void initSeq(const char* param, const char* seq) {
int i; read_parameter_file(param);
c_P = get_scaled_parameters();
c_len = strlen(seq);
c_seq = malloc(c_len+1);
for (i=0; i<c_len; ++i) switch (seq[i]) {
case 'a': c_seq[i]=1; break;
case 'c': c_seq[i]=2; break;
case 'g': c_seq[i]=3; break;
case 'u': c_seq[i]=4; break;
default: exit(1);
}
}
PUBLIC paramT *scale_parameters(void){
model_detailsT md;
set_model_details(&md);
return get_scaled_parameters(temperature, md);
}
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;
}
