float fold(const char *string, char *structure) {
int i, length, energy, bonus=0, bonus_cnt=0;
circ = 0;
length = (int) strlen(string);
if (length>init_length) initialize_fold(length);
if (fabs(P->temperature - temperature)>1e-6) update_fold_params();
encode_seq(string);
BP = (int *)space(sizeof(int)*(length+2));
make_ptypes(S, structure);
energy = fill_arrays(string);
backtrack(string, 0);
#ifdef PAREN
parenthesis_structure(structure, length);
#else
letter_structure(structure, length);
#endif
/* check constraints */
for(i=1;i<=length;i++) {
if((BP[i]<0)&&(BP[i]>-4)) {
bonus_cnt++;
if((BP[i]==-3)&&(structure[i-1]==')')) bonus++;
if((BP[i]==-2)&&(structure[i-1]=='(')) bonus++;
if((BP[i]==-1)&&(structure[i-1]!='.')) bonus++;
}
if(BP[i]>i) {
int l;
bonus_cnt++;
for(l=1; l<=base_pair[0].i; l++)
if((i==base_pair[l].i)&&(BP[i]==base_pair[l].j)) bonus++;
}
}
if (bonus_cnt>bonus) fprintf(stderr,"\ncould not enforce all constraints\n");
bonus*=BONUS;
free(S); free(S1); free(BP);
energy += bonus; /*remove bonus energies from result */
if (backtrack_type=='C')
return (float) c[indx[length]+1]/100.;
else if (backtrack_type=='M')
return (float) fML[indx[length]+1]/100.;
else
return (float) energy/100.;
}
PUBLIC float alifold(const char **strings, char *structure){
int length, energy, s, n_seq;
circular = 0;
length = (int) strlen(strings[0]);
#ifdef _OPENMP
/* always init everything since all global static variables are uninitialized when entering a thread */
init_alifold(length);
#else
if (length>init_length) init_alifold(length);
#endif
if (fabs(P->temperature - temperature)>1e-6) update_alifold_params();
for (s=0; strings[s]!=NULL; s++);
n_seq = s;
alloc_sequence_arrays(strings, &S, &S5, &S3, &a2s, &Ss, circular);
make_pscores((const short **) S, strings, n_seq, structure);
energy = fill_arrays((const char **)strings);
backtrack((const char **)strings, 0);
#ifdef PAREN
parenthesis_structure(structure, base_pair2, length);
#else
letter_structure(structure, base_pair2, length);
#endif
/*
* Backward compatibility:
* This block may be removed if deprecated functions
* relying on the global variable "base_pair" vanishs from within the package!
*/
base_pair = base_pair2;
/*
{
if(base_pair) free(base_pair);
base_pair = (bondT *)space(sizeof(bondT) * (1+length/2));
memcpy(base_pair, base_pair2, sizeof(bondT) * (1+length/2));
}
*/
free_sequence_arrays(n_seq, &S, &S5, &S3, &a2s, &Ss);
if (backtrack_type=='C')
return (float) c[indx[length]+1]/(n_seq*100.);
else if (backtrack_type=='M')
return (float) fML[indx[length]+1]/(n_seq*100.);
else
return (float) f5[length]/(n_seq*100.);
}
