Parse a residue specification. More...

#include <ctype.h>
#include <stdio.h>
#include <string.h>
#include "macros.h"
#include "SysDefs.h"
#include "pdb.h"

Functions
BOOL	blParseResSpec (char spec, char chain, int resnum, char insert)

BOOL	blDoParseResSpec (char inSpec, char chain, int resnum, char insert, BOOL uppercaseresspec)

void	blPrintResSpecHelp (FILE *fp)

void	blBuildResSpec (PDB p, char resspec)

Detailed Description

Parse a residue specification.

Version: V1.15

Date: 11.08.16

Copyright: (c) UCL / Dr. Andrew C. R. Martin 1993-2016

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 01.03.94 Original
V1.1 07.07.95 Now non-destructive
V1.2 17.07.95 Now checks that a number was specified as part of the spec. and returns a BOOL
V1.3 23.10.95 Moved FindResidueSpec() from PDBList.c
V1.4 08.02.96 Added FindResidue() and changed FindResidueSpec() to use it
V1.5 23.07.96 Added AtomNameMatch() and LegalAtomSpec()
V1.6 18.03.98 Added option to include a . to separate chain and residue number so numeric chain names can be used
V1.7 11.10.99 Allow a . to be used to start a number (such that the default blank chain name is used). Allows negative residue numbers
V1.8 29.09.05 Moved ParseResSpec() into DoParseResSpec() with extra param and added wrappers for ParseResSpec() and ParseResSpecNoUpper() (Changes by Tony Lewis) By: TL
V1.9 05.01.12 Default behaviour of ParseResSpec() is now not to upcase the chain label - there are now too many PDB entries with lower case chain names for this to be sensible. By: ACRM
V1.10 12.10.12 insert is now a properly terminated string when there is no insert
V1.11 28.08.13 chain is now a properly terminated string
V1.12 26.02.14 Parsing handles multi-letter chains. By: CTP
V1.13 07.07.14 Use bl prefix for functions By: CTP
V1.14 10.03.15 Added blPrintResSpecHelp() By: ACRM Removed blParseResSpecNoUpper() since blParseResSpec() now does this
V1.15 11.08.16 Added blBuildResSpec()

Definition in file ParseRes.c.

Function Documentation

void blBuildResSpec	(	PDB *	p,
		char *	resspec
	)

Parameters

[in] *p PDB record pointer

Builds a residue specification string for a PDB record

11.08.16 Original By: ACRM

Definition at line 352 of file ParseRes.c.

BOOL blDoParseResSpec	(	char *	inSpec,
		char *	chain,
		int *	resnum,
		char *	insert,
		BOOL	uppercaseresspec
	)

Parameters

[in]	*inSpec	Residue specification
[out]	*chain	Chain label
[out]	*resnum	Residue number
[out]	*insert	Insert label
[in]	uppercaseresspec	Convert spec to upper case.

Returns: Success?

Note that chain and insert must be arrays of at least 2 characters, not character pointers

Splits up a residue specification of the form [c][.]num[i] into chain, resnum and insert. Chain and insert are optional and will be set to spaces if not specified. If uppercaseresspec equals TRUE, the spec is upper cased before processing

Multi-letter chain IDs can be parsed. Additionally, chain IDs with numerical characters can be parsed if a period is used to separate the chain from the residue number.

21.07.93 Original By: ACRM
17.07.95 Added BOOL return
18.03.98 Added option to include a . to separate chain and residue number so numeric chain names can be used
29.09.05 Moved this code to from ParseResSpec() to DoParseResSpec() and made that function just call this new function. This move is to allow this underlying function to have an extra parameter to specify whether or not the residue specification should be upper cased (without affecting code that calls the old function). By: TL
12.10.12 insert is now a properly terminated string when there is no insert
28.08.12 chain is now a properly terminated string The input specification is now copied so that actual strings can be passed into the routine as opposed to string delimited variables. This also removes the need for restoring the string which has now been removed
26.02.14 Parsing handles multi-letter chains and numerical chain IDs. The "Extract chain from spec" section was re-written. If the period separator between the chain id and the residue number is absent then the chain id is set from any non-numeric lead characters. By: CTP
07.07.14 Use bl prefix for functions By: CTP

Definition at line 214 of file ParseRes.c.

BOOL blParseResSpec	(	char *	spec,
		char *	chain,
		int *	resnum,
		char *	insert
	)

Parameters

[in]	*spec	Residue specification
[out]	*chain	Chain label
[out]	*resnum	Residue number
[out]	*insert	Insert label

Returns: Success?

Note that chain and insert must be arrays of at least 2 characters, not character pointers

Splits up a residue specification of the form [c][.]num[i] into chain, resnum and insert. Chain and insert are optional and will be set to spaces if not specified. Converts the resiude specification to upper case before processing.

Moved the code that was here to a new function, DoParseResSpec() and made this function just call that new function. See DoParseResSpec()'s comments for notes on previous changes. This move is to allow the underlying function to have an extra parameter to specify whether or not the residue specification should be upper cased (without affecting code that calls this function).

29.09.05 Original By: TL
05.01.12 Now behaves the same as ParseResSpecNoUpper(). There are now too many PDB files with lower case chain names (e.g. 1gav, 3n9r, etc.) for the old default behaviour or up-casing everything. By: ACRM
07.07.14 Use bl prefix for functions By: CTP

Definition at line 158 of file ParseRes.c.

void blPrintResSpecHelp ( FILE * fp )

Definition at line 330 of file ParseRes.c.

Functions

Detailed Description

Description:

Usage:

Revision History:

Function Documentation