org.jmol.minimize

Class Minimizer

public class Minimizer extends Object implements MinimizerInterface

Nested Class Summary
classMinimizer.MinimizationThread
Field Summary
int[][]angles
intatomCount
intatomCountFull
int[]atomMap
Atom[]atoms
static VectoratomTypes
intbondCount
BitSetbsAtoms
BitSetbsFixed
BitSetbsMinFixed
BitSetbsSelected
BitSetbsTaint
HashtableconstraintMap
Vectorconstraints
double[][]coordSaved
doublecrit
Stringff
MinAtom[]minAtoms
MinBond[]minBonds
booleanminimizationOn
Minimizer.MinimizationThreadminimizationThread
double[]partialCharges
ForceFieldpFF
static intPT_CHARGE
static intPT_CONNECT
static intPT_ELEMENT
intsteps
static Token[][]tokenTypes
int[][]torsions
static intTOKEN_ELEMENT_AROMATIC
static intTOKEN_ELEMENT_CHARGED
static intTOKEN_ELEMENT_CONNECTED
static intTOKEN_ELEMENT_ONLY
static intTOKEN_ELEMENT_SP
static intTOKEN_ELEMENT_SP2
Viewerviewer
Constructor Summary
Minimizer()
Method Summary
voidaddConstraint(Object[] c)
voidclear()
voidendMinimization()
voidgetAngles()
VectorgetAtomTypes()
voidgetEnergyOnly()
ForceFieldgetForceField()
ObjectgetProperty(String propertyName, int param)
BitSetgetSearch(String smarts, int elemnoMax, BitSet bsElements)
voidgetTorsions()
booleanminimize(int steps, double crit, BitSet bsSelected)
voidminimizeWithoutThread()
voidrestoreCoordinates()
voidsaveCoordinates()
voidsetAtomPositions()
voidsetMinimizationOn(boolean minimizationOn)
voidsetProperty(String propertyName, Object value)
booleansetupMinimization()
voidstartMinimization()
booleanstepMinimization()
voidstopMinimization(boolean coordAreOK)
voidupdateAtomXYZ()

Field Detail

angles

public int[][] angles

atomCount

private int atomCount

atomCountFull

private int atomCountFull

atomMap

private int[] atomMap

atoms

public Atom[] atoms

atomTypes

private static Vector atomTypes

bondCount

private int bondCount

bsAtoms

private BitSet bsAtoms

bsFixed

private BitSet bsFixed

bsMinFixed

public BitSet bsMinFixed

bsSelected

private BitSet bsSelected

bsTaint

private BitSet bsTaint

constraintMap

Hashtable constraintMap

constraints

public Vector constraints

coordSaved

double[][] coordSaved

crit

private double crit

ff

private String ff

minAtoms

public MinAtom[] minAtoms

minBonds

public MinBond[] minBonds

minimizationOn

boolean minimizationOn

minimizationThread

private Minimizer.MinimizationThread minimizationThread

partialCharges

public double[] partialCharges

pFF

private ForceField pFF

PT_CHARGE

static final int PT_CHARGE

PT_CONNECT

static final int PT_CONNECT

PT_ELEMENT

static final int PT_ELEMENT

steps

private int steps

tokenTypes

static final Token[][] tokenTypes

torsions

public int[][] torsions

TOKEN_ELEMENT_AROMATIC

static final int TOKEN_ELEMENT_AROMATIC

TOKEN_ELEMENT_CHARGED

static final int TOKEN_ELEMENT_CHARGED

TOKEN_ELEMENT_CONNECTED

static final int TOKEN_ELEMENT_CONNECTED

TOKEN_ELEMENT_ONLY

static final int TOKEN_ELEMENT_ONLY

TOKEN_ELEMENT_SP

static final int TOKEN_ELEMENT_SP

TOKEN_ELEMENT_SP2

static final int TOKEN_ELEMENT_SP2

viewer

public Viewer viewer

Constructor Detail

Minimizer

public Minimizer()

Method Detail

addConstraint

private void addConstraint(Object[] c)

clear

private void clear()

endMinimization

void endMinimization()

getAngles

public void getAngles()

getAtomTypes

public Vector getAtomTypes()

getEnergyOnly

private void getEnergyOnly()

getForceField

public ForceField getForceField()

getProperty

public Object getProperty(String propertyName, int param)

getSearch

private BitSet getSearch(String smarts, int elemnoMax, BitSet bsElements)

getTorsions

public void getTorsions()

minimize

public boolean minimize(int steps, double crit, BitSet bsSelected)

minimizeWithoutThread

private void minimizeWithoutThread()

restoreCoordinates

private void restoreCoordinates()

saveCoordinates

private void saveCoordinates()

setAtomPositions

private void setAtomPositions()

setMinimizationOn

private void setMinimizationOn(boolean minimizationOn)

setProperty

public void setProperty(String propertyName, Object value)

setupMinimization

private boolean setupMinimization()

startMinimization

public void startMinimization()

stepMinimization

boolean stepMinimization()

stopMinimization

private void stopMinimization(boolean coordAreOK)

updateAtomXYZ

void updateAtomXYZ()