PEnergy Class Reference

#include <PExtension.h>

List of all members.

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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

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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.

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Member Data Documentation

const Real PEnergy::DEFAULT_THRESHOLD = 10 [static]

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

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The documentation for this class was generated from the following files:

• src/core/PExtension.h
• src/core/PEnergy.cc

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