#define C_P(atom) (atom->name[0] == 'C')
#define side_chain_c(atom) (atom->name[0] == 'C' && atom->name[1] != ' ' && atom->name[1] != 'A')
#define WATER_ATOM_P(atom) (atom->restype != NULL && (atom->restype->index == first_water_type ||atom->restype->index == second_water_type ))
#define PROTEIN_ATOM_P(atom) (atom->restype != NULL && atom->restype->index <= 19 &&atom->restype->index >= 0 )


#define SELECTED_ATOM_P(atom) !(atom->flags & (DONT_CALCULATE_ATOM | IGNORE_ATOM))
#define NOT_SELECTED_ATOM_P(atom) atom->flags & (DONT_CALCULATE_ATOM | IGNORE_ATOM)


#define LOOP_RESIDUE_ATOMS(res,body)                  \
     {                                               \
	 int _atom_index;                            \
	   residue_record *_res = res ;              \
	   atom_record **_atoms = _res->file->atoms ; \
	                                             \
	       for(_atom_index = _res->start; _atom_index< _res->end ;   \
		   _atom_index++)                                        \
	  {                                                              \
		atom_record *atom = _atoms[_atom_index] ;                \
		                                                         \
		body                                                     \
	  }}

#define MAIN_CHAIN_ATOM_P(atom) (atom->flags & MAIN_CHAIN_ATOM)

#define SET_DOUBLE_FROM_OPTION(var,string)     \
    { char * a = command_line_arg(string) ;    \
	if (a != NULL) var = strtod(a,NULL) ;}


#define SET_INT_FROM_OPTION(var,string)     \
    { char * a = command_line_arg(string) ;    \
	if (a != NULL) var = atoi(a) ;}
    
#define DEBUGGING   debugging &  DEBUG_LEVEL_1

/*   THis does not work for non-standard definitions */

#define PROTEIN_ATOM_DEFINITION_INDEX(ad,rd) (ad - rd->atom_definitions)


#define TRAVERSE_FILES(body) { file_records *file ; while((file = read_next_file_checked(0)) != NULL){  body free_file_records(file) ; }}

#define ATOM_MEASUREMENT_INDEX(ssbond,rdindex,index) 21 * (ssbond ? 20 :rdindex) + index









#define OPERATION_TRANSFORM(so,_tx,_ty,_tz,_sx,_sy,_sz) {\
     symmetry_operation *_so = so ; \
     tx = _sx * _so->xx + _sy * _so->yx + _sz *_so->zx + _so->addx ;  \
     ty = _sx * _so->xy + _sy * _so->yy + _sz *_so->zy + _so->addy ;  \
     tz = _sx * _so->xz + _sy * _so->yz + _sz *_so->zz + _so->addz ;  }

#define MATRIX_TRANSFORM(so,_tx,_ty,_tz,_sx,_sy,_sz) {\
     a_matrix *_so = so ; \
     _tx = _sx * _so->xx + _sy * _so->yx + _sz *_so->zx  ;  \
     _ty = _sx * _so->xy + _sy * _so->yy + _sz *_so->zy  ;  \
     _tz = _sx * _so->xz + _sy * _so->yz + _sz *_so->zz  ;  }

#define LOOP_SG_OPERATIONS(sp,start, body)  {\
        int opnum ;                                 \
        space_group * _sp = sp	;				     \
        for(opnum =start ; opnum < _sp->ops_number; opnum++)  \
	  {                                              \
	    symmetry_operation *so = &_sp->ops[opnum] ;    \
	    body                                         \
	    }}
		
#define LOOP_ALL_SG_OPERATIONS(sp,body) LOOP_SG_OPERATIONS(sp,0,body)
#define LOOP_OTHER_SG_OPERATIONS(sp,body) LOOP_SG_OPERATIONS(sp,1,body)


#define RES_CHAR_TO_INDEX(cc) residue_character_types[cc]