#include "MakeNewAtom.h"

atom_record * RadFileStringToNewAtom(char * string)
{
  if (string == NULL)
    return NULL ;
  else {
    int ii ;
    int type = RECORD_ATOM ;
    char t12 = string[12] ;
    atom_record * newrec = (atom_record *) malloc(sizeof(atom_record)); 
    char *name = newrec->name ;
    int flags = 0 ;
    newrec->atomtype = type ;
    strncpy(newrec->ident,"ATOM  ", 6) ;
    newrec->ident[6] = 0 ; 
    {
      /* From */      
      /*     ======================                        */
      /* int rd_richards_RAD_volume                        */
      /*     ======================                        */
      int ncalc,i,numchn,numfil;
      char atm[10], res3[10];
      int seqnum;
      double x, y, z, rvdw, rcov, volume;
      int ns ;
      char *buf1 = string + 1;
      
      sscanf(buf1,"%5d%5d%3d%3d%6c%6c%5d%8lf%8lf%8lf%5lf%5lf%8lf%5d",
	     &ncalc,&i,&numchn,&numfil,atm,res3,&seqnum,
	     &x,&y,&z,&rvdw,&rcov,&volume,&ns);
      /* fix for volumes of 1000 */
      sscanf(buf1 + 67,"%8lf",&volume);
      newrec->number = i ;
      strcpy(newrec->resname,res3);
      strcpy(newrec->name,atm);
      if (type == RECORD_ATOM &&
	  ((name[0] == 'C' && name[1] == ' ') ||
	   (name[0] == 'C' && name[1] == 'A' && name[2] == ' ')||
	   (name[0] == 'O' && name[1] == ' ') ||
	   (name[0] == 'N' && name[1] == ' ') ))
	flags |= MAIN_CHAIN_ATOM ;
      newrec->extraflag = ' ' ;
      newrec->chain = ' ' ;
      newrec->x_char = ' ';
      newrec->resnum = seqnum ;
      newrec->x = x ;
      newrec->y = y ;
      newrec->z = z ;
      newrec->occ = rvdw ;
      newrec->b = rcov ;
      newrec->restype = find_residue_type(newrec->resname) ; 
      newrec->definition = find_atom_definition(newrec->restype,newrec->name) ;
      newrec->volume = volume ;
      newrec->dumm_solvents = ns ;
      newrec->flags = flags ; 
    }
    return newrec;
  }
}


file_records *ReadRadFile(FILE * ff, int format)
{
  file_records * f = (file_records *) calloc(1,sizeof(file_records)) ;
  int ii;
  int n = 0;
  bool start = false ;
  int tmp_n = 10000 ;
  atom_record ** tmp_atoms =(atom_record **) calloc (tmp_n,sizeof(atom_record *)) ;
  char string[BUFSIZ];
  do {
    char *sa 	= fgets (string, 200, ff) ;
    if (sa == NULL && feof(ff) != 0) {
      STDERR("barf! Bad RAD file format. Couldn't get started.");
      return NULL ;
    } else if (StreqWithSpaces(sa,"BEGIN")) {
      start = true ;
    } 
  } while (!start) ; 
  while (start) {
    char *sa 	= fgets (string, 200, ff) ;
    if (sa == NULL) {
      start = false ;
    } else if (StreqWithSpaces(sa,"TOTAL")) {
      start = false  ;
    } else {
      tmp_atoms[n] = RadFileStringToNewAtom(sa);
      if (tmp_atoms[n] == NULL) 
	start = false  ;
      else 
	n++;
    }
  }
  f->atomnum = n;
  f->atoms =(atom_record **) calloc (n,sizeof(atom_record *)) ;
  for (ii=0; ii<n; ii++) {
    f->atoms[ii] = tmp_atoms[ii];
  } 
  free(tmp_atoms);
  make_residues(f) ;
  f->name = NULL ;
  LinkUp_Residues_Atoms(f);
  return f ;
}


file_records *OpenReadRadFile(char * name,int format)
{
  if (dumm_residue == NULL)
    serious_error(1, "do_initialization was not called before reading a file","") ;
  
  fprintf(stderr,"OpenReadRadFile(): Trying to read %s\n", name) ;
  {
    FILE * ff= fopen(name,"r") ; 
    
    if (ff == NULL) {
      fprintf(stderr,"OpenReadRadFile(): Unable to open file, returning NULL.\n");
      return(NULL) ;
    } else {
      file_records *new = ReadRadFile ( ff, format) ;
      
      fclose(ff) ;
      if (new != NULL) {
	new->name = new_string(name);
	new->header = NULL ;
      }
      return new ;
    }
  }
}