eval = gsl_vector_alloc(3*score);
gsl_vector_set_all(eval, 0);
gsl_vector *eval_t = gsl_vector_alloc(3*score);
gsl_vector_set_all(eval_t, 0);
gsl_matrix *evec = gsl_matrix_alloc (3*score,3*score);
gsl_matrix_set_all(evec, 0);
gsl_matrix *evec_t = gsl_matrix_alloc (3*score,3*score);
gsl_matrix_set_all(evec_t, 0);
diagonalyse_matrix(mini_hess_i, 3*score, eval, evec);
diagonalyse_matrix(mini_hess_t, 3*score, eval_t, evec_t);
gsl_matrix_free(mini_hess_i);
gsl_matrix_free(mini_hess_t);
gsl_matrix *comb_hess = gsl_matrix_alloc(3*score, 3*score);
gsl_matrix_set_all(comb_hess, 0);
double entro = 0.0;
double entro_t = 0.0;
for(i = 0; i < 3*score; i++)
{
if(gsl_vector_get(eval, i) > 0.00001)
{
for(j = 0; j < 3*score; j++)
{
for(k = 0; k < 3*score; k++)
{
gsl_matrix_set(comb_hess, j, k, gsl_matrix_get(comb_hess, j, k) + gsl_matrix_get(evec, j, i)*gsl_matrix_get(evec, k, i)/gsl_vector_get(eval, i));
}
}
entro += log(3.141592653589793238462643383279) - log(beta * gsl_vector_get(eval, i));
}
if(gsl_vector_get(eval_t, i) > 0.00001)
{
for(j = 0; j < 3*score; j++)
{
for(k = 0; k < 3*score; k++)
{
gsl_matrix_set(comb_hess, j, k, gsl_matrix_get(comb_hess, j, k) + gsl_matrix_get(evec_t, j, i)*gsl_matrix_get(evec_t, k, i)/gsl_vector_get(eval_t, i));
}
}
entro_t += log(3.141592653589793238462643383279) - log(beta * gsl_vector_get(eval_t, i));
}
}
gsl_vector_free(eval_t);
gsl_matrix_free(evec_t);
gsl_vector_set_all(eval, 0);
gsl_matrix_set_all(evec, 0);
diagonalyse_matrix(comb_hess, 3*score, eval, evec);
gsl_matrix_set_all(comb_hess, 0);
// double comb_det = 1.0;
for(i = 0; i < 3*score; i++)
{
if(gsl_vector_get(eval, i) > 0.00001)
{
for(j = 0; j < 3*score; j++)
{
for(k = 0; k < 3*score; k++)
{
gsl_matrix_set(comb_hess, j, k, gsl_matrix_get(comb_hess, j, k) + gsl_matrix_get(evec, j, i)*gsl_matrix_get(evec, k, i)/gsl_vector_get(eval, i));
}
}
// comb_det *= beta / (3.141592653589793238462643383279 * gsl_vector_get(eval, i));
}
}
for(i = 0; i < 3*score; i++)
{
for(j = 0; j < 3*score; j++)
{
gsl_vector_set(dummy_conf, i, gsl_vector_get(dummy_conf, i) + gsl_vector_get(copy_conf, j)*gsl_matrix_get(comb_hess, j, i));
}
}
double energy_conf = 0.0;
for(i = 0; i < 3*score; i++)
{
energy_conf += gsl_vector_get(dummy_conf, i)*gsl_vector_get(copy_conf, i);
}
double dummy_energy = 0.0;
double prob_conf = 0.0;
dummy_energy = -1.0 * beta * energy_conf;
prob_conf = exp(dummy_energy);
printf("Weighted probability density of exact conformational change at beta = %1.10f : %1.100f\n", beta, prob_conf);
printf("Delta-S (target - init) : %1.10f\n", entro_t - entro);
printf("Delta-H (target - init) : %1.10f\n", energy_ic - energy_tc);
dummy_energy = -310.25 * (entro_t - entro) + energy_ic - energy_tc;
printf("Delta-G (target - init) : %1.10f\n", dummy_energy);
double K_eq = exp(-1.0 * dummy_energy / (310.25 * 8.3145));
printf("Equilibrium constant (target / init) : %1.10f\n", K_eq);
}
else
{
printf("Energy from init to inter : %1.10f\nEnergy from target to inter : %1.10f\nDelta-H (target - init) : %1.10f\n", energy_ic, energy_tc, energy_ic - energy_tc);
}
gsl_vector_free(copy_conf);
gsl_vector_free(dummy_conf);
}
