#include "MakeNewAtom.h"

atom_record * MakeNewAtom(char * string)
{
  if (string == NULL)
    return NULL ;
  else if (strlen(string) < 6)
    return NULL ;
  else {
    int ii ;
    int type = find_record_type(string) ;   
    if (RECORD_ATOM > type) {
      STDERR("MakeNewAtom(): Barf! I only eat real atoms for dinner.");
    } else {
      char t12 = string[12] ;
      char t13= string[13] ;
      if (t12 == ' ' || isdigit(t12))
	t12 = t13 ;
      
      {
      	atom_record * newrec = (atom_record *) malloc(sizeof(atom_record)); 
	char *name = newrec->name ;
	int flags = 0 ;

 	newrec->atomtype = type ;
	strncpy(newrec->ident,string, 6) ;
	newrec->ident[6] = 0 ; 
	sscanf (string +6 ,"%5d" , &newrec->number) ;
	strncpy(newrec->resname,string+17, 3) ;	
	if (string[12] == ' ') {
	  strncpy(name,string+13, 3) ;
	  name[3] = '\0';
	  if(name[0] == 'S') {
	    if ( name[1] == 'G'  && name[2] == ' ' &&name[3] == '\0' &&
		newrec->resname[0] == 'C' &&
		newrec->resname[1] == 'Y'
		&& newrec->resname[2] == 'S')
	      /* record_sg_atom(newrec) */ ;
	  } else 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 ;
	} else 
	  strncpy(name,string+12, 4) ;
	newrec->extraflag= string[16] ;
	
	if (newrec->extraflag != ' ' && newrec->extraflag != 'A')
	  flags |=  IGNORE_ATOM ;
	
	newrec->resname[3] = 0 ;
	{ 
	  char chain = string[21] ;
	  if (newrec->atomtype != RECORD_ATOM)
	    chain = tolower(chain) ;
	  newrec->chain = chain;
	}
	newrec->x_char = string[26] ;
	sscanf(string+22, "%4d", &newrec->resnum);
	sscanf(string+30, LF_STRING_07, &newrec->x,&newrec->y,&newrec->z,
	       &newrec->occ,&newrec->b);
	newrec->restype = find_residue_type(newrec->resname) ; 
	newrec->definition = find_atom_definition(newrec->restype,newrec->name) ;
	
	sscanf(string+67, LF_STRING_08,&newrec->surface, &newrec->volume) ;
	newrec->flags = flags ; 
	
	return newrec;
      }
    }
  }
}

file_records *ConstructNDummyAtoms(char * string, int n)
{
  file_records * f = (file_records *) calloc(1,sizeof(file_records)) ;
  int ii;
  f->atomnum = n;
  f->atoms =(atom_record **) malloc (n*sizeof(atom_record *)) ;
  for (ii=0; ii<n; ii++) {
    f->atoms[ii] = MakeNewAtom(string);
  } 
  make_residues(f) ;
  f->name = NULL ;
  LinkUp_Residues_Atoms(f);
  return f ;
}


void FreeFileRecordsWithOutFreeingAtoms(file_records *f)
{
  if (f!=NULL) {
    if (f->atoms != NULL && f->atomnum > 0) {
      free (f->atoms);
      if (f->flag &&  f->residue_count > 0) {
	free_file_residues(f) ;
      }
    }
    free(f);
  }
}

file_records *JoinFileRecords_1then2 (file_records *f1,file_records *f2)
{
  int 
    ii,
    n1 = f1->atomnum,
    n2 = f2->atomnum,
    nj = n1 + n2;
  file_records * Join = (file_records *) calloc(1,sizeof(file_records)) ;
  Join->atomnum = nj;
  Join->atoms =(atom_record **) malloc(nj*sizeof(atom_record *)) ;
  for (ii=0; ii<n1; ii++) {
    Join->atoms[ii] = f1->atoms[ii];
  } 
  for(ii=n1; ii<nj; ii++) {
    Join->atoms[ii] = f2->atoms[ii-n1];
  }
  Join->flag = 0;
  Join->LinkUpResiduesFlag  =0;
  make_residues(Join) ;
  Join->name = NULL ;
  LinkUp_Residues_Atoms(Join);
  return Join ;
}

file_records *MoveSelectedToDerivedFileRecord(file_records *f, int flag)
{
  int 
    ii,nn,jj,
    n = f->atomnum;
  for (ii=0; ii<f->atomnum; ii++) {
    atom_record * a = f->atoms[ii] ;
    if (IS_SELECTED_WRT(a,flag) )
      nn++;
  }
  {
    file_records * New = (file_records *) calloc(1,sizeof(file_records)) ;
    New->atomnum = nn;
    New->atoms =(atom_record **) calloc(nn,sizeof(atom_record *)) ;
    for (ii=0, jj=0; ii<f->atomnum; ii++) {
      atom_record * a = f->atoms[ii] ;
      if (IS_SELECTED_WRT(a,flag) ) {
	New->atoms[jj] = f->atoms[ii];
	jj++ ;
      }
    } 
    New->flag = 0;
    New->LinkUpResiduesFlag  =0;
    make_residues(New) ;
    New->name = NULL ;
    LinkUp_Residues_Atoms(New);
    return New ;
  }
}

file_records *NewFileRecWithOutWaterOrSymChain(file_records *f)
{
  int ii;
  for (ii=0; ii<f->atomnum; ii++) {
    atom_record * a = f->atoms[ii] ;
    if (a->name[0] == 'H' || a->name[0] == 'D' ||
	a->extraflag == 'B' || a->chain == '_' ||
	a->chain == 'X' || a->chain == 'Y' || a->chain == 'Z' ||
	a->chain == 'W' ||
	WATER_ATOM_P(a)) 
      SWITCH_ON(a,FLAG_1_DESELECT);
    else 
      SWITCH_OFF(a,FLAG_1_DESELECT);
  }
  return MoveSelectedToDerivedFileRecord(f, FLAG_1_DESELECT) ;
}

file_records *NewFileRecWithOutWater(file_records *f)
{
  int ii;
  for (ii=0; ii<f->atomnum; ii++) {
    atom_record * a = f->atoms[ii] ;
    if (a->name[0] == 'H' || a->name[0] == 'D' ||
	a->extraflag == 'B' || 
	WATER_ATOM_P(a)) 
      SWITCH_ON(a,FLAG_1_DESELECT);
    else 
      SWITCH_OFF(a,FLAG_1_DESELECT);
  }
  return MoveSelectedToDerivedFileRecord(f, FLAG_1_DESELECT) ;
}