HAddPDB.c
Inputs
FILE *fp File pointer to PGP file
Input/Output
PDB *pdb PDB Linked list to which Hs are added
Returns
int Number of Hs added. 0 if error.
HADDINFO gHaddInfo Information on Hs added
Description
This routine adds hydrogens to a PDB linked list. Performs all necessary functions.
N.B. Because of the variation in styles required for N-terminal Hs, this routine adds *no* hydrogens to the N-terminal residue. FixPDB() may be used for this purpose if CHARMM/CONGEN style hydrogens are required.
Created: 16.05.90 Last Modified: 08.03.94
Inputs
FILE *fp Pointer to PGP file.
Returns
int Number of parameters read.
Description
Read a proton generation parameter file. All data are placed in static arrays used by the hydrogen adding routines. Normally this routine is only called by the first call to HAddPDB(). It is only necessary to call this routine explicitly if the PGP file is changed between calls to HAddPDB() and thus needs re-reading.
Created: 16.05.90 Last Modified: 01.09.94
Input/Output
PDB *pdb PDB Linked to which Hs are added
BOOL *err_flag Error flag
Returns
int Number of hydrogens added (0 if error)
Description
Does the actual work of generating a set of hydrogens
Created: 16.05.90 Last Modified: 26.01.96
Inputs
int HType Hydrogen type number
REAL BondLen Length of the bond to the added hydrogen
REAL alpha The first angle defining the H coordinate
REAL beta The second angle defining the H coordinate
REAL firstres If set, don't add a planar hydrogen as it's the first residue of a chain
Returns
PDB * Pointer to linked list of created hydrogens. NULL if memory allocation fails or this is the Nter N where we don't require a planar H or all atoms have been done.
Description
Generate a set of hydrogen coordinates. The antecedent atoms are set in static external variables. A linked list containing the appropriate number of Hs is returned.
Created: 16.05.90 Last Modified: 24.05.99
Inputs
PDB *hlist Linked list of hydrogens to be merged
PDB **position Array of PDB pointers for atoms in this residue
int HType Hydrogen type
Returns
BOOL Success?
Description
AddH() merges a list of hydrogens for this atom into the main pdb structure list. Returns FALSE if the procedure failed.
Created: 16.05.90 Last Modified: 16.05.90
Inputs
char *pgpfile Name of a PGP file or NULL
BOOL AllHyd If name of PGP not specified, this flag specified whether all or explicit hydrogen file required
Returns
FILE * File pointer
Created: 23.08.94 Last Modified: 23.08.94