RdSecPDB.c File Reference

Read secondary structure information from the HELIX, TURN and SHEET records in a PDB file. More...

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

Go to the source code of this file.

Functions
SECSTRUC *	blReadSecPDB (FILE *fp, int *nsec)
SECSTRUC *	blReadSecWholePDB (WHOLEPDB *wpdb, int *nsec)

Detailed Description

Read secondary structure information from the HELIX, TURN and SHEET records in a PDB file.

Version

V1.5

Date

26.02.15

Copyright

(c) UCL / Dr. Andrew C. R. Martin 1990-2015

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:

sec = blReadSecPDB(fp,&nsec)

This routine reads the secondary structure informaton from the header of a .PDB file. It reads from file fp and creates a linked list of type SECSTRUC. The user should include "pdb.h"

On return, the variable nsec, or the value returned by the routine should be checked to ensure some secondary structure was returned. The secondary structure is stored together with ranges of residues to which it applies. The form of the structure should be checked in pdb.h

Input:    fp    *FILE      Pointer to PDB file
Output:   nsec  *int       Number of sec struc regions identified
Returns:  sec   *SECSTRUC  Linked list of type SECSTRUC

Revision History:

• V1.0 22.03.90 Original
• V1.1 20.06.90 Would crash if no secondary structure found—fixed.
• V1.2 09.07.93 Changed allocation scheme. Returns pointer to SECSTRUC. No need to initialise this before calling
• V1.3 18.08.98 Changed SEC to SECSTRUC 'cos of conflict in SunOS
• V1.4 07.07.14 Use bl prefix for functions By: CTP
• V1.5 26.02.15 Added blReadSecWholePDB() By: ACRM

Definition in file RdSecPDB.c.

Function Documentation

SECSTRUC* blReadSecPDB	(	FILE *	fp,
		int *	nsec
	)

Parameters

[in]	*fp	Pointer to PDB file
[out]	*nsec	Number of sec struc regions identified

Returns

Linked list of type SECSTRUC

Reads secondary structure information from the header of a PDB file. Returns a pointer to a linked list of type SECSTRUC.

On return, the variable nsec, or the value returned by the routine should be checked to ensure some secondary structure was returned. The secondary structure is stored together with ranges of residues to which it applies. The form of the structure should be checked in pdb.h

• 22.03.90 Original
• 20.06.90 Would crash if no secondary structure found—fixed.
• 09.07.93 Changed allocation scheme. Returns pointer to SECSTRUC. No need to initialise this before calling. Uses fsscanf()
• 18.08.98 Changed SEC to SECSTRUC 'cos of conflict in SunOS
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 141 of file RdSecPDB.c.

SECSTRUC* blReadSecWholePDB	(	WHOLEPDB *	wpdb,
		int *	nsec
	)

Parameters

[in]	*wpdb	WHOLEPDB structure
[out]	*nsec	Number of sec struc regions identified

Returns

Linked list of type SECSTRUC

Reads secondary structure information from the header of a PDB file stored in a WHOLEPDB structure. Returns a pointer to a linked list of type SECSTRUC.

On return, the variable nsec, or the value returned by the routine should be checked to ensure some secondary structure was returned. The secondary structure is stored together with ranges of residues to which it applies. The form of the structure should be checked in pdb.h

• 26.02.15 Original based on blReadSecPDB()

Definition at line 256 of file RdSecPDB.c.