org.jmol.geodesic

Class EnvelopeCalculation

public final class EnvelopeCalculation extends Object

Field Summary
floataddRadius
intatomCount
AtomDataatomData
BitSetbsMySelected
BitSetbsSurface
Point3fcenterI
Point3fcenterT
Point3f[]currentPoints
floatdiameterP
booleandisregardNeighbors
int[][]dotsConvexMaps
intdotsConvexMax
intgeodesicCount
int[]geodesicMap
intindexI
short[]mads
static int[]mapNull
int[]mapT
floatmaxRadius
booleanmodelZeroBased
static intMAX_LEVEL
Point3f[]neighborCenters
intneighborCount
int[]neighborIndices
float[]neighborPlusProbeRadii2
float[]neighborRadii2
Point3fpointT
static int[]power4
floatradiiIP2
floatradiusI
floatradiusP
floatscale
floatsetRadius
static floatSURFACE_DISTANCE_FOR_CALCULATION
Point3f[]vertexTest
AtomDataServerviewer
Constructor Summary
EnvelopeCalculation(AtomDataServer viewer, int atomCount, short[] mads)
Method Summary
voidaddIncompleteFaces(int[] points)
static int[]allocateBitmap(int count)
voidallocDotsConvexMaps(int max)
voidcalcConvexBits()
voidcalcConvexMap(boolean isSurface)
voidcalculate(float addRadius, float setRadius, float scale, float maxRadius, BitSet bsSelected, BitSet bsIgnore, boolean useVanderwaalsRadius, boolean disregardNeighbors, boolean onlySelectedDots, boolean isSurface, boolean multiModel)
static voidclearBit(int[] bitmap, int i)
static voidclearBitmap(int[] bitmap)
voiddeleteAtoms(int firstAtomDeleted, int nAtomsDeleted, BitSet bsAtoms)
floatgetAppropriateRadius(int atomIndex)
static booleangetBit(int[] bitmap, int i)
BitSetgetBsSurfaceClone()
int[][]getDotsConvexMaps()
intgetDotsConvexMax()
intgetMapStorageCount(int[] map)
voidgetNeighbors()
intgetPointCount(int[] visibilityMap, int dotCount)
Point3f[]getPoints()
floatgetRadius()
voidnewSet()
static voidsetAllBits(int[] bitmap, int count)
voidsetAtomI(int indexI)
static voidsetBit(int[] bitmap, int i)
voidsetDotsConvexMax()
voidsetFromBits(int index, BitSet bs)
voidsetMads(short[] mads)
voidsetRadii(boolean useVanderwaalsRadius)

Field Detail

addRadius

private float addRadius

atomCount

private int atomCount

atomData

private AtomData atomData

bsMySelected

private BitSet bsMySelected

bsSurface

private BitSet bsSurface

centerI

private Point3f centerI

centerT

private Point3f centerT

currentPoints

private Point3f[] currentPoints

diameterP

private float diameterP

disregardNeighbors

private boolean disregardNeighbors

dotsConvexMaps

private int[][] dotsConvexMaps

dotsConvexMax

private int dotsConvexMax

geodesicCount

private int geodesicCount

geodesicMap

private int[] geodesicMap

indexI

private int indexI

mads

private short[] mads

mapNull

private static final int[] mapNull

mapT

private int[] mapT

maxRadius

private float maxRadius

modelZeroBased

private boolean modelZeroBased

MAX_LEVEL

public static final int MAX_LEVEL

neighborCenters

private Point3f[] neighborCenters

neighborCount

private int neighborCount

neighborIndices

private int[] neighborIndices

neighborPlusProbeRadii2

private float[] neighborPlusProbeRadii2

neighborRadii2

private float[] neighborRadii2

pointT

private final Point3f pointT

power4

private static int[] power4

radiiIP2

private float radiiIP2

radiusI

private float radiusI

radiusP

private float radiusP

scale

private float scale

setRadius

private float setRadius

SURFACE_DISTANCE_FOR_CALCULATION

public static final float SURFACE_DISTANCE_FOR_CALCULATION

vertexTest

private final Point3f[] vertexTest

viewer

private AtomDataServer viewer

Constructor Detail

EnvelopeCalculation

public EnvelopeCalculation(AtomDataServer viewer, int atomCount, short[] mads)

Method Detail

addIncompleteFaces

private void addIncompleteFaces(int[] points)

allocateBitmap

private static final int[] allocateBitmap(int count)

allocDotsConvexMaps

public void allocDotsConvexMaps(int max)

calcConvexBits

private void calcConvexBits()

calcConvexMap

private void calcConvexMap(boolean isSurface)

calculate

public void calculate(float addRadius, float setRadius, float scale, float maxRadius, BitSet bsSelected, BitSet bsIgnore, boolean useVanderwaalsRadius, boolean disregardNeighbors, boolean onlySelectedDots, boolean isSurface, boolean multiModel)

clearBit

private static final void clearBit(int[] bitmap, int i)

clearBitmap

private static final void clearBitmap(int[] bitmap)

deleteAtoms

public void deleteAtoms(int firstAtomDeleted, int nAtomsDeleted, BitSet bsAtoms)

getAppropriateRadius

public float getAppropriateRadius(int atomIndex)

getBit

public static final boolean getBit(int[] bitmap, int i)

getBsSurfaceClone

public BitSet getBsSurfaceClone()

getDotsConvexMaps

public int[][] getDotsConvexMaps()

getDotsConvexMax

public int getDotsConvexMax()

getMapStorageCount

private int getMapStorageCount(int[] map)

getNeighbors

private void getNeighbors()

getPointCount

private int getPointCount(int[] visibilityMap, int dotCount)

getPoints

public Point3f[] getPoints()

getRadius

public float getRadius()

newSet

public void newSet()

setAllBits

private static final void setAllBits(int[] bitmap, int count)

setAtomI

private void setAtomI(int indexI)

setBit

private static final void setBit(int[] bitmap, int i)

setDotsConvexMax

private void setDotsConvexMax()

setFromBits

public void setFromBits(int index, BitSet bs)

setMads

public void setMads(short[] mads)

setRadii

private void setRadii(boolean useVanderwaalsRadius)