sVparam_AtomData Struct Reference
[Vparam class]

AtomData sub-class; stores atom data. More...

#include <vparam.h>

Data Fields

char atomName [VMAX_ARGLEN]
char resName [VMAX_ARGLEN]
double charge
double radius
double epsilon

Detailed Description

AtomData sub-class; stores atom data.

Author:
Nathan Baker
Note:
The epsilon and radius members of this class refer use the following formula for calculating the van der Waals energy of atom $i$ interacting with atom $j$:

\[ V_{ij}(r_{ij}) = \epsilon_{ij} \left[ \left( \frac{\sigma_{ij}}{r_{ij}} \right)^{12} - 2 \left( \frac{\sigma_{ij}}{r_{ij}} \right)^{6} \right] \]

where $\epsilon_{ij} = \sqrt{\epsilon_i \epsilon_j}$ is the well-depth (in the desired energy units), $r_{ij}$ is the distance between atoms $i$ and $j$, and $\sigma_{ij} = \sigma_i + \sigma_j$ is the sum of the van der Waals radii.

Field Documentation

char sVparam_AtomData::atomName[VMAX_ARGLEN]

Atom name

Referenced by readFlatFileLine(), readXMLFileAtom(), Vparam_AtomData_copyTo(), and Vparam_getAtomData().

double sVparam_AtomData::charge

Atom charge (in e)

Referenced by readFlatFileLine(), readXMLFileAtom(), Valist_readPDB(), Valist_readPQR(), and Vparam_AtomData_copyTo().

double sVparam_AtomData::epsilon

Atom VdW well depth ($\epsilon_i$ above; in kJ/mol)

Referenced by initAPOL(), readFlatFileLine(), readXMLFileAtom(), Valist_readPDB(), Valist_readPQR(), and Vparam_AtomData_copyTo().

double sVparam_AtomData::radius

Atom VdW radius ($\sigma_i$ above; in Å)

Referenced by initAPOL(), readFlatFileLine(), readXMLFileAtom(), Valist_readPDB(), Valist_readPQR(), and Vparam_AtomData_copyTo().

char sVparam_AtomData::resName[VMAX_ARGLEN]

Residue name

Referenced by readFlatFileLine(), Vparam_AtomData_copyTo(), and Vparam_readFlatFile().

The documentation for this struct was generated from the following file:
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