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calculations.cpp
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calculations.cpp
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#include "calculations.h"
#include <iostream>
// 200612
// - took absolute values of all fitting parameters that correspond to Kd:s
// - N.B. This should never be done when calculating the derivatives!!
// ********************************************************************************************
// Dilute means that total concentration must be taken into account for calculating the signal
// *********************************************************************************************
// One site
// -------
// a0-a1: P and PL signals
// a2: Kd
// a3: [L]start
// a4: [P]start
void fit_one_site_dilution(const double Ltot, const double Ptot, const std::vector<double> &a, double &y, std::vector<double> &dyda)
{
double temp=((Ltot/Ptot)+(((Ptot-Ltot+fabs(a[2]))/2) -
sqrt((((Ptot-Ltot+fabs(a[2]))*(Ptot-Ltot+fabs(a[2])))/4)+fabs(a[2])*Ltot))/Ptot);
y = ((a[0] + (a[1]-a[0])*temp)*Ptot)/a.back() ;
dyda[0]= (1 - temp)*Ptot/a.back();
dyda[1]= temp*Ptot/a.back();
dyda[2]=Ptot*(a[1]-a[0])*(0.5-((((a[2]+Ptot-Ltot)/2)+Ltot) /
sqrt((((a[2]+Ptot-Ltot)*(a[2]+Ptot-Ltot))/4)+Ltot*a[2])))/(Ptot*a.back());
}
double fit_one_site_dilution(const double Ltot, const double Ptot, const std::vector<double> &a)
{
double temp = ((Ltot/Ptot)+(((Ptot-Ltot+fabs(a[2]))/2) -
sqrt((((Ptot-Ltot+fabs(a[2]))*(Ptot-Ltot+fabs(a[2])))/4)+fabs(a[2])*Ltot))/Ptot);
return ((a[0] + (a[1]-a[0])*temp)*Ptot)/a.back() ;
}
//Two-site
// -------
// a0-a2: P - PL2 signals
// a3-a4: Kd1 - Kd2
// a5: [L]start
// a6: [P]start
double ligand_free_two_sites_dilution(const double start_ligand, const double protein_conc, const std::vector<double> &a, const double Lfree);
double protein_free_two_sites_dilution(const double L, const double x2, const std::vector<double> &a);
double secord_deriv(double ligand, unsigned int idx, double protein, VecDoub_I &a,
double fitfunc(double, double, VecDoub_I &));
void fit_two_sites_dilution(const double Ltot, const double Ptot, const std::vector<double> &a, double &y, std::vector<double> &dyda)
{
double root{}, start{a[a.size()-2]}; //a[5] is start conc of the datasets/conc_vector, since we need it to make zbrent
try {
root=zbrent(ligand_free_two_sites_dilution,start,Ltot,1e-12, Ltot,Ptot,a);
} catch (int) {
}
double P=protein_free_two_sites_dilution(root,Ptot,a);
double PL=P*root/fabs(a[3]);
double PL2=PL*root/fabs(a[4]);
y = ((a[0]*P + a[1]*PL + a[2]*PL2)/Ptot)*Ptot/a.back();
dyda[0] = P/a.back();
dyda[1] = PL/a.back();
dyda[2] = PL2/a.back();
for (unsigned int i=3;i<dyda.size();i++)
dyda[i]=secord_deriv(Ltot, i, Ptot, a, fit_two_sites_dilution);
}
double fit_two_sites_dilution(const double Ltot, const double Ptot, const std::vector<double> &a)
{
double root{}, Lstart{a[a.size()-2]}; //a[5] is start conc of the datasets/conc_vector, since we need it to make zbrent
try {
root=zbrent(ligand_free_two_sites_dilution, Lstart, Ltot, 1e-12, Ltot, Ptot,a);
} catch (int) {
}
double P = protein_free_two_sites_dilution(root,Ptot,a);
double PL = P*root/fabs(a[3]);
double PL2 = PL*root/fabs(a[4]);
return (a[0]*P + a[1]*PL + a[2] * PL2)/a.back();
}
double ligand_free_two_sites_dilution(const double Ltot, const double Ptot, const std::vector<double> &a, const double L) {
double sum = L/fabs(a[3]) + 2*L*L/fabs(a[3]*a[4]);
return Ltot - L - Ptot*sum/(1.+sum);
}
double protein_free_two_sites_dilution(const double L, const double Ptot, const std::vector<double> &a){
return Ptot/(1+(L/fabs(a[3]))+(L*L)/fabs(a[3]*a[4]));
}
// Four-site
// ---------
// a0-a4: P - PL4 signals
// a5-a8: Kd1 - Kd4
// a9: [L]start
// a10: [P]start
double ligand_free_four_sites_dilution(double Ltot, double Ptot, VecDoub_I &a, const double L);
double protein_free_four_sites_dilution(double L, double Ptot, VecDoub_I &a);
double secord_deriv(double ligand, unsigned int idx, double protein, VecDoub_I &a,
double fitfunc(double, double, VecDoub_I &));
double fit_four_sites_dilution(const double Ltot, const double Ptot, const std::vector<double> &a)
{
double root{}, Lstart{a[a.size()-2]};
try {
root=zbrent(ligand_free_four_sites_dilution, Lstart, Ltot, 1e-12, Ltot, Ptot, a);
} catch (int) {
}
double P = protein_free_four_sites_dilution(root, Ptot, a);
double PL=P*root/fabs(a[5]);
double PL2=PL*root/fabs(a[6]);
double PL3=PL2*root/fabs(a[7]);
double PL4=PL3*root/fabs(a[8]);
return ((a[0]*P + a[1]*PL + a[2]*PL2 + a[3]*PL3 + a[4]*PL4)/Ptot)*Ptot/a.back();
}
void fit_four_sites_dilution(const double Ltot, const double Ptot, const std::vector<double> &a, double &y, std::vector<double> &dyda)
{
double root{}, Lstart{a[a.size()-2]};
try {
root=zbrent(ligand_free_four_sites_dilution, Lstart, Ltot, 1e-12, Ltot, Ptot, a);
} catch (int) {
}
double P=protein_free_four_sites_dilution(root,Ptot,a);
double PL=P*root/fabs(a[5]);
double PL2=PL*root/fabs(a[6]);
double PL3=PL2*root/fabs(a[7]);
double PL4=PL3*root/fabs(a[8]);
y = (a[0]*P + a[1]*PL + a[2]*PL2 + a[3]*PL3 + a[4]*PL4)/a.back();
dyda[0] = P/a.back();
dyda[1] = PL/a.back();
dyda[2] = PL2/a.back();
dyda[3] = PL3/a.back();
dyda[4] = PL4/a.back();
for (unsigned int i=5;i<dyda.size();i++)
dyda[i]=secord_deriv(Ltot, i, Ptot, a, fit_four_sites_dilution);
}
double ligand_free_four_sites_dilution(double Ltot, double Ptot, VecDoub_I &a, double L){
double sum = L/fabs(a[5]) + 2*L*L/fabs(a[5]*a[6]) + 3*L*L*L/fabs(a[5]*a[6]*a[7]) +
4*L*L*L*L/fabs(a[5]*a[6]*a[7]*a[8]);
return Ltot - L - Ptot*sum/(1.+sum);
}
double protein_free_four_sites_dilution(double L, double Ptot, VecDoub_I &a) {
return Ptot/(1 + L/fabs(a[5]) + L*L/fabs(a[5]*a[6]) + L*L*L/fabs(a[5]*a[6]*a[7]) +
L*L*L*L/fabs(a[5]*a[6]*a[7]*a[8]));
}
// Two site binding + Competitive Binding
// --------------------------------------
// a0-a1: Comp - CompL signals
// a2-a4: Kd1, Kd2, KdComp
// a5: [L]start
// a6: [P]start
// a7: [Comp]start
double secord_deriv_comp(const double Ltot, unsigned int idx, const double Ptot, const std::vector<double> &a,
const double comp);
void fit_comp_dilution(const double Ltot, const double Ptot, const double CompTot, const std::vector<double> &a, double &y, std::vector<double> &dyda)
{
double I{},IL{}, root{}, Lstart{a[a.size()-3]}; //a[5] is start conc of the datasets/conc_vector, since we need it to make zbrent
try {
root=zbrent2(ligand_free_comp,Lstart,Ltot,1e-12, Ltot,Ptot,CompTot,a);
} catch (int) {
}
I = (fabs(a[4])*CompTot)/(fabs(a[4])+root);
IL = CompTot-I;
y = (a[0]*I + a[1]*IL)/a.back();
for (unsigned int i=0;i<dyda.size();i++)
dyda[i]=secord_deriv_comp(Ltot, i, Ptot, a, CompTot);
}
double fit_comp_dilution(const double Ltot, const double Ptot, const double CompTot, const std::vector<double> &a)
{
double I{},IL{}, root{}, Lstart{a[a.size()-3]};
try {
root=zbrent2(ligand_free_comp, Lstart, Ltot, 1e-12, Ltot,Ptot, CompTot, a);
} catch (int) {
}
I=(fabs(a[4])*CompTot)/(fabs(a[4])+root);
IL=CompTot - I;
return (a[0]*I + a[1]*IL)/a.back();
}
double ligand_free_comp(const double start_ligand, const double protein_conc, const double comp_conc, const std::vector<double> &a, const double Lfree)
{
return Lfree+comp_conc*Lfree/(fabs(a[4])+Lfree) + (protein_conc/(1+Lfree/fabs(a[2])+2*(Lfree*Lfree)/fabs(a[2]*a[3]))) *
(Lfree/fabs(a[2])+2*(Lfree*Lfree)/fabs(a[2]*a[3])) - start_ligand;
}
//*********************************************************************************************
// THE FIRST FUNCTIONS BELOW ARE USED TO FIT DATA WHERE THE SIGNAL DOES NOT DEPEND ON CONCENTRATION
// EXAMPLES: CHEMICAL SHIFTS, FLUORESCENCE ANISOTROPY
//*********************************************************************************************
//x1=ligand concentration, x2=proteinconcetration, y=responce, a vector yp(fritt protein) är a[o], y_pl=a[1](signal från PL) och kd= a[2]
// One-site (dilution not important for signal)
// --------------------------------------------
// a0-a1: P - PL signals
// a2: Kd1 - Kd2
// a3: [L]start
// a4: [P]start
void fit_one_site(const double Ltot, const double Ptot, const std::vector<double> &a, double &y, std::vector<double> &dyda)
{
double temp = ((Ltot/Ptot)+(((Ptot-Ltot+fabs(a[2]))/2) -
sqrt((((Ptot-Ltot+fabs(a[2]))*(Ptot-Ltot+fabs(a[2])))/4)+fabs(a[2])*Ltot))/Ptot);
y = a[0] + (a[1]-a[0])*temp;
dyda[0] = 1 - temp;
dyda[1] = temp;
dyda[2] = (a[1]-a[0])*(0.5-((((a[2]+Ptot-Ltot)/2)+Ptot) /
sqrt((((a[2]+Ptot-Ltot)*(a[2]+Ptot-Ltot))/4)+Ltot*a[2])))/Ptot;
}
double fit_one_site(const double Ltot, const double Ptot, const std::vector<double> &a)
{
double temp=((Ltot/Ptot)+(((Ptot-Ltot+a[2])/2) -
sqrt((((Ptot-Ltot+a[2])*(Ptot-Ltot+a[2]))/4)+a[2]*Ltot)) /Ptot);
return a[0] + (a[1]-a[0])*temp;
}
// Two-site (dilution not important for signal)
// --------------------------------------------
// a0-a2: P - PL2 signals
// a3-a4: Kd1 - Kd2
// a5: [L]start
// a6: [P]start
double ligand_free_two_sites(const double start_ligand, const double protein_conc, const std::vector<double> &a, const double Lfree);
double protein_free_two_sites(const double L, const double x2, const std::vector<double> &a);
double secord_deriv(double ligand, unsigned int idx, double protein, VecDoub_I &a,
double fitfunc(double, double, VecDoub_I &));
double fit_two_sites(const double Ltot, const double Ptot, const std::vector<double> &a)
{
double P{}, root{}, y{}, Lstart{a[a.size()-2]}; //a[5] is start conc of the datasets/conc_vector, since we need it to make zbrent
try {
root=zbrent(ligand_free_two_sites, Lstart, Ltot, 1e-12, Ltot, Ptot, a);
} catch (int) {
}
P=protein_free_two_sites(root, Ptot, a);
double PL{}, PL2{};
PL=P*root/fabs(a[3]);
PL2=PL*root/fabs(a[4]);
y = (a[0]*P + a[1]*PL + a[2] * PL2)/Ptot;
return y;
}
void fit_two_sites(const double ligand_conc, const double Ptot, const std::vector<double> &a, double &y, std::vector<double> &dyda)
{
double P{}, root{}, start{a[a.size()-2]}; //a[5] is start conc of the datasets/conc_vector, since we need it to make zbrent
try {
root=zbrent(ligand_free_two_sites, start, ligand_conc, 1e-12, ligand_conc, Ptot, a);
} catch (int) {
}
P=protein_free_two_sites(root, Ptot, a);
double PL{}, PL2{};
PL=P*root/fabs(a[3]);
PL2=PL*root/fabs(a[4]);
y = (a[0]*P + a[1]*PL + a[2] * PL2)/Ptot;
dyda[0] = P/Ptot;
dyda[1] = PL/Ptot;
dyda[2] = PL2/Ptot;
for (unsigned int i=3;i<dyda.size();i++)
dyda[i]=secord_deriv(ligand_conc, i, Ptot, a, fit_two_sites);
}
double ligand_free_two_sites(const double start_ligand, const double protein_conc, const std::vector<double> &a, const double Lfree)
{
return (Lfree*Lfree*Lfree/fabs(a[3]*a[4]))+(Lfree*Lfree)*((1/fabs(a[3]))+(2*protein_conc/(a[3]*a[4]))-1/fabs(a[3]*a[4]))+
Lfree*(1+(protein_conc/fabs(a[3]))-(start_ligand/fabs(a[3])))-start_ligand;
}
double protein_free_two_sites(const double L, const double x2, const std::vector<double> &a)
{
return x2/(1+(L/a[3])+(L*L)/(a[3]*a[4]));
}
double fit_four_sites(const double Ltot, const double Ptot, const std::vector<double> &a)
{
double root{}, Lstart{a[a.size()-2]};
try {
root=zbrent(ligand_free_four_sites_dilution, Lstart, Ltot, 1e-12, Ltot, Ptot, a);
} catch (int) {
}
double P = protein_free_four_sites_dilution(root, Ptot, a);
double PL=P*root/fabs(a[5]);
double PL2=PL*root/fabs(a[6]);
double PL3=PL2*root/fabs(a[7]);
double PL4=PL3*root/fabs(a[8]);
return (a[0]*P + a[1]*PL + a[2]*PL2 + a[3]*PL3 + a[4]*PL4)/Ptot;
}
void fit_four_sites(const double Ltot, const double Ptot, const std::vector<double> &a, double &y, std::vector<double> &dyda)
{
double root{}, start{a[a.size()-2]};
try {
root=zbrent(ligand_free_four_sites_dilution,start,Ltot,1e-12, Ltot,Ptot,a);
} catch (int) {
}
double P=protein_free_four_sites_dilution(root,Ptot,a);
double PL=P*root/fabs(a[5]);
double PL2=PL*root/fabs(a[6]);
double PL3=PL2*root/fabs(a[7]);
double PL4=PL3*root/fabs(a[8]);
y = (a[0]*P + a[1]*PL + a[2]*PL2 + a[3]*PL3 + a[4]*PL4)/Ptot;
dyda[0] = P/Ptot;
dyda[1] = PL/Ptot;
dyda[2] = PL2/Ptot;
dyda[3] = PL3/Ptot;
dyda[4] = PL4/Ptot;
for (unsigned int i=5;i<dyda.size();i++)
dyda[i]=secord_deriv(Ltot, i, Ptot, a, fit_four_sites);
}
void fit_comp(const double Ltot, const double Ptot, const double CompTot, const std::vector<double> &a, double &y, std::vector<double> &dyda)
{
double I{},IL{}, root{}, Lstart{a[a.size()-3]}; //a[5] is start conc of the datasets/conc_vector, since we need it to make zbrent
try {
root=zbrent2(ligand_free_comp,Lstart,Ltot,1e-12, Ltot,Ptot,CompTot,a);
} catch (int) {
}
I = (fabs(a[4])*CompTot)/(fabs(a[4])+root);
IL = CompTot-I;
y = (a[0]*I + a[1]*IL)/CompTot;
for (unsigned int i=0;i<dyda.size();i++)
dyda[i]=secord_deriv_comp(Ltot, i, Ptot, a, CompTot);
}
double fit_comp(const double Ltot, const double Ptot, const double CompTot, const std::vector<double> &a)
{
double I{},IL{}, root{}, Lstart{a[a.size()-3]};
try {
root=zbrent2(ligand_free_comp, Lstart, Ltot, 1e-12, Ltot,Ptot, CompTot, a);
} catch (int) {
}
I=(fabs(a[4])*CompTot)/(fabs(a[4])+root);
IL=CompTot - I;
return (a[0]*I + a[1]*IL)/CompTot;
}
double secord_deriv_comp(const double ligand, unsigned int idx, const double protein, const std::vector<double> &a, const double comp)
{
// Error bound ~eps^2/3
std::vector<double> a_temp{a};
const double eps = std::numeric_limits<double>::epsilon();
double aidx = a_temp[idx];
double h = pow(3*eps, 0.33333333333333);
volatile double temp = a_temp[idx] + h;
h = temp - a_temp[idx];
if (h == 0.0) { h = nextafter(a_temp[idx], std::numeric_limits<double>::max()) - a_temp[idx]; }
a_temp[idx] = aidx + h;
double yh{},ymh{};
yh = fit_comp_dilution(ligand,protein,comp, a_temp);
a_temp[idx] = aidx - h;
ymh = fit_comp_dilution(ligand,protein,comp, a_temp);
double diff = yh - ymh;
a_temp[idx] = aidx;
return diff/(2*h);
}
double secord_deriv(double Ltot, unsigned int idx, double Ptot, VecDoub_I &a,
double fitfunc(double, double, VecDoub_I &))
{
// Error bound ~eps^2/3
std::vector<double> a_temp{a};
const double eps = std::numeric_limits<double>::epsilon();
double aidx = a_temp[idx];
double h = pow(3*eps, 0.33333333333333);
volatile double temp = a_temp[idx] + h;
h = temp - a_temp[idx];
if (h == 0.0) { h = nextafter(a_temp[idx], std::numeric_limits<double>::max()) - a_temp[idx]; }
a_temp[idx] = aidx + h;
double yh{},ymh{};
yh = fitfunc(Ltot, Ptot, a_temp);
a_temp[idx] = aidx - h;
ymh = fitfunc(Ltot, Ptot, a_temp);
double diff = yh - ymh;
a_temp[idx] = aidx;
return diff/(2*h);
}
bool gaussj(MatDoub_IO &a, MatDoub_IO &b)
{
int i,icol,irow,j,k,l,ll,n=a.nrows(),m=b.ncols();
double big,dum,pivinv;
VecInt indxc(n),indxr(n),ipiv(n);
for (j=0;j<n;j++) ipiv[j]=0;
for (i=0;i<n;i++) {
big=0.0;
for (j=0;j<n;j++)
if (ipiv[j] != 1)
for (k=0;k<n;k++) {
if (ipiv[k] == 0) {
if (fabs(a[j][k]) >= big) {
big=fabs(a[j][k]);
irow=j;
icol=k;
}
}
}
++(ipiv[icol]);
if (irow != icol) {
for (l=0;l<n;l++) std::swap(a[irow][l],a[icol][l]);
for (l=0;l<m;l++) std::swap(b[irow][l],b[icol][l]);
}
indxr[i]=irow;
indxc[i]=icol;
if (a[icol][icol] == 0.0) return false;//throw("gaussj: Singular Matrix");
pivinv=1.0/a[icol][icol];
a[icol][icol]=1.0;
for (l=0;l<n;l++) a[icol][l] *= pivinv;
for (l=0;l<m;l++) b[icol][l] *= pivinv;
for (ll=0;ll<n;ll++)
if (ll != icol) {
dum=a[ll][icol];
a[ll][icol]=0.0;
for (l=0;l<n;l++) a[ll][l] -= a[icol][l]*dum;
for (l=0;l<m;l++) b[ll][l] -= b[icol][l]*dum;
}
}
for (l=n-1;l>=0;l--) {
if (indxr[l] != indxc[l])
for (k=0;k<n;k++)
std::swap(a[k][indxr[l]],a[k][indxc[l]]);
}
return true;
}
template<class T>
inline T SIGN(const T &a, const T &b)
{return b >= 0 ? (a >= 0 ? a : -a) : (a >= 0 ? -a : a);}
template <class T>
double zbrent(T &func, const double x1, const double x2, const double tol, const double xx1, const double xx2, const std::vector<double> &aa)
{
const int ITMAX=100;
const double EPS=std::numeric_limits<double>::epsilon();
double a=x1,b=x2,c=x2,d,e,fa=func(xx1,xx2, aa, a),fb=func(xx1,xx2, aa, b),fc,p,q,r,s,tol1,xm;
//std::cout << "fa = " << fa << ", fb = " << fb << ", x1 = "<<x1 << ", x2 = " << x2 << std::endl;
if ((fa > 0.0 && fb > 0.0) || (fa < 0.0 && fb < 0.0))
throw("Root must be bracketed in zbrent");
fc=fb;
for (int iter=0;iter<ITMAX;iter++) {
if ((fb > 0.0 && fc > 0.0) || (fb < 0.0 && fc < 0.0)) {
c=a;
fc=fa;
e=d=b-a;
}
if (fabs(fc) < fabs(fb)) {
a=b;
b=c;
c=a;
fa=fb;
fb=fc;
fc=fa;
}
tol1=2.0*EPS*fabs(b)+0.5*tol;
xm=0.5*(c-b);
if (fabs(xm) <= tol1 || fb == 0.0) return b;
if (fabs(e) >= tol1 && fabs(fa) > fabs(fb)) {
s=fb/fa;
if (a == c) {
p=2.0*xm*s;
q=1.0-s;
} else {
q=fa/fc;
r=fb/fc;
p=s*(2.0*xm*q*(q-r)-(b-a)*(r-1.0));
q=(q-1.0)*(r-1.0)*(s-1.0);
}
if (p > 0.0) q = -q;
p=fabs(p);
double min1=3.0*xm*q-fabs(tol1*q);
double min2=fabs(e*q);
if (2.0*p < (min1 < min2 ? min1 : min2)) {
e=d;
d=p/q;
} else {
d=xm;
e=d;
}
} else {
d=xm;
e=d;
}
a=b;
fa=fb;
if (fabs(d) > tol1)
b += d;
else
b += SIGN(tol1,xm);
fb=func(xx1,xx2, aa, b);
}
throw("Maximum number of iterations exceeded in zbrent");
}
template <class T>
double zbrent2(T &func, const double x1, const double x2, const double tol, const double xx1, const double xx2, const double xx3,const std::vector<double> &aa)
{
const int ITMAX=100;
const double EPS=std::numeric_limits<double>::epsilon();
double a=x1,b=x2,c=x2,d,e,fa=func(xx1,xx2,xx3, aa, a),fb=func(xx1,xx2,xx3, aa, b),fc,p,q,r,s,tol1,xm;
//std::cout << "fa = " << fa << ", fb = " << fb << ", x1 = "<<x1 << ", x2 = " << x2 << std::endl;
if ((fa > 0.0 && fb > 0.0) || (fa < 0.0 && fb < 0.0))
throw("Root must be bracketed in zbrent");
fc=fb;
for (int iter=0;iter<ITMAX;iter++) {
if ((fb > 0.0 && fc > 0.0) || (fb < 0.0 && fc < 0.0)) {
c=a;
fc=fa;
e=d=b-a;
}
if (fabs(fc) < fabs(fb)) {
a=b;
b=c;
c=a;
fa=fb;
fb=fc;
fc=fa;
}
tol1=2.0*EPS*fabs(b)+0.5*tol;
xm=0.5*(c-b);
if (fabs(xm) <= tol1 || fb == 0.0) return b;
if (fabs(e) >= tol1 && fabs(fa) > fabs(fb)) {
s=fb/fa;
if (a == c) {
p=2.0*xm*s;
q=1.0-s;
} else {
q=fa/fc;
r=fb/fc;
p=s*(2.0*xm*q*(q-r)-(b-a)*(r-1.0));
q=(q-1.0)*(r-1.0)*(s-1.0);
}
if (p > 0.0) q = -q;
p=fabs(p);
double min1=3.0*xm*q-fabs(tol1*q);
double min2=fabs(e*q);
if (2.0*p < (min1 < min2 ? min1 : min2)) {
e=d;
d=p/q;
} else {
d=xm;
e=d;
}
} else {
d=xm;
e=d;
}
a=b;
fa=fb;
if (fabs(d) > tol1)
b += d;
else
b += SIGN(tol1,xm);
fb=func(xx1,xx2, xx3,aa, b);
}
throw("Maximum number of iterations exceeded in zbrent");
}
//All guess parameter functions is when the software estimates a starting guess
//All guess parameters_range is when the user has guessed within a range.
void guess_parameters_one_site(Data *&data, QVector<double> kd_testVector, QString mode)
{
double y_calc{};
double chi2{-1.0};
double chi2_temp{};
int best_index_kd{}, best_index_responce{};
QVector<double> test_last_responce{};
double range{data->responceVector.last()/10};
for (int i=0;i<11;i++)
test_last_responce.push_back(data->responceVector.last()+i*range);
double (*dblptr)(const double, const double, const std::vector<double> &){fit_one_site_dilution};
if (mode=="chemshift")
dblptr = fit_one_site;
for (int i=0; i<kd_testVector.size();i++){
std::vector<double> a_temp{data->a};
a_temp[2]=kd_testVector[i];
for (int h=0;h<test_last_responce.size();h++){
a_temp[1]=test_last_responce[h];
for (int i=0; i<data->responceVector.size();i++){
y_calc=dblptr(data->concVector[i],data->protein_conc_vector[i], a_temp);
chi2_temp += ((y_calc - data->responceVector[i]) *
(y_calc - data->responceVector[i]))
/ (data->error_vector[i]*data->error_vector[i]);
}
if(!std::isnan(chi2_temp)){
if (chi2<0){
chi2=chi2_temp;
best_index_kd=i;
best_index_responce=h;
}
else if(chi2>chi2_temp){
chi2=chi2_temp;
best_index_kd=i;
best_index_responce=h;
}
}
chi2_temp=0;
}
}
data->a[2]=kd_testVector[best_index_kd];
data->a[1]=test_last_responce[best_index_responce];
}
void guess_parameters_range(Data *&data, QVector<double> &kd, QVector<double> &start, QVector<double> &end, QString mode)
{
double y_calc{};
double chi2{};
double chi2_temp{};
int best_index_kd{}, best_index_start_responce{}, best_index_end_responce{};
std::vector<double> a_temp{double(),double(),double()};
double (*dblptr)(const double, const double, const std::vector<double> &){fit_one_site_dilution};
if (mode=="chemshift")
dblptr = fit_one_site;
for (int i = 0; i < kd.size();i++) {
a_temp[2]=kd[i];
for (int j=0; j < start.size();j++){
a_temp[0]=start[j];
for (int l=0;l<end.size();l++){
a_temp[1]=end[l];
for (int k=0; k<data->responceVector.size();k++){
y_calc=dblptr(data->concVector[k],data->protein_conc_vector[k], a_temp);
chi2_temp += ((y_calc - data->responceVector[k]) *
(y_calc - data->responceVector[k]))
/ (data->error_vector[k]*data->error_vector[k]);
}
if (chi2==0.0 && i==0 && j==0 && l==0){
chi2=chi2_temp;
best_index_end_responce=l;
best_index_start_responce=j;
best_index_kd=i;
}
else if(chi2>chi2_temp){
chi2=chi2_temp;
best_index_end_responce=l;
best_index_start_responce=j;
best_index_kd=i;
}
chi2_temp=0;
}
}
}
data->a[0]=start[best_index_start_responce];
data->a[1]=end[best_index_end_responce];
data->a[2]=kd[best_index_kd];
}
void guess_parameters_range_2_sites(Data *&data, QVector<double> &kd, QVector<double> &kd2, QVector<double> &start, QVector<double> &inter, QVector<double> &end, QString mode)
{
double y_calc{};
double chi2{-1.0};
double chi2_temp{};
int best_index_kd{}, best_index_start_responce{}, best_index_end_responce{}, best_index_inter_responce{}, best_index_kd2{};
std::vector<double> a_temp{data->a};
double (*dblptr)(const double, const double, const std::vector<double> &){fit_two_sites_dilution};
if (mode=="chemshift")
dblptr = fit_two_sites;
for (int i = 0; i < kd.size();i++) {
a_temp[3]=kd[i];
for (int j=0; j < start.size();j++){
a_temp[0]=start[j];
for (int l=0; l < end.size();l++){
a_temp[2]=end[l];
for (int m=0;m<inter.size();m++){
a_temp[1]=inter[m];
for (int n=0;n<kd2.size();n++){
a_temp[4]=kd2[n];
for (int k=0; k<data->responceVector.size();k++){
y_calc=dblptr(data->concVector[k],data->protein_conc_vector[k], a_temp);
chi2_temp += ((y_calc - data->responceVector[k]) *
(y_calc - data->responceVector[k]))
/ (data->error_vector[k]*data->error_vector[k]);
}
if(!std::isnan(chi2_temp)){
if (chi2<0){
chi2=chi2_temp;
best_index_end_responce=l;
best_index_start_responce=j;
best_index_kd=i;
best_index_inter_responce=m;
best_index_kd2=n;
}
else if(chi2>chi2_temp){
chi2=chi2_temp;
best_index_end_responce=l;
best_index_start_responce=j;
best_index_kd=i;
best_index_inter_responce=m;
best_index_kd2=n;
}
}
chi2_temp=0;
}
}
}
}
}
data->a[0]=start[best_index_start_responce];
data->a[1]=inter[best_index_inter_responce];
data->a[2]=end[best_index_end_responce];
data->a[3]=kd[best_index_kd];
data->a[4]=kd2[best_index_kd2];
}
void guess_parameters_two_sites(Data *&data, QVector<double> kd_testVector, QProgressDialog &progress, QString mode)
{
double y_calc{};
double chi2_temp{};
double chi2{-1.0};
int best_index_kd1{}, best_index_kd2{};
QVector<double> test_last_responce{}, test_intermediate_responce{};
double range{data->responceVector.last()/10};
for (int i=0;i<11;i++)
test_last_responce.push_back(data->responceVector.last()+i*range);
for (int i=0;i<data->responceVector.size();i++)
test_intermediate_responce.push_back(data->responceVector[i]);
for (int i=1;i<11;i++)
test_intermediate_responce.push_back(test_last_responce[i]);
int best_index_a1{}, best_index_a2{};
std::vector<double> a_temp{data->a};
double (*dblptr)(const double, const double, const std::vector<double> &){fit_two_sites_dilution};
if (mode=="chemshift")
dblptr = fit_two_sites;
for (int g = 0; g < test_last_responce.size();g++) {
progress.setValue(g+1);
a_temp[2]=test_last_responce[g];
for (int h=0; h < test_intermediate_responce.size();h++){
a_temp[1]=test_intermediate_responce[h];
for (int i=0; i<kd_testVector.size();i++){
a_temp[3]=kd_testVector[i];
for (int j=0;j<kd_testVector.size();j++){
a_temp[4]=kd_testVector[j];
for (int k=0; k<data->responceVector.size();k++){
y_calc=dblptr(data->concVector[k],data->protein_conc_vector[k], a_temp);
chi2_temp += ((y_calc - data->responceVector[k]) *
(y_calc - data->responceVector[k]))
/ (data->error_vector[k]*data->error_vector[k]);
}
if(!std::isnan(chi2_temp)){
if (chi2<0){
chi2=chi2_temp;
best_index_kd1=i;
best_index_kd2=j;
best_index_a1=h;
best_index_a2=g;
}
else if(chi2>chi2_temp){
chi2=chi2_temp;
best_index_kd1=i;
best_index_kd2=j;
best_index_a1=h;
best_index_a2=g;
}
}
chi2_temp=0;
}
}
}
}
progress.setValue(test_last_responce.size()+1);
data->a[3]=kd_testVector[best_index_kd1];
data->a[4]=kd_testVector[best_index_kd2];
data->a[1]=test_intermediate_responce[best_index_a1];
data->a[2]=test_last_responce[best_index_a2];
}
void guess_parameters_range_four_sites(Data *&data, QVector<double> &kd1_testVector, QVector<double> &kd2_testVector, QVector<double> &kd3_testVector,
QVector<double> &kd4_testVector, QVector<double> &p_resp_testVector, QVector<double> &pl_resp_testVector,
QVector<double> &pl2_resp_testVector, QVector<double> &pl3_resp_testVector, QVector<double> &pl4_resp_testVector,
QString mode)
{
double chi2 = std::numeric_limits<double>::max();
VecInt bestidx{};
double (*dblptr)(const double, const double, const std::vector<double> &){fit_four_sites_dilution};
if (mode=="chemshift")
dblptr = fit_four_sites;
for (int i0=0; i0<p_resp_testVector.size(); ++i0)
for (int i1=0; i1<pl_resp_testVector.size(); ++i1)
for (int i2=0; i2<pl2_resp_testVector.size(); ++i2)
for (int i3=0; i3<pl3_resp_testVector.size(); ++i3)
for (int i4=0; i4<pl4_resp_testVector.size(); ++i4)
for (int i5=0; i5<kd1_testVector.size(); ++i5)
for (int i6=0; i6<kd2_testVector.size(); ++i6)
for (int i7=0; i7<kd3_testVector.size(); ++i7)
for (int i8=0; i8<kd4_testVector.size(); ++i8) {
double chi2_temp = 0.;
VecDoub a_temp = {p_resp_testVector[i0], pl_resp_testVector[i1],
pl2_resp_testVector[i2], pl3_resp_testVector[i3],
pl4_resp_testVector[i4], kd1_testVector[i5],
kd2_testVector[i6], kd3_testVector[i7],
kd4_testVector[i8], data->a[9], data->a[10]};
for (int j=0; j<data->concVector.size(); ++j) {
double y = dblptr(data->concVector[j],
data->protein_conc_vector[j], a_temp);
chi2_temp += ((y - data->responceVector[j]) *
(y - data->responceVector[j]))
/ (data->error_vector[j]*data->error_vector[j]);
}
if (chi2_temp<chi2) {
bestidx = {i0, i1, i2, i3, i4, i5, i6, i7, i8};
chi2 = chi2_temp;
}
}
data->a[0]=p_resp_testVector[bestidx[0]];
data->a[1]=pl_resp_testVector[bestidx[1]];
data->a[2]=pl2_resp_testVector[bestidx[2]];
data->a[3]=pl3_resp_testVector[bestidx[3]];
data->a[4]=pl4_resp_testVector[bestidx[4]];
data->a[5]=kd1_testVector[bestidx[5]];
data->a[6]=kd2_testVector[bestidx[6]];
data->a[7]=kd3_testVector[bestidx[7]];
data->a[8]=kd4_testVector[bestidx[8]];
}
// Fix progress later
void guess_parameters_four_sites(Data *&data, QProgressDialog &progress, QString mode)
{
double chi2 = std::numeric_limits<double>::max();
VecInt bestidx{};
double (*dblptr)(const double, const double, const std::vector<double> &){fit_four_sites_dilution};
if (mode=="chemshift")
dblptr = fit_four_sites;
int maxi1{10}, maxi2{maxi1}, maxi3{maxi1}, maxi4{maxi1}, maxi5{6}, maxi6{maxi5}, maxi7{maxi5}, maxi8{maxi5};
VecDoub response_range{10};
for (int i=0; i<2; ++i) response_range[i] = data->responceVector[0]+i*(data->responceVector.back()-data->responceVector[0])/(maxi1-1);
VecDoub kd_range{0.001, 0.01, 0.1, 1., 10., 100.};
for (int i1=0; i1<maxi1; ++i1)for (int i1=0; i1<maxi1; ++i1) {
progress.setValue(i1+1);
for (int i2=0; i2<maxi2; ++i2)
for (int i3=0; i3<maxi3; ++i3)
for (int i4=0; i4<maxi4; ++i4)
for (int i5=0; i5<maxi5; ++i5)
for (int i6=0; i6<maxi6; ++i6)
for (int i7=0; i7<maxi7; ++i7)
for (int i8=0; i8<maxi8; ++i8) {
double chi2_temp = 0.;
VecDoub a_temp = {data->concVector[0], response_range[i1],
response_range[i2], response_range[i3],
response_range[i4], kd_range[i5],
kd_range[i6], kd_range[i7],
kd_range[i8], data->a[9], data->a[10]};
for (int j=0; j<data->concVector.size(); ++j) {
double y = dblptr(data->concVector[j],
data->protein_conc_vector[j], a_temp);
chi2_temp += ((y - data->responceVector[j]) *
(y - data->responceVector[j]))
/ (data->error_vector[j]*data->error_vector[j]);
}
if (chi2_temp<chi2) {
bestidx = {i1, i2, i3, i4, i5, i6, i7, i8};
chi2 = chi2_temp;
}
}
}
progress.setValue(maxi1+1);
data->a[0]=data->concVector[0];
data->a[1]=response_range[bestidx[0]];
data->a[2]=response_range[bestidx[1]];
data->a[3]=response_range[bestidx[2]];
data->a[4]=response_range[bestidx[3]];
data->a[5]=kd_range[bestidx[4]];
data->a[6]=kd_range[bestidx[5]];
data->a[7]=kd_range[bestidx[6]];
data->a[8]=kd_range[bestidx[7]];
}
void guess_parameters_comp(Data *&data, QVector<double> kd_testVector, QProgressDialog &progress, QString mode)
{
double y_calc{};
double chi2_temp{};
double chi2{(-1.0)};
int best_index_kd1{}, best_index_kd2{}, best_index_kdc{},best_index_a1{};
QVector<double> test_last_responce{};
double range{data->responceVector.last()/10};
if(data->responceVector.back()>data->responceVector[0]){
for (int i=0;i<11;i++)
test_last_responce.push_back(data->responceVector.last()+i*range);
}
else
for (int i=0;i<11;i++)
test_last_responce.push_back(data->responceVector.last()-i*range);
std::vector<double> a_temp{data->a};
double (*dblptr)(const double, const double, const double, const std::vector<double> &){fit_comp_dilution};
if (mode=="chemshift")
dblptr = fit_comp;
for (int g = 0; g < test_last_responce.size();g++) {
a_temp[1]=test_last_responce[g];
progress.setValue(g+1);
for (int i=0; i<kd_testVector.size();i++){
a_temp[2]=kd_testVector[i];
for (int j=i;j<kd_testVector.size();j++){
a_temp[3]=kd_testVector[j];
for (int c=0;c<kd_testVector.size();c++){
a_temp[4]=kd_testVector[c];
for (int k=0; k<data->responceVector.size();k++) {
y_calc=dblptr(data->concVector[k],data->protein_conc_vector[k],data->comp_vector[k], a_temp);
chi2_temp += ((y_calc - data->responceVector[k]) *
(y_calc - data->responceVector[k]))
/ (data->error_vector[k]*data->error_vector[k]);
}
if(!std::isnan(chi2_temp)){
if (chi2<0){
chi2=chi2_temp;
best_index_kd1=i;
best_index_kd2=j;
best_index_a1=g;
best_index_kdc=c;
}
else if(chi2>chi2_temp){
chi2=chi2_temp;
best_index_kd1=i;
best_index_kd2=j;
best_index_a1=g;
best_index_kdc=c;
}
}
chi2_temp=0;
}
}
}
}
progress.setValue(test_last_responce.size()+1);
data->a[2]=kd_testVector[best_index_kd1];
data->a[3]=kd_testVector[best_index_kd2];
data->a[4]=kd_testVector[best_index_kdc];
data->a[1]=test_last_responce[best_index_a1];
}
void guess_parameters_comp_range(Data *&data, QVector<double> &kd, QVector<double> &kd2, QVector<double> &kdc, QVector<double> &start, QVector<double> &end, QString mode)
{
double y_calc{};
double chi2{-1.0};
double chi2_temp{};
int best_index_kd1{}, best_index_start_responce{}, best_index_end_responce{}, best_index_kdc{}, best_index_kd2{};
std::vector<double> a_temp{data->a};
double (*dblptr)(const double, const double, const double, const std::vector<double> &){fit_comp_dilution};
if (mode=="chemshift")
dblptr = fit_comp;
for (int i = 0; i < kd.size();i++) {
a_temp[2]=kd[i];
for (int j=0; j < start.size();j++) {
a_temp[0]=start[j];
for (int l=0; l < end.size();l++) {
a_temp[1]=end[l];
for (int m=0;m<kdc.size();m++) {
a_temp[4]=kdc[m];
for (int n=0;n<kd2.size();n++) {
a_temp[3]=kd2[n];
for (int k=0; k<data->responceVector.size();k++){
y_calc=dblptr(data->concVector[k],data->protein_conc_vector[k],data->comp_vector[k], a_temp);
chi2_temp += ((y_calc - data->responceVector[k]) *
(y_calc - data->responceVector[k]))
/ (data->error_vector[k]*data->error_vector[k]);
}
if(!std::isnan(chi2_temp)) {
if (chi2<0) {
chi2=chi2_temp;
best_index_end_responce=l;
best_index_start_responce=j;
best_index_kd1=i;
best_index_kdc=m;
best_index_kd2=n;