Class Minimizer

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

public class Minimizer extends Object
  • Field Details

    • 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
    • bsBasis

      public javajs.util.BS bsBasis
    • isSilent

      private boolean isSilent
    • constraintMap

      private Map<String,MMConstraint> constraintMap
    • elemnoMax

      private int elemnoMax
    • isQuick

      private boolean isQuick
    • minimizationOn

      private boolean minimizationOn
    • minimizationThread

      private MinimizationThread minimizationThread
    • trustRadius

      private double trustRadius
    • coordSaved

      double[][] coordSaved
    • p

      private javajs.util.P3 p
  • Constructor Details

    • Minimizer

      public Minimizer()
  • Method Details

    • setProperty

      public Minimizer setProperty(String propertyName, Object value)
    • minimize

      public boolean minimize(int steps, double crit, javajs.util.BS bsSelected, javajs.util.BS bsFixed, javajs.util.BS bsBasis, int flags, String ff) throws JmolAsyncException
      Throws:
      JmolAsyncException
    • 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()
    • 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