cct.modelling
Class MolecularEnergy

java.lang.Object
  extended by 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)