org.jmol.minimize
Class Minimizer
public
class
Minimizer
extends Object
implements MinimizerInterface
public int[][] angles
private int atomCount
private int atomCountFull
private int[] atomMap
private static Vector atomTypes
private int bondCount
private BitSet bsAtoms
private BitSet bsFixed
public BitSet bsMinFixed
private BitSet bsSelected
private BitSet bsTaint
Hashtable constraintMap
public Vector constraints
double[][] coordSaved
private double crit
private String ff
boolean minimizationOn
public double[] partialCharges
static final int PT_CHARGE
static final int PT_CONNECT
static final int PT_ELEMENT
private int steps
static final
Token[][] tokenTypes
public int[][] torsions
static final int TOKEN_ELEMENT_AROMATIC
static final int TOKEN_ELEMENT_CHARGED
static final int TOKEN_ELEMENT_CONNECTED
static final int TOKEN_ELEMENT_ONLY
static final int TOKEN_ELEMENT_SP
static final int TOKEN_ELEMENT_SP2
public Minimizer()
private void addConstraint(Object[] c)
private void clear()
void endMinimization()
public void getAngles()
public Vector getAtomTypes()
private void getEnergyOnly()
public Object getProperty(String propertyName, int param)
private BitSet getSearch(String smarts, int elemnoMax, BitSet bsElements)
public void getTorsions()
public boolean minimize(int steps, double crit, BitSet bsSelected)
private void minimizeWithoutThread()
private void restoreCoordinates()
private void saveCoordinates()
private void setAtomPositions()
private void setMinimizationOn(boolean minimizationOn)
public void setProperty(String propertyName, Object value)
private boolean setupMinimization()
public void startMinimization()
boolean stepMinimization()
private void stopMinimization(boolean coordAreOK)
void updateAtomXYZ()