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