Data Structures | |
| struct | sValist |
| Container class for list of atom objects. More... | |
Files | |
| file | valist.h |
| Contains declarations for class Valist. | |
Typedefs | |
| typedef struct sValist | Valist |
| Declaration of the Valist class as the Valist structure. | |
Functions | |
| Vatom * | Valist_getAtomList (Valist *thee) |
| Get actual array of atom objects from the list. | |
| double | Valist_getCenterX (Valist *thee) |
| Get x-coordinate of molecule center. | |
| double | Valist_getCenterY (Valist *thee) |
| Get y-coordinate of molecule center. | |
| double | Valist_getCenterZ (Valist *thee) |
| Get z-coordinate of molecule center. | |
| int | Valist_getNumberAtoms (Valist *thee) |
| Get number of atoms in the list. | |
| Vatom * | Valist_getAtom (Valist *thee, int i) |
| Get pointer to particular atom in list. | |
| unsigned long int | Valist_memChk (Valist *thee) |
| Get total memory allocated for this object and its members. | |
| Valist * | Valist_ctor () |
| Construct the atom list object. | |
| Vrc_Codes | Valist_ctor2 (Valist *thee) |
| FORTRAN stub to construct the atom list object. | |
| void | Valist_dtor (Valist **thee) |
| Destroys atom list object. | |
| void | Valist_dtor2 (Valist *thee) |
| FORTRAN stub to destroy atom list object. | |
| Vrc_Codes | Valist_readPQR (Valist *thee, Vparam *param, Vio *sock) |
| Fill atom list with information from a PQR file. | |
| Vrc_Codes | Valist_readPDB (Valist *thee, Vparam *param, Vio *sock) |
| Fill atom list with information from a PDB file. | |
| Vrc_Codes | Valist_readXML (Valist *thee, Vparam *param, Vio *sock) |
| Fill atom list with information from an XML file. | |
| Vrc_Codes | Valist_getStatistics (Valist *thee) |
| Load up Valist with various statistics. | |
| Valist* Valist_ctor | ( | ) |
Construct the atom list object.
References Valist_ctor2(), and VRC_SUCCESS.
Referenced by loadMolecules().

| Vrc_Codes Valist_ctor2 | ( | Valist * | thee | ) |
FORTRAN stub to construct the atom list object.
| thee | Storage for new atom list |
References sValist::atoms, sValist::number, sValist::vmem, and VRC_SUCCESS.
Referenced by Valist_ctor().
| void Valist_dtor | ( | Valist ** | thee | ) |
Destroys atom list object.
| thee | Pointer to storage for atom list |
References Valist_dtor2().
Referenced by killMolecules(), and loadMolecules().

| void Valist_dtor2 | ( | Valist * | thee | ) |
FORTRAN stub to destroy atom list object.
| thee | Pointer to atom list object |
References sValist::atoms, sValist::number, and sValist::vmem.
Referenced by Valist_dtor().
Get pointer to particular atom in list.
| thee | Atom list object |
| i | Index of atom in list |
References sValist::atoms, and sValist::number.
Referenced by energyMG(), extEnergy(), fillcoChargeSpline1(), fillcoChargeSpline2(), fillcoCoefMolDielNoSmooth(), fillcoCoefMolIon(), fillcoCoefSpline(), fillcoCoefSpline3(), fillcoCoefSpline4(), fillcoPermanentMultipole(), forceAPOL(), initAPOL(), initMG(), qfForceSpline1(), qfForceSpline2(), qfForceSpline4(), storeAtomEnergy(), Vacc_SASA(), Vacc_storeParms(), Vcsm_getAtom(), Vcsm_init(), Vcsm_update(), Vfetk_getAtomColor(), Vfetk_setAtomColors(), Vgreen_coulomb_direct(), Vgreen_coulombD_direct(), Vpbe_ctor2(), Vpbe_getCoulombEnergy1(), Vpmg_dbForce(), Vpmg_ibForce(), Vpmg_polarizEnergy(), Vpmg_qfEnergyPoint(), Vpmg_setPart(), and Vpmg_unsetPart().
Get actual array of atom objects from the list.
| thee | Atom list object |
References sValist::atoms.
| double Valist_getCenterX | ( | Valist * | thee | ) |
Get x-coordinate of molecule center.
| thee | Atom list object |
References sValist::center.
| double Valist_getCenterY | ( | Valist * | thee | ) |
Get y-coordinate of molecule center.
| thee | Atom list object |
References sValist::center.
| double Valist_getCenterZ | ( | Valist * | thee | ) |
Get z-coordinate of molecule center.
| thee | Atom list object |
References sValist::center.
| int Valist_getNumberAtoms | ( | Valist * | thee | ) |
Get number of atoms in the list.
| thee | Atom list object |
References sValist::number.
Referenced by energyMG(), extEnergy(), fillcoChargeSpline1(), fillcoChargeSpline2(), fillcoCoefMolDielNoSmooth(), fillcoCoefMolIon(), fillcoCoefSpline(), fillcoCoefSpline3(), fillcoCoefSpline4(), fillcoPermanentMultipole(), forceAPOL(), forceMG(), initAPOL(), initMG(), loadMolecules(), storeAtomEnergy(), Vacc_allocate(), Vacc_dtor2(), Vacc_SASA(), Vacc_storeParms(), Vacc_wcaEnergy(), Vcsm_init(), Vfetk_getAtomColor(), Vfetk_qfEnergy(), Vfetk_setAtomColors(), Vgreen_coulomb(), Vgreen_coulomb_direct(), Vgreen_coulombD(), Vgreen_coulombD_direct(), Vpbe_ctor2(), Vpbe_getCoulombEnergy1(), Vpmg_polarizEnergy(), Vpmg_qfEnergyPoint(), Vpmg_setPart(), and Vpmg_unsetPart().
| Vrc_Codes Valist_getStatistics | ( | Valist * | thee | ) |
Load up Valist with various statistics.
References sValist::atoms, sValist::center, sVatom::charge, sValist::charge, sValist::maxcrd, sValist::maxrad, sValist::mincrd, sValist::number, sVatom::position, sVatom::radius, VRC_FAILURE, and VRC_SUCCESS.
Referenced by Valist_readPDB(), Valist_readPQR(), and Valist_readXML().
| unsigned long int Valist_memChk | ( | Valist * | thee | ) |
Get total memory allocated for this object and its members.
| thee | Atom list object |
References sValist::vmem.
Fill atom list with information from a PDB file.
| thee | Atom list object |
| param | A pre-initialized parameter object |
| sock | Socket read for reading PDB file |
References sVparam_AtomData::charge, sVparam_AtomData::epsilon, sValist::number, sVparam_AtomData::radius, Valist_getStatistics(), Vatom_setAtomID(), Vatom_setAtomName(), Vatom_setCharge(), Vatom_setEpsilon(), Vatom_setPosition(), Vatom_setRadius(), Vatom_setResName(), sValist::vmem, Vparam_getAtomData(), VRC_FAILURE, and Vstring_strcasecmp().
Referenced by loadMolecules().

Fill atom list with information from a PQR file.
| thee | Atom list object |
| param | A pre-initialized parameter object |
| sock | Socket reading for reading PQR file |
References sVparam_AtomData::charge, sVparam_AtomData::epsilon, sValist::number, sVparam_AtomData::radius, Valist_getStatistics(), Vatom_setAtomID(), Vatom_setAtomName(), Vatom_setCharge(), Vatom_setEpsilon(), Vatom_setPosition(), Vatom_setRadius(), Vatom_setResName(), sValist::vmem, Vparam_getAtomData(), VRC_FAILURE, and Vstring_strcasecmp().
Referenced by loadMolecules().

Fill atom list with information from an XML file.
| thee | Atom list object |
| param | A pre-initialized parameter object |
| sock | Socket reading for reading PQR file |
References sValist::number, Valist_getStatistics(), Vatom_setAtomID(), Vatom_setCharge(), Vatom_setPosition(), Vatom_setRadius(), sValist::vmem, VRC_FAILURE, and Vstring_strcasecmp().
Referenced by loadMolecules().

1.5.7.1