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 java.lang.String units

• pFF

  private ForceField pFF

• ff

  private java.lang.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 java.util.Map<java.lang.String,​MMConstraint> constraintMap

• elemnoMax

  private int elemnoMax

• isQuick

  private boolean isQuick

• minimizationOn

  private boolean minimizationOn

• minimizationThread

  private MinimizationThread minimizationThread

• coordSaved

  double[][] coordSaved

Constructor Detail

• Minimizer

  public Minimizer()

Method Detail

• setProperty

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

• getProperty

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

  Parameters:

  propertyName -

  param -

  Returns:

  Object

• addConstraint

  private void addConstraint​(java.lang.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,
                          int flags,
                          java.lang.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​(java.lang.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​(java.lang.String msg,
                     boolean isEcho)

• calculatePartialCharges

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

  Throws:

  JmolAsyncException