int main(int argc, char *argv[])
{
char *string/*, *line*/;
char *structure=NULL, *cstruc=NULL;
/*char fname[13], ffname[20], gfname[20];*/
/*char *ParamFile=NULL;*/
char *ns_bases=NULL, *c;
int i, length, l, sym/*, r*/;
double energy, min_en;
double kT, sfact=1.07;
int pf=0, noPS=0, istty;
int noconv=0;
int circ=0;
AjPSeq seq = NULL;
AjPFile confile = NULL;
AjPFile paramfile = NULL;
AjPFile outf = NULL;
AjPFile essfile = NULL;
AjPFile dotfilea = NULL;
AjPFile dotfileb = NULL;
AjPStr seqstring = NULL;
AjPStr constring = NULL;
AjPStr seqname = NULL;
float eT = 0.;
AjBool eGU;
AjBool ecirc = ajFalse;
AjBool eclose;
AjBool lonely;
AjBool convert;
AjPStr ensbases = NULL;
AjBool etloop;
AjPStr eenergy = NULL;
char ewt = '\0';
float escale = 0.;
AjPStr edangles = NULL;
char edangle = '\0';
ajint len;
embInitPV("vrnafold",argc,argv,"VIENNA",VERSION);
seqstring = ajStrNew();
constring = ajStrNew();
seqname = ajStrNew();
seq = ajAcdGetSeq("sequence");
confile = ajAcdGetInfile("constraintfile");
paramfile = ajAcdGetInfile("paramfile");
eT = ajAcdGetFloat("temperature");
ecirc = ajAcdGetBoolean("circular");
eGU = ajAcdGetBoolean("gu");
eclose = ajAcdGetBoolean("closegu");
lonely = ajAcdGetBoolean("lp");
convert = ajAcdGetBoolean("convert");
ensbases = ajAcdGetString("nsbases");
etloop = ajAcdGetBoolean("tetraloop");
eenergy = ajAcdGetListSingle("energy");
escale = ajAcdGetFloat("scale");
edangles = ajAcdGetListSingle("dangles");
outf = ajAcdGetOutfile("outfile");
essfile = ajAcdGetOutfile("ssoutfile");
/*
dotfilea = ajAcdGetOutfile("adotoutfile");
dotfileb = ajAcdGetOutfile("bdotoutfile");
*/
do_backtrack = 2;
pf = 0;
string = NULL;
istty = 0;
temperature = (double) eT;
circ = !!ecirc;
noGU = (eGU) ? 0 : 1;
no_closingGU = (eclose) ? 0 : 1;
noLonelyPairs = (lonely) ? 0 : 1;
noconv = (convert) ? 0 : 1;
ns_bases = (ajStrGetLen(ensbases)) ? MAJSTRGETPTR(ensbases) : NULL;
tetra_loop = !!etloop;
ewt = *ajStrGetPtr(eenergy);
if(ewt == '0')
energy_set = 0;
else if(ewt == '1')
energy_set = 1;
else if(ewt == '2')
energy_set = 2;
sfact = (double) escale;
edangle = *ajStrGetPtr(edangles);
if(edangle == '0')
dangles = 0;
else if(edangle == '1')
dangles = 1;
else if(edangle == '2')
dangles = 2;
else if(edangle == '3')
dangles = 3;
if(circ && noLonelyPairs)
{
ajWarn("Depending on the origin of the circular sequence\n"
"some structures may be missed when using -noLP\nTry "
"rotating your sequence a few times\n");
}
if(paramfile)
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++;
}
}
if(confile)
vienna_GetConstraints(confile,&constring);
string = NULL;
structure = NULL;
length = ajSeqGetLen(seq);
string = (char *) space(length+1);
strcpy(string,ajSeqGetSeqC(seq));
len = ajStrGetLen(constring);
structure = (char *) space(length+1);
if(len)
{
fold_constrained = 1;
strcpy(structure,ajStrGetPtr(constring));
}
for (l = 0; l < length; l++) {
string[l] = toupper(string[l]);
if (!noconv && string[l] == 'T') string[l] = 'U';
}
/* initialize_fold(length); */
if (circ)
min_en = circfold(string, structure);
else
min_en = fold(string, structure);
ajFmtPrintF(outf,"%s\n%s", string, structure);
if (istty)
printf("\n minimum free energy = %6.2f kcal/mol\n", min_en);
else
ajFmtPrintF(outf," (%6.2f)\n", min_en);
if (!noPS)
{
if (length<2000)
(void) PS_rna_plot(string, structure, essfile);
else
ajWarn("Structure too long, not doing xy_plot\n");
}
if (length>=2000) free_arrays();
if (pf)
{
char *pf_struc;
pf_struc = (char *) space((unsigned) length+1);
if (dangles==1)
{
dangles=2; /* recompute with dangles as in pf_fold() */
min_en = (circ) ? energy_of_circ_struct(string, structure) :
energy_of_struct(string, structure);
dangles=1;
}
kT = (temperature+273.15)*1.98717/1000.; /* in Kcal */
pf_scale = exp(-(sfact*min_en)/kT/length);
if (length>2000)
ajWarn("scaling factor %f\n", pf_scale);
(circ) ? init_pf_circ_fold(length) : init_pf_fold(length);
if (cstruc!=NULL)
strncpy(pf_struc, cstruc, length+1);
energy = (circ) ? pf_circ_fold(string, pf_struc) :
pf_fold(string, pf_struc);
if (do_backtrack)
{
ajFmtPrintF(outf,"%s", pf_struc);
ajFmtPrintF(outf," [%6.2f]\n", energy);
}
if ((istty)||(!do_backtrack))
ajFmtPrintF(outf," free energy of ensemble = %6.2f kcal/mol\n",
energy);
if (do_backtrack)
{
plist *pl1,*pl2;
char *cent;
double dist, cent_en;
cent = centroid(length, &dist);
cent_en = (circ) ? energy_of_circ_struct(string, cent) :
energy_of_struct(string, cent);
ajFmtPrintF(outf,"%s {%6.2f d=%.2f}\n", cent, cent_en, dist);
free(cent);
pl1 = make_plist(length, 1e-5);
pl2 = b2plist(structure);
(void) PS_dot_plot_list(string, dotfilea, pl1, pl2, "");
free(pl2);
if (do_backtrack==2)
{
pl2 = stackProb(1e-5);
PS_dot_plot_list(string, dotfileb, pl1, pl2,
"Probabilities for stacked pairs (i,j)(i+1,j-1)");
free(pl2);
}
free(pl1);
free(pf_struc);
}
ajFmtPrintF(outf," frequency of mfe structure in ensemble %g; ",
exp((energy-min_en)/kT));
if (do_backtrack)
ajFmtPrintF(outf,"ensemble diversity %-6.2f", mean_bp_dist(length));
ajFmtPrintF(outf,"\n");
free_pf_arrays();
}
if (cstruc!=NULL)
free(cstruc);
free(string);
free(structure);
ajStrDel(&seqstring);
ajStrDel(&constring);
ajStrDel(&seqname);
ajStrDel(&ensbases);
ajStrDel(&eenergy);
ajStrDel(&edangles);
ajSeqDel(&seq);
ajFileClose(&confile);
ajFileClose(¶mfile);
ajFileClose(&outf);
ajFileClose(&essfile);
/*
ajFileClose(&dotfilea);
ajFileClose(&dotfileb);
*/
if (length<2000) free_arrays();
embExit();
return 0;
}
int main(int argc, char *argv[])
{
char *string, *line;
char *structure=NULL, *cstruc=NULL;
char fname[13], ffname[20], gfname[20];
char *ParamFile=NULL;
char *ns_bases=NULL, *c;
int i, length, l, sym, r;
double energy, min_en;
double kT, sfact=1.07;
int pf=0, noPS=0, istty;
int noconv=0;
int circ=0;
do_backtrack = 1;
string=NULL;
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': 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], "-noPS")==0) noPS=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],"%d", &energy_set);
if (!r) usage();
break;
case 'C':
fold_constrained=1;
break;
case 'c':
if ( strcmp(argv[i], "-circ")==0) circ=1;
break;
case 'S':
if(i==argc-1) usage();
r=sscanf(argv[++i],"%lf", &sfact);
if (!r) usage();
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 (circ && noLonelyPairs)
fprintf(stderr, "warning, depending on the origin of the circular sequence, some structures may be missed when using -noLP\nTry rotating your sequence a few times\n");
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));
if ((fold_constrained)&&(istty)) {
printf("Input constraints using the following notation:\n");
printf("| : paired with another base\n");
printf(". : no constraint at all\n");
printf("x : base must not pair\n");
printf("< : base i is paired with a base j<i\n");
printf("> : base i is paired with a base j>i\n");
printf("matching brackets ( ): base i pairs base j\n");
}
do { /* main loop: continue until end of file */
if (istty) {
printf("\nInput string (upper or lower case); @ to quit\n");
printf("%s%s\n", scale1, scale2);
}
fname[0]='\0';
if ((line = get_line(stdin))==NULL) break;
/* skip comment lines and get filenames */
while ((*line=='*')||(*line=='\0')||(*line=='>')) {
if (*line=='>')
(void) sscanf(line, ">%12s", fname);
printf("%s\n", line);
free(line);
if ((line = get_line(stdin))==NULL) break;
}
if ((line ==NULL) || (strcmp(line, "@") == 0)) break;
string = (char *) space(strlen(line)+1);
(void) sscanf(line,"%s",string);
free(line);
length = (int) strlen(string);
structure = (char *) space((unsigned) length+1);
if (fold_constrained) {
cstruc = get_line(stdin);
if (cstruc!=NULL)
strncpy(structure, cstruc, length);
else
fprintf(stderr, "constraints missing\n");
}
for (l = 0; l < length; l++) {
string[l] = toupper(string[l]);
if (!noconv && string[l] == 'T') string[l] = 'U';
}
if (istty)
printf("length = %d\n", length);
/* initialize_fold(length); */
if (circ)
min_en = circfold(string, structure);
else
min_en = fold(string, structure);
printf("%s\n%s", string, structure);
if (istty)
printf("\n minimum free energy = %6.2f kcal/mol\n", min_en);
else
printf(" (%6.2f)\n", min_en);
(void) fflush(stdout);
if (fname[0]!='\0') {
strcpy(ffname, fname);
strcat(ffname, "_ss.ps");
strcpy(gfname, fname);
strcat(gfname, "_ss.g");
} else {
strcpy(ffname, "rna.ps");
strcpy(gfname, "rna.g");
}
if (!noPS) {
if (length<2000)
(void) PS_rna_plot(string, structure, ffname);
else
fprintf(stderr,"INFO: structure too long, not doing xy_plot\n");
}
if (length>2000) free_arrays();
if (pf) {
char *pf_struc;
pf_struc = (char *) space((unsigned) length+1);
if (dangles==1) {
dangles=2; /* recompute with dangles as in pf_fold() */
min_en = (circ) ? energy_of_circ_struct(string, structure) : energy_of_struct(string, structure);
dangles=1;
}
kT = (temperature+273.15)*1.98717/1000.; /* in Kcal */
pf_scale = exp(-(sfact*min_en)/kT/length);
if (length>2000) fprintf(stderr, "scaling factor %f\n", pf_scale);
(circ) ? init_pf_circ_fold(length) : init_pf_fold(length);
if (cstruc!=NULL)
strncpy(pf_struc, cstruc, length+1);
energy = (circ) ? pf_circ_fold(string, pf_struc) : pf_fold(string, pf_struc);
if (do_backtrack) {
printf("%s", pf_struc);
if (!istty) printf(" [%6.2f]\n", energy);
else printf("\n");
}
if ((istty)||(!do_backtrack))
printf(" free energy of ensemble = %6.2f kcal/mol\n", energy);
if (do_backtrack) {
plist *pl1,*pl2;
char *cent;
double dist, cent_en;
cent = centroid(length, &dist);
cent_en = (circ) ? energy_of_circ_struct(string, cent) :energy_of_struct(string, cent);
printf("%s {%6.2f d=%.2f}\n", cent, cent_en, dist);
free(cent);
if (fname[0]!='\0') {
strcpy(ffname, fname);
strcat(ffname, "_dp.ps");
} else strcpy(ffname, "dot.ps");
pl1 = make_plist(length, 1e-5);
pl2 = b2plist(structure);
(void) PS_dot_plot_list(string, ffname, pl1, pl2, "");
free(pl2);
if (do_backtrack==2) {
pl2 = stackProb(1e-5);
if (fname[0]!='\0') {
strcpy(ffname, fname);
strcat(ffname, "_dp2.ps");
} else strcpy(ffname, "dot2.ps");
PS_dot_plot_list(string, ffname, pl1, pl2,
"Probabilities for stacked pairs (i,j)(i+1,j-1)");
free(pl2);
}
free(pl1);
free(pf_struc);
}
printf(" frequency of mfe structure in ensemble %g; ",
exp((energy-min_en)/kT));
if (do_backtrack)
printf("ensemble diversity %-6.2f", mean_bp_dist(length));
printf("\n");
free_pf_arrays();
}
if (cstruc!=NULL) free(cstruc);
(void) fflush(stdout);
free(string);
free(structure);
} while (1);
return 0;
}