PDB2Seq.c File Reference

Conversion from PDB to sequence and other sequence related routines. More...

#include <stdlib.h>
#include <string.h>
#include "macros.h"
#include "pdb.h"
#include "seq.h"

Go to the source code of this file.

Functions
char *	blDoPDB2Seq (PDB *pdb, BOOL DoAsxGlx, BOOL ProtOnly, BOOL NoX)
HASHTABLE *	blDoPDB2SeqByChain (PDB *pdb, BOOL DoAsxGlx, BOOL ProtOnly, BOOL NoX)

Detailed Description

Conversion from PDB to sequence and other sequence related routines.

Version

V1.15

Date

01.12.15

Copyright

(c) UCL / Dr. Andrew C. R. Martin 1993-2015

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:

Revision History:

• V1.0 29.09.92 Original
• V1.1 07.06.93 Corrected allocation
• V1.2 18.06.93 Handles multi-chains and skips NTER and CTER residues. Added SplitSeq()
• V1.3 09.07.93 SplitSeq() cleans up properly if allocation failed
• V1.4 11.05.94 Added TrueSeqLen()
• V1.5 13.05.94 Fixed bug in PDB2Seq(). Added KnownSeqLen().
• V1.6 07.09.94 Fixed allocation bug in SplitSeq()
• V1.7 19.07.95 Added check for ATOM records
• V1.8 24.01.96 Fixed bug when no ATOM records in linked list Returns a blank string
• V1.9 26.08.97 Renamed DoPDB2Seq() with handling of Asx/Glx and protein-only. Added macros to recreate the old PDB2Seq() interface and similar new calls
• V1.10 02.10.00 Added NoX option
• V1.11 30.05.02 Changed PDB field from 'junk' to 'record_type'
• V1.12 10.06.05 Fixed bug - was undercounting by 1 for CA-only chains
• V1.13 04.02.14 Use CHAINMATCH By: CTP
• V1.14 07.07.14 Use bl prefix for functions By: CTP
• V1.15 01.12.15 Added blDoPDB2SeqByChain() By: ACRM

Definition in file PDB2Seq.c.

Function Documentation

char* blDoPDB2Seq	(	PDB *	pdb,
		BOOL	DoAsxGlx,
		BOOL	ProtOnly,
		BOOL	NoX
	)

Parameters

[in]	*pdb	PDB linked list
[in]	DoAsxGlx	Handle Asx and Glx as B and Z rather than X
[in]	ProtOnly	Don't do DNA/RNA; these simply don't get done rather than being handled as X
[in]	NoX	Skip amino acids which would be assigned as X

Returns

Allocated character array containing sequence

malloc()'s an array containing the 1-letter sequence corresponding to an input PDB linked list. Returns NULL if given a NULL parameter or memory allocation fails. Puts *'s in the sequence for multi-chains.

This routine is normally called via the macro interfaces: PDB2Seq(pdb), PDB2SeqX(pdb), PDBProt2Seq(pdb), PDBProt2SeqX(pdb) Those with Prot in their names handle protein only; those with X handle Asx/Glx as B/Z rather than as X

• 29.09.92 Original By: ACRM
• 07.06.93 Corrected allocation.
• 18.06.93 Handles multi-chains and skips NTER and CTER residues
• 13.05.94 Check for chain change before copy residue (!) (Bug reported by Bob MacCullum)
• 19.07.95 Added check for ATOM records
• 24.01.96 Returns blank string (rather than core dumping!) if the linked list contained no ATOM records
• 26.08.97 Changed to doPDB2Seq with extra parameters (DoAsxGlx & ProtOnly). The old calling forms have now become macros
• 02.10.00 Added NoX
• 10.06.05 Changed the initialization of rescount, resnum, etc. so it correctly points to the first residue. This solves a bug with CA-only chains where it was undercounting by 1
• 04.02.14 Use CHAINMATCH By: CTP
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 146 of file PDB2Seq.c.

HASHTABLE* blDoPDB2SeqByChain	(	PDB *	pdb,
		BOOL	DoAsxGlx,
		BOOL	ProtOnly,
		BOOL	NoX
	)

Parameters

[in]	*pdb	PDB linked list
[in]	DoAsxGlx	Handle Asx and Glx as B and Z rather than X
[in]	ProtOnly	Don't do DNA/RNA; these simply don't get done rather than being handled as X
[in]	NoX	Skip amino acids which would be assigned as X

Returns

A hash of 1-letter code sequences indexed by chain label

Reads sequence from ATOM records in 1-letter code, storing the results in a hash indexed by chain label.

This routine is normally called via the macro interfaces: PDB2SeqByCHain(pdb), PDB2SeqXByCHain(pdb), PDBProt2SeqByChain(pdb), PDBProt2SeqXByChain(pdb) Those with Prot in their names handle protein only; those with X handle Asx/Glx as B/Z rather than as X

• 30.11.15 Original based on blDoPDB2Seq() By: ACRM

Definition at line 294 of file PDB2Seq.c.