org.jmol.minimize

Class Minimizer

java.lang.Object

org.jmol.minimize.Minimizer

All Implemented Interfaces:

MinimizerInterface

public class Minimizer
extends java.lang.Object
implements MinimizerInterface

Field Summary

Fields

Modifier and Type	Field and Description
private int	ac
private int[]	atomMap
Atom[]	atoms
private int	bondCount
Bond[]	bonds
BS	bsAtoms
private BS	bsFixed
private BS	bsFixedDefault
BS	bsMinFixed
private BS	bsSelected
private BS	bsTaint
private java.util.Map<java.lang.String,java.lang.Object[]>	constraintMap
javajs.util.Lst<java.lang.Object[]>	constraints
(package private) double[][]	coordSaved
private double	crit
private int	elemnoMax
private java.lang.String	ff
private boolean	isSilent
MinAngle[]	minAngles
MinAtom[]	minAtoms
MinBond[]	minBonds
private boolean	minimizationOn
private MinimizationThread	minimizationThread
MinPosition[]	minPositions
MinTorsion[]	minTorsions
double[]	partialCharges
private ForceField	pFF
int	rawBondCount
private int	steps
java.lang.String	units
Viewer	vwr

Constructor Summary

Constructors

Constructor and Description
Minimizer()

Method Summary

Modifier and Type	Method and Description
private void	addConstraint(java.lang.Object[] c)
void	calculatePartialCharges(Bond[] bonds, int bondCount, Atom[] atoms, BS bsAtoms)
private void	clear()
void	endMinimization()
void	getAngles()
private void	getBonds()
private void	getEnergyOnly()
ForceField	getForceField(java.lang.String ff)
java.lang.Object	getProperty(java.lang.String propertyName, int param)
JmolThread	getThread()
void	getTorsions()
boolean	minimizationOn()
boolean	minimize(int steps, double crit, BS bsSelected, BS bsFixed, boolean haveFixed, boolean forceSilent, java.lang.String ff)
private void	minimizeWithoutThread()
void	report(java.lang.String msg, boolean isEcho)
private void	reportEnergy()
private void	restoreCoordinates()
private void	saveCoordinates()
private void	setAtomPositions()
private void	setEnergyUnits()
private void	setMinimizationOn(boolean minimizationOn)
private boolean	setModel(BS bsElements)
MinimizerInterface	setProperty(java.lang.String propertyName, java.lang.Object value)
private boolean	setupMinimization()
boolean	startMinimization()
boolean	stepMinimization()
void	stopMinimization(boolean coordAreOK)
(package private) void	updateAtomXYZ()

Methods inherited from class java.lang.Object

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

Field Detail

vwr

public Viewer vwr

atoms

public Atom[] atoms

bonds

public Bond[] bonds

rawBondCount

public int rawBondCount

minAtoms

public MinAtom[] minAtoms

minBonds

public MinBond[] minBonds

minAngles

public MinAngle[] minAngles

minTorsions

public MinTorsion[] minTorsions

minPositions

public MinPosition[] minPositions

bsMinFixed

public BS bsMinFixed

ac

private int ac

bondCount

private int bondCount

atomMap

private int[] atomMap

partialCharges

public double[] partialCharges

steps

private int steps

crit

private double crit

units

public java.lang.String units

pFF

private ForceField pFF

ff

private java.lang.String ff

bsTaint

private BS bsTaint

bsSelected

private BS bsSelected

bsAtoms

public BS bsAtoms

bsFixedDefault

private BS bsFixedDefault

bsFixed

private BS bsFixed

constraints

public javajs.util.Lst<java.lang.Object[]> constraints

isSilent

private boolean isSilent

constraintMap

private java.util.Map<java.lang.String,java.lang.Object[]> constraintMap

elemnoMax

private int elemnoMax

minimizationOn

private boolean minimizationOn

minimizationThread

private MinimizationThread minimizationThread

coordSaved

double[][] coordSaved

Constructor Detail

Minimizer

public Minimizer()

Method Detail

setProperty

public MinimizerInterface setProperty(java.lang.String propertyName,
                                      java.lang.Object value)

Specified by:

setProperty in interface MinimizerInterface

getProperty

public java.lang.Object getProperty(java.lang.String propertyName,
                                    int param)

Specified by:

getProperty in interface MinimizerInterface

addConstraint

private void addConstraint(java.lang.Object[] c)

clear

private void clear()

minimize

public boolean minimize(int steps,
                        double crit,
                        BS bsSelected,
                        BS bsFixed,
                        boolean haveFixed,
                        boolean forceSilent,
                        java.lang.String ff)
                 throws JmolAsyncException

Specified by:

minimize in interface MinimizerInterface

Throws:

JmolAsyncException

setEnergyUnits

private void setEnergyUnits()

setupMinimization

private boolean setupMinimization()
                           throws JmolAsyncException

Throws:

JmolAsyncException

setModel

private boolean setModel(BS bsElements)
                  throws JmolAsyncException

Throws:

JmolAsyncException

setAtomPositions

private void setAtomPositions()

getBonds

private void getBonds()

getAngles

public void getAngles()

getTorsions

public void getTorsions()

getForceField

public ForceField getForceField(java.lang.String ff)
                         throws JmolAsyncException

Throws:

JmolAsyncException

minimizationOn

public boolean minimizationOn()

Specified by:

minimizationOn in interface MinimizerInterface

getThread

public JmolThread getThread()

Specified by:

getThread in interface MinimizerInterface

setMinimizationOn

private void setMinimizationOn(boolean minimizationOn)

getEnergyOnly

private void getEnergyOnly()

reportEnergy

private void reportEnergy()

startMinimization

public boolean startMinimization()

Specified by:

startMinimization in interface MinimizerInterface

stepMinimization

public boolean stepMinimization()

Specified by:

stepMinimization in interface MinimizerInterface

endMinimization

public void endMinimization()

Specified by:

endMinimization in interface MinimizerInterface

saveCoordinates

private void saveCoordinates()

restoreCoordinates

private void restoreCoordinates()

stopMinimization

public void stopMinimization(boolean coordAreOK)

updateAtomXYZ

void updateAtomXYZ()

minimizeWithoutThread

private void minimizeWithoutThread()

report

public void report(java.lang.String msg,
                   boolean isEcho)

calculatePartialCharges

public void calculatePartialCharges(Bond[] bonds,
                                    int bondCount,
                                    Atom[] atoms,
                                    BS bsAtoms)
                             throws JmolAsyncException

Specified by:

calculatePartialCharges in interface MinimizerInterface

Throws:

JmolAsyncException