astex
Class EnergyTerm

java.lang.Object
  astex.DynamicArray
      astex.EnergyTerm

public class EnergyTerm
extends DynamicArray

A class for representing an energy term in a force field. The same class is used for storing all energy terms. The objects that the term operates on are identified by integers rather than object references so that they may work efficiently with the optimizer.

Field Summary

DynamicArray	affectedAtoms The list of atoms that are affected by this energy term.
boolean	constrained Is this torsion constrained e.g.
double	forceConstant The force constant for this term.
DynamicArray	signalAtoms The atoms we will optimise to the density.
double	targetValue The target value e.g.

Constructor Summary

EnergyTerm()

Method Summary

Methods inherited from class astex.DynamicArray

add, contains, get, getArray, getIndex, getReverse, print, remove, removeAllElements, removeElement, set, setCapacity, size

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

targetValue

public double targetValue

The target value e.g. bond length, angle, improper torsion.

forceConstant

public double forceConstant

The force constant for this term.

affectedAtoms

public DynamicArray affectedAtoms

The list of atoms that are affected by this energy term.

signalAtoms

public DynamicArray signalAtoms

The atoms we will optimise to the density.

constrained

public boolean constrained

Is this torsion constrained e.g. omega in peptide.

Constructor Detail

EnergyTerm

public EnergyTerm()