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;
}
void main()
{
char *seq1="CGCAGGGAUACCCGCG", *seq2="GCGCCCAUAGGGACGC",
*struct1,* struct2,* xstruc;
float e1, e2, tree_dist, string_dist, profile_dist, kT;
Tree *T1, *T2;
swString *S1, *S2;
float *pf1, *pf2;
FLT_OR_DBL *bppm;
/* fold at 30C instead of the default 37C */
temperature = 30.; /* must be set *before* initializing */
/* allocate memory for structure and fold */
struct1 = (char* ) space(sizeof(char)*(strlen(seq1)+1));
e1 = fold(seq1, struct1);
struct2 = (char* ) space(sizeof(char)*(strlen(seq2)+1));
e2 = fold(seq2, struct2);
free_arrays(); /* free arrays used in fold() */
/* produce tree and string representations for comparison */
xstruc = expand_Full(struct1);
T1 = make_tree(xstruc);
S1 = Make_swString(xstruc);
free(xstruc);
xstruc = expand_Full(struct2);
T2 = make_tree(xstruc);
S2 = Make_swString(xstruc);
free(xstruc);
/* calculate tree edit distance and aligned structures with gaps */
edit_backtrack = 1;
tree_dist = tree_edit_distance(T1, T2);
free_tree(T1); free_tree(T2);
unexpand_aligned_F(aligned_line);
printf("%s\n%s %3.2f\n", aligned_line[0], aligned_line[1], tree_dist);
/* same thing using string edit (alignment) distance */
string_dist = string_edit_distance(S1, S2);
free(S1); free(S2);
printf("%s mfe=%5.2f\n%s mfe=%5.2f dist=%3.2f\n",
aligned_line[0], e1, aligned_line[1], e2, string_dist);
/* for longer sequences one should also set a scaling factor for
partition function folding, e.g: */
kT = (temperature+273.15)*1.98717/1000.; /* kT in kcal/mol */
pf_scale = exp(-e1/kT/strlen(seq1));
/* calculate partition function and base pair probabilities */
e1 = pf_fold(seq1, struct1);
/* get the base pair probability matrix for the previous run of pf_fold() */
bppm = export_bppm();
pf1 = Make_bp_profile_bppm(bppm, strlen(seq1));
e2 = pf_fold(seq2, struct2);
/* get the base pair probability matrix for the previous run of pf_fold() */
bppm = export_bppm();
pf2 = Make_bp_profile_bppm(bppm, strlen(seq2));
free_pf_arrays(); /* free space allocated for pf_fold() */
profile_dist = profile_edit_distance(pf1, pf2);
printf("%s free energy=%5.2f\n%s free energy=%5.2f dist=%3.2f\n",
aligned_line[0], e1, aligned_line[1], e2, profile_dist);
free_profile(pf1); free_profile(pf2);
}