Class EnvelopeCalculation

  • All Implemented Interfaces:
    JmolEnvCalc

    public final class EnvelopeCalculation
    extends java.lang.Object
    implements JmolEnvCalc
    • Field Detail

      • geodesicMap

        private BS geodesicMap
      • mapT

        private BS mapT
      • mads

        private short[] mads
      • ac

        private int ac
      • EMPTY_SET

        private static BS EMPTY_SET
      • maxRadius

        private float maxRadius
      • modelZeroBased

        private boolean modelZeroBased
      • disregardNeighbors

        private boolean disregardNeighbors
      • bsMySelected

        private BS bsMySelected
      • dotsConvexMaps

        private BS[] dotsConvexMaps
      • dotsConvexMax

        private int dotsConvexMax
      • geodesicCount

        private int geodesicCount
      • bsSurface

        private BS bsSurface
      • radiusP

        private float radiusP
      • diameterP

        private float diameterP
      • bsTemp

        private BS bsTemp
      • bsIgnore

        private BS bsIgnore
      • onlySelectedDots

        private boolean onlySelectedDots
      • isSurface

        private boolean isSurface
      • multiModel

        private boolean multiModel
      • currentPoints

        private javajs.util.P3[] currentPoints
      • indexI

        private int indexI
      • centerI

        private javajs.util.P3 centerI
      • radiusI

        private float radiusI
      • radiiIP2

        private float radiiIP2
      • pointT

        private final javajs.util.P3 pointT
      • centerT

        private javajs.util.P3 centerT
      • vertexTest

        private final javajs.util.P3[] vertexTest
      • power4

        private static int[] power4
      • neighborCount

        private int neighborCount
      • neighborIndices

        private int[] neighborIndices
      • neighborCenters

        private javajs.util.P3[] neighborCenters
      • neighborPlusProbeRadii2

        private float[] neighborPlusProbeRadii2
      • neighborRadii2

        private float[] neighborRadii2
    • Constructor Detail

      • EnvelopeCalculation

        public EnvelopeCalculation()
    • Method Detail

      • getDotsConvexMaps

        public BS[] getDotsConvexMaps()
      • getDotsConvexMax

        public int getDotsConvexMax()
      • allocDotsConvexMaps

        public void allocDotsConvexMaps​(int max)
      • setMads

        public void setMads​(short[] mads)
      • setFromBits

        public void setFromBits​(int index,
                                BS bs)
      • newSet

        public void newSet()
      • reCalculate

        public void reCalculate​(BS bs,
                                javajs.util.M3 m)
        problem prior to 12.3.18 was that dots once on the deodesic were not being moved. this isn't perfect, but it's reasonably good. Mostly, you should recreate dots after rotateSelected. This isn't a problem until after a state is saved and reloaded, since only then with atomData.radiusData be null.
        Parameters:
        bs -
        m -
      • calculate

        public void calculate​(RadiusData rd,
                              float maxRadius,
                              BS bsSelected,
                              BS bsIgnore,
                              boolean disregardNeighbors,
                              boolean onlySelectedDots,
                              boolean isSurface,
                              boolean multiModel)
        Specified by:
        calculate in interface JmolEnvCalc
        Parameters:
        rd -
        maxRadius -
        bsSelected -
        bsIgnore -
        disregardNeighbors -
        onlySelectedDots -
        isSurface -
        multiModel -
      • getRadius

        public float getRadius​(int atomIndex)
      • getPoints

        public javajs.util.P3[] getPoints()
        Specified by:
        getPoints in interface JmolEnvCalc
      • setDotsConvexMax

        private void setDotsConvexMax()
      • getAppropriateRadius

        public float getAppropriateRadius​(int atomIndex)
      • setAtomI

        private void setAtomI​(int indexI)
      • calcConvexMap

        private void calcConvexMap​(boolean isSurface)
      • addIncompleteFaces

        private void addIncompleteFaces​(BS points)
      • calcConvexBits

        private void calcConvexBits()
      • checkNewDotsArray

        private void checkNewDotsArray()
      • deleteAtoms

        public void deleteAtoms​(int firstAtomDeleted,
                                int nAtomsDeleted)
        Parameters:
        firstAtomDeleted -
        nAtomsDeleted -