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hbond.h File Reference

Header file for hbond determining code. More...

#include "deprecated.h"

Go to the source code of this file.

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)
 
HBLISTblListAllHBonds (PDB *p, PDB *q)
 

Detailed Description

Header file for hbond determining code.

Version
V1.4
Date
20.07.15
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:

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]*res1First residue
[in]*res2Second residue
[in]typeHBond 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]*res1First residue
[in]*res2Second residue
[in]typeHBond 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]*res1First residue
[in]*res2Second residue
[in]typeHBond 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]*res1Pointer to first residue
[in]*res2Pointer to second residue
Returns
Linked list of hydrogen bonds

Finds all HBonds between two specified residues

Definition at line 781 of file hbond.c.

void blSetMaxProteinHBondDADistance ( REAL  dist)
Parameters
[in]distDistance

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]*AtomHThe hydrogen
[in]*AtomDThe donor (to which the H is attached)
[in]*AtomAThe acceptor
[in]*AtomPThe 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.