#include <PExtension.h>
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 |
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.
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.
const Real PEnergy::DEFAULT_THRESHOLD = 10 [static] |
The default distance threshold used by energyOfChain
if none is provided.