#include "util.h"
#include "pdb.h"


void VectorizeAtoms
(file_records * f)
{
  int ii;
#ifdef OFF
/* 
  for (ii=0; ii<f->atomnum; ii++) {
    atom_record * a = f->atoms[ii];
    a->v = &a->x - 1; 
    assert(
	   a->v[1] == a->x &&	
	   a->v[2] == a->y &&
	   a->v[3] == a->z &&
	   a->v[4] == a->occ &&
	   a->v[5] == a->b 
	   );
  }



Comment from:  MBG : 2.II.94 

This way doesn't work. I tried defining double v[1] before the x field
in the atom_record structure, but it didn't work.

Redone on 3 March 1994. 
*/
#endif

  for (ii=0; ii<f->atomnum; ii++) {
    atom_record * a = f->atoms[ii];
    /* a->v = &a->x - 1; */
    a->v[0] = 0;
    a->footnote = NULL ;
    a->strg71on = NULL ;
    assert(
	   a->v[1] == a->x &&	
	   a->v[2] == a->y &&
	   a->v[3] == a->z &&
	   &(a->v[4]) == &(a->occ) &&
	   &(a->v[5]) == &(a->b) &&
	   &(a->v[6]) == &(a->volume) &&
	   &(a->v[7]) == &(a->surface)
	   );
  }
}

/* Mark Gerstein 6.XI.93  */
/* Links up residues into a doubly linked list, and */
/* links atoms to residues. */

void LinkUp_OneResidue
(residue_record * prev, residue_record * r)
{
  atom_record **atoms = r->file->atoms ;
  int ii;
  r->prev = prev ;
  r->next = NULL ;
  if (prev != NULL) {
    prev->next = r ;
  } 
  for(ii = r->start; ii< r->end ; ii++) {
    atom_record *atom = atoms[ii] ;
    atom->InRes = r ;
    atom->Index = ii ;
  }
}


void LinkUp_Residues_Atoms(file_records * f)
{
  if(!f->flag) {
    fprintf(stderr,"LinkUp_Residues_Atoms(): Residues not set up\n");
  } else {
    int ii,jj;
    int * resnum_vector = f->resnum ;
    residue_record ***residues = f->residues ;
    residue_record * PreviousResidue = NULL ;
    f->FirstResidue = NULL;
    f->LinkCount = 0 ;
    
    for(ii =0 ; ii< 128; ii++)
      if(resnum_vector[ii]) {
	residue_record **chain_residues =  residues[ii] ;
	int limit = resnum_vector[ii] ; 
#       ifdef OFF	
	fprintf(stderr,"ii = %4c = %d  limit = %4d\n",ii,ii,limit);
#       endif	
	for(jj = 0 ; jj< limit ; jj++) {
	  LinkUp_OneResidue(PreviousResidue, chain_residues[jj]);
	  PreviousResidue = chain_residues[jj];
	  if (f->FirstResidue == NULL) 
	    f->FirstResidue = chain_residues[jj] ;
	  f->LinkCount ++ ;
	}
      }
  }
  f->LinkUpResiduesFlag = 1 ;
  VectorizeAtoms(f);

# ifdef OFF
  fprintf(stderr,"LinkUp_Residues_Atoms(): VectorizeAtoms() completed\n");
  if (f->LinkCount != f->residue_count)
    fprintf(stderr,
	    "LinkUp_Residues_Atoms(): (%d = f->LinkCount != f->residue_count = %d)\n",
	    f->LinkCount,f->residue_count);
# endif  
}
  
void PrintResidueRecord (residue_record * r)
{
  {
# ifdef OFF
    residue_description * rt = find_residue_type(r->resname);
    if (rt == NULL) {
      STDERR("rt == NULL");
      return ;
    }
    if (rt != r->restype) {
      STDERR("Not Equal");
      PTOD(r->restype);
    }
    ITOD(r->index);
    ATOD(r->resname);
    ATOD(r->restype->name);
    PTOD(rt) ;
    ITOD(rt);
    ATOD(rt->name);
# endif
    printf("%7s%4d %-4s %-4s%c%4d%c","RESIDUE",r->index,
	 "X",r->resname,r->chain,r->number,r->x_char);
    printf(" : %6d -> %6d : %8x %8x",
	   r->start,r->end,r->flags,r->file);
    if (r->restype != NULL) {
      printf(" : %3s = %3d (%3d atoms)",
	     r->restype->name,r->restype->index,r->restype->atomnum);
    }
    printf("\n");
    if (r->ca != NULL) 
      write_pdb_record(stdout,r->ca,0);
  }
}


void PrintAllResidues(file_records * file)
{
  if(!file->flag) {
    fprintf(stderr,"PrintAllResidues: Residues not set up\n");
  } else {
    int ii,jj;
    int * resnum_vector = file->resnum ;
    residue_record ***residues = file->residues ;
    
    for(ii =0 ; ii< 128; ii++)
      if(resnum_vector[ii]) {
	residue_record **chain_residues =  residues[ii] ;
	int limit = resnum_vector[ii] ; 
#       ifdef OFF
	fprintf(stderr,"ii = %4c = %d  limit = %4d\n",ii,ii,limit);
#       endif
	for(jj = 0 ; jj< limit ; jj++) {
	  PrintResidueRecord(chain_residues[jj]);
	}
      }
  }
}

void NewPrintResidueRecord (residue_record * r)
{
  atom_record * a = r->file->atoms[r->start];
  printf("%7s%4d %-4s %-4s%c%4d%c","RESIDUE",r->index,
	 "X",a->InRes->resname,r->chain,r->number,r->x_char);
  printf(" : %6d -> %6d : %8x %8x",
	 r->start,r->end,r->flags,r->file);
  if (r->restype != NULL) {
    printf(" : %3s = %3d (%3d atoms)",
	   r->restype->name,r->restype->index,r->restype->atomnum);
  }
  printf("\n");
  write_pdb_record(stdout,a,0);
}

void NewPrintAllResidues(file_records * file)
{
  if(!file->LinkUpResiduesFlag) {
    fprintf(stderr,"NewPrintAllResidues: file->LinkUpResiduesFlag != 0\n");
  } else {
    residue_record * r;
    for (r = file->FirstResidue ; r != NULL ; r = r->next )
      NewPrintResidueRecord(r);
  }
}