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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.

VatomVatom_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.


Detailed Description

Atom class for interfacing APBS with PDB files.


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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