# include "pdb.h"


ExtraAtomRecord ** InitExtraAtomRecords(int n, int size)
{
  int ii;
  ExtraAtomRecord ** E ;
  E = (ExtraAtomRecord **) calloc(n+1,sizeof(ExtraAtomRecord *)) ;
  for (ii = 0 ; ii < n ; ii++) {
    E[ii] = (ExtraAtomRecord *) calloc(1,size) ;
    E[ii]->ii = ii ;
  }
  return E ;
}

void CopyAtomVects2To1
  (ExtraAtomRecord ** A0, char * A0Rx,
   ExtraAtomRecord ** B0, char * B0Ry,
   int n)
{
  char * A0R = (char *) *A0 ;
  char * B0R = (char *) *B0 ;
  int
    Ainc    = A0Rx  - A0R,
    Binc    = B0Ry -  B0R,
    i ;
  
  if (n <= 0)
    STDERR("ERROR! n <= 0");
  if (Binc <= 0)
    STDERR("ERROR! Binc <= 0");
  if (Ainc <= 0)
    STDERR("ERROR! Ainc <= 0");

  for(i=0; i<n; i++) {
    ExtraAtomRecord ** Ai = A0 + i;
    ExtraAtomRecord ** Bi = B0 + i;
    double * dAiRx = (double *) ((char *) *Ai + Ainc) ;
    double * dBiRy = (double *) ((char *) *Bi + Binc) ;
    *dAiRx = *dBiRy ;
  }
}

void ThresholdAtomVects
  (ExtraAtomRecord ** A0, char * A0Rx, int n, double t)
{
  char * A0R = (char *) *A0 ;
  int
    Ainc    = A0Rx  - A0R,
    i ;
  
  if (n <= 0)
    STDERR("ERROR! n <= 0");
  if (Ainc <= 0)
    STDERR("ERROR! Ainc <= 0");

  for(i=0; i<n; i++) {
    ExtraAtomRecord ** Ai = A0 + i;
    double * dAiRx = (double *) ((char *) *Ai + Ainc) ;
    if (*dAiRx < t) *dAiRx = t ;
  }
}

void dVToB(file_records * f)
{
  Statistic s;
  int ii;
  InitStats(&s);
  FlagAllAtomsInCYS(f);
  for (ii = 0; ii<f->atomnum; ii++) {
    atom_record * a = f->atoms[ii];
    if (!(a->flags & IGNORE_ATOM)) {
      atom_definition *ad = a->definition ;
      double std_vol = (a->flags & SULPHUR_BRIDGE ? ad->eradsq : ad->eradius) ;
      double dV = (std_vol > 1.0 && a->volume > 1.0 ? a->volume - std_vol : 99.99) ;
      IncrementStats(&s,dV);
      a->b = dV ;
    }
  } 
  s.name = "dV" ;
  DumpStats(&s,stderr);
}

void BDivRefVToOcc (file_records * f)
{
  int ii;
  FlagAllAtomsInCYS(f);
  for (ii = 0; ii<f->atomnum; ii++) {
    atom_record * a = f->atoms[ii];
    if (!(a->flags & IGNORE_ATOM)) {
      atom_definition *ad = a->definition ;
      double std_vol = (a->flags & SULPHUR_BRIDGE ? ad->eradsq : ad->eradius) ;
      if (std_vol > 1.0) 
	a->occ = a->b / std_vol ;
    }
  }
}

void RefVToB(file_records * f)
{
  int ii;
  {
    residue_description * res = find_residue_type("CYS");
    atom_definition * ad = find_atom_definition(res,"SG");
    FTOE(ad->eradius);
    FTOE(ad->eradsq);
  }
  for (ii = 0; ii<f->atomnum; ii++) {
    atom_record * a = f->atoms[ii];
    if (!(a->flags & IGNORE_ATOM)) {
      atom_definition *ad = a->definition ;
      a->b = (a->flags & SULPHUR_BRIDGE ? ad->eradsq : ad->eradius) ;
    }
  }
}

atom_record * InitDummyAtom(atom_record * atom)
{
  atom->atomtype = RECORD_ATOM ;
  strcpy(atom->ident,"ATOM  ");
  strcpy(atom->resname,"RES");
  strcpy(atom->name,"ATM");
  atom->chain = ' ';
  atom->extraflag = ' ';
  atom->x_char = ' ' ;
  atom->number = 1;
  atom->resnum = 1;
  atom->occ = 1 ;
  atom->b = 0 ;
  atom->x =  atom->y = atom->z = 0;
  return atom ;
}



atom_record * find_atom_in_file(const atom_record * atom ,file_records * f2)
{
  int ii;
  
  for (ii = 0 ; ii < f2->atomnum ; ii++) {
    atom_record * a2 = f2->atoms[ii];
    if ((atom->atomtype == a2->atomtype ) &&
 	(atom->chain == a2->chain)  &&
	(atom->resnum == a2->resnum) &&
	StreqWithSpaces(atom->resname,a2->resname) &&
	StreqWithSpaces(atom->name,a2->name))
      return a2 ;
  }
  return NULL ;
}