typedef struct {
  
  /* Information needed to get pointers assignmets              */
                     /* example for water                       */ 
  char name[20];     /* ie, water                               */
  char pdb_nm[4];    /* ie, HOH                                 */
  char atm1[4];      /* ie, O1                                  */
  char atm2[4];      /* used for the second residue on molecule */
  char ctr_atm[4];   /* ie, O1 (the most central atom)          */
  int mod;           /* modified on the number of molecules     */
  int atm_nm;         /* number of atoms in molecule ie. 3       */
} Ptr_Info;

typedef struct {
  double nb_cut;                   /* Cutoff distance                  */
  int 
    nbinx, nbiny, nbinz,           /* # bins in the Cube               */
    atomnum;                       /* # of atoms in theatoms           */
  double sbinx, sbiny, sbinz;      /* size of the bins                 */  
  AtomList 
    **** BinnedAtoms,              /* pointer to 3d array of AtomLists */
    * theatoms;                    /* pointer to array of AtomLists    */
} theCube;

void BasicHistogram 
(double * input, int numinput, double min, double max, double binwidth, int numofbins);
void VaryBySideLength (double num, double * oto, float bxsidel);
double * theDistances (atom_record * center, atom_record * radial, float * bxsidel);
void BoxIt (file_records * f, float *bxsidel);
void FindSideLengths (float * min, float * max, float * bxsidel);
double FindMinDistance (atom_record * a, atom_record * b, float * bxsidel);
int get_mdb_coords ( file_records *f, int * istep, float * min, float * max);
long read_coord_from_traj (file_records * f, long * time, float * min, float * max);
void PrintPtrs (atom_record ** list, int num);
void AssignPtrs (file_records * f, atom_record ** list, Ptr_Info * p);
int count_atom (file_records * f, char * resname, char * name);
int CheckMolecule (file_records * f, char * resname);
Ptr_Info **CreatePtrInfoArray (int argc, char **argv, file_records * f, int *num_A);
void pdb_format (file_records * f);
theCube * SetuptheCube (file_records * f, float * bxsidel, double nb_cutoff);
void BinMoleculesIntheCube (file_records * f, theCube * C, float * box_min);
void FindNeighbors (file_records *f, theCube * C, float * box_min);
void ResettheCube (theCube * C);