--- /dev/null
+/*
+ Interactive access to inverse folding routines
+ c Ivo Hofacker, Peter Stadler
+ Vienna RNA Package
+*/
+/* Last changed Time-stamp: <2000-09-28 14:58:05 ivo> */
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <ctype.h>
+#include <unistd.h>
+#include <string.h>
+#include "inverse.h"
+#include "fold_vars.h"
+#include "fold.h"
+#include "part_func.h"
+#include "utils.h"
+#include "read_epars.h"
+#include "RNAinverse_cmdl.h"
+
+#ifdef dmalloc
+#include "/usr/local/include/dmalloc.h"
+#define space(X) calloc(1,(X))
+#endif
+
+/*@unused@*/
+static char rcsid[] = "$Id: RNAinverse.c,v 1.11 2000/09/28 12:59:21 ivo Rel $";
+
+#define REPEAT_DEFAULT 100
+
+PRIVATE void usage(void);
+extern int inv_verbose;
+
+int main(int argc, char *argv[]){
+ struct RNAinverse_args_info args_info;
+ int input_type;
+ char *input_string, *start, *structure, *rstart, *str2, *line;
+ char *ParamFile=NULL, *c, *ns_bases;
+ int i,j, length, l, hd, sym;
+ double energy=0., kT;
+ int pf, mfe, istty;
+ int repeat, found;
+
+ dangles = 2;
+ do_backtrack = 0;
+ pf = 0;
+ mfe = 1;
+ repeat = 0;
+ input_type = 0;
+ input_string = ns_bases = NULL;
+ init_rand();
+
+ /*
+ #############################################
+ # check the command line parameters
+ #############################################
+ */
+ if(RNAinverse_cmdline_parser (argc, argv, &args_info) != 0) exit(1);
+ /* temperature */
+ if(args_info.temp_given) temperature = args_info.temp_arg;
+ /* do not take special tetra loop energies into account */
+ if(args_info.noTetra_given) 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
+ dangles = args_info.dangles_arg;
+ }
+ /* do not allow wobble pairs (GU) */
+ if(args_info.noGU_given) noGU = 1;
+ /* do not allow weak closing pairs (AU,GU) */
+ if(args_info.noClosingGU_given) no_closingGU = 1;
+ /* set energy model */
+ if(args_info.energyModel_given) energy_set = args_info.energyModel_arg;
+ /* 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);
+ /* alter the alphabet */
+ if(args_info.alphabet_given){
+ symbolset=args_info.alphabet_arg;
+ /* symbolset should only have uppercase characters */
+ for (l = 0; l < (int)strlen(symbolset); l++)
+ symbolset[l] = toupper(symbolset[l]);
+ }
+ /* set function for optimization */
+ if(args_info.function_given){
+ if(strlen(args_info.function_arg) > 2){
+ RNAinverse_cmdline_parser_print_help(); exit(EXIT_FAILURE);
+ }
+ else{
+ if((*args_info.function_arg == 'm') || (*(args_info.function_arg+1) == 'm')) mfe = 1;
+ if((*args_info.function_arg == 'p') || (*(args_info.function_arg+1) == 'p')) pf = 1;
+ }
+ }
+ /* set repeat */
+ if(args_info.repeat_given) repeat = args_info.repeat_arg;
+ /* set final cost */
+ if(args_info.final_given) final_cost = args_info.final_arg;
+ /* do we wannabe verbose */
+ if(args_info.verbose_given) inv_verbose = 1;
+
+ /* free allocated memory of command line data structure */
+ RNAinverse_cmdline_parser_free (&args_info);
+
+ kT = (temperature+273.15)*1.98717/1000.0;
+
+ istty = (isatty(fileno(stdout))&&isatty(fileno(stdin)));
+
+ if (ParamFile!=NULL)
+ read_parameter_file(ParamFile);
+
+ give_up = (repeat<0);
+
+ do {
+ /*
+ ########################################################
+ # handle user input from 'stdin'
+ ########################################################
+ */
+ if(istty)
+ print_tty_input_seq_str("Input structure & start string\n"
+ "(lower case letters for const positions) and 0 or empty line for random start string\n");
+
+ input_type = get_multi_input_line(&input_string, 0);
+ /* we are waiting for a structure (i.e. something like a constraint) so we skip all sequences, fasta-headers and misc lines */
+ while(input_type & (VRNA_INPUT_SEQUENCE | VRNA_INPUT_MISC | VRNA_INPUT_FASTA_HEADER)){
+ if(!istty && (input_type & VRNA_INPUT_FASTA_HEADER)) printf(">%s\n", input_string);
+ free(input_string); input_string = NULL;
+ input_type = get_multi_input_line(&input_string, 0);
+ }
+ if(input_type & (VRNA_INPUT_QUIT | VRNA_INPUT_ERROR)) break;
+
+ if(input_type & (VRNA_INPUT_CONSTRAINT)){
+ structure = (char *)space(sizeof(char) * (strlen(input_string) + 1));
+ (void)sscanf(input_string, "%s", structure); /* scanf gets rid of trailing junk */
+ length = (int)strlen(structure);
+ free(input_string); input_string = NULL;
+ input_type = get_multi_input_line(&input_string, VRNA_INPUT_NOSKIP_BLANK_LINES | VRNA_INPUT_NOSKIP_COMMENTS);
+ }
+ if(input_type & VRNA_INPUT_QUIT) break;
+
+ start = (char *)space(sizeof(char) * (length+1));
+ /* now we assume to get a sequence (input_string may be empty as well) */
+ if(input_type & VRNA_INPUT_SEQUENCE){
+ (void)strncpy(start, input_string, length);
+ start[length] = '\0';
+ free(input_string); input_string = NULL;
+ }
+ /* fallback to empty start sequence */
+ else start[0] = '\0';
+
+ /*
+ ########################################################
+ # done with 'stdin' handling
+ ########################################################
+ */
+
+ 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++;
+ }
+ }
+
+ str2 = (char *) space((unsigned)length+1);
+ if (istty) printf("length = %d\n", length);
+
+ if (repeat!=0) found = (repeat>0)? repeat : (-repeat);
+ else found = 1;
+
+ /* initialize_fold(length); <- obsolete (hopefully commenting this out does not affect anything crucial ;) */
+
+ rstart = (char *) space((unsigned)length+1);
+ while(found>0) {
+ char *string;
+ string = (char *) space((unsigned)length+1);
+ strcpy(string, start);
+ for (i=0; i<length; i++) {
+ /* lower case characters are kept fixed, any other character
+ not in symbolset is replaced by a random character */
+ if (islower(string[i])) continue;
+
+ if (string[i]=='\0' || (strchr(symbolset,string[i])==NULL))
+ string[i]=symbolset[int_urn(0,strlen(symbolset)-1)];
+ }
+ strcpy(rstart, string); /* remember start string */
+
+ if (mfe) {
+ energy = inverse_fold(string, structure);
+ if( (repeat>=0) || (energy<=0.0) ) {
+ found--;
+ hd = hamming(rstart, string);
+ printf("%s %3d", string, hd);
+ if (energy>0) { /* no solution found */
+ printf(" d= %g\n", energy);
+ if(istty) {
+ energy = fold(string,str2);
+ printf("%s\n", str2);
+ }
+ } else printf("\n");
+ }
+ }
+ if (pf) {
+ if (!(mfe && give_up && (energy>0))) {
+ /* unless we gave up in the mfe part */
+ double prob, min_en, sfact=1.07;
+
+ /* get a reasonable pf_scale */
+ min_en = fold(string,str2);
+ pf_scale = exp(-(sfact*min_en)/kT/length);
+ /* init_pf_fold(length); <- obsolete (hopefully commenting this out does not affect anything crucial ;) */
+
+ energy = inverse_pf_fold(string, structure);
+ prob = exp(-energy/kT);
+ hd = hamming(rstart, string);
+ printf("%s %3d (%g)\n", string, hd, prob);
+ free_pf_arrays();
+ }
+ if (!mfe) found--;
+ }
+ (void) fflush(stdout);
+ free(string);
+ }
+ free(rstart);
+ free_arrays();
+
+ free(structure);
+ free(str2);
+ free(start);
+ (void) fflush(stdout);
+ } while (1);
+ return 0;
+}
+
+
+PRIVATE void usage(void)
+{
+ nrerror("usage: RNAinverse [-F[mp]] [-a ALPHABET] [-R [repeats]] [-f final]\n"
+ " [-T temp] [-4] [-d[2]] [-noGU] [-P paramfile] [-e e_set] [-v]");
+}
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