Routine to add C-terminal oxygens. More...

#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "SysDefs.h"
#include "MathType.h"
#include "pdb.h"
#include "macros.h"

Macros
#define	MAXBUFF 160

Functions
BOOL	blFixCterPDB (PDB *pdb, int style)

Detailed Description

Routine to add C-terminal oxygens.

Version: V1.10

Date: 05.03.15

Copyright: (c) UCL / Dr. Andrew C. R. Martin 1994-2015

Author: Dr. Andrew C. R. Martin

: Institute of Structural & Molecular Biology, University College London, Gower Street, London. WC1E 6BT.

: andre.nosp@m.w@bi.nosp@m.oinf..nosp@m.org..nosp@m.uk andre.nosp@m.w.ma.nosp@m.rtin@.nosp@m.ucl..nosp@m.ac.uk

This code is NOT IN THE PUBLIC DOMAIN, but it may be copied according to the conditions laid out in the accompanying file COPYING.DOC.

The code may be modified as required, but any modifications must be documented so that the person responsible can be identified.

The code may not be sold commercially or included as part of a commercial product except as described in the file COPYING.DOC.

Description:

Usage:

BOOL FixCterPDB(PDB *pdb, int style)

Renames Cter oxygens in the required style (CTER_STYLE_STD, CTER_STYLE_GROMOS or CTER_STYLE_CHARMM) and generates a second oxygen if required. If the style is CHARMM an extra CTER residue will be created. Input may be in any of the 3 styles.

Revision History:

V1.0 24.08.94 Original By: ACRM
V1.1 05.10.94 Removed unused variables
V1.2 12.11.96 If any of the antecedant coordinates are undefined, set the terminal oxygen to NULL coordinates
V1.3 13.11.96 Also checks for missing CA,C and O1 records
V1.4 06.02.03 Handles atnam_raw
V1.5 03.06.05 Handles altpos
V1.6 04.02.14 Use CHAINMATCH By: CTP
V1.7 07.07.14 Use bl prefix for functions By: CTP
V1.8 17.02.15 Added check on memory allocation By: ACRM
V1.9 25.02.15 Ensures terminal oxygens are only added to amino acids not HETATM groups
V1.10 05.03.15 Replaced blFindEndPDB() with blFindNextResidue()

Definition in file FixCterPDB.c.

Macro Definition Documentation

#define MAXBUFF 160

Definition at line 96 of file FixCterPDB.c.

Function Documentation

BOOL blFixCterPDB	(	PDB *	pdb,
		int	style
	)

Parameters

[in,out]	*pdb	PDB linked list to modify
[in]	style	CTER_STYLE_STD, CTER_STYLE_GROMOS or CTER_STYLE_CHARMM

Returns: Memory allocation OK?

Renames C-ter atoms in required style and calls CalcCterCoords() as required to calculate coordinates ans splices them in. The input PDB linked list may have standard, CHARMM or GROMOS style.

24.08.94 Original By: ACRM
05.10.94 Removed unused variables
12.11.96 If any of the antecedant coordinates are undefined, set the terminal oxygen to NULL coordinates
13.11.96 Added check on finding CA,C and O1 If no C or O1 present, OXT not added
06.02.03 Handles atnam_raw
03.06.05 Handles altpos
04.02.14 Use CHAINMATCH By: CTP
07.07.14 Use bl prefix for functions By: CTP
17.02.15 Checks INIT() succeeded By: ACRM
25.02.15 Ensures terminal oxygens are only added to amino acids not HETATM groups
05.03.15 Replaced blFindEndPDB() with blFindNextResidue()

Definition at line 138 of file FixCterPDB.c.