#include "pdb.h"

void set_atom_selection_on (atom_record *atom, int what,int index)
{
	atom->flags |= what ;
}	


void set_atom_selection_off(atom_record *atom, int what,int index)
{
	atom->flags &= what ;
}	

/* set the selction bit of all atoms to be on with the given bits */

void turn_selection_on(file_records *file, int what)
{
	traverse_file_atom_records(file,set_atom_selection_on,what);
}

void turn_selection_off(file_records *file, int what)
{
	traverse_file_atom_records(file,set_atom_selection_off, ~what);
}


void setup_flags_from_file(file_records* file, FILE *ff, int flag,int do_and)
{
  char string [200] ;
  char chain ;
  int resnum ;
  
  while(fgets(string,200,ff) != NULL)
    {
      int ii = 0 ;
      int x_char  = ' ' ;
	 while(string[ii] != 0 )
	   {
	     string[ii] = toupper(string[ii]) ;
	     ii++;
	   }
      if (string[ii-1] == '\n') string[ii -1] = '\0' ;
	 ii = 0 ;
	 while(isspace(string[ii])|| string[ii] == '_' ) ii++;
	 if(isdigit(string[ii]))
	   {
	     resnum =atoi(string+ii);
	     while (isdigit(string[ii])) ii++;
	     if (string[ii])
	       chain= string[ii++] ;
	     else chain = ' ';
	     if (chain == '_') chain = ' ' ;
	   }
	 else
	   {
	     chain = string[ii++];
	     resnum =atoi(string+ii);
	     while (isdigit(string[ii])) ii++;
	     if (string[ii] && string[ii] != '\n' && string[ii] != '_')
	       x_char = string[ii++] ; 
	   }

	 { residue_record * res = residue_by_number(file,resnum,chain,x_char);
	   
	   if(res == NULL)
	     serious_error(ARG_TYPE_STRING, "Failed to find residue for selection", string);
	   while (isspace(string[ii])|| string[ii] == '_') ii++;
	   if(string[ii])
	     {
	       while(string[ii])
		 {
		   int here = ii ;
		   
		   while(!isspace(string[ii]) && string[ii] && string[ii] != '_') ii++;
		   if (string[ii]) string[ii++] = 0 ;
		   {
		     atom_record *atom = find_atom_in_residue(res,string +here);
		     
		     if(atom == NULL)
		       serious_error(ARG_TYPE_STRING, "Failed to find atom in residue for selection", string);
		     
		     atom->flags = do_and ? atom->flags & flag :
		                            atom->flags | flag;
		   }
		   while(isspace(string[ii]) || string[ii] == '_') ii++;
		 }
	     }
	   else
	     traverse_residue_atoms(res,do_and ? set_atom_selection_off :
				    set_atom_selection_on,
				    flag) ;
	 }
    }
}


void select_residues_for_calculation (file_records *file, char *what,int fromfile)
{
   FILE *ff ;
  atom_record *atom ;
  int number ;

  if (!fromfile)
     {
       char * poi = what ;

       while( *poi) 
	 {
	   if (*poi == '|') *poi = '\n' ;
	   poi++;
	 }
	ff = stream_from_string (what) ;
     }
   else
     {
	ff = fopen(what,"r");
	if (ff == NULL) serious_error (1,"Failed to open residue file",what);
     }

   turn_selection_on(file, DONT_CALCULATE_ATOM) ;
   setup_flags_from_file(file,ff, ~DONT_CALCULATE_ATOM, 1);
   fclose(ff) ;
 }








void select_atoms_for_calculation (file_records *file, char *what)
{
   int from_string = isdigit(what[0]) ;
   FILE *ff ;
  atom_record *atom ;
  int number ;

  if (from_string)
     {
	ff = stream_from_string (what) ;
     }
   else
     {
	ff = fopen(what,"r");
	if (ff == NULL) serious_error (1,"Failed to open selection file",what);
     }

  turn_selection_on(file, DONT_CALCULATE_ATOM) ;

  while (fscanf(ff,"%d",&number) > 0)
    {
	atom = atom_by_number (file, number) ;
	if (atom == NULL)
	   warning(2,"Failed to find atom  for selection", number) ;
	else SWITCH_OFF(atom , DONT_CALCULATE_ATOM) ;
    }

  fclose (ff) ;
}








char * selection_argument = NULL ;
char * residue_selection_argument = NULL;
char * residue_selection_file  = NULL ;






void setup_selection (file_records *file)
{



  if(selection_argument != NULL)
    select_atoms_for_calculation (file, selection_argument);
  if (residue_selection_argument != NULL)
    select_residues_for_calculation (file, residue_selection_argument,0);
  if (residue_selection_file != NULL)
    select_residues_for_calculation (file, residue_selection_file,1);
}

void select_protein_atoms(file_records *file)
{

	  turn_selection_on(file, DONT_CALCULATE_ATOM) ;

	  traverse_file_protein_atoms(file,set_atom_selection_off, ~ DONT_CALCULATE_ATOM) ;
}



void ignore_water_atoms(file_records *file)
{
  traverse_file_water_atoms(file,set_atom_selection_on,  IGNORE_ATOM) ;
}
	

void ignore_hetatm(atom_record *atom, void *ignore , int index)
{
  if (atom->atomtype != RECORD_ATOM)
    SWITCH_ON(atom, IGNORE_ATOM) ;
}

void ignore_hetatms(file_records *file)
{
  traverse_file_atom_records(file, ignore_hetatm, NULL);
}