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:

• record_type - Record Type (ATOM/HETATM)
• atnum - Atom serial number.
• atnam - Atom name.
• altpos - Alternate location indicator.
• resnam - Residue name.
• chain - Chain identifier.
• resnum - Residue sequence number.
• insert - Code for insertion of residues.
• x - X Coordinate in Angstroms.
• y - Y Coordinate in Angstroms.
• z - Z Coordinate in Angstroms.
• occ - Occupancy.
• bval - Temperature factor.
• element - Element symbol.
• formal_charge - Charge on the atom.

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

• next - Next ATOM/HETATM record in list.

Additionally the following values are included:

• access - Solvent accessibility.
• radius - Atom radius for solvent accessibility calculations.
• partial_charge - Partial charge

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

typedef struct
{
   REAL angle;
   BOOL flag;
}  EXTRAS;
PDB *p;

for(p=pdb; p!=NULL; NEXT(p))
{
   if((p->extras = (APTR)malloc(sizeof(EXTRAS)))==NULL)
      return(FALSE);
}

for(p=pdb; p!=NULL; NEXT(p))
{
   ((EXTRAS *)p->extras)->flag = FALSE;
   ((EXTRAS *)p->extras)->angle = (REAL)0.0;
}