int main(int argc, char *argv[]) {
struct RNAfold_args_info args_info;
char *string, *input_string, *structure=NULL, *cstruc=NULL;
char fname[80], ffname[80], gfname[80], *ParamFile=NULL;
char *ns_bases=NULL, *c;
int i, j, ii, jj, mu, length, l, sym, r, pf=0, noconv=0;
unsigned int input_type;
double energy, min_en, kT, sfact=1.07;
int doMEA=0, circular = 0, N;
char *pf_struc;
double dist;
plist *pl;
FILE * filehandle;
FILE * statsfile;
char* line;
double tau = 0.01; /* Variance of energy parameters */
double sigma = 0.01; /* Variance of experimental constraints */
double *gradient; /* Gradient for steepest descent search
epsilon[i+1]= epsilon[i] - gradient *
step_size */
double initial_step_size = 0.5; /* Initial step size for steepest
descent search */
double step_size;
double D; /* Discrepancy (i.e. value of objective
function) for the current
prediction */
int iteration, max_iteration = 2000; /* Current and maximum number of
iterations after which
algorithm stops */
double precision = 0.1; /* cutoff used for stop conditions */
double tolerance = 0.1; /* Parameter used by various GSL minimizers */
int method_id = 1; /* Method to use for minimization, 0 and 1
are custom steepest descent, the rest
are GSL implementations (see below)*/
int initial_guess_method = 0;
int sample_N = 1000;
double *prev_epsilon;
double *prev_gradient;
double DD, prev_D, sum, norm;
int status;
double* gradient_numeric;
double* gradient_numeric_gsl;
/* Minimizer vars */
const gsl_multimin_fdfminimizer_type *T;
gsl_multimin_fdfminimizer *minimizer;
gsl_vector *minimizer_x;
gsl_vector *minimizer_g;
gsl_multimin_function_fdf minimizer_func;
minimizer_pars_struct minimizer_pars;
char *constraints;
char outfile[256];
char constraints_file[256];
char epsilon_file[256];
FILE* fh;
double last_non_nan_lnQ;
pf_overflow = 0;
pf_underflow = 0;
dangles=2;
do_backtrack = 1;
string = NULL;
noPS = 0;
outfile[0]='\0';
epsilon_file[0]='\0';
strcpy(psDir, "dotplots");
if(RNAfold_cmdline_parser (argc, argv, &args_info) != 0) exit(1);
/* RNAbpfold specific options */
if (args_info.tau_given) tau = args_info.tau_arg;
if (args_info.sigma_given) sigma = args_info.sigma_arg;
if (args_info.precision_given) precision = args_info.precision_arg;
if (args_info.step_given) initial_step_size = args_info.step_arg;
if (args_info.maxN_given) max_iteration = args_info.maxN_arg;
if (args_info.minimization_given) method_id = args_info.minimization_arg;
if (args_info.init_given) initial_guess_method = args_info.init_arg;
if (args_info.tolerance_given) tolerance = args_info.tolerance_arg;
if (args_info.outfile_given) strcpy(outfile, args_info.outfile_arg);
if (args_info.constraints_given) strcpy(constraints_file, args_info.constraints_arg);
if (args_info.epsilon_given) strcpy(epsilon_file, args_info.epsilon_arg);
if (args_info.sampleGradient_given) sample_conditionals=1;
if (args_info.hybridGradient_given) {
sample_conditionals=1;
hybrid_conditionals=1;
}
if (args_info.numericalGradient_given) numerical=1;
if (args_info.sampleStructure_given) sample_structure=1;
if (args_info.psDir_given) strcpy(psDir, args_info.psDir_arg);
if (args_info.sparsePS_given) sparsePS=args_info.sparsePS_arg;
if (args_info.gridSearch_given) grid_search = 1;
/* Generic RNAfold options */
if (args_info.temp_given) temperature = args_info.temp_arg;
if (args_info.reference_given) fold_constrained=1;
if (args_info.noTetra_given) tetra_loop=0;
if (args_info.dangles_given) dangles = args_info.dangles_arg;
if (args_info.noLP_given) noLonelyPairs = 1;
if (args_info.noGU_given) noGU = 1;
if (args_info.noClosingGU_given) no_closingGU = 1;
if (args_info.noconv_given) noconv = 1;
if (args_info.energyModel_given) energy_set = args_info.energyModel_arg;
if (args_info.paramFile_given) ParamFile = strdup(args_info.paramFile_arg);
if (args_info.nsp_given) ns_bases = strdup(args_info.nsp_arg);
if (args_info.pfScale_given) sfact = args_info.pfScale_arg;
if (args_info.noPS_given) noPS=1;
/* Create postscript directory */
if (!noPS) {
struct stat stat_p;
if (stat (psDir, &stat_p) != 0) {
if (mkdir(psDir, S_IRWXU|S_IROTH|S_IRGRP ) !=0) {
fprintf(stderr, "WARNING: Could not create directory: %s", psDir);
}
}
}
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++;
}
}
/*Read sequence*/
fname[0] = '\0';
while((input_type = get_input_line(&input_string, 0)) & VRNA_INPUT_FASTA_HEADER) {
(void) sscanf(input_string, "%42s", fname);
free(input_string);
}
length = (int) strlen(input_string);
string = strdup(input_string);
free(input_string);
structure = (char *) space((unsigned) length+1);
/* For testing purpose pass dot bracket structure of reference structure via -C */
if (fold_constrained) {
input_type = get_input_line(&input_string, VRNA_INPUT_NOSKIP_COMMENTS);
if(input_type & VRNA_INPUT_QUIT) {
exit(1);
}
else if((input_type & VRNA_INPUT_MISC) && (strlen(input_string) > 0)) {
cstruc = strdup(input_string);
free(input_string);
}
else warn_user("-C was given but reference structure is missing");
}
if(noconv) {
str_RNA2RNA(string);
} else {
str_DNA2RNA(string);
}
/* Allocating space */
epsilon = (double *) space(sizeof(double)*(length+1));
exp_pert = (double **)space(sizeof(double *)*(length+1));
perturbations = (double **)space(sizeof(double *)*(length+1));
prev_epsilon = (double *) space(sizeof(double)*(length+1));
gradient = (double *) space(sizeof(double)*(length+1));
gradient_numeric = (double *) space(sizeof(double)*(length+1));
gradient_numeric_gsl = (double *) space(sizeof(double)*(length+1));
prev_gradient = (double *) space(sizeof(double)*(length+1));
q_unpaired = (double *) space(sizeof(double)*(length+1));
p_unpaired_cond = (double **)space(sizeof(double *)*(length+1));
p_unpaired_cond_sampled = (double **)space(sizeof(double *)*(length+1));
p_pp = (double **)space(sizeof(double *)*(length+1));
p_unpaired = (double *) space(sizeof(double)*(length+1));
p_unpaired_tmp = (double *) space(sizeof(double)*(length+1));
for (i=0; i <= length; i++) {
epsilon[i] = gradient[i] = q_unpaired[i] = 0.0;
p_unpaired_cond[i] = (double *) space(sizeof(double)*(length+1));
p_unpaired_cond_sampled[i] = (double *) space(sizeof(double)*(length+1));
p_pp[i] = (double *) space(sizeof(double)*(length+1));
exp_pert[i] = (double *) space(sizeof(double)*(length+1));
perturbations[i] = (double *) space(sizeof(double)*(length+1));
for (j=0; j <= length; j++) {
p_pp[i][j]=p_unpaired_cond[i][j] = 0.0;
p_unpaired_cond_sampled[i][j] = 0.0;
}
}
/*** If file with perturbation vector epsilon is given we fold using
this epsilon and are done ***/
if (args_info.epsilon_given) {
plist *pl, *pl1,*pl2;
filehandle = fopen (epsilon_file,"r");
if (filehandle == NULL) {
nrerror("Could not open file with perturbation vector.");
}
i=1;
while (1) {
double t;
line = get_line(filehandle);
if (line == NULL) break;
if (i>length) nrerror("Too many values in perturbation vector file.");
if (sscanf(line, "%lf", &epsilon[i]) !=1) {
nrerror("Error while reading perturbation vector file.");
}
i++;
}
if (i-1 != length) {
nrerror("Too few values in perturbation vector file.");
}
init_pf_fold(length);
pf_fold_pb(string, NULL);
sprintf(fname,"%s/dot.ps", psDir);
pl1 = make_plist(length, 1e-5);
(void) PS_dot_plot_list_epsilon(string, fname, NULL, pl1, epsilon, "");
exit(0);
}
/*** Get constraints from reference structure or from external file ***/
/* Structure was given by -C */
if (fold_constrained) {
for (i=0; i<length; i++) {
if (cstruc[i] == '(' || cstruc[i] == ')') {
q_unpaired[i+1] = 0.0;
} else {
q_unpaired[i+1] = 1.0;
}
}
/*Read constraints from file*/
} else {
filehandle = fopen (constraints_file,"r");
if (filehandle == NULL) {
nrerror("No constraints given as dot bracket or wrong file name");
}
i=1;
while (1) {
double t;
line = get_line(filehandle);
if (line == NULL) break;
if (i>length) nrerror("Too many values in constraints.dat");
if (sscanf(line, "%lf", &q_unpaired[i]) !=1) {
nrerror("Error while reading constraints.dat");
}
i++;
}
if (i-1 != length) {
nrerror("Too few values in constraints.dat");
}
}
/* Create file handle */
if (outfile[0] !='\0') {
statsfile = fopen (outfile,"w");
} else {
statsfile = fopen ("stats.dat","w");
}
setvbuf(statsfile, NULL, _IONBF, 0);
if (!grid_search) {
fprintf(statsfile, "Iteration\tDiscrepancy\tNorm\tdfCount\tMEA\tSampled_structure\tSampled_energy\tSampled_distance\tEpsilon\ttimestamp\n");
} else {
/* If we do a grid search we have a different output. */
fprintf(statsfile, "Dummy\tm\tb\tdummy\tMEA\tepsilon\n");
}
if (statsfile == NULL) {
nrerror("Could not open stats.dat for writing.");
}
fprintf(stderr, "tau^2 = %.4f; sigma^2 = %.4f; precision = %.4f; tolerance = %.4f; step-size: %.4f\n\n",
tau, sigma, precision, tolerance, initial_step_size);
st_back=1;
min_en = fold(string, structure);
(void) fflush(stdout);
if (length>2000) free_arrays();
pf_struc = (char *) space((unsigned) length+1);
kT = (temperature+273.15)*1.98717/1000.; /* in Kcal */
pf_scale = exp(-(sfact*min_en)/kT/length);
/* Set up minimizer */
minimizer_x = gsl_vector_alloc (length+1);
minimizer_g = gsl_vector_alloc (length+1);
for (i=0; i <= length; i++) {
epsilon[i] = 0.0;
gsl_vector_set (minimizer_g, i, 0.0);
gsl_vector_set (minimizer_x, i, epsilon[i]);
}
minimizer_pars.length=length;
minimizer_pars.seq = string;
minimizer_pars.tau=tau;
minimizer_pars.sigma=sigma;
minimizer_pars.kT=kT;
minimizer_func.n = length+1;
minimizer_func.f = calculate_f;
minimizer_func.df = numerical ? calculate_df_numerically: calculate_df;
minimizer_func.fdf = calculate_fdf;
minimizer_func.params = &minimizer_pars;
//min_en = fold_pb(string, structure);
//fprintf(stderr, "%f", min_en);
//exit(0);
/* Calling test functions for debugging */
for (i=1; i <= length; i++) {
if (i%2==0) {
epsilon[i] = +0.2*i;
} else {
epsilon[i] = -0.2*i;
}
}
//test_folding(string, length);
/* //test_stochastic_backtracking(string, length); */
/* //test_gradient(minimizer_func, minimizer_pars); */
/* //test_gradient_sampling(minimizer_func, minimizer_pars); */
//exit(1);
count_df_evaluations=0;
/* Initial guess for epsilon */
if (initial_guess_method !=0 && initial_guess_method !=3) {
/* Vars for inital guess methods */
double m,b;
double* curr_epsilon;
double* best_epsilon;
double best_m, best_b, best_scale;
double curr_D;
double min_D = 999999999.0;
double inc = +0.25;
double cut;
if (initial_guess_method == 1) fprintf(stderr, "Mathew's constant perturbations\n");
if (initial_guess_method == 2) fprintf(stderr, "Perturbations proportional to q-p\n");
curr_epsilon = (double *) space(sizeof(double)*(length+1));
best_epsilon = (double *) space(sizeof(double)*(length+1));
last_non_nan_lnQ = min_en;
// Calculate p_unpaired for unperturbed state which we need later
// for the proportinal method
if (initial_guess_method == 2) {
init_pf_fold(length);
for (i=0; i <= length; i++) {
epsilon[i] = 0.0;
}
pf_fold_pb(string, NULL);
for (i = 1; i < length; i++) {
for (j = i+1; j<= length; j++) {
p_pp[i][j]=p_pp[j][i]=pr[iindx[i]-j];
}
}
get_pair_prob_vector(p_pp, p_unpaired_tmp, length, 1);
free_pf_arrays();
}
/* We do the same grid search as in the Mathews paper Fig. 4*/
for (m=0.25; m <=7.0; m+=0.25) {
// Weird way of writing this inner loop for the grid search. We
// traverse the grid without big jumps in the parameters to make
// sure that the updated scaling factor is accurate all the time.
inc*=-1;
for (b = inc < 0.0 ? 0.0 : -3.0; inc < 0.0 ? b >= -3.0 : b<= 0.0 ; b+=inc) {
// calculate cut point with x-axis and skip parameter pairs
// which give a cut point outside the range of
// q_unpaired (0 to 1). They gave frequently overflows and the
// idea is that we both want positive and negative perturbations
cut = exp( (-1) * b / m ) - 1;
fprintf(stderr, "\nm = %.2f, b = %.2f, cut=%.2f\n", m, b, cut);
if (cut > 1.0 || cut < 0.01) {
fprintf(stderr, "\nSkipping m = %.2f, b = %.2f\n", m, b);
continue;
}
/* Mathew's constant perturbations */
if (initial_guess_method == 1) {
for (i=0; i <= length; i++) {
/* We add epsilon to unpaired regions (as opposed to
paired regions as in the Mathews paper) so we multiply
by -1; if missing data we set it to 0.0 */
if (q_unpaired[i] < -0.5) {
curr_epsilon[i] = 0.0;
} else {
curr_epsilon[i] = (m *(log(q_unpaired[i]+1))+b) *(-1);
}
gsl_vector_set (minimizer_x, i, curr_epsilon[i]);
}
/* Perturbations proportional to q-p */
} else {
for (i=0; i <= length; i++) {
curr_epsilon[i] = (m *(log(q_unpaired[i]+1)-log(p_unpaired_tmp[i]+1))+ b ) * (-1);
gsl_vector_set (minimizer_x, i, curr_epsilon[i]);
}
}
// Repeat and adjust scaling factor until we get result without over-/underflows
do {
// First we use default scaling factor
if (pf_underflow == 0 && pf_overflow == 0) {
sfact = 1.070;
}
if (pf_underflow) {
sfact *= 0.8;
fprintf(stderr,"Underflow, adjusting sfact to %.4f\n", sfact );
}
if (pf_overflow) {
sfact *= 1.2;
fprintf(stderr,"Overflow, adjusting sfact to %.4f\n", sfact );
}
pf_scale = exp(-(sfact*last_non_nan_lnQ)/kT/length);
//fprintf(stderr,"Scaling factor is now: %.4e\n", pf_scale);
curr_D = calculate_f(minimizer_x, (void*)&minimizer_pars);
if (!isnan(last_lnQ)) last_non_nan_lnQ = last_lnQ;
// Give up when even extreme scaling does not give results
// (for some reason I could not get rid of overflows even with high scaling factors)
if (sfact < 0.1 || sfact > 2.0) break;
} while (pf_underflow == 1 || pf_overflow == 1);
// We have not given up so everything is ok now
if (!(sfact < 0.1 || sfact > 2.0)) {
if (curr_D < min_D) {
min_D = curr_D;
for (i=0; i <= length; i++) {
best_epsilon[i] = curr_epsilon[i];
}
best_m = m;
best_b = b;
best_scale = pf_scale;
}
/*If we are interested in the grid search we misuse the
print_stats function and report m and b together with MEA*/
if (grid_search) {
for (i=0; i <= length; i++) {
epsilon[i] = curr_epsilon[i];
}
print_stats(statsfile, string, cstruc, length, 0, 0, m, 0.0, b, 0);
}
fprintf(stderr, "curr D: %.2f, minimum D: %.2f\n", curr_D, min_D);
// Adjust pf_scale with default scaling factor but lnQ from
// previous step
sfact = 1.070;
pf_scale = exp(-(sfact*last_lnQ)/kT/length);
} else {
sfact = 1.070;
fprintf(stderr, "Skipping m = %.2f, b = %.2f; did not get stable result.\n", m, b);
}
} // for b
} // for m
fprintf(stderr, "Minimum found: m=%.2f, b=%.2f: %.2f\n", best_m, best_b, min_D);
for (i=0; i <= length; i++) {
epsilon[i] = best_epsilon[i];
gsl_vector_set (minimizer_x, i, best_epsilon[i]);
}
pf_scale = best_scale;
}
if (initial_guess_method == 3) {
srand((unsigned)time(0));
for (i=0; i <= length; i++) {
double r = (double)rand()/(double)RAND_MAX * 4 - 2;
epsilon[i] = r;
gsl_vector_set (minimizer_x, i, epsilon[i]);
}
}
/* If we just wanted a grid search we are done now. */
if (grid_search) {
exit(0);
}
prev_D = calculate_f(minimizer_x, (void*)&minimizer_pars);
print_stats(statsfile, string, cstruc, length, 0 , count_df_evaluations , prev_D, -1.0, 0.0,1);
/* GSL minimization */
if (method_id !=0) {
if (method_id > 2) {
char name[100];
// Available algorithms
// 3 gsl_multimin_fdfminimizer_conjugate_fr
// 4 gsl_multimin_fdfminimizer_conjugate_pr
// 5 gsl_multimin_fdfminimizer_vector_bfgs
// 6 gsl_multimin_fdfminimizer_vector_bfgs2
// 7 gsl_multimin_fdfminimizer_steepest_descent
// http://www.gnu.org/software/gsl/manual/html_node/Multimin-Algorithms-with-Derivatives.html
switch (method_id) {
case 2:
minimizer = gsl_multimin_fdfminimizer_alloc (gsl_multimin_fdfminimizer_conjugate_fr, length+1);
strcpy(name, "Fletcher-Reeves conjugate gradient");
break;
case 3:
minimizer = gsl_multimin_fdfminimizer_alloc (gsl_multimin_fdfminimizer_conjugate_pr, length+1);
strcpy(name, "Polak-Ribiere conjugate gradient");
break;
case 4:
minimizer = gsl_multimin_fdfminimizer_alloc ( gsl_multimin_fdfminimizer_vector_bfgs, length+1);
strcpy(name, "Broyden-Fletcher-Goldfarb-Shanno");
break;
case 5:
minimizer = gsl_multimin_fdfminimizer_alloc ( gsl_multimin_fdfminimizer_vector_bfgs2, length+1);
strcpy(name, "Broyden-Fletcher-Goldfarb-Shanno (improved version)");
break;
case 6:
minimizer = gsl_multimin_fdfminimizer_alloc (gsl_multimin_fdfminimizer_steepest_descent, length+1);
strcpy(name, "Gradient descent (GSL implmementation)");
break;
}
fprintf(stderr, "Starting minimization via GSL implementation of %s...\n\n", name);
// The last two parmeters are step size and tolerance (with
// different meaning for different algorithms
gsl_multimin_fdfminimizer_set (minimizer, &minimizer_func, minimizer_x, initial_step_size, tolerance);
iteration = 1;
do {
status = gsl_multimin_fdfminimizer_iterate (minimizer);
D = minimizer->f;
norm = gsl_blas_dnrm2(minimizer->gradient);
print_stats(statsfile, string, cstruc, length,iteration, count_df_evaluations, D, prev_D, norm, iteration%sparsePS == 0);
prev_D = D;
if (status) {
fprintf(stderr, "An unexpected error has occured in the iteration (status:%i)\n", status);
break;
}
status = gsl_multimin_test_gradient (minimizer->gradient, precision);
if (status == GSL_SUCCESS) fprintf(stderr, "Minimum found stopping.\n");
iteration++;
} while (status == GSL_CONTINUE && iteration < max_iteration);
gsl_multimin_fdfminimizer_free (minimizer);
gsl_vector_free (minimizer_x);
/* Custom implementation of steepest descent */
} else {
if (method_id == 1) {
fprintf(stderr, "Starting custom implemented steepest descent search...\n\n");
} else {
fprintf(stderr, "Starting custom implemented steepest descent search with Barzilai Borwein step size...\n\n");
}
iteration = 0;
D = 0.0;
while (iteration++ < max_iteration) {
for (i=1; i <= length; i++) {
gsl_vector_set (minimizer_x, i, epsilon[i]);
}
D = calculate_f(minimizer_x, (void*)&minimizer_pars);
if (numerical) {
calculate_df_numerically(minimizer_x, (void*)&minimizer_pars, minimizer_g);
} else {
calculate_df(minimizer_x, (void*)&minimizer_pars, minimizer_g);
}
for (i=1; i <= length; i++) {
gradient[i] = gsl_vector_get (minimizer_g, i);
}
// Do line search
fprintf(stderr, "\nLine search:\n");
// After the first iteration, use Barzilai-Borwain (1988) step size (currently turned off)
if (iteration>1 && method_id==2) {
double denominator=0.0;
double numerator=0.0;
for (i=1; i <= length; i++) {
numerator += (epsilon[i]-prev_epsilon[i]) * (gradient[i]-prev_gradient[i]);
denominator+=(gradient[i]-prev_gradient[i]) * (gradient[i]-prev_gradient[i]);
}
step_size = numerator / denominator;
norm =1.0;
} else {
// Use step sized given by the user (normalize it first)
step_size = initial_step_size / calculate_norm(gradient, length);
}
for (i=1; i <= length; i++) {
prev_epsilon[i] = epsilon[i];
prev_gradient[i] = gradient[i];
}
do {
for (mu=1; mu <= length; mu++) {
epsilon[mu] = prev_epsilon[mu] - step_size * gradient[mu];
}
for (i=1; i <= length; i++) {
gsl_vector_set (minimizer_x, i, epsilon[i]);
}
DD = calculate_f(minimizer_x, (void*)&minimizer_pars);
if (step_size > 0.0001) {
fprintf(stderr, "Old D: %.4f; New D: %.4f; Step size: %.4f\n", D, DD, step_size);
} else {
fprintf(stderr, "Old D: %.4f; New D: %.4f; Step size: %.4e\n", D, DD, step_size);
}
step_size /= 2;
} while (step_size > 1e-12 && DD > D);
norm = calculate_norm(gradient,length);
if (DD > D) {
fprintf(stderr, "Line search did not improve D in iteration %i. Stop.\n", iteration);
if (hybrid_conditionals) {
sample_conditionals=0;
} else {
break;
}
}
print_stats(statsfile, string, cstruc, length,iteration, count_df_evaluations, DD, prev_D, norm, iteration%sparsePS == 0);
if (norm<precision && iteration>1) {
fprintf(stderr, "Minimum found stopping.\n");
break;
}
prev_D = DD;
}
}
/* Force last dotplot to be printed */
print_stats(statsfile, string, cstruc, length,iteration, count_df_evaluations, DD, prev_D, norm, 1);
}
free(pf_struc);
if (cstruc!=NULL) free(cstruc);
(void) fflush(stdout);
free(string);
free(structure);
RNAfold_cmdline_parser_free (&args_info);
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;
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;
}
void print_stats(FILE* statsfile, char* seq, char* struc, int length, int iteration, int count_df_evaluations, double D, double prev_D, double norm, int printPS) {
plist *pl, *pl1,*pl2;
char fname[100];
char title[100];
char* ss;
double MEAgamma, mea, mea_en;
char* output;
int i,j;
static char timestamp[40];
const struct tm *tm;
time_t now;
ss = (char *) space((unsigned) length+1);
memset(ss,'.',length);
init_pf_fold(length);
pf_fold_pb(seq, NULL);
for (i = 1; i < length; i++) {
for (j = i+1; j<= length; j++) {
p_pp[i][j]=p_pp[j][i]=pr[iindx[i]-j];
}
}
get_pair_prob_vector(p_pp, p_unpaired, length, 1);
fprintf (stderr, "\nITERATION: %i\n", iteration);
fprintf(stderr, "DISCREPANCY: %.4f\n", D);
fprintf(stderr, "NORM: %.2f\n", norm);
if (prev_D > -1.0) {
fprintf(stderr, "IMPROVEMENT: %.4f%%\n\n", (1-(D/prev_D))*100);
}
fprintf(statsfile, "%i\t%.4f\t%.4f\t%i\t", iteration, D, norm, count_df_evaluations);
for (MEAgamma=1e-5; MEAgamma<1e+6; MEAgamma*=10 ) {
pl = make_plist(length, 1e-4/(1+MEAgamma));
mea = MEA(pl, ss, MEAgamma);
mea_en = energy_of_struct(seq, ss);
fprintf(statsfile,"%s,%.2e;", ss, MEAgamma);
free(pl);
}
fprintf(statsfile, "\t");
// Stochastic backtracking
fprintf(stderr, "Sampling structures...\n");
if (sample_structure) {
char* best_structure;
char* curr_structure;
double x;
double curr_energy = 0.0;
double min_energy = +1.0;
int curr_distance = 0;
int min_distance = 999999;
best_structure = (char *) space((unsigned) length+1);
for (i=1; i<=10000; i++) {
curr_structure = pbacktrack_pb(seq);
curr_energy = energy_of_struct(seq, curr_structure);
curr_distance = 0.0;
//fprintf(stderr, "%s%.2f ", curr_structure, curr_energy);
for (j = 1; j <= length; j++) {
if (q_unpaired[j] > -0.5) {
x = (curr_structure[j-1] == '.') ? 1.0 : 0.0;
curr_distance += abs(x-q_unpaired[j]);
}
}
if (curr_distance < min_distance) {
min_distance = curr_distance;
min_energy = curr_energy;
strcpy(best_structure, curr_structure);
}
if (curr_distance == min_distance) {
if (curr_energy < min_energy) {
min_energy = curr_energy;
strcpy(best_structure, curr_structure);
}
}
//fprintf(stderr, "%i\n", curr_distance);
free(curr_structure);
}
//fprintf(stderr, "\n%s %.2f %i\n", best_structure, min_energy, min_distance);
fprintf(statsfile, "\t%s\t%.2f\t%i\t", best_structure, min_energy, min_distance);
} else {
fprintf(statsfile, "NA\tNA\tNA\t");
}
for (i = 1; i <= length; i++) {
fprintf(statsfile, "%.4f", epsilon[i]);
if (!(i==length)) {
fprintf(statsfile, ",");
}
}
now = time ( NULL );
tm = localtime ( &now );
strftime ( timestamp, 40, "%Y-%m-%d %X", tm );
fprintf(statsfile, "\t%s\n", timestamp);
/* Print dotplot only if not noPS is given and function call asks for it */
if (!noPS && printPS) {
/* Print dotplot */
sprintf(fname,"%s/iteration%i.ps", psDir, iteration);
pl1 = make_plist(length, 1e-5);
if (struc != NULL) {
pl2 = b2plist(struc);
} else {
pl2 = NULL;
}
sprintf(title,"Iteration %i, D = %.4f", iteration, D);
(void) PS_dot_plot_list_epsilon(seq, fname, pl2, pl1, epsilon, title);
}
free_pf_arrays();
}
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;
}
