cct.modelling
Class MolecularEnergy

java.lang.Object
  cct.modelling.MolecularEnergy

All Implemented Interfaces:

MinimizedFunctionInterface

public class MolecularEnergy
extends java.lang.Object
implements MinimizedFunctionInterface

Title:

Description:

Copyright: Copyright (c) 2006

Company: ANU

Field Summary

protected double	angleBendEnergy
protected double	bondStretchEnergy
protected boolean	calculate14Energy
protected boolean	calculateAngleBendEnergy
protected boolean	calculateBondStretchEnergy
protected boolean	calculateNonbondEnergy
protected boolean	calculateTorsionEnergy
protected int	dynamicAtoms
protected FFMolecule	ffMolecule
protected boolean	gradAllocated
protected vPoint3f[]	Gradients
protected int[][]	indexes
protected double	nonbond_1_4_Energy
protected double	nonbondEnergy
(package private) boolean	numericalGradients
static int	SFF_PARAMETERS
protected double	torsionEnergy
protected double	totalEnergy

Constructor Summary

MolecularEnergy(FFMolecule ffmol)

Method Summary

double	calculateEnergy(boolean andGrads)
void	enable14Energy(boolean enable)
void	enable1NonbondEnergy(boolean enable)
void	enableAngleBendEnergy(boolean enable)
void	enableBondStretchEnergy(boolean enable)
void	enableNumericalGradients(boolean enable)
void	enableTorsionEnergy(boolean enable)
double	function(int n, double[] X)
double	function(int n, double[] X, double[] Grads)
float	function(int n, float[] X)
float	function(int n, float[] X, float[] Grads)
float[][]	getCoordinates(int n, float[] X)
vPoint3f[]	getGradients()
void	printEnergyDecomposition()
void	setIndexes(int[][] ind)
(package private) void	setupCoordinates(int n, float[] X)
(package private) void	setupGradinents(int n, float[] Grads)

Methods inherited from class java.lang.Object

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

Field Detail

SFF_PARAMETERS

public static final int SFF_PARAMETERS

See Also:

Constant Field Values

gradAllocated

protected boolean gradAllocated

ffMolecule

protected FFMolecule ffMolecule

Gradients

protected vPoint3f[] Gradients

dynamicAtoms

protected int dynamicAtoms

totalEnergy

protected double totalEnergy

bondStretchEnergy

protected double bondStretchEnergy

angleBendEnergy

protected double angleBendEnergy

torsionEnergy

protected double torsionEnergy

nonbond_1_4_Energy

protected double nonbond_1_4_Energy

nonbondEnergy

protected double nonbondEnergy

calculateBondStretchEnergy

protected boolean calculateBondStretchEnergy

calculateAngleBendEnergy

protected boolean calculateAngleBendEnergy

calculateTorsionEnergy

protected boolean calculateTorsionEnergy

calculate14Energy

protected boolean calculate14Energy

calculateNonbondEnergy

protected boolean calculateNonbondEnergy

numericalGradients

boolean numericalGradients

indexes

protected int[][] indexes

Constructor Detail

MolecularEnergy

public MolecularEnergy(FFMolecule ffmol)

Method Detail

enableNumericalGradients

public void enableNumericalGradients(boolean enable)

enableBondStretchEnergy

public void enableBondStretchEnergy(boolean enable)

enableAngleBendEnergy

public void enableAngleBendEnergy(boolean enable)

enableTorsionEnergy

public void enableTorsionEnergy(boolean enable)

enable14Energy

public void enable14Energy(boolean enable)

enable1NonbondEnergy

public void enable1NonbondEnergy(boolean enable)

getGradients

public vPoint3f[] getGradients()

setIndexes

public void setIndexes(int[][] ind)

calculateEnergy

public double calculateEnergy(boolean andGrads)
                       throws java.lang.Exception

Throws:

java.lang.Exception

printEnergyDecomposition

public void printEnergyDecomposition()

function

public double function(int n,
                       double[] X,
                       double[] Grads)

Specified by:

function in interface MinimizedFunctionInterface

function

public float function(int n,
                      float[] X,
                      float[] Grads)

Specified by:

function in interface MinimizedFunctionInterface

function

public double function(int n,
                       double[] X)

Specified by:

function in interface MinimizedFunctionInterface

function

public float function(int n,
                      float[] X)

Specified by:

function in interface MinimizedFunctionInterface

setupCoordinates

void setupCoordinates(int n,
                      float[] X)

getCoordinates

public float[][] getCoordinates(int n,
                                float[] X)

setupGradinents

void setupGradinents(int n,
                     float[] Grads)