PUBLIC duplexT *duplex_subopt(const char *s1, const char *s2, int delta, int w) {
int i,j, n1, n2, thresh, E, n_subopt=0, n_max;
char *struc;
duplexT mfe;
duplexT *subopt;
n_max=16;
subopt = (duplexT *) space(n_max*sizeof(duplexT));
delay_free=1;
mfe = duplexfold(s1, s2);
free(mfe.structure);
thresh = (int) mfe.energy*100+0.1 + delta;
n1 = strlen(s1); n2=strlen(s2);
for (i=n1; i>0; i--) {
for (j=1; j<=n2; j++) {
int type;
type = pair[S2[j]][S1[i]];
if (!type) continue;
E = c[i][j];
if (i<n1) E += P->dangle3[type][SS1[i+1]];
if (j>1) E += P->dangle5[type][SS2[j-1]];
if (type>2) E += P->TerminalAU;
if (E<=thresh) {
struc = backtrack(i,j);
#if 0
int l1;
l1 = strchr(struc, '&')-struc;
printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", struc, i+2-l1, i+1,
j-1, j+strlen(struc)-l1-3, E*0.01);
#endif
if (n_subopt+1>=n_max) {
n_max *= 2;
subopt = (duplexT *) xrealloc(subopt, n_max*sizeof(duplexT));
}
subopt[n_subopt].i = MIN2(i+1,n1);
subopt[n_subopt].j = MAX2(j-1,1);
subopt[n_subopt].energy = E * 0.01;
subopt[n_subopt++].structure = struc;
}
}
}
for (i=1; i<=n1; i++) free(c[i]);
free(c);
free(S1); free(S2); free(SS1); free(SS2);
delay_free=0;
if (subopt_sorted) qsort(subopt, n_subopt, sizeof(duplexT), compare);
subopt[n_subopt].i =0;
subopt[n_subopt].j =0;
subopt[n_subopt].structure = NULL;
return subopt;
}
void ffiwrap_duplexfold (duplexT * x, char * linp, char * rinp)
{
*x = duplexfold (linp, rinp);
return;
}
int main(int argc, char *argv[])
{
char *s1, *s2, *line;
char fname[13];
char *ParamFile=NULL;
char *ns_bases=NULL, *c;
int i, l, sym, r;
double deltaf;
double kT, sfact=1.07;
int pf=0, istty, delta=-1;
int noconv=0;
for (i=1; i<argc; i++) {
if (argv[i][0]=='-')
switch ( argv[i][1] )
{
case 'T': if (argv[i][2]!='\0') usage();
if(i==argc-1) usage();
r=sscanf(argv[++i], "%lf", &temperature);
if (!r) usage();
break;
case 'p':
fprintf(stderr, "partition function folding not yet implemented\n");
usage();
pf=1;
if (argv[i][2]!='\0')
(void) sscanf(argv[i]+2, "%d", &do_backtrack);
break;
case 'n':
if ( strcmp(argv[i], "-noGU")==0) noGU=1;
if ( strcmp(argv[i], "-noCloseGU")==0) no_closingGU=1;
if ( strcmp(argv[i], "-noLP")==0) noLonelyPairs=1;
if ( strcmp(argv[i], "-nsp") ==0) {
if (i==argc-1) usage();
ns_bases = argv[++i];
}
if ( strcmp(argv[i], "-noconv")==0) noconv=1;
break;
case '4':
tetra_loop=0;
break;
case 'e':
if (i>=argc-1) usage();
r=sscanf(argv[++i], "%lf", &deltaf);
if (r!=1) usage();
delta = (int) (0.1+deltaf*100);
break;
case 's': subopt_sorted=1;
break;
case 'd': dangles=0;
if (argv[i][2]!='\0') {
r=sscanf(argv[i]+2, "%d", &dangles);
if (r!=1) usage();
}
break;
case 'P':
if (i==argc-1) usage();
ParamFile = argv[++i];
break;
default: usage();
}
}
if (ParamFile != NULL)
read_parameter_file(ParamFile);
if (ns_bases != NULL) {
nonstandards = space(33);
c=ns_bases;
i=sym=0;
if (*c=='-') {
sym=1; c++;
}
while (*c!='\0') {
if (*c!=',') {
nonstandards[i++]=*c++;
nonstandards[i++]=*c;
if ((sym)&&(*c!=*(c-1))) {
nonstandards[i++]=*c;
nonstandards[i++]=*(c-1);
}
}
c++;
}
}
istty = isatty(fileno(stdout))&&isatty(fileno(stdin));
do { /* main loop: continue until end of file */
duplexT mfe, *subopt;
if (istty) {
printf("\nInput two sequences (one line each); @ to quit\n");
printf("%s\n", scale);
}
fname[0]='\0';
if ((line = get_line(stdin))==NULL) break;
/* skip empty lines, comment lines, name lines */
while (line && ((*line=='*')||(*line=='\0')||(*line=='>'))) {
printf("%s\n", line); free(line);
if ((line = get_line(stdin))==NULL) break;
}
if ((line ==NULL) || (strcmp(line, "@") == 0)) break;
s1 = (char *) space(strlen(line)+1);
(void) sscanf(line,"%s",s1); free(line);
if ((line = get_line(stdin))==NULL) break;
/* skip comment lines and get filenames */
while ((*line=='*')||(*line=='\0')||(*line=='>')) {
printf("%s\n", line); free(line);
if ((line = get_line(stdin))==NULL) break;
}
if ((line ==NULL) || (strcmp(line, "@") == 0)) break;
s2 = (char *) space(strlen(line)+1);
(void) sscanf(line,"%s",s2); free(line);
for (l = 0; l < strlen(s1); l++) {
s1[l] = toupper(s1[l]);
if (!noconv && s1[l] == 'T') s1[l] = 'U';
}
for (l = 0; l < strlen(s2); l++) {
s2[l] = toupper(s2[l]);
if (!noconv && s2[l] == 'T') s2[l] = 'U';
}
if (istty)
printf("lengths = %d,%d\n", strlen(s1), strlen(s2));
/* initialize_fold(length); */
update_fold_params();
if (delta>=0) {
duplexT *sub;
subopt = duplex_subopt(s1, s2, delta, 5);
for (sub=subopt; sub->i >0; sub++) {
print_struc(sub);
free(sub->structure);
}
free(subopt);
}
else {
mfe = duplexfold(s1, s2);
print_struc(&mfe);
free(mfe.structure);
}
(void) fflush(stdout);
(void) fflush(stdout);
free(s1); free(s2);
} while (1);
return 0;
}
PRIVATE void print_interaction(interact *Int, char *s1, char *s2, pu_contrib *p_c, pu_contrib *p_c2, int w, int incr3, int incr5) {
char *i_long,*i_short;
int i,len, l_l, l_s, len1, end5, end3, i_min, j_min, l1, add_a, add_b,nix_up;
double p_c_S;
double G_min,Gi_min,Gul, G_sum, Gus, diff;
duplexT mfe;
char *struc;
G_min = Int->Gikjl;
Gi_min = Int->Gikjl_wo;
len1 = Int->length;
len=strlen(s1)+strlen(s2);
/* use duplexfold() to fold the interaction site */
l_l = (Int->i-Int->k+1);
i_long = (char*)space(sizeof(char)*(l_l+1));
l_s = (Int->l-Int->j+1);
i_short = (char*)space(sizeof(char)*(l_s+1));
strncpy(i_long,&s1[Int->k-1],l_l);
i_long[l_l] = '\0';
strncpy(i_short,&s2[Int->j-1],l_s);
i_short[l_s] = '\0';
mfe = duplexfold(i_long,i_short);
i_min = mfe.i;
j_min = mfe.j ;
l1 = strchr(mfe.structure, '&')-mfe.structure;
/* printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", mfe.structure, i_min+1-l1,
i_min, j_min, j_min+strlen(mfe.structure)-l1-2, mfe.energy ); */
/* structure by duplexfold is shorter than structure by RNAup:*/
add_a = add_b = 0; /* length difference in longer / shorter sequence*/
nix_up = 0;
if(((i_min+1-l1) - i_min) != ( Int->k - Int->i)) {
add_a = Int->i - Int->k + 2;
}
if(((j_min+strlen(mfe.structure)-l1-2) - j_min) != (Int->l - Int->j)) {
add_b = Int->l - Int->j +2;
}
/* printf("add_a %d add_b %d\n",add_a,add_b); */
if( add_a || add_b ) {
nix_up = 1;
if(add_a && add_b == 0) add_b = Int->l - Int->j + 2;
if(add_a == 0 && add_b) add_a = Int->i - Int->k + 2;
struc = (char*)space(sizeof(char)*(add_a+add_b+3));
for(i=0;i<(add_a+add_b-1);i++) {
if(i != l_l) struc[i] = '.';
if(i == l_l) struc[i] = '&';
}
struc[i] = '\0';
} else {
l1=strlen(mfe.structure);
struc = (char*)space(sizeof(char)*(l1+1));
strcpy(struc,mfe.structure);
}
end5 = MAX(1,Int->k-incr5);
end3 = MIN(MIN(l_l-1+incr3,w+incr3+incr5),len1);
p_c_S = p_c->H[end5][end3]+p_c->I[end5][end3]+p_c->M[end5][end3]+p_c->E[end5][end3];
Gul = -RT*log(p_c_S);
if (p_c2 == NULL) {
G_sum = Gi_min + Gul;
/* printf("dG = dGint + dGu_l\n"); */
printf("%s %3d,%-3d : %3d,%-3d (%.2f = %.2f + %.2f)\n",
struc, Int->k, Int->i, Int->j, Int->l, G_min, Gi_min, Gul);
printf("%s&%s\n",i_long,i_short);
} else {
p_c_S = p_c2->H[Int->j][(Int->l)-(Int->j)]+
p_c2->I[Int->j][(Int->l)-(Int->j)]+
p_c2->M[Int->j][(Int->l)-(Int->j)]+
p_c2->E[Int->j][(Int->l)-(Int->j)];
Gus = -RT*log(p_c_S);
G_sum = Gi_min + Gul +Gus;
/* printf("dG = dGint + dGu_l + dGu_s\n"); */
printf("%s %3d,%-3d : %3d,%-3d (%.2f = %.2f + %.2f + %.2f)\n",
struc, Int->k, Int->i, Int->j, Int->l, G_min, Gi_min, Gul, Gus);
printf("%s&%s\n",i_long,i_short);
}
if (!EQUAL(G_min,G_sum)) {
printf("ERROR\n");
diff = fabs((G_min)-(G_sum));
printf("diff %.18f\n",diff);
}
if(nix_up) fprintf(stderr,"RNAduplex structure doesn't match any structure of RNAup structure ensemble\n");
free(i_long);
free(i_short);
free(mfe.structure);
free(struc);
}
