java.lang.Object
- org.jmol.minimize.Minimizer

```
public class Minimizer
extends Object
```

Field Summary

Fields
Modifier and Type	Field	Description
`private int`	`ac`
`private int[]`	`atomMap`
`Atom[]`	`atoms`
`private int`	`bondCount`
`Bond[]`	`bonds`
`javajs.util.BS`	`bsAtoms`
`private javajs.util.BS`	`bsFixed`
`private javajs.util.BS`	`bsFixedDefault`
`javajs.util.BS`	`bsMinFixed`
`private javajs.util.BS`	`bsSelected`
`private javajs.util.BS`	`bsTaint`
`private Map<String,MMConstraint>`	`constraintMap`
`javajs.util.Lst<MMConstraint>`	`constraints`
`(package private) double[][]`	`coordSaved`
`private double`	`crit`
`private int`	`elemnoMax`
`private 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`
`String`	`units`
`Viewer`	`vwr`

Constructor Summary

Constructors
Constructor Description

Minimizer()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`addConstraint(Object[] o)`
`void`	`calculatePartialCharges(ModelSet ms, javajs.util.BS bsAtoms, javajs.util.BS bsReport)`
`private void`	`clear()`
`void`	`endMinimization()`
`void`	`getAngles()`
`private void`	`getBonds()`
`private void`	`getEnergyOnly()`
`ForceField`	`getForceField(String ff)`
`Object`	`getProperty(String propertyName, int param)`
`JmolThread`	`getThread()`
`void`	`getTorsions()`
`boolean`	`minimizationOn()`
`boolean`	`minimize(int steps, double crit, javajs.util.BS bsSelected, javajs.util.BS bsFixed, boolean haveFixed, boolean forceSilent, String ff)`
`private void`	`minimizeWithoutThread()`
`void`	`report(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(javajs.util.BS bsElements)`
`Minimizer`	`setProperty(String propertyName, 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 javajs.util.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 String units
```

pFF
```
private ForceField pFF
```

ff
```
private String ff
```

bsTaint
```
private javajs.util.BS bsTaint
```

bsSelected
```
private javajs.util.BS bsSelected
```

bsAtoms
```
public javajs.util.BS bsAtoms
```

bsFixedDefault
```
private javajs.util.BS bsFixedDefault
```

bsFixed
```
private javajs.util.BS bsFixed
```

constraints

public javajs.util.Lst<MMConstraint> constraints

isSilent
```
private boolean isSilent
```

constraintMap

private Map<String,MMConstraint> 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 Minimizer setProperty(String propertyName,
                             Object value)

getProperty

public Object getProperty(String propertyName,
                          int param)

Parameters:: propertyName -; param -
Returns:: Object

addConstraint
```
private void addConstraint(Object[] o)
```
Parameters:

o - [ [natoms a1 a2 a3...] value ]

clear
```
private void clear()
```

minimize

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

Throws:: JmolAsyncException

setEnergyUnits
```
private void setEnergyUnits()
```

setupMinimization

private boolean setupMinimization()
                           throws JmolAsyncException

Throws:: JmolAsyncException

setModel

private boolean setModel(javajs.util.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(String ff)
                         throws JmolAsyncException

Throws:: JmolAsyncException

minimizationOn
```
public boolean minimizationOn()
```

getThread
```
public JmolThread getThread()
```

setMinimizationOn

private void setMinimizationOn(boolean minimizationOn)

getEnergyOnly
```
private void getEnergyOnly()
```

reportEnergy
```
private void reportEnergy()
```

startMinimization
```
public boolean startMinimization()
```

stepMinimization
```
public boolean stepMinimization()
```

endMinimization
```
public void endMinimization()
```

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(String msg,
                   boolean isEcho)

calculatePartialCharges

public void calculatePartialCharges(ModelSet ms,
                                    javajs.util.BS bsAtoms,
                                    javajs.util.BS bsReport)
                             throws JmolAsyncException

Throws:: JmolAsyncException

Class Minimizer

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

vwr

atoms

bonds

rawBondCount

minAtoms

minBonds

minAngles

minTorsions

minPositions

bsMinFixed

ac

bondCount

atomMap

partialCharges

steps

crit

units

pFF

ff

bsTaint

bsSelected

bsAtoms

bsFixedDefault

bsFixed

constraints

isSilent

constraintMap

elemnoMax

minimizationOn

minimizationThread

coordSaved

Constructor Detail

Minimizer

Method Detail

setProperty

getProperty

addConstraint

clear

minimize

setEnergyUnits

setupMinimization

setModel

setAtomPositions

getBonds

getAngles

getTorsions

getForceField

minimizationOn

getThread

setMinimizationOn

getEnergyOnly

reportEnergy

startMinimization

stepMinimization

endMinimization

saveCoordinates

restoreCoordinates

stopMinimization

updateAtomXYZ

minimizeWithoutThread

report

calculatePartialCharges