#include "pdb.h"
int debugging = 0 ;

double maximum_x, maximum_y,maximum_z, maximum_r,minimum_x,minimum_y,minimum_z ,minimum_r ;

void print_an_atom(atom_record * atom, FILE *ff)
{

  if(atom == NULL)
    fprintf(ff, " NULL atom") ;
  else fprintf(ff , " %3.3s%-4d/%4.4s", atom->resname,atom->resnum, atom->name);
}



void serious_error (int arg_type, char *major_message, void *minor)
{
     switch (arg_type)
        {
	  case ARG_TYPE_STRING : fprintf(stderr, "serious error: %s [ %s ]\n" , major_message, minor) ; break;
	  case ARG_TYPE_INTEGER : fprintf(stderr, "serious error: %s [ %d ]\n" , major_message, minor) ; break;
	  case ARG_TYPE_ATOM : fprintf(stderr, "serious error: %s [ ", major_message);			  print_an_atom(minor,stderr) ;
		  fprintf(stderr," ]\n") ;
		  break ;
        }
   call_exit(100) ;
}

int give_warning = 0 ;
void warning (int arg_type, char *major_message, void *minor)
{

     switch (arg_type)
        {
	  case ARG_TYPE_STRING :
	     fprintf(stderr,"warning: %s [ %s ]\n" , major_message, minor) ; 
		break;
	  case ARG_TYPE_INTEGER:
	    fprintf(stderr, "warning :  %s [ %d ]\n" , major_message, minor) ;
		 break;
	 case ARG_TYPE_ATOM :
		 fprintf(stderr, "warning : %s [ ", major_message);
		  print_an_atom(minor,stderr) ;
		  fprintf(stderr," ]\n") ;
		  break ;
        }

}


void soft_warning (int arg_type, char *major_message, void *minor)
{
  if(!give_warning) return ;
  warning(arg_type,major_message,minor) ;
}


atom_record * nth_atom(file_records * file, int index)
{


      	if (file->atomnum > index)
	   return file->atoms[index] ;
	return NULL ;
}

atom_record *atom_by_number (file_records *file,int  number)
{
   int atomnum = file->atomnum;
   atom_record * atom ;
   atom_record **atoms =  file->atoms;
   int ii ;

  if((atomnum > number)  && atoms[number]->number == number)
	return atoms[number] ;
  for (ii = 0 ; ii< atomnum ; ii++)
    if (atoms[ii]->number == number)
	return atoms[ii] ;
  return NULL;   
}



double atoms_distance (atom_record *atoma, atom_record *atomb)
{
	double xdist = atoma->x - atomb->x ;
	double ydist = atoma->y - atomb->y ;
	double zdist = atoma->z - atomb->z ;

	return sqrt (xdist * xdist + ydist * ydist + zdist * zdist) ;
}



int is_cb(atom_record *atom)
{

 return ( atom->name[0]== 'C' && atom->name[1]== 'B') ;
}



int is_ca(atom_record *atom)
{

 return ( atom->name[0]== 'C' && atom->name[1]== 'A') ;
}


int is_c(atom_record *atom)
{

 return ( atom->name[0]== 'C' && atom->name[1]== ' ') ;
}



int is_n(atom_record *atom)
{

 return ( atom->name[0]== 'N' && atom->name[1]== ' ') ;
}

int is_o(atom_record *atom)
{

 return ( atom->name[0]== 'O' && atom->name[1]== ' ') ;
}

/**
 **  MBG: Added this 2.II.94 to handle nucleic acids.
 */

int isCAorP(atom_record *a)
{
# ifdef OFF
  return (is_ca(a) || (a->name[0] == 'P'));
# endif
  return (is_ca(a) || (a->name[0] == 'O' && a->name[1] == '5' && a->name[2] == '*'));
}


void maybe_free(void *pointer)
{
	if (pointer != NULL)
		free(pointer) ;
}


/*  Take a string and return a FILE * to read from it. This is quite a 
    stupid way of doing this, and there should be a standard C function to
    do this, but I didn't fint It. 
*/

FILE *stream_from_string (char *string)
{

	FILE * tt = tmpfile() ;

	fwrite(string,1,strlen(string), tt) ;

	rewind (tt);

	return tt ;
}


/*  if malloc reset the area it allocates, this is redundant.  */
char * malloc_and_zero (int len)
{
  char *new = (char *)malloc(len) ;
  bzero(new, len) ;
  return new;
}




char *new_string (char *string)
{
	char *nn = (char *)malloc(strlen (string) + 1) ;
	
	strcpy(nn,string);

	return nn;
}


void read_residue_spec(char *string, int *number, int *chain, int * x_char)
{
  int ii = 0 ;
  *chain = string[ii++];
  *number  = atoi(string+ii);
  while (isspace(string[ii])) ii++;
  while (isdigit(string[ii])) ii++;
  if (string[ii] && string[ii] != '\n')
    * x_char = string[ii++] ; 
}