Data Structures | Files | Defines | Typedefs | Functions

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.


Defines

#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 VatomVatom_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.


Define Documentation

#define VMAX_RECLEN   64

Residue name length.

Author:
Nathan Baker, David Gohara, Mike Schneiders

Definition at line 66 of file vatom.h.


Function Documentation

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 167 of file vatom.c.

Here is the call graph for this function:

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 158 of file vatom.c.

Here is the caller graph for this function:

VEXTERNC Vatom* Vatom_ctor (  )

Constructor for the Vatom class.

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

Definition at line 123 of file vatom.c.

Here is the call graph for this function:

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 134 of file vatom.c.

Here is the caller graph for this function:

VEXTERNC void Vatom_dtor ( Vatom **  thee )

Object destructor.

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

Definition at line 139 of file vatom.c.

Here is the call graph for this function:

VEXTERNC void Vatom_dtor2 ( Vatom thee )

FORTRAN stub object destructor.

Author:
Nathan Baker
Parameters:
theePointer to object to be destroyed

Definition at line 147 of file vatom.c.

Here is the caller graph for this function:

VEXTERNC double Vatom_getAtomID ( Vatom thee )

Get atom ID.

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

Definition at line 77 of file vatom.c.

Here is the caller graph for this function:

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

Retrieve atom name.

Author:
Jason Wagoner
Parameters:
theeVatom object
atomNameAtom name

Definition at line 195 of file vatom.c.

VEXTERNC double Vatom_getCharge ( Vatom thee )

Get atomic charge.

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

Definition at line 112 of file vatom.c.

Here is the caller graph for this function:

VEXTERNC double Vatom_getEpsilon ( Vatom thee )

Get atomic epsilon.

Author:
David Gohara
Parameters:
theeVatom object
Returns:
Atomic epsilon (in Å)
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 63 of file vatom.c.

Here is the caller graph for this function:

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 56 of file vatom.c.

Here is the caller graph for this function:

VEXTERNC double Vatom_getRadius ( Vatom thee )

Get atomic position.

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

Definition at line 98 of file vatom.c.

Here is the caller graph for this function:

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

Retrieve residue name.

Author:
Jason Wagoner
Parameters:
theeVatom object
resNameResidue Name

Definition at line 180 of file vatom.c.

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 119 of file vatom.c.

VEXTERNC void Vatom_setAtomID ( Vatom thee,
int  id 
)

Set atom ID.

Author:
Nathan Baker
Parameters:
theeVatom object
idUnique non-negative number

Definition at line 84 of file vatom.c.

Here is the caller graph for this function:

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

Set atom name.

Author:
Jason Wagoner
Parameters:
theeVatom object
atomNameAtom name

Definition at line 188 of file vatom.c.

Here is the caller graph for this function:

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 105 of file vatom.c.

Here is the caller graph for this function:

VEXTERNC void Vatom_setEpsilon ( Vatom thee,
double  epsilon 
)

Set atomic epsilon.

Author:
David Gohara
Parameters:
theeVatom object
epsilonAtomic epsilon (in Å)

Here is the caller graph for this function:

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 70 of file vatom.c.

Here is the caller graph for this function:

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 149 of file vatom.c.

Here is the caller graph for this function:

VEXTERNC void Vatom_setRadius ( Vatom thee,
double  radius 
)

Set atomic radius.

Author:
Nathan Baker
Parameters:
theeVatom object
radiusAtomic radius (in Å)

Definition at line 91 of file vatom.c.

Here is the caller graph for this function:

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

Set residue name.

Author:
Jason Wagoner
Parameters:
theeVatom object
resNameResidue Name

Definition at line 173 of file vatom.c.

Here is the caller graph for this function: