Vatom class

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...
Typedefs
typedef sVatom	Vatom
	Declaration of the Vatom class as the Vatom structure.
Functions
double *	Vatom_getPosition (Vatom *thee)
	Get atomic position.
void	Vatom_setRadius (Vatom *thee, double radius)
	Set atomic radius.
double	Vatom_getRadius (Vatom *thee)
	Get atomic position.
void	Vatom_setPartID (Vatom *thee, int partID)
	Set partition ID.
double	Vatom_getPartID (Vatom *thee)
	Get partition ID.
void	Vatom_setAtomID (Vatom *thee, int id)
	Set atom ID.
double	Vatom_getAtomID (Vatom *thee)
	Get atom ID.
void	Vatom_setCharge (Vatom *thee, double charge)
	Set atomic charge.
double	Vatom_getCharge (Vatom *thee)
	Get atomic charge.
void	Vatom_setEpsilon (Vatom *thee, double epsilon)
	Set atomic epsilon.
double	Vatom_getEpsilon (Vatom *thee)
	Get atomic epsilon.
unsigned long int	Vatom_memChk (Vatom *thee)
	Return the memory used by this structure (and its contents) in bytes.
void	Vatom_setResName (Vatom *thee, char resName[VMAX_RECLEN])
	Set residue name.
void	Vatom_setAtomName (Vatom *thee, char atomName[VMAX_RECLEN])
	Set atom name.
void	Vatom_getResName (Vatom *thee, char resName[VMAX_RECLEN])
	Retrieve residue name.
void	Vatom_getAtomName (Vatom *thee, char atomName[VMAX_RECLEN])
	Retrieve atom name.
Vatom *	Vatom_ctor ()
	Constructor for the Vatom class.
int	Vatom_ctor2 (Vatom *thee)
	FORTRAN stub constructor for the Vatom class.
void	Vatom_dtor (Vatom **thee)
	Object destructor.
void	Vatom_dtor2 (Vatom *thee)
	FORTRAN stub object destructor.
void	Vatom_setPosition (Vatom *thee, double position[3])
	Set the atomic position.
void	Vatom_copyTo (Vatom *thee, Vatom *dest)
	Copy information to another atom.
void	Vatom_copyFrom (Vatom *thee, Vatom *src)
	Copy information to another atom.

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Detailed Description

Atom class for interfacing APBS with PDB files.

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Function Documentation

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

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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

Vatom* Vatom_ctor (   )

Constructor for the Vatom class. Author: Nathan Baker Returns: Pointer to newly allocated Vatom object

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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

void Vatom_dtor (  Vatom **  thee  )

Object destructor. Author: Nathan Baker Parameters: thee  Pointer to memory location of object to be destroyed

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void Vatom_dtor2 (  Vatom *  thee  )

FORTRAN stub object destructor. Author: Nathan Baker Parameters: thee  Pointer to object to be destroyed

double Vatom_getAtomID (  Vatom *  thee  )

Get atom ID. Author: Nathan Baker Parameters: thee  Vatom object Returns: Unique non-negative number

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

Retrieve atom name. Author: Jason Wagoner Parameters: atomName  Vatom object Atom name

double Vatom_getCharge (  Vatom *  thee  )

Get atomic charge. Author: Nathan Baker Parameters: thee  Vatom object Returns: Atom partial charge (in e)

double Vatom_getEpsilon (  Vatom *  thee  )

Get atomic epsilon. Author: David Gohara Parameters: thee  Vatom object Returns: Atomic epsilon (in Å)

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

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)

double Vatom_getRadius (  Vatom *  thee  )

Get atomic position. Author: Nathan Baker Parameters: thee  Vatom object Returns: Atomic radius (in Å)

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

Retrieve residue name. Author: Jason Wagoner Parameters: thee  Vatom object resName  Residue Name

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

void Vatom_setAtomID (  Vatom *  thee, int  id )

Set atom ID. Author: Nathan Baker Parameters: thee  Vatom object id  Unique non-negative number

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

Set atom name. Author: Jason Wagoner Parameters: atomName  Vatom object Atom name

void Vatom_setCharge (  Vatom *  thee, double  charge )

Set atomic charge. Author: Nathan Baker Parameters: thee  Vatom object charge  Atom partial charge (in e)

void Vatom_setEpsilon (  Vatom *  thee, double  epsilon )

Set atomic epsilon. Author: David Gohara Parameters: thee  Vatom object epsilon  Atomic epsilon (in Å)

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

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)

void Vatom_setRadius (  Vatom *  thee, double  radius )

Set atomic radius. Author: Nathan Baker Parameters: thee  Vatom object radius  Atomic radius (in Å)

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

Set residue name. Author: Jason Wagoner Parameters: thee  Vatom object resName  Residue Name

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