Package org.jmol.minimize

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