OrderPDB.c
Inputs
PDB *pdb PDB linked list to fix atom order
BOOL pad TRUE: Create dummy coordinate atoms for any missing atoms in standard residues
BOOL Renum TRUE: Renumber the atoms
Returns
PDB * Corrected PDB linked list
Description
Runs through a PDB linked list and corrects the atom order to match the N,CA,C,O,s/c standard. Only standard amino acids are processed. The input linked list is modified (i.e. a new list is not built), but the return value from the routine should be used for the corrected list rather than the input PDB pointer, since the start of the list may have changed. i.e. the routine should be called with the form:
pdb = FixOrderPDB(pdb,TRUE,TRUE);
Created: 08.07.93 Last Modified: 08.07.93
Inputs
PDB *start Start of residue to be shuffled
PDB *end Start of next residue in linked list (NULL for last residue)
BOOL Pad TRUE: Create dummy records for missing atoms
Returns
PDB * Pointer to new start of linked list
Description
Shuffle atoms within a residue into the standard order. Returns a pointer to the new first atom in the residue. Atoms not in the known list are discarded. If we fail to allocate memory for extra atom records, no action is taken.
Created: 08.07.93 Last Modified: 17.03.94
Inputs
char *resnam Residue name for which to search
Outputs
char **AtomTypes Array of atom names contained in the residue
Returns
BOOL Success
Description
Fill in atom types for a given residue. AtomTypes must be pre-allocated and must be set up as an array of character pointers using Array2D() (or equivalent) rather than being created as a simple char types[][] - THIS WILL NOT WORK!
Created: 08.07.93 Last Modified: 08.07.93
Inputs
PDB *pdb Input PDB linked list
Returns
PDB * Start of shuffled PDB linked list
Description
Shuffles the PDB list to match the standard of N,CA,C,O,CB,other. Basically designed to be used with backbones only since the sidechain order is not modified. Returns the start of the shuffled PDB linked list.
Created: 13.05.92 Last Modified: 13.05.92