/*Use the Abate-Whitt for numerical inversion of the Laplace transform*/
static double SumAW(double expiry,
double sg, double r, double aa, int terms, int totterms, int nummoment)
{
int k;
double h=sg*sg*expiry/4.0;
double Eulero;
dcomplex term;
dcomplex sum;
double *sum_r;
sum_r = malloc((totterms-terms+2)*sizeof(double));
sum =Complex(0.0, 0.0);
Eulero = 0.0;
sum =RCmul(1.0/2.0,dermellin(Complex(aa/(2.0*h),0), sg, r,nummoment));
for (k=1;k<=totterms;k++)
{
term = RCmul(PNL_ALTERNATE(k) ,dermellin(Complex(aa/(2.0*h) , k*M_PI/h),sg, r,nummoment ));
sum = Cadd(term, sum);
if(terms<= k) sum_r[k-terms+1]= sum.r;
}
for (k=0;k<=totterms-terms;k++)
{
Eulero = Eulero + bico(totterms-terms,k) * pow( 2.0, -(totterms-terms) ) * sum_r[k+1];
}
free(sum_r);
return exp(aa/2.0)*Eulero/h;
}
void newmomentsAM(int model, double rf, double dt, int maxmoment,
int ndates, double parameters[], double **momtable)
{
int i,ii,k;
double sum;
for(i = 1; i < maxmoment + 1; i++)
{momtable[1][i] = Creal(cfrn(model,rf, dt, Complex(0,-i), parameters)); }
for(ii = 2;ii < ndates + 1; ii++)
{for(i = 1; i < maxmoment + 1; i++)
{
sum=0;
for(k=1;k<=i;k++)
{sum=sum+momtable[ii - 1][ k]*bico(i, i-k);
}
momtable[ii][ i] = momtable[1][ i]*(1 + sum);
}
}
}
/*************************************************************************************************************
Procedure: getIsoDist
************************************************************************************************************/
double getIsoDist(int ii, ISOTAB *element, int num, double *peptide, ISODIST *dist)
{
double mult, power, probj, probk, probl, probm;
double probjk, probkl, probjkl, probklm, probjklm;
int i, j, k, l, m;
/* get monoisotopic mass and it's probabilty */
dist[ii].mass[0] = 0.0;
dist[ii].prob[0] = 100.0;
for (i = 0; i < num; i++)
{
power = peptide[i];
dist[ii].mass[0] = dist[ii].mass[0] + peptide[i]*element[i].isotope[0];
dist[ii].prob[0] = dist[ii].prob[0] * pow(element[i].abundance[0], power);
}
/* get probabilty of monoisotopic mass plus 1 */
dist[ii].prob[1] = 0.0;
for (j = 0; j < num; j++)
{
power = peptide[j] - 1.0;
mult = peptide[j];
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[1];
for (i = 0; i < num; i++)
{
if (i != j)
{
power = peptide[i];
probj = probj * pow(element[i].abundance[0], power);
}
}
dist[ii].prob[1] = dist[ii].prob[1] + probj;
}
dist[ii].prob[1] = dist[ii].prob[1]*100.0;
/* get probabilty of monoisotopic mass plus 2 */
dist[ii].prob[2] = 0.0;
for (j = 0; j < num; j++)
{
power = peptide[j] - 1.0;
mult = peptide[j];
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[2];
for (i = 0; i < num; i++)
{
if (i != j)
{
power = peptide[i];
probj = probj * pow(element[i].abundance[0], power);
}
}
dist[ii].prob[2] = dist[ii].prob[2] + probj;
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 2.0;
mult = bico(peptide[j], 2);
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[1]*element[j].abundance[1];
for (i = 0; i < num; i++)
{
if (i != j)
{
power = peptide[i];
probj = probj * pow(element[i].abundance[0], power);
}
}
dist[ii].prob[2] = dist[ii].prob[2] + probj;
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 1.0;
mult = peptide[j];
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[1];
for (k = 0; k < num; k++)
{
probk = 0.0;
if (k > j)
{
power = peptide[k] - 1.0;
mult = peptide[k];
probk = mult * pow(element[k].abundance[0], power)*element[k].abundance[1];
}
for (i = 0; i < num; i++)
{
if ((i != j) && (i != k))
{
power = peptide[i];
probk = probk * pow(element[i].abundance[0], power);
}
}
probjk = probj*probk;
dist[ii].prob[2] = dist[ii].prob[2] + probjk;
}
}
dist[ii].prob[2] = dist[ii].prob[2]*100.0;
/* get probabilty of monoisotopic mass plus 3 */
dist[ii].prob[3] = 0.0;
for (j = 0; j < num; j++)
{
power = peptide[j] - 1.0;
mult = peptide[j];
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[3];
for (i = 0; i < num; i++)
{
if (i != j)
{
power = peptide[i];
probj = probj * pow(element[i].abundance[0], power);
}
}
dist[ii].prob[3] = dist[ii].prob[3] + probj;
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 2.0;
mult = peptide[j]*(peptide[j]-1);
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[1]*element[j].abundance[2];
for (i = 0; i < num; i++)
{
if (i != j)
{
power = peptide[i];
probj = probj * pow(element[i].abundance[0], power);
}
}
dist[ii].prob[3] = dist[ii].prob[3] + probj;
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 3.0;
mult = bico(peptide[j], 3);
probj = mult * pow(element[j].abundance[0], power)*pow(element[j].abundance[1],3);
for (i = 0; i < num; i++)
{
if (i != j)
{
power = peptide[i];
probj = probj * pow(element[i].abundance[0], power);
}
}
dist[ii].prob[3] = dist[ii].prob[3] + probj;
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 1.0;
mult = peptide[j];
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[2];
for (k = 0; k < num; k++)
{
probk = 0.0;
if (k != j)
{
power = peptide[k] - 1.0;
mult = peptide[k];
probk = mult * pow(element[k].abundance[0], power)*element[k].abundance[1];
}
for (i = 0; i < num; i++)
{
if ((i != j) && (i != k))
{
power = peptide[i];
probk = probk * pow(element[i].abundance[0], power);
}
}
probjk = probj*probk;
dist[ii].prob[3] = dist[ii].prob[3] + probjk;
}
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 2.0;
mult = bico(peptide[j], 2);
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[1]*element[j].abundance[1];
for (k = 0; k < num; k++)
{
probk = 0.0;
if (k != j)
{
power = peptide[k] - 1.0;
mult = peptide[k];
probk = mult * pow(element[k].abundance[0], power)*element[k].abundance[1];
}
for (i = 0; i < num; i++)
{
if ((i != j) && (i != k))
{
power = peptide[i];
probk = probk * pow(element[i].abundance[0], power);
}
}
probjk = probj*probk;
dist[ii].prob[3] = dist[ii].prob[3] + probjk;
}
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 1.0;
mult = peptide[j];
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[1];
for (k = 0; k < num; k++)
{
probk = 0.0;
if (k > j)
{
power = peptide[k] - 1.0;
mult = peptide[k];
probk = mult * pow(element[k].abundance[0], power)*element[k].abundance[1];
}
for (l = 0; l < num; l++)
{
probl = 0.0;
if (l > k)
{
power = peptide[l] - 1.0;
mult = peptide[l];
probl = mult * pow(element[l].abundance[0], power)*element[l].abundance[1];
}
probkl = probk*probl;
for (i = 0; i < num; i++)
{
if ((i != j) && (i != k) && (i != l))
{
power = peptide[i];
probkl = probkl * pow(element[i].abundance[0], power);
}
}
probjkl = probj*probkl;
dist[ii].prob[3] = dist[ii].prob[3] + probjkl;
}
}
}
dist[ii].prob[3] = dist[ii].prob[3]*100.0;
/* get probabilty of monoisotopic mass plus 4 */
dist[ii].prob[4] = 0.0;
/* note there is no abundance for iso 4 or more */
for (j = 0; j < num; j++)
{
power = peptide[j] - 2.0;
mult = peptide[j]*(peptide[j]-1);
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[1]*element[j].abundance[3];
for (i = 0; i < num; i++)
{
if (i != j)
{
power = peptide[i];
probj = probj * pow(element[i].abundance[0], power);
}
}
dist[ii].prob[4] = dist[ii].prob[4] + probj;
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 2.0;
mult = bico(peptide[j], 2);
probj = mult * pow(element[j].abundance[0], power)*pow(element[j].abundance[2],2);
for (i = 0; i < num; i++)
{
if (i != j)
{
power = peptide[i];
probj = probj * pow(element[i].abundance[0], power);
}
}
dist[ii].prob[4] = dist[ii].prob[4] + probj;
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 3.0;
mult = peptide[j]*bico(peptide[j]-1, 2);
probj = mult * pow(element[j].abundance[0], power)*pow(element[j].abundance[1],2)*element[j].abundance[2];
for (i = 0; i < num; i++)
{
if (i != j)
{
power = peptide[i];
probj = probj * pow(element[i].abundance[0], power);
}
}
dist[ii].prob[4] = dist[ii].prob[4] + probj;
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 4;
mult = bico(peptide[j], 4);
probj = mult * pow(element[j].abundance[0], power)*pow(element[j].abundance[1],4);
for (i = 0; i < num; i++)
{
if (i != j)
{
power = peptide[i];
probj = probj * pow(element[i].abundance[0], power);
}
}
dist[ii].prob[4] = dist[ii].prob[4] + probj;
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 1.0;
mult = peptide[j];
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[3];
for (k = 0; k < num; k++)
{
probk = 0.0;
if (k != j)
{
power = peptide[k] - 1.0;
mult = peptide[k];
probk = mult * pow(element[k].abundance[0], power)*element[k].abundance[1];
}
for (i = 0; i < num; i++)
{
if ((i != j) && (i != k))
{
power = peptide[i];
probk = probk * pow(element[i].abundance[0], power);
}
}
probjk = probj*probk;
dist[ii].prob[4] = dist[ii].prob[4] + probjk;
}
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 1.0;
mult = peptide[j];
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[2];
for (k = 0; k < num; k++)
{
probk = 0.0;
if (k > j)
{
power = peptide[k] - 1.0;
mult = peptide[k];
probk = mult * pow(element[k].abundance[0], power)*element[k].abundance[2];
}
for (i = 0; i < num; i++)
{
if ((i != j) && (i != k))
{
power = peptide[i];
probk = probk * pow(element[i].abundance[0], power);
}
}
probjk = probj*probk;
dist[ii].prob[4] = dist[ii].prob[4] + probjk;
}
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 2.0;
mult = peptide[j]*(peptide[j]-1);
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[2]*element[j].abundance[1];
for (k = 0; k < num; k++)
{
probk = 0.0;
if (k != j)
{
power = peptide[k] - 1.0;
mult = peptide[k];
probk = mult * pow(element[k].abundance[0], power)*element[k].abundance[1];
}
for (i = 0; i < num; i++)
{
if ((i != j) && (i != k))
{
power = peptide[i];
probk = probk * pow(element[i].abundance[0], power);
}
}
probjk = probj*probk;
dist[ii].prob[4] = dist[ii].prob[4] + probjk;
}
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 1.0;
mult = peptide[j];
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[2];
for (k = 0; k < num; k++)
{
probk = 0.0;
if (k > j)
{
power = peptide[k] - 1.0;
mult = peptide[k];
probk = mult * pow(element[k].abundance[0], power)*element[k].abundance[1];
}
for (l = 0; l < num; l++)
{
probl = 0.0;
if (l > k)
{
power = peptide[l] - 1.0;
mult = peptide[l];
probl = mult * pow(element[l].abundance[0], power)*element[l].abundance[1];
}
probkl = probk*probl;
for (i = 0; i < num; i++)
{
if ((i != j) && (i != k) && (i != l))
{
power = peptide[i];
probkl = probkl * pow(element[i].abundance[0], power);
}
}
probjkl = probj*probkl;
dist[ii].prob[4] = dist[ii].prob[4] + probjkl;
}
}
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 1.0;
mult = peptide[j];
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[2];
for (k = 0; k < num; k++)
{
probk = 0.0;
if (k != j)
{
power = peptide[k] - 2.0;
mult = bico(peptide[k], 2);
probk = mult * pow(element[k].abundance[0], power)*element[k].abundance[1]*element[k].abundance[1];
}
for (i = 0; i < num; i++)
{
if ((i != j) && (i != k))
{
power = peptide[i];
probk = probk * pow(element[i].abundance[0], power);
}
}
probjk = probj*probk;
dist[ii].prob[4] = dist[ii].prob[4] + probjk;
}
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 3.0;
mult = bico(peptide[j],3);
probj = mult * pow(element[j].abundance[0], power)*pow(element[j].abundance[1],3);
for (k = 0; k < num; k++)
{
probk = 0.0;
if (k != j)
{
power = peptide[k] - 1.0;
mult = peptide[k];
probk = mult * pow(element[k].abundance[0], power)*element[k].abundance[1];
}
for (i = 0; i < num; i++)
{
if ((i != j) && (i != k))
{
power = peptide[i];
probk = probk * pow(element[i].abundance[0], power);
}
}
probjk = probj*probk;
dist[ii].prob[4] = dist[ii].prob[4] + probjk;
}
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 2.0;
mult = bico(peptide[j], 2);
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[1]*element[j].abundance[1];
for (k = 0; k < num; k++)
{
probk = 0.0;
if (k > j)
{
power = peptide[k] - 2.0;
mult = bico(peptide[k], 2);
probk = mult * pow(element[k].abundance[0], power)*element[k].abundance[1]*element[k].abundance[1];
}
for (i = 0; i < num; i++)
{
if ((i != j) && (i != k))
{
power = peptide[i];
probk = probk * pow(element[i].abundance[0], power);
}
}
probjk = probj*probk;
dist[ii].prob[4] = dist[ii].prob[4] + probjk;
}
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 2.0;
mult = bico(peptide[j], 2);
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[1]*element[j].abundance[1];
for (k = 0; k < num; k++)
{
probk = 0.0;
if (k != j)
{
power = peptide[k] - 1.0;
mult = peptide[k];
probk = mult * pow(element[k].abundance[0], power)*element[k].abundance[1];
}
for (l = 0; l < num; l++)
{
probl = 0.0;
if ((l != j) && (l > k))
{
power = peptide[l] - 1.0;
mult = peptide[l];
probl = mult * pow(element[l].abundance[0], power)*element[l].abundance[1];
}
probkl = probk*probl;
for (i = 0; i < num; i++)
{
if ((i != j) && (i != k) && (i != l))
{
power = peptide[i];
probkl = probkl * pow(element[i].abundance[0], power);
}
}
probjkl = probj*probkl;
dist[ii].prob[4] = dist[ii].prob[4] + probjkl;
}
}
}
for (j = 0; j < num; j++)
{
power = peptide[j] - 1.0;
mult = peptide[j];
probj = mult * pow(element[j].abundance[0], power)*element[j].abundance[1];
for (k = 0; k < num; k++)
{
probk = 0.0;
if (k > j)
{
power = peptide[k] - 1.0;
mult = peptide[k];
probk = mult * pow(element[k].abundance[0], power)*element[k].abundance[1];
}
for (l = 0; l < num; l++)
{
probl = 0.0;
if (l > k)
{
power = peptide[l] - 1.0;
mult = peptide[l];
probl = mult * pow(element[l].abundance[0], power)*element[l].abundance[1];
}
probkl = probk*probl;
for (m = 0; m < num; m++)
{
probm = 0.0;
if (m > l)
{
power = peptide[m] - 1.0;
mult = peptide[m];
probm = mult * pow(element[m].abundance[0], power)*element[m].abundance[1];
}
probklm = probkl*probm;
for (i = 0; i < num; i++)
{
if ((i != j) && (i != k) && (i != l) && (i != m))
{
power = peptide[i];
probklm = probklm * pow(element[i].abundance[0], power);
}
}
probjklm = probj*probklm;
dist[ii].prob[4] = dist[ii].prob[4] + probjklm;
}
}
}
}
dist[ii].prob[4] = dist[ii].prob[4]*100.0;
double max = 0.0;
for (i = 0; i < 5; i++)
{
if (dist[ii].prob[i] > max) max = dist[ii].prob[i];
}
for (i = 0; i < 5; i++)
{
dist[ii].prob[i] = dist[ii].prob[i]/max;
}
return(dist[ii].mass[0]);
}
