access.c File Reference

Accessibility calculation code. More...

#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "macros.h"
#include "SysDefs.h"
#include "pdb.h"
#include "access.h"

Go to the source code of this file.

Macros
#define	MAXBUFF   160 /* I/O buffer */
#define	MAX_INTERSECT
#define	MAX_INTERSECT_EXP   100 /* Amount to expand intersect array by */
#define	MAX_ATOM_IN_CUBE
#define	FREE_ACCESS_STORAGE
#define	EXPAND_INTERSECT_ARRAYS

Functions
RESRAD *	blSetAtomRadii (PDB *pdb, FILE *fpRad)
BOOL	blCalcAccess (PDB *pdb, int natoms, REAL integrationAccuracy, REAL probeRadius, BOOL doAccessibility)
RESACCESS *	blCalcResAccess (PDB *pdb, RESRAD *resrad)

Detailed Description

Accessibility calculation code.

Version

V1.2

Date

17.06.15

Copyright

(c) UCL, Dr. Andrew C.R. Martin, 1999-2015

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:

Calculation of solvent accessibility by the method of Lee and Richards. Based loosely on PMCL code by Peter McLaughlin

Usage:

RESRAD *blSetAtomRadii(PDB *pdb, FILE *fpRad)

Read the radius file and set the radii in the PDB linked list. Also returns the data from the radius file for use by blCalcResAccess()

BOOL blCalcAccess(PDB *pdb, int natoms, 
                  REAL integrationAccuracy, REAL probeRadius,
                  BOOL doAccessibility)

Does the accessibilty calculations. integrationAccuracy can be set to zero to use the default value

RESACCESS *blCalcResAccess(PDB *pdb, RESRAD *resrad)

Calculates residue accessibility and relative accessibility

Revision History:

• V1.0 21.04.99 Original By: ACRM
• V1.1 17.07.14 Extracted from XMAS code
• V1.2 17.06.15 Added sidechain residues access

Definition in file access.c.

Macro Definition Documentation

#define EXPAND_INTERSECT_ARRAYS

Value:

do {  int newMaxIntersect = (maxIntersect+MAX_INTERSECT_EXP),            \
          iexpand;                                                       \
   neighbours = (int  *)realloc(neighbours,                              \
                                (newMaxIntersect+1)*sizeof(int));        \
   flag = (int  *)realloc(flag, (newMaxIntersect+1)*sizeof(int));        \
   arci = (REAL *)realloc(arci, (newMaxIntersect+1)*sizeof(REAL));       \
   arcf = (REAL *)realloc(arcf, (newMaxIntersect+1)*sizeof(REAL));       \
   deltaX = (REAL *)realloc(deltaX, (newMaxIntersect+1)*sizeof(REAL));   \
   deltaY = (REAL *)realloc(deltaY, (newMaxIntersect+1)*sizeof(REAL));   \
   dist   = (REAL *)realloc(dist,   (newMaxIntersect+1)*sizeof(REAL));   \
   distSquared = (REAL *)realloc(distSquared,                            \
                                 (newMaxIntersect+1)*sizeof(REAL));      \
   if(neighbours==NULL || flag==NULL   || arci==NULL || arcf==NULL ||    \
      deltaX==NULL     || deltaY==NULL || dist==NULL ||                  \
      distSquared==NULL)                                                 \
   {  FREE_ACCESS_STORAGE;                                               \
      return(FALSE);                                                     \
   }                                                                     \
   for(iexpand=maxIntersect+1; iexpand<=newMaxIntersect; iexpand++)      \
   {  neighbours[iexpand]  = 0;                                          \
      flag[iexpand]        = 0;                                          \
      arci[iexpand]        = 0.0;                                        \
      arcf[iexpand]        = 0.0;                                        \
      deltaX[iexpand]      = 0.0;                                        \
      deltaY[iexpand]      = 0.0;                                        \
      dist[iexpand]        = 0.0;                                        \
      distSquared[iexpand] = 0.0;                                        \
   }                                                                     \
   maxIntersect = newMaxIntersect;                                       \
} while(0)

Definition at line 139 of file access.c.

#define FREE_ACCESS_STORAGE

Value:

do {                                                                     \
   if(cube)         free(cube);                                          \
   if(radii)        free(radii);                                         \
   if(radiiSquared) free(radiiSquared);                                  \
   if(neighbours)   free(neighbours);                                    \
   if(flag)         free(flag);                                          \
   if(arci)         free(arci);                                          \
   if(arcf)         free(arcf);                                          \
   if(deltaX)       free(deltaX);                                        \
   if(deltaY)       free(deltaY);                                        \
   if(dist)         free(dist);                                          \
   if(distSquared)  free(distSquared);                                   \
   if(atomTable)    free(atomTable);                                     \
   if(atomsInCube)  {                                                    \
      for(i=0;i<=maxAtomInCube;i++)                                      \
      {  if(atomsInCube[i]) free(atomsInCube[i]);                        \
         else        break;                                              \
      }                                                                  \
      free(atomsInCube);                                                 \
   }                                                                     \
}  while(0);

Definition at line 115 of file access.c.

#define MAX_ATOM_IN_CUBE

Value:

100 /* Initial max no. of atoms in a cube -
                                  expands as required                   */

Definition at line 112 of file access.c.

#define MAX_INTERSECT

Value:

10000 /* Initial max no. of intersections of 
                                  neighbouring spheres - expands as
                                  required                              */

Definition at line 108 of file access.c.

#define MAX_INTERSECT_EXP   100 /* Amount to expand intersect array by */

Definition at line 111 of file access.c.

#define MAXBUFF   160 /* I/O buffer */

Definition at line 107 of file access.c.

Function Documentation

BOOL blCalcAccess	(	PDB *	pdb,
		int	natoms,
		REAL	integrationAccuracy,
		REAL	probeRadius,
		BOOL	doAccessibility
	)

Parameters

[in,out]	*pdb	PDB linked list
[in]	natoms	Number of atoms
[in]	integrationAccuracy	Integration accuracy
[in]	probeRadius	Probe radius
[in]	doAccessibility	Accessibility or contact area

Returns

Success

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
	)

Parameters

[in,out]	*pdb	PDB linked list
[in]	*resrad	Linked list of atom radius information

Returns

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
	)

Parameters

[in,out]	*pdb	PDB linked list
[in]	*fpRad	Radius file pointer

Returns

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.