Atom class for interfacing APBS with PDB files.
More...
|
file | vatom.c |
| Class Vatom methods.
|
|
file | vatom.h |
| Contains declarations for class Vatom.
|
|
|
struct | sVatom |
| Contains public data members for Vatom class/module. More...
|
|
|
typedef struct sVatom | Vatom |
| Declaration of the Vatom class as the Vatom structure.
|
|
|
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 Vatom * | Vatom_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.
|
|
Atom class for interfacing APBS with PDB files.
◆ VMAX_RECLEN
Residue name length.
- Author
- Nathan Baker, David Gohara, Mike Schneiders
Definition at line 77 of file vatom.h.
◆ Vatom
Declaration of the Vatom class as the Vatom structure.
Definition at line 114 of file vatom.h.
◆ Vatom_copyFrom()
VEXTERNC 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 |
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
-
thee | Source for atom information |
dest | Destination 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
-
thee | Pointer 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
-
thee | Pointer 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
-
thee | Pointer 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
-
- 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
-
thee | Vatom object |
atomName | Atom name |
Definition at line 214 of file vatom.c.
◆ Vatom_getCharge()
VEXTERNC double Vatom_getCharge |
( |
Vatom * | thee | ) |
|
Get atomic charge.
- Author
- Nathan Baker
- Parameters
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
thee | Vatom object |
resName | Residue 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
-
- 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
-
thee | Vatom object |
id | Unique 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
-
thee | Vatom object |
atomName | Atom 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
-
thee | Vatom object |
charge | Atom 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
-
thee | Vatom object |
epsilon | Atomic 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
-
thee | Vatom object |
partID | Partition 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
-
thee | Vatom object to be modified |
position | Coordinates (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
-
thee | Vatom object |
radius | Atomic 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
-
thee | Vatom object |
resName | Residue Name |
Definition at line 192 of file vatom.c.