/*
c Ivo Hofacker
Vienna RNA package
*/
#include <config.h>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include "energy_par.h"
#include "fold_vars.h"
#include "utils.h"
#include "params.h"
/**
*** \file params.c
*** <P>
*** This file provides functions that return temperature scaled energy parameters and
*** Boltzmann weights packed in datastructures
*** </P>
***/
/*@unused@*/
static char rcsid[] UNUSED = "$Id: params.c,v 1.9 2008/07/04 14:29:14 ivo Exp $";
PRIVATE paramT p;
PRIVATE int id=-1;
/* variables for partition function */
PRIVATE pf_paramT pf;
PRIVATE int pf_id=-1;
#ifdef _OPENMP
#pragma omp threadprivate(id, pf_id)
#endif
PUBLIC paramT *scale_parameters(void){
model_detailsT md;
set_model_details(&md);
return get_scaled_parameters(temperature, md);
}
PUBLIC paramT *get_scaled_parameters( double temp,
model_detailsT md){
unsigned int i,j,k,l;
double tempf;
paramT *params;
params = (paramT *)space(sizeof(paramT));
/* store the model details */
params->model_details = md;
params->temperature = temp;
tempf = ((params->temperature+K0)/Tmeasure);
for(i = VRNA_GQUAD_MIN_STACK_SIZE; i <= VRNA_GQUAD_MAX_STACK_SIZE; i++)
for(j = 3*VRNA_GQUAD_MIN_LINKER_LENGTH; j <= 3*VRNA_GQUAD_MAX_LINKER_LENGTH; j++){
double GQuadAlpha_T = (double)GQuadAlphadH - (double)(GQuadAlphadH - GQuadAlpha37) * tempf;
double GQuadBeta_T = (double)GQuadBetadH - (double)(GQuadBetadH - GQuadBeta37) * tempf;
params->gquad[i][j] = (int)GQuadAlpha_T*(i-1) + (int)(((double)GQuadBeta_T)*log(j - 2));
}
for (i=0; i<31; i++)
params->hairpin[i] = hairpindH[i] - (hairpindH[i] - hairpin37[i])*tempf;
for (i=0; i<=MIN2(30,MAXLOOP); i++) {
params->bulge[i] = bulgedH[i] - (bulgedH[i] - bulge37[i]) * tempf;
params->internal_loop[i] = internal_loopdH[i] - (internal_loopdH[i] - internal_loop37[i]) * tempf;
}
params->lxc = lxc37*tempf;
for (; i<=MAXLOOP; i++) {
params->bulge[i] = params->bulge[30]+(int)(params->lxc*log((double)(i)/30.));
params->internal_loop[i] = params->internal_loop[30]+(int)(params->lxc*log((double)(i)/30.));
}
params->ninio[2] = niniodH - (niniodH - ninio37) * tempf;
params->TripleC = TripleCdH - (TripleCdH - TripleC37) * tempf;
params->MultipleCA = MultipleCAdH - (MultipleCAdH - MultipleCA37) * tempf;
params->MultipleCB = MultipleCBdH - (MultipleCBdH - MultipleCB37) * tempf;
for (i=0; (i*7)<strlen(Tetraloops); i++)
params->Tetraloop_E[i] = TetraloopdH[i] - (TetraloopdH[i]-Tetraloop37[i])*tempf;
for (i=0; (i*5)<strlen(Triloops); i++)
params->Triloop_E[i] = TriloopdH[i] - (TriloopdH[i]-Triloop37[i])*tempf;
for (i=0; (i*9)<strlen(Hexaloops); i++)
params->Hexaloop_E[i] = HexaloopdH[i] - (HexaloopdH[i]-Hexaloop37[i])*tempf;
params->TerminalAU = TerminalAUdH - (TerminalAUdH - TerminalAU37) * tempf;
params->DuplexInit = DuplexInitdH - (DuplexInitdH - DuplexInit37) *tempf;
params->MLbase = ML_BASEdH - (ML_BASEdH - ML_BASE37) * tempf;
for (i=0; i<=NBPAIRS; i++)
params->MLintern[i] = ML_interndH - (ML_interndH - ML_intern37) * tempf;
params->MLclosing = ML_closingdH - (ML_closingdH - ML_closing37) * tempf;
/* stacks G(T) = H - [H - G(T0)]*T/T0 */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=NBPAIRS; j++)
params->stack[i][j] = stackdH[i][j] - (stackdH[i][j] - stack37[i][j])*tempf;
/* mismatches */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<5; j++)
for (k=0; k<5; k++) {
int mm;
params->mismatchI[i][j][k] = mismatchIdH[i][j][k] - (mismatchIdH[i][j][k] - mismatchI37[i][j][k])*tempf;
params->mismatchH[i][j][k] = mismatchHdH[i][j][k] - (mismatchHdH[i][j][k] - mismatchH37[i][j][k])*tempf;
params->mismatch1nI[i][j][k] = mismatch1nIdH[i][j][k]-(mismatch1nIdH[i][j][k]-mismatch1nI37[i][j][k])*tempf;/* interior nx1 loops */
params->mismatch23I[i][j][k] = mismatch23IdH[i][j][k]-(mismatch23IdH[i][j][k]-mismatch23I37[i][j][k])*tempf;/* interior 2x3 loops */
if(md.dangles){
mm = mismatchMdH[i][j][k] - (mismatchMdH[i][j][k] - mismatchM37[i][j][k])*tempf;
params->mismatchM[i][j][k] = (mm > 0) ? 0 : mm;
mm = mismatchExtdH[i][j][k] - (mismatchExtdH[i][j][k] - mismatchExt37[i][j][k])*tempf;
params->mismatchExt[i][j][k] = (mm > 0) ? 0 : mm;
}
else{
params->mismatchM[i][j][k] = params->mismatchExt[i][j][k] = 0;
}
}
/* dangles */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<5; j++) {
int dd;
dd = dangle5_dH[i][j] - (dangle5_dH[i][j] - dangle5_37[i][j])*tempf;
params->dangle5[i][j] = (dd>0) ? 0 : dd; /* must be <= 0 */
dd = dangle3_dH[i][j] - (dangle3_dH[i][j] - dangle3_37[i][j])*tempf;
params->dangle3[i][j] = (dd>0) ? 0 : dd; /* must be <= 0 */
}
/* interior 1x1 loops */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=NBPAIRS; j++)
for (k=0; k<5; k++)
for (l=0; l<5; l++)
params->int11[i][j][k][l] = int11_dH[i][j][k][l] - (int11_dH[i][j][k][l] - int11_37[i][j][k][l])*tempf;
/* interior 2x1 loops */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=NBPAIRS; j++)
for (k=0; k<5; k++)
for (l=0; l<5; l++) {
int m;
for (m=0; m<5; m++)
params->int21[i][j][k][l][m] = int21_dH[i][j][k][l][m] - (int21_dH[i][j][k][l][m] - int21_37[i][j][k][l][m])*tempf;
}
/* interior 2x2 loops */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=NBPAIRS; j++)
for (k=0; k<5; k++)
for (l=0; l<5; l++) {
int m,n;
for (m=0; m<5; m++)
for (n=0; n<5; n++)
params->int22[i][j][k][l][m][n] = int22_dH[i][j][k][l][m][n] - (int22_dH[i][j][k][l][m][n]-int22_37[i][j][k][l][m][n])*tempf;
}
strncpy(params->Tetraloops, Tetraloops, 281);
strncpy(params->Triloops, Triloops, 241);
strncpy(params->Hexaloops, Hexaloops, 361);
params->id = ++id;
return params;
}
/*------------------------------------------------------------------------*/
#define SCALE 10
/**
*** dangling ends should never be destabilizing, i.e. expdangle>=1<BR>
*** specific heat needs smooth function (2nd derivative)<BR>
*** we use a*(sin(x+b)+1)^2, with a=2/(3*sqrt(3)), b=Pi/6-sqrt(3)/2,
*** in the interval b<x<sqrt(3)/2
*/
#define SMOOTH(X) ((X)/SCALE<-1.2283697)?0:(((X)/SCALE>0.8660254)?(X):\
SCALE*0.38490018*(sin((X)/SCALE-0.34242663)+1)*(sin((X)/SCALE-0.34242663)+1))
/* #define SMOOTH(X) ((X)<0 ? 0 : (X)) */
PUBLIC pf_paramT *get_scaled_pf_parameters(void){
model_detailsT md;
set_model_details(&md);
return get_boltzmann_factors(temperature, 1.0, md, pf_scale);
}
PUBLIC pf_paramT *get_boltzmann_factors(double temp,
double betaScale,
model_detailsT md,
double pf_scale){
unsigned int i, j, k, l;
double kT, TT;
double GT;
pf_paramT *pf;
pf = (pf_paramT *)space(sizeof(pf_paramT));
pf->model_details = md;
pf->temperature = temp;
pf->alpha = betaScale;
pf->kT = kT = betaScale*(temp+K0)*GASCONST; /* kT in cal/mol */
pf->pf_scale = pf_scale;
TT = (temp+K0)/(Tmeasure);
for(i = VRNA_GQUAD_MIN_STACK_SIZE; i <= VRNA_GQUAD_MAX_STACK_SIZE; i++)
for(j = 3*VRNA_GQUAD_MIN_LINKER_LENGTH; j <= 3*VRNA_GQUAD_MAX_LINKER_LENGTH; j++){
double GQuadAlpha_T = (double)GQuadAlphadH - (double)(GQuadAlphadH - GQuadAlpha37) * TT;
double GQuadBeta_T = (double)GQuadBetadH - (double)(GQuadBetadH - GQuadBeta37) * TT;
GT = ((double)GQuadAlpha_T)*((double)(i-1)) + ((double)GQuadBeta_T)*log(((double)j) - 2.);
pf->expgquad[i][j] = exp( -GT*10./kT);
}
/* loop energies: hairpins, bulges, interior, mulit-loops */
for (i=0; i<31; i++){
GT = hairpindH[i] - (hairpindH[i] - hairpin37[i])*TT;
pf->exphairpin[i] = exp( -GT*10./kT);
}
for (i=0; i<=MIN2(30, MAXLOOP); i++) {
GT = bulgedH[i]- (bulgedH[i] - bulge37[i])*TT;
pf->expbulge[i] = exp( -GT*10./kT);
GT = internal_loopdH[i] - (internal_loopdH[i] - internal_loop37[i])*TT;
pf->expinternal[i] = exp( -GT*10./kT);
}
/* special case of size 2 interior loops (single mismatch) */
if (james_rule) pf->expinternal[2] = exp ( -80*10./kT);
pf->lxc = lxc37*TT;
GT = DuplexInitdH - (DuplexInitdH - DuplexInit37)*TT;
pf->expDuplexInit = exp( -GT*10./kT);
for (i=31; i<=MAXLOOP; i++) {
GT = bulge37[30]*TT + (pf->lxc*log( i/30.));
pf->expbulge[i] = exp( -GT*10./kT);
GT = internal_loop37[30]*TT + (pf->lxc*log( i/30.));
pf->expinternal[i] = exp( -GT*10./kT);
}
GT = niniodH - (niniodH - ninio37)*TT;
for (j=0; j<=MAXLOOP; j++)
pf->expninio[2][j]=exp(-MIN2(MAX_NINIO,j*GT)*10./kT);
for (i=0; (i*7)<strlen(Tetraloops); i++) {
GT = TetraloopdH[i] - (TetraloopdH[i]-Tetraloop37[i])*TT;
pf->exptetra[i] = exp( -GT*10./kT);
}
for (i=0; (i*5)<strlen(Triloops); i++) {
GT = TriloopdH[i] - (TriloopdH[i]-Triloop37[i])*TT;
pf->exptri[i] = exp( -GT*10./kT);
}
for (i=0; (i*9)<strlen(Hexaloops); i++) {
GT = HexaloopdH[i] - (HexaloopdH[i]-Hexaloop37[i])*TT;
pf->exphex[i] = exp( -GT*10./kT);
}
GT = ML_closingdH - (ML_closingdH - ML_closing37)*TT;
pf->expMLclosing = exp( -GT*10./kT);
for (i=0; i<=NBPAIRS; i++) {
GT = ML_interndH - (ML_interndH - ML_intern37)*TT;
/* if (i>2) GT += TerminalAU; */
pf->expMLintern[i] = exp( -GT*10./kT);
}
GT = TerminalAUdH - (TerminalAUdH - TerminalAU37)*TT;
pf->expTermAU = exp(-GT*10./kT);
GT = ML_BASEdH - (ML_BASEdH - ML_BASE37)*TT;
pf->expMLbase=exp(-10.*GT/kT);
/* if dangles==0 just set their energy to 0,
don't let dangle energies become > 0 (at large temps),
but make sure go smoothly to 0 */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=4; j++) {
if (md.dangles) {
GT = dangle5_dH[i][j] - (dangle5_dH[i][j] - dangle5_37[i][j])*TT;
pf->expdangle5[i][j] = exp(SMOOTH(-GT)*10./kT);
GT = dangle3_dH[i][j] - (dangle3_dH[i][j] - dangle3_37[i][j])*TT;
pf->expdangle3[i][j] = exp(SMOOTH(-GT)*10./kT);
} else
pf->expdangle3[i][j] = pf->expdangle5[i][j] = 1;
}
/* stacking energies */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=NBPAIRS; j++) {
GT = stackdH[i][j] - (stackdH[i][j] - stack37[i][j])*TT;
pf->expstack[i][j] = exp( -GT*10./kT);
}
/* mismatch energies */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<5; j++)
for (k=0; k<5; k++) {
GT = mismatchIdH[i][j][k] - ( mismatchIdH[i][j][k] - mismatchI37[i][j][k])*TT;
pf->expmismatchI[i][j][k] = exp(-GT*10.0/kT);
GT = mismatch1nIdH[i][j][k] - (mismatch1nIdH[i][j][k] - mismatch1nI37[i][j][k])*TT;
pf->expmismatch1nI[i][j][k] = exp(-GT*10.0/kT);
GT = mismatchHdH[i][j][k] - (mismatchHdH[i][j][k] - mismatchH37[i][j][k])*TT;
pf->expmismatchH[i][j][k] = exp(-GT*10.0/kT);
if (md.dangles) {
GT = mismatchMdH[i][j][k] - (mismatchMdH[i][j][k] - mismatchM37[i][j][k])*TT;
pf->expmismatchM[i][j][k] = exp(SMOOTH(-GT)*10.0/kT);
GT = mismatchExtdH[i][j][k] - (mismatchExtdH[i][j][k] - mismatchExt37[i][j][k])*TT;
pf->expmismatchExt[i][j][k] = exp(SMOOTH(-GT)*10.0/kT);
}
else{
pf->expmismatchM[i][j][k] = pf->expmismatchExt[i][j][k] = 1.;
}
GT = mismatch23IdH[i][j][k] - (mismatch23IdH[i][j][k] - mismatch23I37[i][j][k])*TT;
pf->expmismatch23I[i][j][k] = exp(-GT*10.0/kT);
}
/* interior lops of length 2 */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=NBPAIRS; j++)
for (k=0; k<5; k++)
for (l=0; l<5; l++) {
GT = int11_dH[i][j][k][l] -
(int11_dH[i][j][k][l] - int11_37[i][j][k][l])*TT;
pf->expint11[i][j][k][l] = exp(-GT*10./kT);
}
/* interior 2x1 loops */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=NBPAIRS; j++)
for (k=0; k<5; k++)
for (l=0; l<5; l++) {
int m;
for (m=0; m<5; m++) {
GT = int21_dH[i][j][k][l][m] -
(int21_dH[i][j][k][l][m] - int21_37[i][j][k][l][m])*TT;
pf->expint21[i][j][k][l][m] = exp(-GT*10./kT);
}
}
/* interior 2x2 loops */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=NBPAIRS; j++)
for (k=0; k<5; k++)
for (l=0; l<5; l++) {
int m,n;
for (m=0; m<5; m++)
for (n=0; n<5; n++) {
GT = int22_dH[i][j][k][l][m][n] -
(int22_dH[i][j][k][l][m][n]-int22_37[i][j][k][l][m][n])*TT;
pf->expint22[i][j][k][l][m][n] = exp(-GT*10./kT);
}
}
strncpy(pf->Tetraloops, Tetraloops, 281);
strncpy(pf->Triloops, Triloops, 241);
strncpy(pf->Hexaloops, Hexaloops, 361);
return pf;
}
PUBLIC pf_paramT *get_scaled_alipf_parameters(unsigned int n_seq){
model_detailsT md;
set_model_details(&md);
return get_boltzmann_factors_ali(n_seq, temperature, 1.0, md, pf_scale);
}
PUBLIC pf_paramT *get_boltzmann_factors_ali(unsigned int n_seq,
double temperature,
double betaScale,
model_detailsT md,
double pf_scale){
/* scale energy parameters and pre-calculate Boltzmann weights */
unsigned int i, j, k, l;
double kTn, TT;
double GT;
pf_paramT *pf;
pf = (pf_paramT *)space(sizeof(pf_paramT));
pf->model_details = md;
pf->alpha = betaScale;
pf->temperature = temperature;
pf->pf_scale = pf_scale;
pf->kT = kTn = ((double)n_seq)*betaScale*(temperature+K0)*GASCONST; /* kT in cal/mol */
TT = (temperature+K0)/(Tmeasure);
/* loop energies: hairpins, bulges, interior, mulit-loops */
for (i=0; i<31; i++) {
GT = hairpindH[i] - (hairpindH[i] - hairpin37[i])*TT;
pf->exphairpin[i] = exp( -GT*10./kTn);
}
/*add penalty for too short hairpins*/
for (i=0; i<3; i++) {
GT= 600/*Penalty*/*TT;
pf->exphairpin[i] = exp( -GT*10./kTn);
}
for (i=0; i<=MIN2(30, MAXLOOP); i++) {
GT = bulgedH[i]- (bulgedH[i] - bulge37[i])*TT;
pf->expbulge[i] = exp( -GT*10./kTn);
GT = internal_loopdH[i] - (internal_loopdH[i] - internal_loop37[i])*TT;
pf->expinternal[i] = exp( -GT*10./kTn);
}
/* special case of size 2 interior loops (single mismatch) */
if (james_rule) pf->expinternal[2] = exp ( -80*10./kTn);
pf->lxc = lxc37*TT;
GT = DuplexInitdH - (DuplexInitdH - DuplexInit37)*TT;
pf->expDuplexInit = exp( -GT*10./kTn);
for (i=31; i<=MAXLOOP; i++) {
GT = bulge37[30]*TT + (pf->lxc*log( i/30.));
pf->expbulge[i] = exp( -GT*10./kTn);
GT = internal_loop37[30]*TT + (pf->lxc*log( i/30.));
pf->expinternal[i] = exp( -GT*10./kTn);
}
GT = niniodH - (niniodH - ninio37)*TT;
for (j=0; j<=MAXLOOP; j++)
pf->expninio[2][j]=exp(-MIN2(MAX_NINIO,j*GT)*10./kTn);
for (i=0; (i*7)<strlen(Tetraloops); i++) {
GT = TetraloopdH[i] - (TetraloopdH[i]-Tetraloop37[i])*TT;
pf->exptetra[i] = exp( -GT*10./kTn);
}
for (i=0; (i*5)<strlen(Triloops); i++) {
GT = TriloopdH[i] - (TriloopdH[i]-Triloop37[i])*TT;
pf->exptri[i] = exp( -GT*10./kTn);
}
for (i=0; (i*9)<strlen(Hexaloops); i++) {
GT = HexaloopdH[i] - (HexaloopdH[i]-Hexaloop37[i])*TT;
pf->exphex[i] = exp( -GT*10./kTn);
}
GT = ML_closingdH - (ML_closingdH - ML_closing37)*TT;
pf->expMLclosing = exp( -GT*10./kTn);
for (i=0; i<=NBPAIRS; i++) { /* includes AU penalty */
GT = ML_interndH - (ML_interndH - ML_intern37)*TT;
/* if (i>2) GT += TerminalAU; */
pf->expMLintern[i] = exp( -GT*10./kTn);
}
GT = TerminalAUdH - (TerminalAUdH - TerminalAU37)*TT;
pf->expTermAU = exp(-GT*10./kTn);
GT = ML_BASEdH - (ML_BASEdH - ML_BASE37)*TT;
pf->expMLbase=exp(-10.*GT/(kTn/n_seq));
/* if dangle_model==0 just set their energy to 0,
don't let dangle energies become > 0 (at large temps),
but make sure go smoothly to 0 */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=4; j++) {
if (md.dangles) {
GT = dangle5_dH[i][j] - (dangle5_dH[i][j] - dangle5_37[i][j])*TT;
pf->expdangle5[i][j] = exp(SMOOTH(-GT)*10./kTn);
GT = dangle3_dH[i][j] - (dangle3_dH[i][j] - dangle3_37[i][j])*TT;
pf->expdangle3[i][j] = exp(SMOOTH(-GT)*10./kTn);
} else
pf->expdangle3[i][j] = pf->expdangle5[i][j] = 1;
}
/* stacking energies */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=NBPAIRS; j++) {
GT = stackdH[i][j] - (stackdH[i][j] - stack37[i][j])*TT;
pf->expstack[i][j] = exp( -GT*10./kTn);
}
/* mismatch energies */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<5; j++)
for (k=0; k<5; k++) {
GT = mismatchIdH[i][j][k] - ( mismatchIdH[i][j][k] - mismatchI37[i][j][k])*TT;
pf->expmismatchI[i][j][k] = exp(-GT*10.0/kTn);
GT = mismatch1nIdH[i][j][k] - (mismatch1nIdH[i][j][k] - mismatch1nI37[i][j][k])*TT;
pf->expmismatch1nI[i][j][k] = exp(-GT*10.0/kTn);
GT = mismatchHdH[i][j][k] - (mismatchHdH[i][j][k] - mismatchH37[i][j][k])*TT;
pf->expmismatchH[i][j][k] = exp(-GT*10.0/kTn);
if (md.dangles) {
GT = mismatchMdH[i][j][k] - (mismatchMdH[i][j][k] - mismatchM37[i][j][k])*TT;
pf->expmismatchM[i][j][k] = exp(SMOOTH(-GT)*10.0/kTn);
GT = mismatchExtdH[i][j][k] - (mismatchExtdH[i][j][k] - mismatchExt37[i][j][k])*TT;
pf->expmismatchExt[i][j][k] = exp(SMOOTH(-GT)*10.0/kTn);
}
else{
pf->expmismatchM[i][j][k] = pf->expmismatchExt[i][j][k] = 1.;
}
GT = mismatch23IdH[i][j][k] - (mismatch23IdH[i][j][k] - mismatch23I37[i][j][k])*TT;
pf->expmismatch23I[i][j][k] = exp(-GT*10.0/kTn);
}
/* interior lops of length 2 */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=NBPAIRS; j++)
for (k=0; k<5; k++)
for (l=0; l<5; l++) {
GT = int11_dH[i][j][k][l] -
(int11_dH[i][j][k][l] - int11_37[i][j][k][l])*TT;
pf->expint11[i][j][k][l] = exp(-GT*10./kTn);
}
/* interior 2x1 loops */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=NBPAIRS; j++)
for (k=0; k<5; k++)
for (l=0; l<5; l++) {
int m;
for (m=0; m<5; m++) {
GT = int21_dH[i][j][k][l][m] -
(int21_dH[i][j][k][l][m] - int21_37[i][j][k][l][m])*TT;
pf->expint21[i][j][k][l][m] = exp(-GT*10./kTn);
}
}
/* interior 2x2 loops */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=NBPAIRS; j++)
for (k=0; k<5; k++)
for (l=0; l<5; l++) {
int m,n;
for (m=0; m<5; m++)
for (n=0; n<5; n++) {
GT = int22_dH[i][j][k][l][m][n] -
(int22_dH[i][j][k][l][m][n]-int22_37[i][j][k][l][m][n])*TT;
pf->expint22[i][j][k][l][m][n] = exp(-GT*10./kTn);
}
}
strncpy(pf->Tetraloops, Tetraloops, 281);
strncpy(pf->Triloops, Triloops, 241);
strncpy(pf->Hexaloops, Hexaloops, 361);
return pf;
}
PUBLIC pf_paramT *get_boltzmann_factor_copy(pf_paramT *par){
pf_paramT *copy = NULL;
if(par){
copy = (pf_paramT *) space(sizeof(pf_paramT));
memcpy(copy, par, sizeof(pf_paramT));
}
return copy;
}
PUBLIC paramT *get_parameter_copy(paramT *par){
paramT *copy = NULL;
if(par){
copy = (paramT *) space(sizeof(paramT));
memcpy(copy, par, sizeof(paramT));
}
return copy;
}
/*###########################################*/
/*# deprecated functions below #*/
/*###########################################*/
PUBLIC paramT *copy_parameters(void){
paramT *copy;
if (p.id != id) scale_parameters();
copy = (paramT *) space(sizeof(paramT));
memcpy(copy, &p, sizeof(paramT));
return copy;
}
PUBLIC paramT *set_parameters(paramT *dest){
memcpy(&p, dest, sizeof(paramT));
return &p;
}
PUBLIC pf_paramT *copy_pf_param(void){
pf_paramT *copy;
if (pf.id != pf_id) scale_pf_parameters();
copy = (pf_paramT *) space(sizeof(pf_paramT));
memcpy(copy, &pf, sizeof(pf_paramT));
return copy;
}
PUBLIC pf_paramT *set_pf_param(paramT *dest){
memcpy(&pf, dest, sizeof(pf_paramT));
return &pf;
}
PUBLIC pf_paramT *scale_pf_parameters(void){
return get_scaled_pf_parameters();
#if 0
/* scale energy parameters and pre-calculate Boltzmann weights */
unsigned int i, j, k, l;
double kT, TT;
double GT;
/* scale pf_params() in partfunc.c is only a wrapper, that calls
this functions !! */
pf.temperature = temperature;
kT = (pf.temperature+K0)*GASCONST; /* kT in cal/mol */
TT = (pf.temperature+K0)/(Tmeasure);
/* loop energies: hairpins, bulges, interior, mulit-loops */
for (i=0; i<31; i++) {
GT = hairpin37[i]*TT;
pf.exphairpin[i] = exp( -GT*10./kT);
}
for (i=0; i<=MIN2(30, MAXLOOP); i++) {
GT = bulge37[i]*TT;
pf.expbulge[i] = exp( -GT*10./kT);
GT = internal_loop37[i]*TT;
pf.expinternal[i] = exp( -GT*10./kT);
}
/* special case of size 2 interior loops (single mismatch) */
if (james_rule) pf.expinternal[2] = exp ( -80*10./kT);
pf.lxc = lxc37*TT;
GT = DuplexInitdH - (DuplexInitdH - DuplexInit37)*TT;
pf.expDuplexInit = exp( -GT*10./kT);
for (i=31; i<=MAXLOOP; i++) {
GT = bulge37[30]*TT + (pf.lxc*log( i/30.));
pf.expbulge[i] = exp( -GT*10./kT);
GT = internal_loop37[30]*TT + (pf.lxc*log( i/30.));
pf.expinternal[i] = exp( -GT*10./kT);
}
GT = niniodH - (niniodH - ninio37)*TT;
for (j=0; j<=MAXLOOP; j++)
pf.expninio[2][j]=exp(-MIN2(MAX_NINIO,j*GT)*10./kT);
for (i=0; (i*7)<strlen(Tetraloops); i++) {
GT = TetraloopdH[i] - (TetraloopdH[i]-Tetraloop37[i])*TT;
pf.exptetra[i] = exp( -GT*10./kT);
}
for (i=0; (i*5)<strlen(Triloops); i++) {
GT = TriloopdH[i] - (TriloopdH[i]-Triloop37[i])*TT;
pf.exptri[i] = exp( -GT*10./kT);
}
for (i=0; (i*9)<strlen(Hexaloops); i++) {
GT = HexaloopdH[i] - (HexaloopdH[i]-Hexaloop37[i])*TT;
pf.exphex[i] = exp( -GT*10./kT);
}
GT = ML_closing37*TT;
pf.expMLclosing = exp( -GT*10./kT);
for (i=0; i<=NBPAIRS; i++) { /* includes AU penalty */
GT = ML_intern37*TT;
/* if (i>2) GT += TerminalAU; */
pf.expMLintern[i] = exp( -GT*10./kT);
}
GT = TerminalAUdH - (TerminalAUdH - TerminalAU37)*TT;
pf.expTermAU = exp(-GT*10./kT);
GT = ML_BASE37*TT;
pf.expMLbase=exp(-10.*GT/kT);
/* if dangle_model==0 just set their energy to 0,
don't let dangle energies become > 0 (at large temps),
but make sure go smoothly to 0 */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=4; j++) {
if (dangles) {
GT = dangle5_dH[i][j] - (dangle5_dH[i][j] - dangle5_37[i][j])*TT;
pf.expdangle5[i][j] = exp(SMOOTH(-GT)*10./kT);
GT = dangle3_dH[i][j] - (dangle3_dH[i][j] - dangle3_37[i][j])*TT;
pf.expdangle3[i][j] = exp(SMOOTH(-GT)*10./kT);
} else
pf.expdangle3[i][j] = pf.expdangle5[i][j] = 1;
if (i>2) /* add TermAU penalty into dangle3 */
pf.expdangle3[i][j] *= pf.expTermAU;
}
/* stacking energies */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=NBPAIRS; j++) {
GT = stackdH[i][j] - (stackdH[i][j] - stack37[i][j])*TT;
pf.expstack[i][j] = exp( -GT*10./kT);
}
/* mismatch energies */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<5; j++)
for (k=0; k<5; k++) {
GT = mismatchIdH[i][j][k] - ( mismatchIdH[i][j][k] - mismatchI37[i][j][k])*TT;
pf.expmismatchI[i][j][k] = exp(-GT*10./kT);
GT = mismatch1nIdH[i][j][k] - (mismatch1nIdH[i][j][k] - mismatch1nI37[i][j][k])*TT;
pf.expmismatch1nI[i][j][k] = exp(-GT*10./kT);
GT = mismatchHdH[i][j][k] - (mismatchHdH[i][j][k] - mismatchH37[i][j][k])*TT;
pf.expmismatchH[i][j][k] = exp(-GT*10./kT);
GT = mismatch23IdH[i][j][k] - (mismatch23IdH[i][j][k] - mismatch23I37[i][j][k])*TT;
pf.expmismatch23I[i][j][k] = exp(-GT*10./kT);
if (dangles) {
GT = mismatchMdH[i][j][k] - (mismatchMdH[i][j][k] - mismatchM37[i][j][k])*TT;
pf.expmismatchM[i][j][k] = exp(-GT*10./kT);
GT = mismatchExtdH[i][j][k] - ( mismatchExtdH[i][j][k] - mismatchExt37[i][j][k])*TT;
pf.expmismatchExt[i][j][k] = exp(-GT*10./kT);
}
else{
pf.expmismatchM[i][j][k] = pf.expmismatchExt[i][j][k] = 1.;
}
}
/* interior lops of length 2 */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=NBPAIRS; j++)
for (k=0; k<5; k++)
for (l=0; l<5; l++) {
GT = int11_dH[i][j][k][l] -
(int11_dH[i][j][k][l] - int11_37[i][j][k][l])*TT;
pf.expint11[i][j][k][l] = exp(-GT*10./kT);
}
/* interior 2x1 loops */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=NBPAIRS; j++)
for (k=0; k<5; k++)
for (l=0; l<5; l++) {
int m;
for (m=0; m<5; m++) {
GT = int21_dH[i][j][k][l][m] -
(int21_dH[i][j][k][l][m] - int21_37[i][j][k][l][m])*TT;
pf.expint21[i][j][k][l][m] = exp(-GT*10./kT);
}
}
/* interior 2x2 loops */
for (i=0; i<=NBPAIRS; i++)
for (j=0; j<=NBPAIRS; j++)
for (k=0; k<5; k++)
for (l=0; l<5; l++) {
int m,n;
for (m=0; m<5; m++)
for (n=0; n<5; n++) {
GT = int22_dH[i][j][k][l][m][n] -
(int22_dH[i][j][k][l][m][n]-int22_37[i][j][k][l][m][n])*TT;
pf.expint22[i][j][k][l][m][n] = exp(-GT*10./kT);
}
}
strncpy(pf.Tetraloops, Tetraloops, 281);
strncpy(pf.Triloops, Triloops, 241);
strncpy(pf.Hexaloops, Hexaloops, 361);
pf.id = ++pf_id;
return &pf;
#endif
}