APBS  1.5
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...
 

Macros

#define VMAX_RECLEN   64
 Residue name length. More...
 

Typedefs

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

Functions

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

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.

Function Documentation

◆ Vatom_copyFrom()

VEXTERNC void Vatom_copyFrom ( Vatom thee,
Vatom src 
)

Copy information to another atom.

Author
Nathan Baker
Parameters
theeDestination for atom information
srcSource 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
theeSource for atom information
destDestination 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
theePointer 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
theePointer 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
theePointer 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
theeVatom 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
theeVatom object
atomNameAtom name

Definition at line 214 of file vatom.c.

◆ Vatom_getCharge()

VEXTERNC double Vatom_getCharge ( Vatom thee)

Get atomic charge.

Author
Nathan Baker
Parameters
theeVatom 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
theeVatom 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
theeVatom 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
theeVatom 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
theeVatom 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
theeVatom object
resNameResidue 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
theeVpmg 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
theeVatom object
idUnique 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
theeVatom object
atomNameAtom 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
theeVatom object
chargeAtom 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
theeVatom object
epsilonAtomic 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
theeVatom object
partIDPartition 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
theeVatom object to be modified
positionCoordinates (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
theeVatom object
radiusAtomic 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
theeVatom object
resNameResidue Name

Definition at line 192 of file vatom.c.