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. | |
Copy information to another atom.
| thee | Destination for atom information | |
| src | Source for atom information |
References Vatom_copyTo().

Copy information to another atom.
| thee | Source for atom information | |
| dest | Destination for atom information |
Referenced by Vatom_copyFrom().
| Vatom* Vatom_ctor | ( | ) |
Constructor for the Vatom class.
References Vatom_ctor2().

| int Vatom_ctor2 | ( | Vatom * | thee | ) |
FORTRAN stub constructor for the Vatom class.
| thee | Pointer to Vatom allocated memory location |
References sVatom::partID.
Referenced by Vatom_ctor().
| void Vatom_dtor | ( | Vatom ** | thee | ) |
Object destructor.
| thee | Pointer to memory location of object to be destroyed |
References Vatom_dtor2().

| void Vatom_dtor2 | ( | Vatom * | thee | ) |
FORTRAN stub object destructor.
| thee | Pointer to object to be destroyed |
Referenced by Vatom_dtor().
| double Vatom_getAtomID | ( | Vatom * | thee | ) |
Get atom ID.
| thee | Vatom object |
Referenced by Vacc_atomSASA(), Vacc_atomSASPoints(), Vacc_atomSurf(), Vacc_fastMolAcc(), Vacc_totalAtomdSASA(), and Vacc_totalAtomdSAV().
| void Vatom_getAtomName | ( | Vatom * | thee, | |
| char | atomName[VMAX_RECLEN] | |||
| ) |
| double Vatom_getCharge | ( | Vatom * | thee | ) |
Get atomic charge.
| thee | Vatom object |
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.
| thee | Vatom object |
| double Vatom_getPartID | ( | Vatom * | thee | ) |
Get partition ID.
| thee | Vatom object |
References sVatom::partID.
Referenced by Vfetk_getAtomColor().
| double* Vatom_getPosition | ( | Vatom * | thee | ) |
Get atomic position.
| thee | Vatom object |
References sVatom::position.
Referenced by fillcoChargeSpline1(), fillcoChargeSpline2(), fillcoCoefMolDielNoSmooth(), fillcoCoefMolIon(), fillcoCoefSpline(), fillcoCoefSpline3(), fillcoCoefSpline4(), fillcoPermanentMultipole(), forceAPOL(), initAPOL(), qfForceSpline1(), qfForceSpline2(), qfForceSpline4(), Vacc_atomSurf(), Vacc_SASA(), 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.
| thee | Vatom object |
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.
| 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.
| thee | Vpmg object |
| void Vatom_setAtomID | ( | Vatom * | thee, | |
| int | id | |||
| ) |
Set atom ID.
| 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.
| 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.
| 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.
| 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.
| 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.
| 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.
| 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.
| thee | Vatom object | |
| resName | Residue Name |
References sVatom::resName.
Referenced by Valist_readPDB(), and Valist_readPQR().
1.5.7.1