PRIVATE cofoldF do_partfunc(char *string, int length, int Switch, struct plist **tpr, struct plist **mfpl, pf_paramT *parameters){
/*compute mfe and partition function of dimere or monomer*/
char *Newstring;
char *tempstruc;
double min_en;
double sfact=1.07;
double kT;
pf_paramT *par;
FLT_OR_DBL *probs;
cofoldF X;
kT = parameters->kT/1000.;
switch (Switch)
{
case 1: /*monomer*/
cut_point=-1;
tempstruc = (char *) space((unsigned)length+1);
min_en = fold(string, tempstruc);
assign_plist_from_db(mfpl, tempstruc, 0.95);
free_arrays();
/*En=pf_fold(string, tempstruc);*/
/* init_co_pf_fold(length); <- obsolete */
par = get_boltzmann_factor_copy(parameters);
par->pf_scale = exp(-(sfact*min_en)/kT/(length));
X=co_pf_fold_par(string, tempstruc, par, 1, fold_constrained);
probs = export_co_bppm();
assign_plist_from_pr(tpr, probs, length, bppmThreshold);
free_co_pf_arrays();
free(tempstruc);
free(par);
break;
case 2: /*dimer*/
Newstring=(char *)space(sizeof(char)*(length*2+1));
strcat(Newstring,string);
strcat(Newstring,string);
cut_point=length+1;
tempstruc = (char *) space((unsigned)length*2+1);
min_en = cofold(Newstring, tempstruc);
assign_plist_from_db(mfpl, tempstruc, 0.95);
free_co_arrays();
/* init_co_pf_fold(2*length); <- obsolete */
par = get_boltzmann_factor_copy(parameters);
par->pf_scale =exp(-(sfact*min_en)/kT/(2*length));
X=co_pf_fold_par(Newstring, tempstruc, par, 1, fold_constrained);
probs = export_co_bppm();
assign_plist_from_pr(tpr, probs, 2*length, bppmThreshold);
free_co_pf_arrays();
free(Newstring);
free(tempstruc);
free(par);
break;
default:
printf("Error in get_partfunc\n, computing neither mono- nor dimere!\n");
exit (42);
}
return X;
}
PRIVATE cofoldF do_partfunc(char *string, int length, int Switch, struct plist **tpr, struct plist **mfpl) {
/*compute mfe and partition function of dimere or monomer*/
char *Newstring;
char *tempstruc;
double min_en;
double sfact=1.07;
double kT;
cofoldF X;
kT = (temperature+273.15)*1.98717/1000.;
switch (Switch)
{
case 1: /*monomer*/
cut_point=-1;
tempstruc = (char *) space((unsigned)length+1);
min_en = fold(string, tempstruc);
pf_scale = exp(-(sfact*min_en)/kT/(length));
*mfpl=get_mfe_plist(*mfpl);
free_arrays();
/*En=pf_fold(string, tempstruc);*/
init_co_pf_fold(length);
X=co_pf_fold(string, tempstruc);
*tpr=get_plist(*tpr, length,0.00001);
free_co_pf_arrays();
free(tempstruc);
break;
case 2: /*dimer*/
Newstring=(char *)space(sizeof(char)*(length*2+1));
strcat(Newstring,string);
strcat(Newstring,string);
cut_point=length+1;
tempstruc = (char *) space((unsigned)length*2+1);
min_en = cofold(Newstring, tempstruc);
pf_scale =exp(-(sfact*min_en)/kT/(2*length));
*mfpl=get_mfe_plist(*mfpl);
free_co_arrays();
init_co_pf_fold(2*length);
X=co_pf_fold(Newstring, tempstruc);
*tpr=get_plist(*tpr, 2*length,0.00001);
free_co_pf_arrays();
free(Newstring);
free(tempstruc);
break;
default:
printf("Error in get_partfunc\n, computing neither mono- nor dimere!\n");
exit (42);
}
return X;
}
int main(int argc, char *argv[])
{
struct RNAcofold_args_info args_info;
unsigned int input_type;
char *string, *input_string;
char *structure, *cstruc, *rec_sequence, *orig_sequence, *rec_id, **rec_rest;
char fname[FILENAME_MAX_LENGTH], ffname[FILENAME_MAX_LENGTH];
char *ParamFile;
char *ns_bases, *c;
char *Concfile;
int i, length, l, sym, r, cl;
double min_en;
double kT, sfact, betaScale;
int pf, istty;
int noconv, noPS;
int doT; /*compute dimere free energies etc.*/
int doC; /*toggle to compute concentrations*/
int doQ; /*toggle to compute prob of base being paired*/
int cofi; /*toggle concentrations stdin / file*/
plist *prAB;
plist *prAA; /*pair probabilities of AA dimer*/
plist *prBB;
plist *prA;
plist *prB;
plist *mfAB;
plist *mfAA; /*pair mfobabilities of AA dimer*/
plist *mfBB;
plist *mfA;
plist *mfB;
double *ConcAandB;
unsigned int rec_type, read_opt;
pf_paramT *pf_parameters;
model_detailsT md;
/*
#############################################
# init variables and parameter options
#############################################
*/
dangles = 2;
sfact = 1.07;
bppmThreshold = 1e-5;
noconv = 0;
noPS = 0;
do_backtrack = 1;
pf = 0;
doT = 0;
doC = 0;
doQ = 0;
cofi = 0;
betaScale = 1.;
gquad = 0;
ParamFile = NULL;
pf_parameters = NULL;
string = NULL;
Concfile = NULL;
structure = NULL;
cstruc = NULL;
ns_bases = NULL;
rec_type = read_opt = 0;
rec_id = rec_sequence = orig_sequence = NULL;
rec_rest = NULL;
set_model_details(&md);
/*
#############################################
# check the command line prameters
#############################################
*/
if(RNAcofold_cmdline_parser (argc, argv, &args_info) != 0) exit(1);
/* temperature */
if(args_info.temp_given) temperature = args_info.temp_arg;
/* structure constraint */
if(args_info.constraint_given) fold_constrained=1;
/* do not take special tetra loop energies into account */
if(args_info.noTetra_given) md.special_hp = tetra_loop=0;
/* set dangle model */
if(args_info.dangles_given){
if((args_info.dangles_arg < 0) || (args_info.dangles_arg > 3))
warn_user("required dangle model not implemented, falling back to default dangles=2");
else
md.dangles = dangles = args_info.dangles_arg;
}
/* do not allow weak pairs */
if(args_info.noLP_given) md.noLP = noLonelyPairs = 1;
/* do not allow wobble pairs (GU) */
if(args_info.noGU_given) md.noGU = noGU = 1;
/* do not allow weak closing pairs (AU,GU) */
if(args_info.noClosingGU_given) md.noGUclosure = no_closingGU = 1;
/* gquadruplex support */
if(args_info.gquad_given) md.gquad = gquad = 1;
/* enforce canonical base pairs in any case? */
if(args_info.canonicalBPonly_given) md.canonicalBPonly = canonicalBPonly = 1;
/* do not convert DNA nucleotide "T" to appropriate RNA "U" */
if(args_info.noconv_given) noconv = 1;
/* set energy model */
if(args_info.energyModel_given) energy_set = args_info.energyModel_arg;
/* */
if(args_info.noPS_given) noPS = 1;
/* take another energy parameter set */
if(args_info.paramFile_given) ParamFile = strdup(args_info.paramFile_arg);
/* Allow other pairs in addition to the usual AU,GC,and GU pairs */
if(args_info.nsp_given) ns_bases = strdup(args_info.nsp_arg);
/* set pf scaling factor */
if(args_info.pfScale_given) sfact = args_info.pfScale_arg;
if(args_info.all_pf_given) doT = pf = 1;
/* concentrations from stdin */
if(args_info.concentrations_given) doC = doT = pf = 1;
/* set the bppm threshold for the dotplot */
if(args_info.bppmThreshold_given)
bppmThreshold = MIN2(1., MAX2(0.,args_info.bppmThreshold_arg));
/* concentrations in file */
if(args_info.betaScale_given) betaScale = args_info.betaScale_arg;
if(args_info.concfile_given){
Concfile = strdup(args_info.concfile_arg);
doC = cofi = doT = pf = 1;
}
/* partition function settings */
if(args_info.partfunc_given){
pf = 1;
if(args_info.partfunc_arg != -1)
do_backtrack = args_info.partfunc_arg;
}
/* free allocated memory of command line data structure */
RNAcofold_cmdline_parser_free (&args_info);
/*
#############################################
# begin initializing
#############################################
*/
if(pf && gquad){
nrerror("G-Quadruplex support is currently not available for partition function computations");
}
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));
/* print user help if we get input from tty */
if(istty){
printf("Use '&' to connect 2 sequences that shall form a complex.\n");
if(fold_constrained){
print_tty_constraint(VRNA_CONSTRAINT_DOT | VRNA_CONSTRAINT_X | VRNA_CONSTRAINT_ANG_BRACK | VRNA_CONSTRAINT_RND_BRACK);
print_tty_input_seq_str("Input sequence (upper or lower case) followed by structure constraint\n");
}
else print_tty_input_seq();
}
/* set options we wanna pass to read_record */
if(istty) read_opt |= VRNA_INPUT_NOSKIP_BLANK_LINES;
if(!fold_constrained) read_opt |= VRNA_INPUT_NO_REST;
/*
#############################################
# main loop: continue until end of file
#############################################
*/
while(
!((rec_type = read_record(&rec_id, &rec_sequence, &rec_rest, read_opt))
& (VRNA_INPUT_ERROR | VRNA_INPUT_QUIT))){
/*
########################################################
# init everything according to the data we've read
########################################################
*/
if(rec_id){
if(!istty) printf("%s\n", rec_id);
(void) sscanf(rec_id, ">%" XSTR(FILENAME_ID_LENGTH) "s", fname);
}
else fname[0] = '\0';
cut_point = -1;
rec_sequence = tokenize(rec_sequence); /* frees input_string and sets cut_point */
length = (int) strlen(rec_sequence);
structure = (char *) space((unsigned) length+1);
/* parse the rest of the current dataset to obtain a structure constraint */
if(fold_constrained){
cstruc = NULL;
int cp = cut_point;
unsigned int coptions = (rec_id) ? VRNA_CONSTRAINT_MULTILINE : 0;
coptions |= VRNA_CONSTRAINT_DOT | VRNA_CONSTRAINT_X | VRNA_CONSTRAINT_ANG_BRACK | VRNA_CONSTRAINT_RND_BRACK;
getConstraint(&cstruc, (const char **)rec_rest, coptions);
cstruc = tokenize(cstruc);
if(cut_point != cp) nrerror("cut point in sequence and structure constraint differs");
cl = (cstruc) ? (int)strlen(cstruc) : 0;
if(cl == 0) warn_user("structure constraint is missing");
else if(cl < length) warn_user("structure constraint is shorter than sequence");
else if(cl > length) nrerror("structure constraint is too long");
if(cstruc) strncpy(structure, cstruc, sizeof(char)*(cl+1));
}
/* convert DNA alphabet to RNA if not explicitely switched off */
if(!noconv) str_DNA2RNA(rec_sequence);
/* store case-unmodified sequence */
orig_sequence = strdup(rec_sequence);
/* convert sequence to uppercase letters only */
str_uppercase(rec_sequence);
if(istty){
if (cut_point == -1)
printf("length = %d\n", length);
else
printf("length1 = %d\nlength2 = %d\n", cut_point-1, length-cut_point+1);
}
/*
########################################################
# begin actual computations
########################################################
*/
if (doC) {
FILE *fp;
if (cofi) { /* read from file */
fp = fopen(Concfile, "r");
if (fp==NULL) {
fprintf(stderr, "could not open concentration file %s", Concfile);
nrerror("\n");
}
ConcAandB = read_concentrations(fp);
fclose(fp);
} else {
printf("Please enter concentrations [mol/l]\n format: ConcA ConcB\n return to end\n");
ConcAandB = read_concentrations(stdin);
}
}
/*compute mfe of AB dimer*/
min_en = cofold(rec_sequence, structure);
assign_plist_from_db(&mfAB, structure, 0.95);
{
char *pstring, *pstruct;
if (cut_point == -1) {
pstring = strdup(orig_sequence);
pstruct = strdup(structure);
} else {
pstring = costring(orig_sequence);
pstruct = costring(structure);
}
printf("%s\n%s", pstring, pstruct);
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 (!noPS) {
char annot[512] = "";
if (fname[0]!='\0') {
strcpy(ffname, fname);
strcat(ffname, "_ss.ps");
} else {
strcpy(ffname, "rna.ps");
}
if (cut_point >= 0)
sprintf(annot,
"1 %d 9 0 0.9 0.2 omark\n%d %d 9 1 0.1 0.2 omark\n",
cut_point-1, cut_point+1, length+1);
if(gquad){
if (!noPS) (void) PS_rna_plot_a_gquad(pstring, pstruct, ffname, annot, NULL);
} else {
if (!noPS) (void) PS_rna_plot_a(pstring, pstruct, ffname, annot, NULL);
}
}
free(pstring);
free(pstruct);
}
if (length>2000) free_co_arrays();
/*compute partition function*/
if (pf) {
cofoldF AB, AA, BB;
FLT_OR_DBL *probs;
if (dangles==1) {
dangles=2; /* recompute with dangles as in pf_fold() */
min_en = energy_of_structure(rec_sequence, structure, 0);
dangles=1;
}
kT = (betaScale*((temperature+K0)*GASCONST))/1000.; /* in Kcal */
pf_scale = exp(-(sfact*min_en)/kT/length);
if (length>2000) fprintf(stderr, "scaling factor %f\n", pf_scale);
pf_parameters = get_boltzmann_factors(temperature, betaScale, md, pf_scale);
if (cstruc!=NULL)
strncpy(structure, cstruc, length+1);
AB = co_pf_fold_par(rec_sequence, structure, pf_parameters, do_backtrack, fold_constrained);
if (do_backtrack) {
char *costruc;
costruc = (char *) space(sizeof(char)*(strlen(structure)+2));
if (cut_point<0) printf("%s", structure);
else {
strncpy(costruc, structure, cut_point-1);
strcat(costruc, "&");
strcat(costruc, structure+cut_point-1);
printf("%s", costruc);
}
if (!istty) printf(" [%6.2f]\n", AB.FAB);
else printf("\n");/*8.6.04*/
}
if ((istty)||(!do_backtrack))
printf(" free energy of ensemble = %6.2f kcal/mol\n", AB.FAB);
printf(" frequency of mfe structure in ensemble %g",
exp((AB.FAB-min_en)/kT));
printf(" , delta G binding=%6.2f\n", AB.FcAB - AB.FA - AB.FB);
probs = export_co_bppm();
assign_plist_from_pr(&prAB, probs, length, bppmThreshold);
/* if (doQ) make_probsum(length,fname); */ /*compute prob of base paired*/
/* free_co_arrays(); */
if (doT) { /* cofold of all dimers, monomers */
int Blength, Alength;
char *Astring, *Bstring, *orig_Astring, *orig_Bstring;
char *Newstring;
char Newname[30];
char comment[80];
if (cut_point<0) {
printf("Sorry, i cannot do that with only one molecule, please give me two or leave it\n");
free(mfAB);
free(prAB);
continue;
}
if (dangles==1) dangles=2;
Alength=cut_point-1; /*length of first molecule*/
Blength=length-cut_point+1; /*length of 2nd molecule*/
Astring=(char *)space(sizeof(char)*(Alength+1));/*Sequence of first molecule*/
Bstring=(char *)space(sizeof(char)*(Blength+1));/*Sequence of second molecule*/
strncat(Astring,rec_sequence,Alength);
strncat(Bstring,rec_sequence+Alength,Blength);
orig_Astring=(char *)space(sizeof(char)*(Alength+1));/*Sequence of first molecule*/
orig_Bstring=(char *)space(sizeof(char)*(Blength+1));/*Sequence of second molecule*/
strncat(orig_Astring,orig_sequence,Alength);
strncat(orig_Bstring,orig_sequence+Alength,Blength);
/* compute AA dimer */
AA=do_partfunc(Astring, Alength, 2, &prAA, &mfAA, pf_parameters);
/* compute BB dimer */
BB=do_partfunc(Bstring, Blength, 2, &prBB, &mfBB, pf_parameters);
/*free_co_pf_arrays();*/
/* compute A monomer */
do_partfunc(Astring, Alength, 1, &prA, &mfA, pf_parameters);
/* compute B monomer */
do_partfunc(Bstring, Blength, 1, &prB, &mfB, pf_parameters);
compute_probabilities(AB.F0AB, AB.FA, AB.FB, prAB, prA, prB, Alength);
compute_probabilities(AA.F0AB, AA.FA, AA.FA, prAA, prA, prA, Alength);
compute_probabilities(BB.F0AB, BB.FA, BB.FA, prBB, prA, prB, Blength);
printf("Free Energies:\nAB\t\tAA\t\tBB\t\tA\t\tB\n%.6f\t%6f\t%6f\t%6f\t%6f\n",
AB.FcAB, AA.FcAB, BB.FcAB, AB.FA, AB.FB);
if (doC) {
do_concentrations(AB.FcAB, AA.FcAB, BB.FcAB, AB.FA, AB.FB, ConcAandB);
free(ConcAandB);/*freeen*/
}
if (fname[0]!='\0') {
strcpy(ffname, fname);
strcat(ffname, "_dp5.ps");
} else strcpy(ffname, "dot5.ps");
/*output of the 5 dot plots*/
/*AB dot_plot*/
/*write Free Energy into comment*/
sprintf(comment,"\n%%Heterodimer AB FreeEnergy= %.9f\n", AB.FcAB);
/*reset cut_point*/
cut_point=Alength+1;
/*write New name*/
strcpy(Newname,"AB");
strcat(Newname,ffname);
(void)PS_dot_plot_list(orig_sequence, Newname, prAB, mfAB, comment);
/*AA dot_plot*/
sprintf(comment,"\n%%Homodimer AA FreeEnergy= %.9f\n",AA.FcAB);
/*write New name*/
strcpy(Newname,"AA");
strcat(Newname,ffname);
/*write AA sequence*/
Newstring=(char*)space((2*Alength+1)*sizeof(char));
strcpy(Newstring,orig_Astring);
strcat(Newstring,orig_Astring);
(void)PS_dot_plot_list(Newstring, Newname, prAA, mfAA, comment);
free(Newstring);
/*BB dot_plot*/
sprintf(comment,"\n%%Homodimer BB FreeEnergy= %.9f\n",BB.FcAB);
/*write New name*/
strcpy(Newname,"BB");
strcat(Newname,ffname);
/*write BB sequence*/
Newstring=(char*)space((2*Blength+1)*sizeof(char));
strcpy(Newstring,orig_Bstring);
strcat(Newstring,orig_Bstring);
/*reset cut_point*/
cut_point=Blength+1;
(void)PS_dot_plot_list(Newstring, Newname, prBB, mfBB, comment);
free(Newstring);
/*A dot plot*/
/*reset cut_point*/
cut_point=-1;
sprintf(comment,"\n%%Monomer A FreeEnergy= %.9f\n",AB.FA);
/*write New name*/
strcpy(Newname,"A");
strcat(Newname,ffname);
/*write BB sequence*/
(void)PS_dot_plot_list(orig_Astring, Newname, prA, mfA, comment);
/*B monomer dot plot*/
sprintf(comment,"\n%%Monomer B FreeEnergy= %.9f\n",AB.FB);
/*write New name*/
strcpy(Newname,"B");
strcat(Newname,ffname);
/*write BB sequence*/
(void)PS_dot_plot_list(orig_Bstring, Newname, prB, mfB, comment);
free(Astring); free(Bstring); free(orig_Astring); free(orig_Bstring);
free(prAB); free(prAA); free(prBB); free(prA); free(prB);
free(mfAB); free(mfAA); free(mfBB); free(mfA); free(mfB);
} /*end if(doT)*/
free(pf_parameters);
}/*end if(pf)*/
if (do_backtrack) {
if (fname[0]!='\0') {
strcpy(ffname, fname);
strcat(ffname, "_dp.ps");
} else strcpy(ffname, "dot.ps");
if (!doT) {
if (pf) { (void) PS_dot_plot_list(rec_sequence, ffname, prAB, mfAB, "doof");
free(prAB);}
free(mfAB);
}
}
if (!doT) free_co_pf_arrays();
(void) fflush(stdout);
/* clean up */
if(cstruc) free(cstruc);
if(rec_id) free(rec_id);
free(rec_sequence);
free(orig_sequence);
free(structure);
/* free the rest of current dataset */
if(rec_rest){
for(i=0;rec_rest[i];i++) free(rec_rest[i]);
free(rec_rest);
}
rec_id = rec_sequence = orig_sequence = structure = cstruc = NULL;
rec_rest = NULL;
/* print user help for the next round if we get input from tty */
if(istty){
printf("Use '&' to connect 2 sequences that shall form a complex.\n");
if(fold_constrained){
print_tty_constraint(VRNA_CONSTRAINT_DOT | VRNA_CONSTRAINT_X | VRNA_CONSTRAINT_ANG_BRACK | VRNA_CONSTRAINT_RND_BRACK);
print_tty_input_seq_str("Input sequence (upper or lower case) followed by structure constraint\n");
}
else print_tty_input_seq();
}
}
return EXIT_SUCCESS;
}
int main(int argc, char *argv[])
{
char *string/*, *line*/;
char *structure=NULL, *cstruc=NULL;
/*char fname[53], ffname[60]; */
/*char *ParamFile=NULL; */
char *ns_bases=NULL, *c;
char *Concfile;
int i, length, l, sym/*, r*/;
double min_en;
double kT, sfact=1.07;
int pf=0, istty;
int noconv=0;
int doT=0; /*compute dimere free energies etc.*/
int doC=0; /*toggle to compute concentrations*/
int doQ=0; /*toggle to compute prob of base being paired*/
int cofi=0; /*toggle concentrations stdin / file*/
struct plist *prAB;
struct plist *prAA; /*pair probabilities of AA dimer*/
struct plist *prBB;
struct plist *prA;
struct plist *prB;
struct plist *mfAB;
struct plist *mfAA; /*pair mfobabilities of AA dimer*/
struct plist *mfBB;
struct plist *mfA;
struct plist *mfB;
double *ConcAandB;
AjPSeq seq1 = NULL;
AjPFile confile1 = NULL;
AjPSeq seq2 = NULL;
AjPFile confile2 = NULL;
AjPFile concfile = NULL;
AjPFile paramfile = NULL;
AjPFile outf = NULL;
AjPFile essfile = NULL;
AjPFile dotfile = NULL;
AjPFile aoutf = NULL;
AjPFile aaoutf = NULL;
AjPFile boutf = NULL;
AjPFile bboutf = NULL;
AjPFile aboutf = NULL;
AjPStr seqstring1 = NULL;
AjPStr constring1 = NULL;
AjPStr constring2 = NULL;
float eT = 0.;
AjBool eGU;
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';
/* AjBool dimers; */
/* AjBool paired; */
embInitPV("vrnacofold",argc,argv,"VIENNA",VERSION);
seqstring1 = ajStrNew();
constring1 = ajStrNew();
constring2 = ajStrNew();
seq1 = ajAcdGetSeq("asequence");
confile1 = ajAcdGetInfile("aconstraintfile");
seq2 = ajAcdGetSeq("bsequence");
confile2 = ajAcdGetInfile("bconstraintfile");
paramfile = ajAcdGetInfile("paramfile");
eT = ajAcdGetFloat("temperature");
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");
/* dimers = ajAcdGetBoolean("dimers"); */
/* paired = ajAcdGetBoolean("paired"); */
outf = ajAcdGetOutfile("outfile");
essfile = ajAcdGetOutfile("ssoutfile");
/* concfile = ajAcdGetInfile("concentrationfile"); */
/* dotfile = ajAcdGetOutfile("dotoutfile"); */
/*
aoutf = ajAcdGetOutfile("aoutfile");
aaoutf = ajAcdGetOutfile("aaoutfile");
boutf = ajAcdGetOutfile("boutfile");
bboutf = ajAcdGetOutfile("bboutfile");
aboutf = ajAcdGetOutfile("aboutfile");
*/
do_backtrack = 1;
pf = 0;
doT = 0;
doC = 0;
cofi = 0;
doQ = 0;
string = NULL;
Concfile = NULL;
istty = 0;
temperature = (double) eT;
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(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++;
}
}
cut_point = -1;
ajFmtPrintS(&seqstring1,"%s&%s",ajSeqGetSeqC(seq1),ajSeqGetSeqC(seq2));
string = tokenize(MAJSTRGETPTR(seqstring1)); /* frees line */
length = (int) strlen(string);
if (doC)
{
ConcAandB = read_concentrations(concfile);
}
structure = (char *) space((unsigned) length+1);
if(confile1)
{
vienna_GetConstraints(confile1,&constring1);
vienna_GetConstraints(confile2,&constring2);
ajStrAppendK(&constring1,'&');
ajStrAppendS(&constring1,constring2);
cstruc = tokenize(MAJSTRGETPTR(constring1));
if (cstruc!=NULL)
strncpy(structure, cstruc, length);
else
ajFatal("Constraints missing\n");
}
for (l = 0; l < length; l++)
{
string[l] = toupper(string[l]);
if (!noconv && string[l] == 'T') string[l] = 'U';
}
/*compute mfe of AB dimer*/
min_en = cofold(string, structure);
mfAB=(struct plist *) space(sizeof(struct plist) * (length+1));
mfAB=get_mfe_plist(mfAB);
if (cut_point == -1)
ajFmtPrintF(outf,"%s\n%s", string, structure); /*no cofold*/
else
{
char *pstring, *pstruct;
pstring = costring(string);
pstruct = costring(structure);
ajFmtPrintF(outf,"%s\n%s", pstring, pstruct);
free(pstring);
free(pstruct);
}
ajFmtPrintF(outf," (%6.2f)\n", min_en);
if (length<2000)
(void) PS_rna_plot(string, structure, essfile);
else
{
ajWarn("Structure too long, not doing xy_plot\n");
free_co_arrays();
}
/*compute partition function*/
if (pf)
{
cofoldF AB, AA, BB;
if (dangles==1)
{
dangles=2; /* recompute with dangles as in pf_fold() */
min_en = 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);
init_co_pf_fold(length);
if (cstruc!=NULL)
strncpy(structure, cstruc, length+1);
AB = co_pf_fold(string, structure);
if (do_backtrack)
{
char *costruc;
costruc = (char *) space(sizeof(char)*(strlen(structure)+2));
if (cut_point<0)
ajFmtPrintF(outf,"%s", structure);
else
{
strncpy(costruc, structure, cut_point-1);
strcat(costruc, "&");
strcat(costruc, structure+cut_point-1);
ajFmtPrintF(outf,"%s", costruc);
}
ajFmtPrintF(outf," [%6.2f]\n", AB.FAB);
}
if ((istty)||(!do_backtrack))
ajFmtPrintF(outf," free energy of ensemble = %6.2f kcal/mol\n",
AB.FAB);
ajFmtPrintF(outf," frequency of mfe structure in ensemble %g",
exp((AB.FAB-min_en)/kT));
ajFmtPrintF(outf," , delta G binding=%6.2f\n", AB.FcAB - AB.FA - AB.FB);
prAB=(struct plist *) space(sizeof(struct plist) * (2*length));
prAB=get_plist(prAB, length,0.00001);
/* if (doQ) make_probsum(length,fname); */ /*compute prob of base paired*/
/* free_co_arrays(); */
if (doT)
{ /* cofold of all dimers, monomers */
int Blength, Alength;
char *Astring, *Bstring;
char *Newstring;
/*char Newname[30];*/
char comment[80];
if (cut_point<0)
{
free(mfAB);
free(prAB);
ajFatal("Sorry, I cannot do that with only one molecule, "
"please give me two\n");
}
if (dangles==1)
dangles=2;
Alength=cut_point-1; /*length of first molecule*/
Blength=length-cut_point+1; /*length of 2nd molecule*/
/*Sequence of first molecule*/
Astring=(char *)space(sizeof(char)*(Alength+1));
/*Sequence of second molecule*/
Bstring=(char *)space(sizeof(char)*(Blength+1));
strncat(Astring,string,Alength);
strncat(Bstring,string+Alength,Blength);
/* compute AA dimer */
prAA=(struct plist *) space(sizeof(struct plist) * (4*Alength));
mfAA=(struct plist *) space(sizeof(struct plist) * (Alength+1));
AA=do_partfunc(Astring, Alength, 2, &prAA, &mfAA);
/* compute BB dimer */
prBB=(struct plist *) space(sizeof(struct plist) * (4*Blength));
mfBB=(struct plist *) space(sizeof(struct plist) * (Blength+1));
BB=do_partfunc(Bstring, Blength, 2, &prBB, &mfBB);
/*free_co_pf_arrays();*/
/* compute A monomer */
prA=(struct plist *) space(sizeof(struct plist) * (2*Alength));
mfA=(struct plist *) space(sizeof(struct plist) * (Alength+1));
do_partfunc(Astring, Alength, 1, &prA, &mfA);
/* compute B monomer */
prB=(struct plist *) space(sizeof(struct plist) * (2*Blength));
mfB=(struct plist *) space(sizeof(struct plist) * (Blength+1));
do_partfunc(Bstring, Blength, 1, &prB, &mfB);
compute_probabilities(AB.F0AB, AB.FA, AB.FB, prAB, prA, prB,
Alength);
compute_probabilities(AA.F0AB, AA.FA, AA.FA, prAA, prA, prA,
Alength);
compute_probabilities(BB.F0AB, BB.FA, BB.FA, prBB, prA, prB,
Blength);
ajFmtPrintF(outf,"Free Energies:\nAB\t\tAA\t\tBB\t\tA\t\tB\n%.6f"
"\t%6f\t%6f\t%6f\t%6f\n",
AB.FcAB, AA.FcAB, BB.FcAB, AB.FA, AB.FB);
if (doC)
{
do_concentrations(AB.FcAB, AA.FcAB, BB.FcAB, AB.FA, AB.FB,
ConcAandB, outf);
free(ConcAandB);/*freeen*/
}
/*AB dot_plot*/
/*write Free Energy into comment*/
sprintf(comment,"\n%%Heterodimer AB FreeEnergy= %.9f\n", AB.FcAB);
/*reset cut_point*/
cut_point=Alength+1;
(void)PS_dot_plot_list(string, aboutf, prAB, mfAB, comment);
/*AA dot_plot*/
sprintf(comment,"\n%%Homodimer AA FreeEnergy= %.9f\n",AA.FcAB);
/*write AA sequence*/
Newstring=(char*)space((2*Alength+1)*sizeof(char));
strcpy(Newstring,Astring);
strcat(Newstring,Astring);
(void)PS_dot_plot_list(Newstring, aaoutf, prAA, mfAA, comment);
free(Newstring);
/*BB dot_plot*/
sprintf(comment,"\n%%Homodimer BB FreeEnergy= %.9f\n",BB.FcAB);
/*write BB sequence*/
Newstring=(char*)space((2*Blength+1)*sizeof(char));
strcpy(Newstring,Bstring);
strcat(Newstring,Bstring);
/*reset cut_point*/
cut_point=Blength+1;
(void)PS_dot_plot_list(Newstring, bboutf, prBB, mfBB, comment);
free(Newstring);
/*A dot plot*/
/*reset cut_point*/
cut_point=-1;
sprintf(comment,"\n%%Monomer A FreeEnergy= %.9f\n",AB.FA);
/*write A sequence*/
(void)PS_dot_plot_list(Astring, aoutf, prA, mfA, comment);
/*B monomer dot plot*/
sprintf(comment,"\n%%Monomer B FreeEnergy= %.9f\n",AB.FB);
/*write B sequence*/
(void)PS_dot_plot_list(Bstring, boutf, prB, mfB, comment);
free(Astring);
free(Bstring);
free(prAB);
free(prAA);
free(prBB);
free(prA);
free(prB);
free(mfAB);
free(mfAA);
free(mfBB);
free(mfA);
free(mfB);
} /*end if(doT)*/
}/*end if(pf)*/
if (do_backtrack)
{
if (!doT)
{
if (pf)
{
(void) PS_dot_plot_list(string, dotfile, prAB, mfAB, "doof");
free(prAB);
}
free(mfAB);
}
}
if (!doT)
free_co_pf_arrays();
if (cstruc!=NULL)
free(cstruc);
free(string);
free(structure);
ajStrDel(&seqstring1);
ajStrDel(&constring1);
ajStrDel(&constring2);
ajSeqDel(&seq1);
ajSeqDel(&seq2);
ajStrDel(&ensbases);
ajStrDel(&eenergy);
ajStrDel(&edangles);
ajFileClose(&confile1);
ajFileClose(&confile2);
ajFileClose(¶mfile);
ajFileClose(&outf);
ajFileClose(&essfile);
if (length<2000)
free_co_arrays();
embExit();
return 0;
}
int main(int argc, char *argv[])
{
char *string, *line;
char *structure=NULL, *cstruc=NULL;
char fname[53], ffname[60];
char *ParamFile=NULL;
char *ns_bases=NULL, *c;
char *Concfile;
int i, length, l, sym, r;
double min_en;
double kT, sfact=1.07;
int pf=0, istty;
int noconv=0;
int doT=0; /*compute dimere free energies etc.*/
int doC=0; /*toggle to compute concentrations*/
int doQ=0; /*toggle to compute prob of base being paired*/
int cofi=0; /*toggle concentrations stdin / file*/
struct plist *prAB;
struct plist *prAA; /*pair probabilities of AA dimer*/
struct plist *prBB;
struct plist *prA;
struct plist *prB;
struct plist *mfAB;
struct plist *mfAA; /*pair mfobabilities of AA dimer*/
struct plist *mfBB;
struct plist *mfA;
struct plist *mfB;
double *ConcAandB;
do_backtrack = 1;
string=NULL;
Concfile=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], "-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 '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;
case 'a':
doT=1;
pf=1;
break;
case 'c':/*concentrations from stdin*/
doC=1;
doT=1;
pf=1;
break;
case 'f':/*concentrations in file*/
if (i==argc-1) usage();
Concfile = argv[++i];
doC=1;
cofi=1;
doT=1;
pf=1;
break;
case 'q':
pf=1;
doQ=1;
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));
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 */
cut_point = -1;
if (istty) {
printf("\nInput sequence(s); @ to quit\n");
printf("Use '&' as spearator between 2 sequences that shall form a complex.\n");
printf("%s\n", scale);
}
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, ">%51s", fname);
printf("%s\n", line);
free(line);
if ((line = get_line(stdin))==NULL) break;
}
if ((line ==NULL) || (strcmp(line, "@") == 0)) break;
string = tokenize(line); /* frees line */
length = (int) strlen(string);
if (doC) {
FILE *fp;
if (cofi) { /* read from file */
fp = fopen(Concfile, "r");
if (fp==NULL) {
fprintf(stderr, "could not open concentration file %s", Concfile);
nrerror("\n");
}
ConcAandB = read_concentrations(fp);
fclose(fp);
} else {
printf("Please enter concentrations [mol/l]\n format: ConcA ConcB\n return to end\n");
ConcAandB = read_concentrations(stdin);
}
}
structure = (char *) space((unsigned) length+1);
if (fold_constrained) {
cstruc = tokenize(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) {
if (cut_point == -1)
printf("length = %d\n", length);
else
printf("length1 = %d\nlength2 = %d\n",
cut_point-1, length-cut_point+1);
}
/*compute mfe of AB dimer*/
min_en = cofold(string, structure);
mfAB=(struct plist *) space(sizeof(struct plist) * (length+1));
mfAB=get_mfe_plist(mfAB);
if (cut_point == -1) printf("%s\n%s", string, structure); /*no cofold*/
else {
char *pstring, *pstruct;
pstring = costring(string);
pstruct = costring(structure);
printf("%s\n%s", pstring, pstruct);
free(pstring);
free(pstruct);
}
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");
} else {
strcpy(ffname, "rna.ps");
}
if (length<2000)
(void) PS_rna_plot(string, structure, ffname);
else {
fprintf(stderr,"INFO: structure too long, not doing xy_plot\n");
free_co_arrays();
}
/*compute partition function*/
if (pf) {
cofoldF AB, AA, BB;
if (dangles==1) {
dangles=2; /* recompute with dangles as in pf_fold() */
min_en = 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);
init_co_pf_fold(length);
if (cstruc!=NULL)
strncpy(structure, cstruc, length+1);
AB = co_pf_fold(string, structure);
if (do_backtrack) {
char *costruc;
costruc = (char *) space(sizeof(char)*(strlen(structure)+2));
if (cut_point<0) printf("%s", structure);
else {
strncpy(costruc, structure, cut_point-1);
strcat(costruc, "&");
strcat(costruc, structure+cut_point-1);
printf("%s", costruc);
}
if (!istty) printf(" [%6.2f]\n", AB.FAB);
else printf("\n");/*8.6.04*/
}
if ((istty)||(!do_backtrack))
printf(" free energy of ensemble = %6.2f kcal/mol\n", AB.FAB);
printf(" frequency of mfe structure in ensemble %g",
exp((AB.FAB-min_en)/kT));
printf(" , delta G binding=%6.2f\n", AB.FcAB - AB.FA - AB.FB);
prAB=(struct plist *) space(sizeof(struct plist) * (2*length));
prAB=get_plist(prAB, length,0.00001);
/* if (doQ) make_probsum(length,fname); */ /*compute prob of base paired*/
/* free_co_arrays(); */
if (doT) { /* cofold of all dimers, monomers */
int Blength, Alength;
char *Astring, *Bstring;
char *Newstring;
char Newname[30];
char comment[80];
if (cut_point<0) {
printf("Sorry, i cannot do that with only one molecule, please give me two or leave it\n");
free(mfAB);
free(prAB);
continue;
}
if (dangles==1) dangles=2;
Alength=cut_point-1; /*length of first molecule*/
Blength=length-cut_point+1; /*length of 2nd molecule*/
Astring=(char *)space(sizeof(char)*(Alength+1));/*Sequence of first molecule*/
Bstring=(char *)space(sizeof(char)*(Blength+1));/*Sequence of second molecule*/
strncat(Astring,string,Alength);
strncat(Bstring,string+Alength,Blength);
/* compute AA dimer */
prAA=(struct plist *) space(sizeof(struct plist) * (4*Alength));
mfAA=(struct plist *) space(sizeof(struct plist) * (Alength+1));
AA=do_partfunc(Astring, Alength, 2, &prAA, &mfAA);
/* compute BB dimer */
prBB=(struct plist *) space(sizeof(struct plist) * (4*Blength));
mfBB=(struct plist *) space(sizeof(struct plist) * (Blength+1));
BB=do_partfunc(Bstring, Blength, 2, &prBB, &mfBB);
/*free_co_pf_arrays();*/
/* compute A monomer */
prA=(struct plist *) space(sizeof(struct plist) * (2*Alength));
mfA=(struct plist *) space(sizeof(struct plist) * (Alength+1));
do_partfunc(Astring, Alength, 1, &prA, &mfA);
/* compute B monomer */
prB=(struct plist *) space(sizeof(struct plist) * (2*Blength));
mfB=(struct plist *) space(sizeof(struct plist) * (Blength+1));
do_partfunc(Bstring, Blength, 1, &prB, &mfB);
compute_probabilities(AB.F0AB, AB.FA, AB.FB, prAB, prA, prB, Alength);
compute_probabilities(AA.F0AB, AA.FA, AA.FA, prAA, prA, prA, Alength);
compute_probabilities(BB.F0AB, BB.FA, BB.FA, prBB, prA, prB, Blength);
printf("Free Energies:\nAB\t\tAA\t\tBB\t\tA\t\tB\n%.6f\t%6f\t%6f\t%6f\t%6f\n",
AB.FcAB, AA.FcAB, BB.FcAB, AB.FA, AB.FB);
if (doC) {
do_concentrations(AB.FcAB, AA.FcAB, BB.FcAB, AB.FA, AB.FB, ConcAandB);
free(ConcAandB);/*freeen*/
}
if (fname[0]!='\0') {
strcpy(ffname, fname);
strcat(ffname, "_dp5.ps");
} else strcpy(ffname, "dot5.ps");
/*output of the 5 dot plots*/
/*AB dot_plot*/
/*write Free Energy into comment*/
sprintf(comment,"\n%%Heterodimer AB FreeEnergy= %.9f\n", AB.FcAB);
/*reset cut_point*/
cut_point=Alength+1;
/*write New name*/
strcpy(Newname,"AB");
strcat(Newname,ffname);
(void)PS_dot_plot_list(string, Newname, prAB, mfAB, comment);
/*AA dot_plot*/
sprintf(comment,"\n%%Homodimer AA FreeEnergy= %.9f\n",AA.FcAB);
/*write New name*/
strcpy(Newname,"AA");
strcat(Newname,ffname);
/*write AA sequence*/
Newstring=(char*)space((2*Alength+1)*sizeof(char));
strcpy(Newstring,Astring);
strcat(Newstring,Astring);
(void)PS_dot_plot_list(Newstring, Newname, prAA, mfAA, comment);
free(Newstring);
/*BB dot_plot*/
sprintf(comment,"\n%%Homodimer BB FreeEnergy= %.9f\n",BB.FcAB);
/*write New name*/
strcpy(Newname,"BB");
strcat(Newname,ffname);
/*write BB sequence*/
Newstring=(char*)space((2*Blength+1)*sizeof(char));
strcpy(Newstring,Bstring);
strcat(Newstring,Bstring);
/*reset cut_point*/
cut_point=Blength+1;
(void)PS_dot_plot_list(Newstring, Newname, prBB, mfBB, comment);
free(Newstring);
/*A dot plot*/
/*reset cut_point*/
cut_point=-1;
sprintf(comment,"\n%%Monomer A FreeEnergy= %.9f\n",AB.FA);
/*write New name*/
strcpy(Newname,"A");
strcat(Newname,ffname);
/*write BB sequence*/
(void)PS_dot_plot_list(Astring, Newname, prA, mfA, comment);
/*B monomer dot plot*/
sprintf(comment,"\n%%Monomer B FreeEnergy= %.9f\n",AB.FB);
/*write New name*/
strcpy(Newname,"B");
strcat(Newname,ffname);
/*write BB sequence*/
(void)PS_dot_plot_list(Bstring, Newname, prB, mfB, comment);
free(Astring);
free(Bstring);
free(prAB);
free(prAA);
free(prBB);
free(prA);
free(prB);
free(mfAB);
free(mfAA);
free(mfBB);
free(mfA);
free(mfB);
} /*end if(doT)*/
}/*end if(pf)*/
if (do_backtrack) {
if (fname[0]!='\0') {
strcpy(ffname, fname);
strcat(ffname, "_dp.ps");
} else strcpy(ffname, "dot.ps");
if (!doT) {
if (pf) {
(void) PS_dot_plot_list(string, ffname, prAB, mfAB, "doof");
free(prAB);
}
free(mfAB);
}
}
if (!doT) free_co_pf_arrays();
if (cstruc!=NULL) free(cstruc);
(void) fflush(stdout);
free(string);
free(structure);
} while (1);
return 0;
}