/*
c Ivo Hofacker
Vienna RNA package
*/
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include "ViennaRNA/energy_par.h"
#include "ViennaRNA/fold_vars.h"
#include "ViennaRNA/utils.h"
#include "ViennaRNA/params.h"
/**
*** \file params.c
*** <P>
*** This file provides functions that return temperature scaled energy parameters and
*** Boltzmann weights packed in datastructures
*** </P>
***/
/*------------------------------------------------------------------------*/
#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)) */
/*
#################################
# PRIVATE VARIABLES #
#################################
*/
PRIVATE vrna_param_t p;
PRIVATE int id=-1;
/* variables for partition function */
PRIVATE vrna_exp_param_t pf;
PRIVATE int pf_id=-1;
#ifdef _OPENMP
#pragma omp threadprivate(id, pf_id)
#endif
/*
#################################
# PRIVATE FUNCTION DECLARATIONS #
#################################
*/
PRIVATE vrna_param_t *get_scaled_params(vrna_md_t *md);
PRIVATE vrna_exp_param_t *get_scaled_exp_params(vrna_md_t *md, double pfs);
PRIVATE vrna_exp_param_t *get_exp_params_ali(vrna_md_t *md, unsigned int n_seq, double pfs);
PRIVATE void rescale_params(vrna_fold_compound_t *vc);
/*
#################################
# BEGIN OF FUNCTION DEFINITIONS #
#################################
*/
PUBLIC vrna_param_t *
vrna_params(vrna_md_t *md){
if(md){
return get_scaled_params(md);
} else {
vrna_md_t md;
vrna_md_set_default(&md);
return get_scaled_params(&md);
}
}
PUBLIC vrna_exp_param_t *
vrna_exp_params(vrna_md_t *md){
if(md){
return get_scaled_exp_params(md, -1.);
} else {
vrna_md_t md;
vrna_md_set_default(&md);
return get_scaled_exp_params(&md, -1.);
}
}
PUBLIC vrna_exp_param_t *
vrna_exp_params_comparative(unsigned int n_seq, vrna_md_t *md){
if(md){
return get_exp_params_ali(md, n_seq, -1.);
} else {
vrna_md_t md;
vrna_md_set_default(&md);
return get_exp_params_ali(&md, n_seq, -1.);
}
}
PUBLIC vrna_param_t *
vrna_params_copy(vrna_param_t *par){
vrna_param_t *copy = NULL;
if(par){
copy = (vrna_param_t *) vrna_alloc(sizeof(vrna_param_t));
memcpy(copy, par, sizeof(vrna_param_t));
}
return copy;
}
PUBLIC vrna_exp_param_t *
vrna_exp_params_copy(vrna_exp_param_t *par){
vrna_exp_param_t *copy = NULL;
if(par){
copy = (vrna_exp_param_t *) vrna_alloc(sizeof(vrna_exp_param_t));
memcpy(copy, par, sizeof(vrna_exp_param_t));
}
return copy;
}
PUBLIC void
vrna_params_subst( vrna_fold_compound_t *vc,
vrna_param_t *parameters){
if(vc){
if(vc->params)
free(vc->params);
if(parameters){
vc->params = vrna_params_copy(parameters);
} else {
switch(vc->type){
case VRNA_FC_TYPE_SINGLE: /* fall through */
case VRNA_FC_TYPE_COMPARATIVE: vc->params = vrna_params(NULL);
break;
default: break;
}
}
}
}
PUBLIC void
vrna_params_reset(vrna_fold_compound_t *vc,
vrna_md_t *md_p){
if(vc){
switch(vc->type){
case VRNA_FC_TYPE_SINGLE: /* fall through */
case VRNA_FC_TYPE_COMPARATIVE: if(vc->params)
free(vc->params);
vc->params = vrna_params(md_p);
break;
default: break;
}
}
}
PUBLIC void
vrna_exp_params_reset(vrna_fold_compound_t *vc,
vrna_md_t *md_p){
if(vc){
switch(vc->type){
case VRNA_FC_TYPE_SINGLE: /* fall through */
case VRNA_FC_TYPE_COMPARATIVE: if(vc->exp_params)
free(vc->exp_params);
vc->exp_params = vrna_exp_params(md_p);
break;
default: break;
}
}
}
PUBLIC void
vrna_exp_params_subst(vrna_fold_compound_t *vc,
vrna_exp_param_t *params){
if(vc){
if(vc->exp_params)
free(vc->exp_params);
if(params){
vc->exp_params = vrna_exp_params_copy(params);
} else {
switch(vc->type){
case VRNA_FC_TYPE_SINGLE: vc->exp_params = vrna_exp_params(NULL);
if(vc->cutpoint > 0)
vc->exp_params->model_details.min_loop_size = 0;
break;
case VRNA_FC_TYPE_COMPARATIVE: vc->exp_params = vrna_exp_params_comparative(vc->n_seq, NULL);
break;
default: break;
}
}
/* fill additional helper arrays for scaling etc. */
vrna_exp_params_rescale(vc, NULL);
}
}
PUBLIC void
vrna_exp_params_rescale(vrna_fold_compound_t *vc,
double *mfe){
vrna_exp_param_t *pf;
double kT;
vrna_md_t *md;
if(vc){
if(!vc->exp_params){
switch(vc->type){
case VRNA_FC_TYPE_SINGLE:
vc->exp_params = vrna_exp_params(&(vc->params->model_details));
break;
case VRNA_FC_TYPE_COMPARATIVE:
vc->exp_params = vrna_exp_params_comparative(vc->n_seq, &(vc->params->model_details));
break;
}
}
pf = vc->exp_params;
if(pf){
kT = pf->kT;
md = &(pf->model_details);
if(vc->type == VRNA_FC_TYPE_COMPARATIVE)
kT /= vc->n_seq;
if(mfe){
kT /= 1000.;
pf->pf_scale = exp(-(md->sfact * *mfe)/ kT / vc->length);
} else if(pf->pf_scale < 1.){ /* mean energy for random sequences: 184.3*length cal */
pf->pf_scale = exp(-(-185+(pf->temperature-37.)*7.27)/kT);
}
if(pf->pf_scale < 1.)
pf->pf_scale = 1.;
rescale_params(vc);
}
}
}
/*
#####################################
# BEGIN OF STATIC HELPER FUNCTIONS #
#####################################
*/
PRIVATE vrna_param_t *
get_scaled_params(vrna_md_t *md){
unsigned int i,j,k,l;
double tempf;
vrna_param_t *params;
params = (vrna_param_t *)vrna_alloc(sizeof(vrna_param_t));
params->model_details = *md; /* copy over the model details */
params->temperature = md->temperature;
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;
}
PRIVATE vrna_exp_param_t *
get_scaled_exp_params(vrna_md_t *md,
double pfs){
unsigned int i, j, k, l;
double kT, TT;
double GT;
vrna_exp_param_t *pf;
pf = (vrna_exp_param_t *)vrna_alloc(sizeof(vrna_exp_param_t));
pf->model_details = *md;
pf->temperature = md->temperature;
pf->alpha = md->betaScale;
pf->kT = kT = md->betaScale * (md->temperature + K0) * GASCONST; /* kT in cal/mol */
pf->pf_scale = pfs;
TT = (md->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) * 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;
}
PRIVATE vrna_exp_param_t *
get_exp_params_ali( vrna_md_t *md,
unsigned int n_seq,
double pfs){
/* scale energy parameters and pre-calculate Boltzmann weights */
unsigned int i, j, k, l;
double kTn, TT;
double GT;
vrna_exp_param_t *pf;
pf = (vrna_exp_param_t *)vrna_alloc(sizeof(vrna_exp_param_t));
pf->model_details = *md;
pf->alpha = md->betaScale;
pf->temperature = md->temperature;
pf->pf_scale = pfs;
pf->kT = kTn = ((double)n_seq)*md->betaScale*(md->temperature+K0)*GASCONST; /* kT in cal/mol */
TT = (md->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;
}
PRIVATE void
rescale_params(vrna_fold_compound_t *vc){
int i;
vrna_exp_param_t *pf = vc->exp_params;
vrna_mx_pf_t *m = vc->exp_matrices;
if(m && pf){
m->scale[0] = 1.;
m->scale[1] = (FLT_OR_DBL)(1./pf->pf_scale);
m->expMLbase[0] = 1;
m->expMLbase[1] = (FLT_OR_DBL)(pf->expMLbase / pf->pf_scale);
for (i=2; i<=vc->length; i++) {
m->scale[i] = m->scale[i/2]*m->scale[i-(i/2)];
m->expMLbase[i] = (FLT_OR_DBL)pow(pf->expMLbase, (double)i) * m->scale[i];
}
}
}
#ifdef VRNA_BACKWARD_COMPAT
/*###########################################*/
/*# deprecated functions below #*/
/*###########################################*/
PUBLIC vrna_param_t *
scale_parameters(void){
vrna_md_t md;
set_model_details(&md);
return vrna_params(&md);
}
PUBLIC vrna_param_t *
get_scaled_parameters(double temp,
vrna_md_t md){
md.temperature = temp;
return get_scaled_params(&md);
}
PUBLIC vrna_exp_param_t *
get_boltzmann_factors(double temp,
double betaScale,
vrna_md_t md,
double pfs){
md.temperature = temp;
md.betaScale = betaScale;
pf_scale = pfs;
return get_scaled_exp_params(&md, pfs);
}
PUBLIC vrna_exp_param_t *
get_scaled_pf_parameters(void){
vrna_md_t md;
vrna_exp_param_t *pf;
set_model_details(&md);
pf = vrna_exp_params(&md);
pf->pf_scale = pf_scale;
return pf;
}
PUBLIC vrna_exp_param_t *
get_boltzmann_factors_ali(unsigned int n_seq,
double temp,
double betaScale,
vrna_md_t md,
double pfs){
md.temperature = temp;
md.betaScale = betaScale;
pf_scale = pfs;
return get_exp_params_ali(&md, n_seq, pfs);
}
PUBLIC vrna_exp_param_t *
get_scaled_alipf_parameters(unsigned int n_seq){
vrna_md_t md;
set_model_details(&md);
return get_exp_params_ali(&md, n_seq, pf_scale);
}
PUBLIC vrna_exp_param_t *
get_boltzmann_factor_copy(vrna_exp_param_t *par){
return vrna_exp_params_copy(par);
}
PUBLIC vrna_param_t *get_parameter_copy(vrna_param_t *par){
return vrna_params_copy(par);
}
PUBLIC vrna_param_t *copy_parameters(void){
vrna_param_t *copy;
if (p.id != id){
vrna_md_t md;
set_model_details(&md);
return vrna_params(&md);
} else {
copy = (vrna_param_t *) vrna_alloc(sizeof(vrna_param_t));
memcpy(copy, &p, sizeof(vrna_param_t));
}
return copy;
}
PUBLIC vrna_param_t *set_parameters(vrna_param_t *dest){
memcpy(&p, dest, sizeof(vrna_param_t));
return &p;
}
PUBLIC vrna_exp_param_t *copy_pf_param(void){
vrna_exp_param_t *copy;
if (pf.id != pf_id){
vrna_md_t md;
set_model_details(&md);
copy = vrna_exp_params(&md);
copy->pf_scale = pf_scale;
return copy;
}
else{
copy = (vrna_exp_param_t *) vrna_alloc(sizeof(vrna_exp_param_t));
memcpy(copy, &pf, sizeof(vrna_exp_param_t));
}
return copy;
}
PUBLIC vrna_exp_param_t *set_pf_param(vrna_param_t *dest){
memcpy(&pf, dest, sizeof(vrna_exp_param_t));
return &pf;
}
PUBLIC vrna_exp_param_t *scale_pf_parameters(void){
vrna_md_t md;
vrna_exp_param_t *pf;
set_model_details(&md);
pf = vrna_exp_params(&md);
pf->pf_scale = pf_scale;
return pf;
}
#endif