Header file for hbond determining code. More...

#include "deprecated.h"

Data Structures
struct	_hblist

Macros
#define	HBOND_BACK1 0x01

#define	HBOND_BACK2 0x02

#define	HBOND_SIDE1 0x04

#define	HBOND_SIDE2 0x08

#define	HBOND_BB (HBOND_BACK1 \| HBOND_BACK2)

#define	HBOND_BS (HBOND_BACK1 \| HBOND_SIDE2)

#define	HBOND_SS (HBOND_SIDE1 \| HBOND_SIDE2)

#define	HBOND_SB (HBOND_SIDE1 \| HBOND_BACK2)

#define	HBOND_SIDECHAIN (HBOND_SIDE1 \| HBOND_SIDE2 \| HBOND_BACK2)

#define	HBOND_BACKBONE (HBOND_BACK1 \| HBOND_SIDE2 \| HBOND_BACK2)

#define	HBOND_ANY (HBOND_BACK1 \| HBOND_BACK2 \| HBOND_SIDE1 \| HBOND_SIDE2)

#define	_HBOND_H_DEPRECATED

Typedefs
typedef struct _hblist	HBLIST

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 p, PDB q)

Detailed Description

Header file for hbond determining code.

Version: V1.4

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:

Revision History:

V1.0 26.01.96 Original By: ACRM
V1.1 07.07.14 Use bl prefix for functions By: CTP
V1.2 31.07.14 Updated deprecation: Removed deprecated.h and added prototypes for renamed functions. By: CTP
V1.3 14.08.14 Moved deprecated function prototypes to deprecated.h By: CTP
V1.4 20.07.15 Added blListAllHBonds() By: ACRM

Definition in file hbond.h.

Macro Definition Documentation

#define _HBOND_H_DEPRECATED

Definition at line 98 of file hbond.h.

#define HBOND_ANY (HBOND_BACK1 | HBOND_BACK2 | HBOND_SIDE1 | HBOND_SIDE2)

Definition at line 76 of file hbond.h.

#define HBOND_BACK1 0x01

Definition at line 64 of file hbond.h.

#define HBOND_BACK2 0x02

Definition at line 65 of file hbond.h.

#define HBOND_BACKBONE (HBOND_BACK1 | HBOND_SIDE2 | HBOND_BACK2)

Definition at line 74 of file hbond.h.

#define HBOND_BB (HBOND_BACK1 | HBOND_BACK2)

Definition at line 69 of file hbond.h.

#define HBOND_BS (HBOND_BACK1 | HBOND_SIDE2)

Definition at line 70 of file hbond.h.

#define HBOND_SB (HBOND_SIDE1 | HBOND_BACK2)

Definition at line 72 of file hbond.h.

#define HBOND_SIDE1 0x04

Definition at line 66 of file hbond.h.

#define HBOND_SIDE2 0x08

Definition at line 67 of file hbond.h.

#define HBOND_SIDECHAIN (HBOND_SIDE1 | HBOND_SIDE2 | HBOND_BACK2)

Definition at line 73 of file hbond.h.

#define HBOND_SS (HBOND_SIDE1 | HBOND_SIDE2)

Definition at line 71 of file hbond.h.

Typedef Documentation

typedef struct _hblist HBLIST

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.

Data Structures

Macros

Typedefs

Functions

Detailed Description

Description:

Usage:

Revision History:

Macro Definition Documentation

Typedef Documentation

Function Documentation