Class Minimizer


  • public class Minimizer
    extends Object
    • Field Detail

      • atoms

        public Atom[] atoms
      • bonds

        public Bond[] bonds
      • rawBondCount

        public int rawBondCount
      • minAtoms

        public MinAtom[] minAtoms
      • minBonds

        public MinBond[] minBonds
      • minAngles

        public MinAngle[] minAngles
      • 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
      • 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
      • elemnoMax

        private int elemnoMax
      • minimizationOn

        private boolean minimizationOn
      • coordSaved

        double[][] coordSaved
    • Constructor Detail

      • Minimizer

        public Minimizer()
    • Method Detail

      • 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()
      • minimize

        public boolean minimize​(int steps,
                                double crit,
                                javajs.util.BS bsSelected,
                                javajs.util.BS bsFixed,
                                boolean haveFixed,
                                boolean forceSilent,
                                String ff)
                         throws JmolAsyncException
        Throws:
        JmolAsyncException
      • setEnergyUnits

        private void setEnergyUnits()
      • setAtomPositions

        private void setAtomPositions()
      • getBonds

        private void getBonds()
      • getAngles

        public void getAngles()
      • getTorsions

        public void getTorsions()
      • minimizationOn

        public boolean minimizationOn()
      • 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)