org.jmol.geodesic
Class EnvelopeCalculation
public final
class
EnvelopeCalculation
extends Object
Method Summary |
void | addIncompleteFaces(int[] points) |
static int[] | allocateBitmap(int count) |
void | allocDotsConvexMaps(int max) |
void | calcConvexBits() |
void | calcConvexMap(boolean isSurface) |
void | calculate(float addRadius, float setRadius, float scale, float maxRadius, BitSet bsSelected, BitSet bsIgnore, boolean useVanderwaalsRadius, boolean disregardNeighbors, boolean onlySelectedDots, boolean isSurface, boolean multiModel) |
static void | clearBit(int[] bitmap, int i) |
static void | clearBitmap(int[] bitmap) |
void | deleteAtoms(int firstAtomDeleted, int nAtomsDeleted, BitSet bsAtoms) |
float | getAppropriateRadius(int atomIndex) |
static boolean | getBit(int[] bitmap, int i) |
BitSet | getBsSurfaceClone() |
int[][] | getDotsConvexMaps() |
int | getDotsConvexMax() |
int | getMapStorageCount(int[] map) |
void | getNeighbors() |
int | getPointCount(int[] visibilityMap, int dotCount) |
Point3f[] | getPoints() |
float | getRadius() |
void | newSet() |
static void | setAllBits(int[] bitmap, int count) |
void | setAtomI(int indexI) |
static void | setBit(int[] bitmap, int i) |
void | setDotsConvexMax() |
void | setFromBits(int index, BitSet bs) |
void | setMads(short[] mads) |
void | setRadii(boolean useVanderwaalsRadius) |
private float addRadius
private int atomCount
private BitSet bsMySelected
private BitSet bsSurface
private Point3f centerI
private Point3f centerT
private Point3f[] currentPoints
private float diameterP
private boolean disregardNeighbors
private int[][] dotsConvexMaps
private int dotsConvexMax
private int geodesicCount
private int[] geodesicMap
private int indexI
private short[] mads
private static final int[] mapNull
private int[] mapT
private float maxRadius
private boolean modelZeroBased
public static final int MAX_LEVEL
private Point3f[] neighborCenters
private int neighborCount
private int[] neighborIndices
private float[] neighborPlusProbeRadii2
private float[] neighborRadii2
private final Point3f pointT
private static int[] power4
private float radiiIP2
private float radiusI
private float radiusP
private float scale
private float setRadius
public static final float SURFACE_DISTANCE_FOR_CALCULATION
private final Point3f[] vertexTest
public EnvelopeCalculation(
AtomDataServer viewer, int atomCount, short[] mads)
private void addIncompleteFaces(int[] points)
private static final int[] allocateBitmap(int count)
public void allocDotsConvexMaps(int max)
private void calcConvexBits()
private void calcConvexMap(boolean isSurface)
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)
private static final void clearBit(int[] bitmap, int i)
private static final void clearBitmap(int[] bitmap)
public void deleteAtoms(int firstAtomDeleted, int nAtomsDeleted, BitSet bsAtoms)
public float getAppropriateRadius(int atomIndex)
public static final boolean getBit(int[] bitmap, int i)
public BitSet getBsSurfaceClone()
public int[][] getDotsConvexMaps()
public int getDotsConvexMax()
private int getMapStorageCount(int[] map)
private void getNeighbors()
private int getPointCount(int[] visibilityMap, int dotCount)
public Point3f[] getPoints()
public float getRadius()
public void newSet()
private static final void setAllBits(int[] bitmap, int count)
private void setAtomI(int indexI)
private static final void setBit(int[] bitmap, int i)
private void setDotsConvexMax()
public void setFromBits(int index, BitSet bs)
public void setMads(short[] mads)
private void setRadii(boolean useVanderwaalsRadius)