Build connectivity information in PDB linked list. More...

#include <math.h>
#include <stdlib.h>
#include "macros.h"
#include "pdb.h"

Data Structures
struct	_covalentradii

Functions
BOOL	blAddConect (PDB p, PDB q)

BOOL	blAddOneDirectionConect (PDB p, PDB q)

BOOL	blBuildConectData (PDB *pdb, REAL tol)

BOOL	blIsBonded (PDB p, PDB q, REAL tol)

BOOL	blAreResiduesBonded (PDB pdb, char chain1, int resnum1, char insert1, char chain2, int resnum2, char *insert2, REAL tol)

BOOL	blAreResiduePointersBonded (PDB res1, PDB res2, REAL tol)

BOOL	blDeleteAConect (PDB p, PDB q)

BOOL	blDeleteAConectByNum (PDB *pdb, int cNum)

void	blDeleteAtomConects (PDB *pdb)

BOOL	blCopyConects (PDB out, PDB in)

BOOL	blIsConected (PDB p, PDB q)

Detailed Description

Build connectivity information in PDB linked list.

Version: V1.5

Date: 03.10.16

Copyright: (c) UCL / Dr. Andrew C. R. Martin 2002-2016

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 19.02.15 Original
V1.1 16.03.15 Added blDeleteAConect() and blDeleteAConectByNum()
V1.2 12.05.15 Fixed to add conects between C and N if either is a HETATM
V1.3 23.06.15 Added blAreResiduesBonded() and blAreResiduePointersBonded()
V1.4 22.07.15 Added blIsConnected()
V1.5 03.10.16 Added <stdlib.h>

Definition in file BuildConect.c.

Function Documentation

BOOL blAddConect	(	PDB *	p,
		PDB *	q
	)

Parameters

[in,out]	*p	First PDB item
[in,out]	*q	Second PDB item

Returns: Success?

Adds a conect bteween p and q (i.e. in both directions) Fails if there are too many CONECTs

19.02.15 Original By: ACRM

Definition at line 173 of file BuildConect.c.

BOOL blAddOneDirectionConect	(	PDB *	p,
		PDB *	q
	)

Parameters

[in,out]	*p	First PDB item
[in,out]	*q	Second PDB item

Returns: Success?

Adds a conect from p to q (i.e. one direction only) Fails if there are too many CONECTs

19.02.15 Original By: ACRM

Definition at line 200 of file BuildConect.c.

BOOL blAreResiduePointersBonded	(	PDB *	res1,
		PDB *	res2,
		REAL	tol
	)

Parameters

[in]	*res1	Start of first residue
[in]	*res2	Start of second residue
[in]	tol	Tolerance for distances

Returns: Are they bonded

Tests whether two residue are bonded using pointers to start of residues

23.06.15 Original By: ACRM

Definition at line 394 of file BuildConect.c.

BOOL blAreResiduesBonded	(	PDB *	pdb,
		char *	chain1,
		int	resnum1,
		char *	insert1,
		char *	chain2,
		int	resnum2,
		char *	insert2,
		REAL	tol
	)

Parameters

[in]	*pdb	PDB linked list
[in]	*chain1	First chain label
[in]	resnum1	First residue number
[in]	*insert1	First insert code
[in]	*chain2	Second chain label
[in]	resnum2	Second residue number
[in]	*insert2	Second insert code
[in]	tol	Tolerance for distances

Returns: Are they bonded

Tests whether two residue are bonded

23.06.15 Original By: ACRM

Definition at line 360 of file BuildConect.c.

BOOL blBuildConectData	(	PDB *	pdb,
		REAL	tol
	)

Parameters

[in,out]	*pdb	PDB linked list
[in]	tol	Tolerence for distance between atoms

Returns: Were all CONECTs added OK

Deletes all current connectivity data and rebuilds it using covalent radii data. A return of FALSE indicates that there were too many connections for an atom. If this happens, MAXCONECT needs to be increased in pdb.h

19.02.15 Original By: ACRM
26.02.15 Added tol paramater
12.05.15 Conects are built involving backbone C and N if either atom is a HETATM

Definition at line 251 of file BuildConect.c.

BOOL blCopyConects	(	PDB *	out,
		PDB *	in
	)

Parameters

[out]	*out	PDB linked list containing new CONECT records
[in]	*in	PDB linked list containing original CONECT records

Returns: Success

Updates the CONECT information in the out PDB linked list based on those in the in linked list. This is used when we have copied a PDB linked list (e.g. in the bl...AsCopy() routines) to make sure the CONECT data points to records in the new linked list instead of the old one.

17.04.15 Original By: ACRM

Definition at line 574 of file BuildConect.c.

BOOL blDeleteAConect	(	PDB *	p,
		PDB *	q
	)

Parameters

[in]	*p	First PDB pointer
[in]	*q	Second PDB pointer

Returns: Success

Deletes the CONECT information between the two specified atoms

16.03.15 Original By: ACRM

Definition at line 458 of file BuildConect.c.

BOOL blDeleteAConectByNum	(	PDB *	pdb,
		int	cNum
	)

Parameters

[in]	*pdb	PDB pointer
[in]	cNum	Index into the ->conect[] array for the CONECT to be deleted

Returns: Success

Deletes the link for the specified CONECT. Other CONECTs are shuffled down.

16.03.15 Original By: ACRM

Definition at line 500 of file BuildConect.c.

void blDeleteAtomConects ( PDB * pdb )

Parameters

[in] *pdb PDB pointer

Deletes all CONECT information associated with a PDB pointer. Also deletes the relevant CONECTs (back to this atom) from the partner atoms

17.03.15 Original By: ACRM

Definition at line 536 of file BuildConect.c.

BOOL blIsBonded	(	PDB *	p,
		PDB *	q,
		REAL	tol
	)

Parameters

[in]	*p	First PDB atom
[in]	*q	Second PDB atom
[in]	tol	Telerance for separation between atoms

Returns: Bonded?

Test whether two atoms are bonded

19.02.15 Original By: ACRM
26.02.15 Added tol parameter. Changed to used squared distances

Definition at line 326 of file BuildConect.c.

BOOL blIsConected	(	PDB *	p,
		PDB *	q
	)

Parameters

[in]	*p	First atom
[in]	*q	Second atom

Returns: Connected?

Tests whether there is a link between the specified atoms in the CONECT list

07.06.99 Original By: ACRM

Definition at line 629 of file BuildConect.c.

Data Structures

Functions

Detailed Description

Description:

Usage:

Revision History:

Function Documentation