access.h File Reference

Accessibility calculation code. More...

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Data Structures
struct	_resrad
struct	_resaccess

Macros
#define	ACCESS_MAX_ATOMS_PER_RESIDUE   50
#define	ACCESS_DEF_INTACC   0.05
#define	VERY_SMALL   (REAL)1e-6

Typedefs
typedef struct _resrad	RESRAD
typedef struct _resaccess	RESACCESS

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

17.06.16

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:

Usage:

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 scAccess and scRelAccess to RESACCESS structure Added stdaccessSc to RESRAD structure

Definition in file access.h.

Macro Definition Documentation

#define ACCESS_DEF_INTACC   0.05

Definition at line 58 of file access.h.

#define ACCESS_MAX_ATOMS_PER_RESIDUE   50

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
	)

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.