PEnergy Class Reference

#include <PExtension.h>

List of all members.


Detailed Description

PEnergy contains methods to calculate the free energy for pairs of atoms and proteins.


Static Public Member Functions

static Real vanDerWaalsEnergy (const PAtom *a1, const PAtom *a2)
static Real energyOfChain (PChain *chain, EnergyCalcFn energyFn=vanDerWaalsEnergy, Real threshold=DEFAULT_THRESHOLD)
static Real collisionEnergy (const PAtom *a1, const PAtom *a2)

Static Public Attributes

static const Real DEFAULT_THRESHOLD = 10


Member Function Documentation

Real PEnergy::vanDerWaalsEnergy ( const PAtom a1,
const PAtom a2 
) [static]

Calculates the van der Waals energy between atoms a1 and a2.

Real PEnergy::energyOfChain ( PChain chain,
EnergyCalcFn  energyFn = vanDerWaalsEnergy,
Real  threshold = DEFAULT_THRESHOLD 
) [static]

Calculates the potential energy for the entire chain specified by chain, ignoring pairs of bonded atoms as well as pairs of atoms more than threshold Angstroms apart. A user-defined EnergyCalcFn may be specified to define the potential energy of a pair of atoms, or the default vanDerWaalsEnergy will be used.

Real PEnergy::collisionEnergy ( const PAtom a1,
const PAtom a2 
) [static]

Calculates the collision energy between atoms a1 and a2. If the radius of a1 and a2 are r1 and r2 respectively, the collision energy is 1/d^2 - 1/d0^2, where d is the distance between two atom centers, and d0=COLLISION_THRESHOLD*(r1+r2). The COLLISION_THRESHOLD is set to 0.75 in PConstants.h.


Member Data Documentation

const Real PEnergy::DEFAULT_THRESHOLD = 10 [static]

The default distance threshold used by energyOfChain if none is provided.


The documentation for this class was generated from the following files:
Generated on Wed May 16 20:22:13 2007 for LoopTK: Protein Loop Kinematic Toolkit by  doxygen 1.5.1