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The PDB Data Structure

Bioplib - The PDB Data Structure and Linked Lists.

The PDB Data Structure

The main data structure used by bioplib is the PDB linked list.

typedef struct pdb_entry
REAL x, y, z, /* Coordinates */
occ, bval, /* Occupancy and B-value */
access, radius, /* Accessibility and radius - populated by
Bioplib routines */
partial_charge; /* Reserved for future use */
APTR extras; /* Pointer for users to add information */
blATOMTYPE *atomType; /* Reserved for future use */
struct pdb_entry *next; /* Forward linked list */
int atnum; /* Atom number */
int resnum; /* Residue number */
int formal_charge; /* Formal charge - used in XML files */
char record_type[8]; /* ATOM / HETATM */
char atnam[8]; /* Atom name, left justified */
char atnam_raw[8]; /* Atom name as it appears in the PDB file */
char resnam[8]; /* Residue name */
char insert[8]; /* Numbering insert code */
char chain[8]; /* Chain label */
char element[8]; /* Element type */
char altpos; /* Alternate position indicator */
} PDB;

The PDB data structure contains the data for each ATOM or HETATM record in the PDB file. The structure contains a link to the next atom in the list and the following data corresponding to the fields in the ATOM/HETATM record in a PDB file:

The structure contains a link to the next node in the linked list:

Additionally the following values are included:

The extras field is used to attach additional data structure or array to each atom record. For example:

typedef struct
REAL angle;
BOOL flag;
PDB *p;
for(p=pdb; p!=NULL; NEXT(p))
if((p->extras = (APTR)malloc(sizeof(EXTRAS)))==NULL)
for(p=pdb; p!=NULL; NEXT(p))
((EXTRAS *)p->extras)->flag = FALSE;
((EXTRAS *)p->extras)->angle = (REAL)0.0;