Exemple #1
0
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;
}
Exemple #2
0
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;
}
Exemple #3
0
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;
}
Exemple #4
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;

    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(&paramfile);
    ajFileClose(&outf);
    ajFileClose(&essfile);

    if (length<2000)
        free_co_arrays();

    embExit();

    return 0;
}
Exemple #5
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;
}