meshi.energy.solvate.hydrogenBonds
Class AbstractHydrogenBond

java.lang.Object
  meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBond

Direct Known Subclasses:

HydrogenBondDahiyat

public abstract class AbstractHydrogenBond
extends java.lang.Object

A super class with the most general treatment of hydrogen bond. A specific implementation should put content to these abstract methods. The constructor gets a distance matrix object, and an AtomList object of all the atoms participating in the bond. The only condition on the list is that the donor and acceptor must be its first two elements (their relative order is not important). IPORTANT IMPORTANT IMPORTANT NOTE: The distance matrix must be in an updated state before any of this class's methods are called. If it is not up to date, the results would be meaningless!!! This class does not update the distance matrix on its own at any time!!

Field Summary

protected AtomList	atomList
protected double[][]	derivatives derivatives[i][0] is the derivative of the HB value relative to the X coordinate of atom i.
protected DistanceMatrix	dm
protected double	hbVal

Constructor Summary

AbstractHydrogenBond()

AbstractHydrogenBond(DistanceMatrix dm, AtomList atomList)

Method Summary

void	applyForcesToAtoms(double factor) FOLLOWING the activation of "update" this method can be activated, where it will apply the forces to the atoms participating in the HB.
AtomList	atomList()
double[][]	derivatives()
double	derivatives(int atomInd, int xyz)
Atom	getFirstPolar()
Atom	getSecondPolar()
double	hbVal()
java.lang.String	toString()
abstract void	updateHBvalueAndDerivatives() This update method should be used if a change to the atoms coordinates has occured.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

atomList

protected AtomList atomList

dm

protected DistanceMatrix dm

hbVal

protected double hbVal

derivatives

protected double[][] derivatives

derivatives[i][0] is the derivative of the HB value relative to the X coordinate of atom i. derivatives[i][1] is the derivative of the HB value relative to the Y coordinate of atom i. derivatives[i][2] is the derivative of the HB value relative to the Z coordinate of atom i.

Constructor Detail

AbstractHydrogenBond

public AbstractHydrogenBond()

AbstractHydrogenBond

public AbstractHydrogenBond(DistanceMatrix dm,
                            AtomList atomList)

Method Detail

updateHBvalueAndDerivatives

public abstract void updateHBvalueAndDerivatives()

This update method should be used if a change to the atoms coordinates has occured. Only after this update, the getter methods can produce correct values. This class assume the distance matrix is updated.

applyForcesToAtoms

public void applyForcesToAtoms(double factor)

FOLLOWING the activation of "update" this method can be activated, where it will apply the forces to the atoms participating in the HB. The forces are: factor*(minus derivative). This class is useful in energy terms that make use of the hydrogen bond.

hbVal

public double hbVal()

derivatives

public double derivatives(int atomInd,
                          int xyz)

derivatives

public final double[][] derivatives()

atomList

public final AtomList atomList()

getFirstPolar

public final Atom getFirstPolar()

getSecondPolar

public final Atom getSecondPolar()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object