ExtractZonePDB.c File Reference

PDB linked list manipulation. More...

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

Go to the source code of this file.

Functions
PDB *	blExtractZonePDBAsCopy (PDB *inpdb, char *chain1, int resnum1, char *insert1, char *chain2, int resnum2, char *insert2)
PDB *	blExtractZoneSpecPDBAsCopy (PDB *pdb, char *firstRes, char *lastRes)
PDB *	blExtractNotZonePDBAsCopy (PDB *inpdb, char *chain1, int resnum1, char *insert1, char *chain2, int resnum2, char *insert2)
PDB *	blExtractNotZoneSpecPDBAsCopy (PDB *pdb, char *firstRes, char *lastRes)

Detailed Description

PDB linked list manipulation.

Version

V1.19

Date

17.02.16

Copyright

(c) UCL / Dr. Andrew C. R. Martin 1992-2016

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:

Revision History:

• V1.0 22.02.94 Original release
• V1.1 23.05.94 Added FindNextChainPDB()
• V1.2 05.10.94 KillSidechain() uses BOOL rather than int
• V1.3 24.07.95 Added TermPDB()
• V1.4 25.07.95 Added GetPDBChainLabels()
• V1.5 26.09.95 Fixed bug in TermPDB()
• V1.6 12.10.95 Added DupePDB(), CopyPDBCoords()
• V1.7 23.10.95 Moved FindResidueSpec() to ParseRes.c
• V1.8 10.01.96 Added ExtractZonePDB()
• V1.9 14.03.96 Added FindAtomInRes()
• V1.10 08.10.99 Initialised some variables
• V1.11 22.03.05 Extracted range is limited by specified residues
• V1.12 22.03.06 Modified ExtractZonePDB() to allow non-exact ranges
• V1.13 29.10.10 Fixed bug when end of zone was last residue in a chain
• V1.14 04.02.14 Use CHAINMATCH By: CTP
• V1.15 07.07.14 Use bl prefix for functions By: CTP
• V1.16 19.08.14 Renamed function to blExtractZonePDBAsCopy() By: CTP
• V1.17 07.10.15 Added function blExtractNotZonePDBAsCopy() and blExtractNotZonePDBAsCopy() By: ACRM
• V1.18 08.12.15 Modified blExtractZoneAsCopy() to check for exact match first

Definition in file ExtractZonePDB.c.

Function Documentation

PDB* blExtractNotZonePDBAsCopy	(	PDB *	inpdb,
		char *	chain1,
		int	resnum1,
		char *	insert1,
		char *	chain2,
		int	resnum2,
		char *	insert2
	)

Parameters

[in]	*inpdb	Input PDB linked list
[in]	*chain1	Start residue chain name
[in]	resnum1	Start residue number
[in]	*insert1	Start residue insert code
[in]	*chain2	End residue chain name
[in]	resnum2	End residue number
[in]	*insert2	End residue insert code

Returns

PDB linked list of the region of interest.

Reduces a PDB linked list to those residues outside a specified zone. Note that the PDB linked list is duplicated before extraction so pointers do not match those in the input PDB linked list. Excess records in the new PDB linked list are freed.

• 07.10.15 Original By: ACRM
• 08.10.15 Fixed return(FALSE) to return(NULL)

Definition at line 341 of file ExtractZonePDB.c.

PDB* blExtractNotZoneSpecPDBAsCopy	(	PDB *	pdb,
		char *	firstRes,
		char *	lastRes
	)

Parameters

[in]	pdb	PDB linked list
[in]	firstRes	Residue spec ([chain]resnum[insert])
[in]	lastRes	Residue spec ([chain]resnum[insert])

Extracts atoms outside a zone from a PDB linked list, making a copy of the original list.

• 07.10.15 Original By: ACRM

Definition at line 417 of file ExtractZonePDB.c.

PDB* blExtractZonePDBAsCopy	(	PDB *	inpdb,
		char *	chain1,
		int	resnum1,
		char *	insert1,
		char *	chain2,
		int	resnum2,
		char *	insert2
	)

Parameters

[in]	*inpdb	Input PDB linked list
[in]	*chain1	Start residue chain name
[in]	resnum1	Start residue number
[in]	*insert1	Start residue insert code
[in]	*chain2	End residue chain name
[in]	resnum2	End residue number
[in]	*insert2	End residue insert code

Returns

PDB linked list of the region of interest.

Reduces a PDB linked list to those residues within a specified zone. Note that the PDB linked list is duplicated before extraction so pointers do not match those in the input PDB linked list. Excess records in the new PDB linked list are freed.

• 10.01.96 Original By: ACRM
• 22.03.06 Modified to allow non-exact zones. i.e. the extracted zone will be the widest subset of the specified zone. So, if you specifiy 30-35Z and the PDB file only has 30-35B then that will be extracted.
• 29.10.10 Fixed extraction where end of zone matched last residue in a chain
• 04.02.14 Use CHAINMATCH By: CTP
• 07.07.14 Use bl prefix for functions By: CTP
• 19.08.14 Renamed function to blExtractZonePDBAsCopy() By: CTP
• 08.12.15 Now checks for an exact match first to deal with 6INS that uses the insert code for something different! By: ACRM

• 17.02.16 Added fix on check for exact match - prev wasn't being set correctly if the match was to the first residue in the file

  TODO - This doesn't deal with CONECT information properly! ***

Definition at line 158 of file ExtractZonePDB.c.

PDB* blExtractZoneSpecPDBAsCopy	(	PDB *	pdb,
		char *	firstRes,
		char *	lastRes
	)

Parameters

[in]	pdb	PDB linked list
[in]	firstRes	Residue spec ([chain]resnum[insert])
[in]	lastRes	Residue spec ([chain]resnum[insert])

Extracts a zone from a PDB linked list, making a copy of the original list.

• 08.10.14 Original By: ACRM

Definition at line 300 of file ExtractZonePDB.c.