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access.h File Reference

Accessibility calculation code. More...

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Data Structures

struct  _resrad
struct  _resaccess


#define ACCESS_DEF_INTACC   0.05
#define VERY_SMALL   (REAL)1e-6


typedef struct _resrad RESRAD
typedef struct _resaccess RESACCESS


RESRADblSetAtomRadii (PDB *pdb, FILE *fpRad)
BOOL blCalcAccess (PDB *pdb, int natoms, REAL integrationAccuracy, REAL probeRadius, BOOL doAccessibility)
RESACCESSblCalcResAccess (PDB *pdb, RESRAD *resrad)

Detailed Description

Accessibility calculation code.

Dr. Andrew C.R. Martin
Institute of Structural & Molecular Biology, University College London, Gower Street, London. WC1E 6BT.

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.



Revision History:

Definition in file access.h.

Macro Definition Documentation

#define ACCESS_DEF_INTACC   0.05

Definition at line 58 of file access.h.


Definition at line 57 of file access.h.

#define VERY_SMALL   (REAL)1e-6

Definition at line 61 of file access.h.

Typedef Documentation

typedef struct _resaccess RESACCESS
typedef struct _resrad RESRAD

Function Documentation

BOOL blCalcAccess ( PDB pdb,
int  natoms,
REAL  integrationAccuracy,
REAL  probeRadius,
BOOL  doAccessibility 
[in,out]*pdbPDB linked list
[in]natomsNumber of atoms
[in]integrationAccuracyIntegration accuracy
[in]probeRadiusProbe radius
[in]doAccessibilityAccessibility or contact area

Allocates arrays and calls routines to populate them, do the access calculations and populate into the PDB linked list

  • 22.04.99 Original By: ACRM

Definition at line 331 of file access.c.

RESACCESS* blCalcResAccess ( PDB pdb,
RESRAD resrad 
[in,out]*pdbPDB linked list
[in]*resradLinked list of atom radius information
Linked list of residue accessibilities

Calculates and populates the residue totals and relative values using standards stored in resrad

  • 22.04.99 Original By: ACRM
  • 04.08.99 Changed check on return from GetStandardAccess() to check for < VERY_SMALL rather than ==0.0 Set relative access to -1 if the standard accessibility is unknown rather than to 0.0
  • 17.06.15 Added calculation of sidechain accessibility

Definition at line 673 of file access.c.

RESRAD* blSetAtomRadii ( PDB pdb,
FILE *  fpRad 
[in,out]*pdbPDB linked list
[in]*fpRadRadius file pointer
Linked list of radius information

Set atom radii from the radius file in the PDB linked list Returns the radius lookup information since it also contains the standard accessibilities

  • 22.04.99 Original By: ACRM
  • 16.06.99 Initialise radii to NULL
  • 22.06.99 Changed to call DefaultRadius() with element type rather than atom name
  • 16.07.14 Rewritten to work outside XMAS format and now takes the file pointer to the radii file rather than the filename

Definition at line 259 of file access.c.