hbond.c File Reference

Report whether two residues are H-bonded using Baker & Hubbard criteria. More...

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

Go to the source code of this file.

Macros
#define	DADIST   3.5
#define	DADISTSQ   (DADIST*DADIST)
#define	HADIST   2.5
#define	HADISTSQ   (HADIST*HADIST)

Functions
int	blIsHBonded (PDB *res1, PDB *res2, int type)
BOOL	blValidHBond (PDB *AtomH, PDB *AtomD, PDB *AtomA, PDB *AtomP)
int	blIsMCDonorHBonded (PDB *res1, PDB *res2, int type)
int	blIsMCAcceptorHBonded (PDB *res1, PDB *res2, int type)
void	blSetMaxProteinHBondDADistance (REAL dist)
HBLIST *	blListAllHBonds (PDB *res1, PDB *res2)

Detailed Description

Report whether two residues are H-bonded using Baker & Hubbard criteria.

Version

V1.8

Date

20.07.15

Copyright

(c) UCL / Dr. Andrew C. R. Martin 1996-2015

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:

NOTE, explicit hydrogens must be added to the PDB linked list before calling this routine.

The only external entry points are blIsHBonded() and blValidHBond()

Revision History:

• V1.0 26.01.96 Original By: ACRM
• V1.1 09.02.96 Added #ifdef'd code to allow AE1/AE2 AD1/AD2
• V1.2 19.12.02 Fixed bug in walking over multiple H atoms
• V1.3 18.08.05 Fixed bug relating to sidechains like GLN/ASN
• V1.4 03.01.06 Proline backbone nitrogen cannot act as donor! Also incorporated fix in ValidHBond() from 02.06.99 Inpharmatica version to handle NULL antecedent atoms
• V1.5 17.01.06 Added IsMCDonorHBonded() and IsMCAcceptorHBonded()
• V1.6 20.03.14 Updated message in Demo code. By: CTP
• V1.7 07.07.14 Use bl prefix for functions By: CTP
• V1.8 20.08.14 Added blSetMaxProteinHBondDADistance() Added blFindHBond() By: ACRM

Definition in file hbond.c.

Macro Definition Documentation

#define DADIST   3.5

Definition at line 112 of file hbond.c.

#define DADISTSQ   (DADIST*DADIST)

Definition at line 113 of file hbond.c.

#define HADIST   2.5

Definition at line 114 of file hbond.c.

#define HADISTSQ   (HADIST*HADIST)

Definition at line 115 of file hbond.c.

Function Documentation

int blIsHBonded	(	PDB *	res1,
		PDB *	res2,
		int	type
	)

Parameters

[in]	*res1	First residue
[in]	*res2	Second residue
[in]	type	HBond type to search for

Returns

HBond type found or 0 if none

Determines whether 2 residues are H-bonded using the crude criteria of Baker & Hubbard, 1984 (Prog. Biophys. & Mol. Biol, 44, 97-179)

N.B. Explicit hydrogens must be added to the PDB linked list before calling this routine!

Searches may be made for any H-bond, or just for those involving backbone or sidechain. These requirements may be combined in any way for the two residues by ORing the appropriate flags in the type variable.

  The flags are:
  HBOND_BACK1 (res1 b/b)
  HBOND_BACK2 (res2 b/b)
  HBOND_SIDE1 (res1 s/c)
  HBOND_SIDE2 (res2 s/c)


  The most common flag combinations are already provided:
  HBOND_BB         (b/b -- b/b)
  HBOND_BS         (b/b -- s/c)
  HBOND_SS         (s/c -- s/c)
  HBOND_SB         (s/c -- b/b)
  HBOND_SIDECHAIN  (s/c -- any)
  HBOND_BACKBONE   (b/b -- any)
  HBOND_ANY        (any -- any)

• 25.01.96 Original By: ACRM
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 173 of file hbond.c.

int blIsMCAcceptorHBonded	(	PDB *	res1,
		PDB *	res2,
		int	type
	)

Parameters

[in]	*res1	First residue
[in]	*res2	Second residue
[in]	type	HBond type to search for

Returns

HBond type found or 0 if none

Determines whether 2 residues are H-bonded using the crude criteria of Baker & Hubbard, 1984 (Prog. Biophys. & Mol. Biol, 44, 97-179)

N.B. Explicit hydrogens must be added to the PDB linked list before calling this routine!

Searches for HBonds, in which the first residue is a mainchain acceptor and the second residue is a donor. Type should be HBOND_BACK2 or HBOND_SIDE2 depending whether the second residue (the acceptor) is backbond or sidechain

• 17.01.06 Original By: ACRM
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 717 of file hbond.c.

int blIsMCDonorHBonded	(	PDB *	res1,
		PDB *	res2,
		int	type
	)

Parameters

[in]	*res1	First residue
[in]	*res2	Second residue
[in]	type	HBond type to search for

Returns

HBond type found or 0 if none

Determines whether 2 residues are H-bonded using the crude criteria of Baker & Hubbard, 1984 (Prog. Biophys. & Mol. Biol, 44, 97-179)

N.B. Explicit hydrogens must be added to the PDB linked list before calling this routine!

Searches for HBonds, in which the first residue is a mainchain donor and the second residue is an acceptor. Type should be HBOND_BACK2 or HBOND_SIDE2 depending whether the second residue (the acceptor) is backbond or sidechain

• 17.01.06 Original modified from IsHbonded() By: ACRM
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 660 of file hbond.c.

HBLIST* blListAllHBonds	(	PDB *	res1,
		PDB *	res2
	)

Parameters

[in]	*res1	Pointer to first residue
[in]	*res2	Pointer to second residue

Returns

Linked list of hydrogen bonds

Finds all HBonds between two specified residues

• 20.07.15 Original By: ACRM
• 21.07.15 Corrected to blValidHBond()

Definition at line 781 of file hbond.c.

void blSetMaxProteinHBondDADistance

(

REAL

dist

)

Parameters

[in]

dist

Distance

Wrapper to set the static variable for maximum D-A distance

16.06.99 Original By: ACRM

Definition at line 761 of file hbond.c.

BOOL blValidHBond	(	PDB *	AtomH,
		PDB *	AtomD,
		PDB *	AtomA,
		PDB *	AtomP
	)

Parameters

[in]	*AtomH	The hydrogen
[in]	*AtomD	The donor (to which the H is attached)
[in]	*AtomA	The acceptor
[in]	*AtomP	The antecedent to the acceptor

Returns

Valid?

Determines whether a set of atoms form a valid H-bond using the Baker and Hubbard criteria

• 25.01.96 Original By: ACRM
• 02.06.99 Added NULL antecedent handling to allow calculation of HBonds with missing antecedents. Previously AtomP==NULL was handled as an invalid HBond.
• 07.07.14 Use bl prefix for functions By: CTP
• 20.07.15 Changed DADISTSQ to sDADistSq By: ACRM

Definition at line 303 of file hbond.c.