Field Detail

• geodesicMap

  private BS geodesicMap

• mapT

  private BS mapT

• mads

  private short[] mads

• atomData

  private AtomData atomData

• vwr

  private AtomDataServer vwr

• 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

• set

  public EnvelopeCalculation set​(AtomDataServer vwr,
                                 int ac,
                                 short[] mads)

  Specified by:

  set in interface JmolEnvCalc

  Parameters:

  vwr -

  ac -

  mads -

  Returns:

  this

• getDotsConvexMaps

  public BS[] getDotsConvexMaps()

• getDotsConvexMax

  public int getDotsConvexMax()

• allocDotsConvexMaps

  public void allocDotsConvexMaps​(int max)

• getBsSurfaceClone

  public BS getBsSurfaceClone()

  Specified by:

  getBsSurfaceClone in interface JmolEnvCalc

• 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()

• getNeighbors

  private AtomIndexIterator getNeighbors​(AtomIndexIterator iter)

• deleteAtoms

  public void deleteAtoms​(int firstAtomDeleted,
                          int nAtomsDeleted)

  Parameters:

  firstAtomDeleted -

  nAtomsDeleted -