Vatom class

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

Data Structures

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

Files

file  vatom.h
 

Contains declarations for class Vatom.


file  vatom.c
 

Class Vatom methods.


Typedefs

typedef struct 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.

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

References Vatom_copyTo().

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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

Referenced by Vatom_copyFrom().

Vatom* Vatom_ctor (  ) 

Constructor for the Vatom class.

Author:
Nathan Baker
Returns:
Pointer to newly allocated Vatom object

References Vatom_ctor2().

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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

References sVatom::partID.

Referenced by Vatom_ctor().

void Vatom_dtor ( Vatom **  thee  ) 

Object destructor.

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

References Vatom_dtor2().

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void Vatom_dtor2 ( Vatom *  thee  ) 

FORTRAN stub object destructor.

Author:
Nathan Baker
Parameters:
thee Pointer to object to be destroyed

Referenced by Vatom_dtor().

double Vatom_getAtomID ( Vatom *  thee  ) 

Get atom ID.

Author:
Nathan Baker
Parameters:
thee Vatom object
Returns:
Unique non-negative number

Referenced by Vacc_atomSASA(), Vacc_atomSASPoints(), Vacc_atomSurf(), Vacc_fastMolAcc(), Vacc_totalAtomdSASA(), and Vacc_totalAtomdSAV().

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

Retrieve atom name.

Author:
Jason Wagoner
Parameters:
atomName Vatom object Atom name

References sVatom::atomName.

double Vatom_getCharge ( Vatom *  thee  ) 

Get atomic charge.

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

References sVatom::charge.

Referenced by fillcoChargeSpline1(), fillcoChargeSpline2(), fillcoPermanentMultipole(), initAPOL(), initMG(), qfForceSpline1(), qfForceSpline2(), qfForceSpline4(), Vfetk_PDE_delta(), Vgreen_coulomb_direct(), Vgreen_coulombD_direct(), Vpbe_ctor2(), Vpbe_getCoulombEnergy1(), Vpmg_polarizEnergy(), Vpmg_qfAtomEnergy(), and Vpmg_qfEnergyPoint().

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

References sVatom::partID.

Referenced by Vfetk_getAtomColor().

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)

References sVatom::position.

Referenced by fillcoChargeSpline1(), fillcoChargeSpline2(), fillcoCoefMolDielNoSmooth(), fillcoCoefMolIon(), fillcoCoefSpline(), fillcoCoefSpline3(), fillcoCoefSpline4(), fillcoPermanentMultipole(), forceAPOL(), initAPOL(), qfForceSpline1(), qfForceSpline2(), qfForceSpline4(), Vacc_atomSurf(), Vacc_splineAccAtom(), Vacc_splineAccGradAtomNorm(), Vacc_splineAccGradAtomNorm3(), Vacc_splineAccGradAtomNorm4(), Vacc_splineAccGradAtomUnnorm(), Vacc_totalAtomdSASA(), Vacc_totalAtomdSAV(), Vacc_wcaForceAtom(), Vcsm_init(), Vcsm_update(), Vfetk_PDE_delta(), Vgreen_coulomb_direct(), Vgreen_coulombD_direct(), Vpbe_ctor2(), Vpbe_getCoulombEnergy1(), Vpmg_dbForce(), Vpmg_ibForce(), Vpmg_polarizEnergy(), Vpmg_qfAtomEnergy(), and Vpmg_qfEnergyPoint().

double Vatom_getRadius ( Vatom *  thee  ) 

Get atomic position.

Author:
Nathan Baker
Parameters:
thee Vatom object
Returns:
Atomic radius (in Å)

References sVatom::radius.

Referenced by fillcoCoefMolDielNoSmooth(), fillcoCoefMolIon(), fillcoCoefSpline(), fillcoCoefSpline3(), fillcoCoefSpline4(), initAPOL(), Vacc_atomSurf(), Vacc_splineAccAtom(), Vacc_splineAccGradAtomNorm(), Vacc_splineAccGradAtomNorm3(), Vacc_splineAccGradAtomNorm4(), Vacc_splineAccGradAtomUnnorm(), Vacc_storeParms(), Vacc_totalAtomdSASA(), Vacc_totalAtomdSAV(), Vpbe_ctor2(), Vpmg_dbForce(), and Vpmg_ibForce().

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

Retrieve residue name.

Author:
Jason Wagoner
Parameters:
thee Vatom object
resName Residue Name

References sVatom::resName.

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

Referenced by Valist_readPDB(), Valist_readPQR(), and Valist_readXML().

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

Set atom name.

Author:
Jason Wagoner
Parameters:
atomName Vatom object Atom name

References sVatom::atomName.

Referenced by Valist_readPDB(), and Valist_readPQR().

void Vatom_setCharge ( Vatom *  thee,
double  charge 
)

Set atomic charge.

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

References sVatom::charge.

Referenced by Valist_readPDB(), Valist_readPQR(), and Valist_readXML().

void Vatom_setEpsilon ( Vatom *  thee,
double  epsilon 
)

Set atomic epsilon.

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

Referenced by Valist_readPDB(), and Valist_readPQR().

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

References sVatom::partID.

Referenced by Vfetk_setAtomColors().

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)

References sVatom::position.

Referenced by Valist_readPDB(), Valist_readPQR(), and Valist_readXML().

void Vatom_setRadius ( Vatom *  thee,
double  radius 
)

Set atomic radius.

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

References sVatom::radius.

Referenced by Valist_readPDB(), Valist_readPQR(), and Valist_readXML().

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

Set residue name.

Author:
Jason Wagoner
Parameters:
thee Vatom object
resName Residue Name

References sVatom::resName.

Referenced by Valist_readPDB(), and Valist_readPQR().

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