Atom class for interfacing APBS with PDB files. More...

Files
file	vatom.c
	Class Vatom methods.

file	vatom.h
	Contains declarations for class Vatom.

Data Structures
struct	sVatom
	Contains public data members for Vatom class/module. More...

Macros
#define	VMAX_RECLEN 64
	Residue name length.

Typedefs
typedef struct sVatom	Vatom
	Declaration of the Vatom class as the Vatom structure.

Functions
VEXTERNC double *	Vatom_getPosition (Vatom *thee)
	Get atomic position.

VEXTERNC void	Vatom_setRadius (Vatom *thee, double radius)
	Set atomic radius.

VEXTERNC double	Vatom_getRadius (Vatom *thee)
	Get atomic position.

VEXTERNC void	Vatom_setPartID (Vatom *thee, int partID)
	Set partition ID.

VEXTERNC double	Vatom_getPartID (Vatom *thee)
	Get partition ID.

VEXTERNC void	Vatom_setAtomID (Vatom *thee, int id)
	Set atom ID.

VEXTERNC double	Vatom_getAtomID (Vatom *thee)
	Get atom ID.

VEXTERNC void	Vatom_setCharge (Vatom *thee, double charge)
	Set atomic charge.

VEXTERNC double	Vatom_getCharge (Vatom *thee)
	Get atomic charge.

VEXTERNC void	Vatom_setEpsilon (Vatom *thee, double epsilon)
	Set atomic epsilon.

VEXTERNC double	Vatom_getEpsilon (Vatom *thee)
	Get atomic epsilon.

VEXTERNC unsigned long int	Vatom_memChk (Vatom *thee)
	Return the memory used by this structure (and its contents) in bytes.

VEXTERNC void	Vatom_setResName (Vatom *thee, char resName[VMAX_RECLEN])
	Set residue name.

VEXTERNC void	Vatom_setAtomName (Vatom *thee, char atomName[VMAX_RECLEN])
	Set atom name.

VEXTERNC void	Vatom_getResName (Vatom *thee, char resName[VMAX_RECLEN])
	Retrieve residue name.

VEXTERNC void	Vatom_getAtomName (Vatom *thee, char atomName[VMAX_RECLEN])
	Retrieve atom name.

VEXTERNC Vatom *	Vatom_ctor ()
	Constructor for the Vatom class.

VEXTERNC int	Vatom_ctor2 (Vatom *thee)
	FORTRAN stub constructor for the Vatom class.

VEXTERNC void	Vatom_dtor (Vatom **thee)
	Object destructor.

VEXTERNC void	Vatom_dtor2 (Vatom *thee)
	FORTRAN stub object destructor.

VEXTERNC void	Vatom_setPosition (Vatom *thee, double position[3])
	Set the atomic position.

VEXTERNC void	Vatom_copyTo (Vatom thee, Vatom dest)
	Copy information to another atom.

VEXTERNC void	Vatom_copyFrom (Vatom thee, Vatom src)
	Copy information to another atom.

Detailed Description

Atom class for interfacing APBS with PDB files.

Macro Definition Documentation

◆ VMAX_RECLEN

#define VMAX_RECLEN 64

Residue name length.

Author: Nathan Baker, David Gohara, Mike Schneiders

Definition at line 77 of file vatom.h.

Typedef Documentation

◆ Vatom

typedef struct sVatom Vatom

Declaration of the Vatom class as the Vatom structure.

Definition at line 114 of file vatom.h.

Function Documentation

◆ Vatom_copyFrom()

VEXTERNC void Vatom_copyFrom	(	Vatom *	thee,
		Vatom *	src )

Copy information to another atom.

Author: Nathan Baker

Parameters

thee	Destination for atom information
src	Source for atom information

Definition at line 186 of file vatom.c.

◆ Vatom_copyTo()

VEXTERNC void Vatom_copyTo	(	Vatom *	thee,
		Vatom *	dest )

Copy information to another atom.

Author: Nathan Baker

Parameters

thee	Source for atom information
dest	Destination for atom information

Definition at line 177 of file vatom.c.

◆ Vatom_ctor()

VEXTERNC Vatom * Vatom_ctor ( )

Constructor for the Vatom class.

Author: Nathan Baker

Returns: Pointer to newly allocated Vatom object

Definition at line 142 of file vatom.c.

◆ Vatom_ctor2()

VEXTERNC int Vatom_ctor2 ( Vatom * thee )

FORTRAN stub constructor for the Vatom class.

Author: Nathan Baker

Parameters

thee	Pointer to Vatom allocated memory location

Returns: 1 if succesful, 0 otherwise

Definition at line 153 of file vatom.c.

◆ Vatom_dtor()

VEXTERNC void Vatom_dtor ( Vatom ** thee )

Object destructor.

Author: Nathan Baker

Parameters

thee	Pointer to memory location of object to be destroyed

Definition at line 158 of file vatom.c.

◆ Vatom_dtor2()

VEXTERNC void Vatom_dtor2 ( Vatom * thee )

FORTRAN stub object destructor.

Author: Nathan Baker

Parameters

thee	Pointer to object to be destroyed

Definition at line 166 of file vatom.c.

◆ Vatom_getAtomID()

VEXTERNC double Vatom_getAtomID ( Vatom * thee )

Get atom ID.

Author: Nathan Baker

Parameters

thee	Vatom object

Returns: Unique non-negative number

Definition at line 84 of file vatom.c.

◆ Vatom_getAtomName()

VEXTERNC void Vatom_getAtomName	(	Vatom *	thee,
		char	atomName[VMAX_RECLEN] )

Retrieve atom name.

Author: Jason Wagoner

Parameters

thee	Vatom object
atomName	Atom name

Definition at line 214 of file vatom.c.

◆ Vatom_getCharge()

VEXTERNC double Vatom_getCharge ( Vatom * thee )

Get atomic charge.

Author: Nathan Baker

Parameters

thee	Vatom object

Returns: Atom partial charge (in e)

Definition at line 119 of file vatom.c.

◆ Vatom_getEpsilon()

VEXTERNC double Vatom_getEpsilon ( Vatom * thee )

Get atomic epsilon.

Author: David Gohara

Parameters

thee	Vatom object

Returns: Atomic epsilon (in Å)

Definition at line 132 of file vatom.c.

◆ Vatom_getPartID()

VEXTERNC double Vatom_getPartID ( Vatom * thee )

Get partition ID.

Author: Nathan Baker

Parameters

thee	Vatom object

Returns: Partition ID; a negative value means this atom is not assigned to any partition

Definition at line 70 of file vatom.c.

◆ Vatom_getPosition()

VEXTERNC double * Vatom_getPosition ( Vatom * thee )

Get atomic position.

Author: Nathan Baker

Parameters

thee	Vatom object

Returns: Pointer to 3*double array of atomic coordinates (in Å)

Definition at line 63 of file vatom.c.

◆ Vatom_getRadius()

VEXTERNC double Vatom_getRadius ( Vatom * thee )

Get atomic position.

Author: Nathan Baker

Parameters

thee	Vatom object

Returns: Atomic radius (in Å)

Definition at line 105 of file vatom.c.

◆ Vatom_getResName()

VEXTERNC void Vatom_getResName	(	Vatom *	thee,
		char	resName[VMAX_RECLEN] )

Retrieve residue name.

Author: Jason Wagoner

Parameters

thee	Vatom object
resName	Residue Name

Definition at line 199 of file vatom.c.

◆ Vatom_memChk()

VEXTERNC unsigned long int Vatom_memChk ( Vatom * thee )

Return the memory used by this structure (and its contents) in bytes.

Author: Nathan Baker

Parameters

thee	Vpmg object

Returns: The memory used by this structure and its contents in bytes

Definition at line 138 of file vatom.c.

◆ Vatom_setAtomID()

VEXTERNC void Vatom_setAtomID	(	Vatom *	thee,
		int	id )

Set atom ID.

Author: Nathan Baker

Parameters

thee	Vatom object
id	Unique non-negative number

Definition at line 91 of file vatom.c.

◆ Vatom_setAtomName()

VEXTERNC void Vatom_setAtomName	(	Vatom *	thee,
		char	atomName[VMAX_RECLEN] )

Set atom name.

Author: Jason Wagoner

Parameters

thee	Vatom object
atomName	Atom name

Definition at line 207 of file vatom.c.

◆ Vatom_setCharge()

VEXTERNC void Vatom_setCharge	(	Vatom *	thee,
		double	charge )

Set atomic charge.

Author: Nathan Baker

Parameters

thee	Vatom object
charge	Atom partial charge (in e)

Definition at line 112 of file vatom.c.

◆ Vatom_setEpsilon()

VEXTERNC void Vatom_setEpsilon	(	Vatom *	thee,
		double	epsilon )

Set atomic epsilon.

Author: David Gohara

Parameters

thee	Vatom object
epsilon	Atomic epsilon (in Å)

Definition at line 126 of file vatom.c.

◆ Vatom_setPartID()

VEXTERNC void Vatom_setPartID	(	Vatom *	thee,
		int	partID )

Set partition ID.

Author: Nathan Baker

Parameters

thee	Vatom object
partID	Partition ID; a negative value means this atom is not assigned to any partition

Definition at line 77 of file vatom.c.

◆ Vatom_setPosition()

VEXTERNC void Vatom_setPosition	(	Vatom *	thee,
		double	position[3] )

Set the atomic position.

Author: Nathan Baker

Parameters

thee	Vatom object to be modified
position	Coordinates (in Å)

Definition at line 168 of file vatom.c.

◆ Vatom_setRadius()

VEXTERNC void Vatom_setRadius	(	Vatom *	thee,
		double	radius )

Set atomic radius.

Author: Nathan Baker

Parameters

thee	Vatom object
radius	Atomic radius (in Å)

Definition at line 98 of file vatom.c.

◆ Vatom_setResName()

VEXTERNC void Vatom_setResName	(	Vatom *	thee,
		char	resName[VMAX_RECLEN] )

Set residue name.

Author: Jason Wagoner

Parameters

thee	Vatom object
resName	Residue Name

Definition at line 192 of file vatom.c.

Files

Data Structures

Macros

Typedefs

Functions

Detailed Description

Macro Definition Documentation

◆ VMAX_RECLEN

Typedef Documentation

◆ Vatom

Function Documentation

◆ Vatom_copyFrom()

◆ Vatom_copyTo()

◆ Vatom_ctor()

◆ Vatom_ctor2()

◆ Vatom_dtor()

◆ Vatom_dtor2()

◆ Vatom_getAtomID()

◆ Vatom_getAtomName()

◆ Vatom_getCharge()

◆ Vatom_getEpsilon()

◆ Vatom_getPartID()

◆ Vatom_getPosition()

◆ Vatom_getRadius()

◆ Vatom_getResName()

◆ Vatom_memChk()

◆ Vatom_setAtomID()

◆ Vatom_setAtomName()

◆ Vatom_setCharge()

◆ Vatom_setEpsilon()

◆ Vatom_setPartID()

◆ Vatom_setPosition()

◆ Vatom_setRadius()

◆ Vatom_setResName()