Package org.jmol.minimize

Class Minimizer

java.lang.Object
org.jmol.minimize.Minimizer
public class Minimizer extends Object

  • Field Details

    • staticID

      public static int staticID

    • id

      public int id

    • vwr

      public Viewer vwr

    • atoms

      public Atom[] atoms

    • bonds

      public Bond[] bonds

    • rawBondCount

      public int rawBondCount

    • bsAtoms

      public BS bsAtoms

    • constraints

      public Lst<MMConstraint> constraints

    • minAtoms

      public MinAtom[] minAtoms

    • minBonds

      public MinBond[] minBonds

    • minAngles

      public MinAngle[] minAngles

    • minTorsions

      public MinTorsion[] minTorsions

    • bsMinFixed

      public BS bsMinFixed

    • units

      public String units

  • Constructor Details

    • Minimizer

      public Minimizer()

  • Method Details

    • setProperty

      public Minimizer setProperty(String propertyName, Object value)

    • minimize

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

    • getProperty

      public Object getProperty(String propertyName, int param)
      Parameters:
      propertyName -
      param -
      Returns:
      Object

    • getAngles

      public void getAngles()

    • getTorsions

      public void getTorsions(boolean isMMFF)

    • getForceField

      public ForceField getForceField(String ff) throws JmolAsyncException
      Throws:
      JmolAsyncException

    • minimizationOn

      public boolean minimizationOn()

    • getThread

      public JmolThread getThread()

    • startMinimization

      public boolean startMinimization()

    • stepMinimization

      public boolean stepMinimization()

    • endMinimization

      public void endMinimization(boolean normalFinish)

    • stopMinimization

      public void stopMinimization(boolean coordAreOK)

    • updateAtomXYZ

      public void updateAtomXYZ(boolean isEnd)

    • report

      public void report(String msg, boolean isEcho)

    • calculatePartialCharges

      public void calculatePartialCharges(ModelSet ms, BS bsAtoms, BS bsReport) throws JmolAsyncException
      Throws:
      JmolAsyncException

    • getForceFieldUsed

      public String getForceFieldUsed()

    • isLoggable

      public Boolean isLoggable(int[] iData, int n)

    • toString

      public String toString()
      Overrides:
      toString in class Object