Write a PDB file from a linked list. More...

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

Macros
#define	WRITEPDB_MAIN

Functions
int	blWritePDB (FILE fp, PDB pdb)

BOOL	blFormatCheckWritePDB (PDB *pdb)

int	blWritePDBAsPDBorGromos (FILE fp, PDB pdb, BOOL doGromos)

void	blWriteTerCard (FILE fp, PDB p)

void	blWritePDBRecord (FILE fp, PDB pdb)

void	blWritePDBRecordAtnam (FILE fp, PDB pdb)

BOOL	blWritePDBAsPDBML (FILE fp, PDB pdb)

void	blSetElementSymbolFromAtomName (char element, char atom_name)

void	blWriteGromosPDB (FILE fp, PDB pdb)

void	blWriteGromosPDBRecord (FILE fp, PDB pdb)

BOOL	blWriteWholePDB (FILE fp, WHOLEPDB wpdb)

void	blWriteWholePDBHeader (FILE fp, WHOLEPDB wpdb)

void	blWriteWholePDBTrailer (FILE fp, WHOLEPDB wpdb, int numTer)

void	blWriteWholePDBHeaderNoRes (FILE fp, WHOLEPDB wpdb)

Detailed Description

Write a PDB file from a linked list.

Version: V1.29

Date: 29.07.15

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:

This routine will write a .PDB file of any size from a linked list of the protein structure. This list is contained in a linked set of structures of type pdb_entry. The structure is set up by including the file "pdb.h". For details of the structure, see this file.

Usage:

blWritePDB(fp, pdb)

Parameters

[in]	*fp	A pointer to the file to write
[in]	*pdb	The start of the PDB linked list.

Revision History:

V1.0 08.03.89 Original
V1.2 28.03.90 Modified to match the correct column definition of ReadPDB V1.2 (N.B. There was no V1.1)
V1.3 01.06.92 Corrected header, to match standard. Autodoc'd, ANSIed. Added FPU check.
V1.4 10.06.93 Changed to use NEXT() macro. void types
V1.5 22.02.94 Added TER card at end of file
V1.6 15.02.01 Writes using atnam_raw so atom name is unchanged from input
V1.7 30.05.02 Changed PDB field from 'junk' to 'record_type'
V1.8 03.06.05 'atnam_raw' no longer includes the alternate indicator which is now in 'altpos'
V1.9 22.09.06 Added WritePDBRecordAtnam()
V1.10 04.02.14 Use CHAINMATCH macro. By: CTP
V1.11 01.06.14 Added WritePDBML() By: CTP
V1.12 21.06.14 Added blWritePDB(), blFormatCheckWritePDB() and blWriteAsPDB(). Renamed WritePDBML() to blWriteAsPDBML() and deprecated WritePDB(). Defined WRITEPDB_MAIN. By: CTP
V1.13 07.07.14 Renamed functions to use bl prefix. Moved WritePDB() to deprecated.h By: CTP
V1.14 17.07.14 Added blSetElementSymbolFromAtomName() By: CTP
V1.15 16.08.14 Added writing element and charge. By: CTP
V1.16 18.08.14 Added XML_SUPPORT option allowing compilation without support for PDBML format. By: CTP
V1.17 17.02.15 Handles segid and the element and formal charge in blWritePDBRecordAtnam() By: ACRM
V1.18 23.02.15 Modified blWriteAsPDB() to do proper TER cards - now returns an int - the number of TER cards written
V1.19 24.02.15 Renamed blWriteAsPDB() to blWritePDBAsPDBorGromos() and integrated Gromos support into this routine. Now takes a new BOOL flag
V1.20 25.02.15 blWritePDBAsPDBML() now returns BOOL and checks all memory allocations
V1.21 02.03.15 Corrected counting of ORIGX, SCALE and MTRIX records in WriteMaster(). Added blWriteWholePDBHeaderNoRes() Added space padding to TER in blWriteTerCard() Added space padding to END and to CONECT in blWriteWholePDBTrailer()
V1.22 09.03.15 blWriteWholePDBHeaderNoRes() now skips more header lines
V1.23 10.03.15 blWriteWholePDBHeaderNoRes() now skips more header lines
V1.24 02.04.15 WriteMaster() Padded MASTER record to 80 cols. By: CTP
V1.25 13.05.15 Updated blWritePDBAsPDBML() to write CONECT records, Added output of COMPND and SOURCE records. By: CTP
V1.26 08.06.15 Updated XML check for output format. By: CTP
V1.27 21.06.15 Added blMapChainsToEntity(). blDoWritePDBAsPDBML() sets entity_id based on COMPND records if entty_id not already set. By: CTP
V1.28 10.07.15 Added return value for blWritePDBAsPDBML() and blDoWritePDBAsPDBML() when XML_SUPPORT not defined By: ACRM
V1.29 29.07.15 Added output of PDBML seqres records from wpdb->header. Added ReadSeqresChainLabelWholePDB() and ReadSeqresResidueListWholePDB(). By: CTP

Definition in file WritePDB.c.

Macro Definition Documentation

#define WRITEPDB_MAIN

Definition at line 173 of file WritePDB.c.

Function Documentation

BOOL blFormatCheckWritePDB ( PDB * pdb )

Parameters

[in] *pdb PDB linked list to write

Checks PDB linked list is compatible with PDB-formatted text file.

21.06.14 Original By: CTP

Definition at line 269 of file WritePDB.c.

void blSetElementSymbolFromAtomName	(	char *	element,
		char *	atom_name
	)

Parameters

[out]	*element	Element symbol
[in]	*atom_name	Atom name

Set the element symbol (columns 77-78 of a pdb file) based on the atom name (columns 13-16 of a pdb file).

The atom name is stored in the PDB data stucture as atnam_raw.

17.07.14 Original. By: CTP

Definition at line 1433 of file WritePDB.c.

void blWriteGromosPDB	(	FILE *	fp,
		PDB *	pdb
	)

Parameters

[in]	*fp	PDB file pointer to be written
[in]	*pdb	PDB linked list to write

Write a PDB linked list by calls to WritePDBRecord()

08.03.89 Original
01.06.92 ANSIed and autodoc'd
10.06.93 Uses NEXT macro; void type
08.07.93 Added insertion of TER cards
22.02.94 And a TER card at the end of the file
15.02.01 This is the old WritePDB()
04.02.14 Use CHAINMATCH macro. By: CTP
07.07.14 Use bl prefix for functions By: CTP
23.02.15 Proper TER card support By: ACRM
24.02.15 Now just uses blWritePDBAsPDBorGromos()

Definition at line 1491 of file WritePDB.c.

void blWriteGromosPDBRecord	(	FILE *	fp,
		PDB *	pdb
	)

Parameters

[in]	*fp	PDB file pointer to be written
[in]	*pdb	PDB linked list record to write

Write a PDB record

08.03.89 Original
28.03.90 Changed to match ReadPDB() V1.2 for column widths
01.06.92 ANSIed and autodoc'd
10.06.93 void type
22.06.93 Changed to lf. Ljust strings
11.03.94 lf back to f (!)
12.02.01 This is the old WritePDBRecord()
07.07.14 Use bl prefix for functions By: CTP

Definition at line 1517 of file WritePDB.c.

int blWritePDB	(	FILE *	fp,
		PDB *	pdb
	)

Parameters

[in]	*fp	PDB file pointer to be written
[in]	*pdb	PDB linked list to write

Returns: int Number of TER cards written (0 indicates error)

Write a PDB linked list...

21.06.14 Original By: CTP
18.08.14 Added XML_SUPPORT option. Return error if attempting to write PDBML format. By: CTP
23.02.15 Now returns an int
24.02.15 Changed to call blWritePDBAsPDBorGromos() and blWritePDBAsPDBML()

Definition at line 223 of file WritePDB.c.

BOOL blWritePDBAsPDBML	(	FILE *	fp,
		PDB *	pdb
	)

Parameters

[in]	*fp	PDB file pointer to be written
[in]	*pdb	PDB linked list to write

Returns: Success

Write a PDB linked list in PDBML format.

02.06.14 Original. By: CTP
21.06.14 Renamed blWriteAsPDBML() and updated symbol handling. By: CTP
17.07.14 Use blSetElementSymbolFromAtomName() By: CTP
16.08.14 Use element and charge data. By: CTP
17.02.15 Added segid support By: ACRM
24.02.15 Changed name to blWritePDBAsPDBML()
25.02.15 Changed to type BOOL and checks all memory allocations
29.04.15 Updated to write CONECT records. By: CTP
11.05.15 Made function into wrapper for blDoWritePDBAsPDBML(). By: CTP
10.07.15 Added return value for no XML_SUPPORT By: ACRM

Definition at line 525 of file WritePDB.c.

int blWritePDBAsPDBorGromos	(	FILE *	fp,
		PDB *	pdb,
		BOOL	doGromos
	)

Parameters

[in]	*fp	PDB file pointer to be written
[in]	*pdb	PDB linked list to write

Returns: Number of TER cards written (0=error)

Write a PDB linked list by calls to WritePDBRecord()

08.03.89 Original
01.06.92 ANSIed and autodoc'd
10.06.93 Uses NEXT macro; void type
08.07.93 Added insertion of TER cards
22.02.94 And a TER card at the end of the file
04.02.14 Use CHAINMATCH macro. By: CTP
17.06.14 Renamed to blWriteAsPDB() By: CTP
07.07.14 Use blWritePDBRecord() By: CTP
23.02.15 Write correct format TER cards. Now returns int By: ACRM
24.02.15 Renamed to blWritePDBAsPDBorGromos() and added doGromos flag

Definition at line 308 of file WritePDB.c.

void blWritePDBRecord	(	FILE *	fp,
		PDB *	pdb
	)

Parameters

[in]	*fp	PDB file pointer to be written
[in]	*pdb	PDB linked list record to write

Write a PDB record

08.03.89 Original
28.03.90 Changed to match ReadPDB() V1.2 for column widths
01.06.92 ANSIed and autodoc'd
10.06.93 void type
22.06.93 Changed to lf. Ljust strings
11.03.94 lf back to f (!)
15.02.01 Modified to use atnam_raw
03.06.05 Modified to use altpos
07.07.14 Renamed to blWritePDBRecord() By: CTP
16.08.14 Write element and formal charge. By: CTP
17.02.15 Added segid support By: ACRM

Definition at line 415 of file WritePDB.c.

void blWritePDBRecordAtnam	(	FILE *	fp,
		PDB *	pdb
	)

Parameters

[in]	*fp	PDB file pointer to be written
[in]	*pdb	PDB linked list record to write

Write a PDB record using the data in atnam rather than atnam_raw

08.03.89 Original
28.03.90 Changed to match ReadPDB() V1.2 for column widths
01.06.92 ANSIed and autodoc'd
10.06.93 void type
22.06.93 Changed to lf. Ljust strings
11.03.94 lf back to f (!)
15.02.01 Modified to use atnam_raw
03.06.05 Modified to use altpos
22.09.05 This is like the old version which used atnam rather than atnam_raw
07.07.14 Renamed to blWritePDBRecordAtnam() By: CTP
17.02.15 Added element, formalcharge and segid support By: ACRM

Definition at line 471 of file WritePDB.c.

void blWriteTerCard	(	FILE *	fp,
		PDB *	p
	)

Parameters

[in]	*fp	File pointer
[in]	*p	PDB record pointer

Prints a TER card in the new PDB format - i.e. with the residue information for the previous ATOM/HETATM, rather than just printing TER

23.02.15 Original By: ACRM
02.03.15 Added space padding

Definition at line 382 of file WritePDB.c.

BOOL blWriteWholePDB	(	FILE *	fp,
		WHOLEPDB *	wpdb
	)

Parameters

[in]	*fp	File pointer
[in]	*wpdb	Whole PDB structure pointer

Writes a PDB file including header and trailer information. Output in PDBML-format if flags set.

21.06.14 Original By: CTP
18.08.14 Added XML_SUPPORT option. Return error if attempting to write PDBML format. By: CTP
12.02.15 Now a wrapper to blDoWriteWhilePDB()
24.02.15 blWriteAsPDBML() changed to blWritePDBAsPDBML() blWriteAsPDB() changed to blWritePDBAsPDBorGromos()
25.02.15 No longer a wrapper
04.03.15 Added check on wpdb and wpdb->pdb being non-NULL
11.05.15 Updated to use blDoWritePDBAsPDBML(). By: CTP

Definition at line 1557 of file WritePDB.c.

void blWriteWholePDBHeader	(	FILE *	fp,
		WHOLEPDB *	wpdb
	)

Parameters

[in]	*fp	File pointer
[in]	*wpdb	Whole PDB structure pointer

Writes the header of a PDB file

30.05.02 Original By: ACRM
21.06.14 Renamed to blWriteWholePDBHeader() By: CTP
12.02.15 Added XML check By: ACRM
06.08.15 Updated XML check. By: CTP

Definition at line 1608 of file WritePDB.c.

void blWriteWholePDBHeaderNoRes	(	FILE *	fp,
		WHOLEPDB *	wpdb
	)

Parameters

[in]	*fp	File pointer
[in]	*wpdb	Whole PDB structure pointer

Writes the header of a PDB file, but skips any records that include residue numbers for cases where these may have changed.

Skips: REMARK 500 DBREF HELIX SHEET SSBOND CISPEP SEQADV MODRES HET SITE REMARK 465 REMARK 470 REMARK 475 REMARK 480 REMARK 525 REMARK 610 REMARK 615 REMARK 620 REMARK 630 REMARK 3

02.03.15 Original By: ACRM
09.03.15 Additionally skips SEQADV, MODRES, HET, SITE
10.03.15 Additionally skips REMARK 3,465,470,475,480,525,610,615,620,630
06.08.15 Updated XML check. By: CTP

Definition at line 1809 of file WritePDB.c.

void blWriteWholePDBTrailer	(	FILE *	fp,
		WHOLEPDB *	wpdb,
		int	numTer
	)

Parameters

[in]	*fp	File pointer
[in]	*wpdb	Whole PDB structure pointer
[in]	numTer	Number of TER cards

Writes the trailer of a PDB file

30.05.02 Original By: ACRM
21.06.14 Renamed to blWriteWholePDBTrailer() By: CTP
12.02.15 Added XML check By: ACRM
18.02.15 Complete rewrite to use the parsed CONECT data rather than simply rewriting what was read in
23.02.15 Added numTer parameter
02.03.15 Padded END and CONECT
06.08.15 Updated XML check. By: CTP

Definition at line 1643 of file WritePDB.c.

Macros

Functions

Detailed Description

Description:

Usage:

Revision History:

Macro Definition Documentation

Function Documentation