PRIVATE void heat_capacity(char *string, float T_min, float T_max,
float h, int m)
{
int length, i;
char *structure;
float hc, kT, min_en;
length = (int) strlen(string);
do_backtrack = 0;
temperature = T_min -m*h;
/* initialize_fold(length); <- obsolete */
structure = (char *) vrna_alloc((unsigned) length+1);
min_en = fold(string, structure);
free(structure); free_arrays();
kT = (temperature+K0)*GASCONST/1000; /* in kcal */
pf_scale = exp(-(1.07*min_en)/kT/length );
/* init_pf_fold(length); <- obsolete */
vrna_exp_param_t *pf_parameters = NULL;
vrna_md_t md;
set_model_details(&md);
pf_parameters = get_boltzmann_factors(temperature, 1.0, md, pf_scale);
update_pf_params_par(length, pf_parameters);
for (i=0; i<2*m+1; i++) {
F[i] = pf_fold_par(string, NULL, pf_parameters, 0, 0, 0); /* T_min -2h */
md.temperature = temperature += h;
kT = (temperature+K0)*GASCONST/1000;
pf_scale=exp(-(F[i]/length +h*0.00727)/kT); /* try to extrapolate F */
free(pf_parameters);
pf_parameters = get_boltzmann_factors(temperature, 1.0, md, pf_scale);
update_pf_params_par(length, pf_parameters);
}
while (temperature <= (T_max+m*h+h)) {
hc = - ddiff(F,h,m)* (temperature +K0 - m*h -h);
printf("%g %g\n", (temperature-m*h-h), hc);
for (i=0; i<2*m; i++)
F[i] = F[i+1];
F[2*m] = pf_fold_par(string, NULL, pf_parameters, 0, 0, 0);
/* printf("%g\n", F[2*m]);*/
temperature += h;
kT = (temperature+K0)*GASCONST/1000;
pf_scale=exp(-(F[i]/length +h*0.00727)/kT);
free(pf_parameters);
md.temperature = temperature;
pf_parameters = get_boltzmann_factors(temperature, 1.0, md, pf_scale);
update_pf_params_par(length, pf_parameters);
}
free_pf_arrays();
}
float ffiwrap_pf_circ_fold_constrained (const char *sequence, char *structure, int constrained)
{
return pf_fold_par (sequence, structure, 0, 1, constrained, 1);
}
double score_seq( int s, char* seq, int ip )
{
double score = 0.0;
if( !is_legal( seq ) ) return score;
int length = strlen( seq );
int* ix = get_iindx( length );
double betaScale = 1.0;
double kT = ( betaScale*( ( temperature+K0 )*GASCONST ) )/1000.; /* in Kcal */
model_detailsT md;
set_model_details( &md );
char* secstr = strdup( seq );
secstr[0] = 0;
fold_constrained = 0;
paramT* params = get_scaled_parameters( temperature, md );
double min_en = fold_par( seq, secstr, params, fold_constrained, 0 );
if( strncmp( secstr + ip,
cnf->hairpin_ss, strlen( cnf->hairpin_ss ) ) != 0
|| strcmp( secstr + length - strlen( cnf->tail3p_ss ),
cnf->tail3p_ss ) != 0 ) {
free( params );
free( secstr );
free( ix );
return score;
}
if( !is_legal_pair_content( seq, secstr, ip ) ) {
free( params );
free( secstr );
free( ix );
return score;
}
#pragma omp atomic update
num_scored++;
double pf_scale = exp( -( 1.07*min_en )/kT/length );
pf_paramT* pf_params = get_boltzmann_factors( temperature, betaScale, md, pf_scale );
// Either patch fold_vars.h by inserting following at line 166
//
// #ifdef _OPENMP
// #pragma omp threadprivate(iindx)
// #endif
//
// or uncomment this pragma below
//
// #pragma omp critical(pf_fold)
double e = pf_fold_par( seq, NULL, pf_params, 1, fold_constrained, 0 );
FLT_OR_DBL* ppm = export_bppm();
#define pr_ij(i,j) (i == j? 0.0 : (i < j ? ppm[ix[i]-j] : ppm[ix[j]-i]))
score = cnf->s_max;
int i, o;
for( i = 1; i <= length; i++ ) {
for( o = 1; o <= strlen( cnf->hairpin_ss ); o++ ) {
int j = ip + o;
double v = pr_ij( i, j );
score -= v * ( 1.0 - v );
}
}
score *= cnf->s_scale;
free( pf_params );
free( params );
free( secstr );
free( ix );
return score;
}
