org.jmol.geodesic
Class EnvelopeCalculation
java.lang.Object
org.jmol.geodesic.EnvelopeCalculation
public final class EnvelopeCalculation
- extends Object
Method Summary |
private void |
addIncompleteFaces(FastBitSet points)
|
void |
allocDotsConvexMaps(int max)
|
private void |
calcConvexBits()
|
private void |
calcConvexMap(boolean isSurface)
|
void |
calculate(RadiusData rd,
float maxRadius,
BitSet bsSelected,
BitSet bsIgnore,
boolean disregardNeighbors,
boolean onlySelectedDots,
boolean isSurface,
boolean multiModel)
|
void |
deleteAtoms(int firstAtomDeleted,
int nAtomsDeleted,
BitSet bsAtoms)
|
float |
getAppropriateRadius(int atomIndex)
|
BitSet |
getBsSurfaceClone()
|
FastBitSet[] |
getDotsConvexMaps()
|
int |
getDotsConvexMax()
|
private AtomIndexIterator |
getNeighbors(AtomIndexIterator iter)
|
Point3f[] |
getPoints()
|
float |
getRadius(int atomIndex)
|
void |
newSet()
|
void |
reCalculate(BitSet bs)
|
private void |
setAtomI(int indexI)
|
private void |
setDotsConvexMax()
|
void |
setFromBits(int index,
BitSet bs)
|
void |
setMads(short[] mads)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
geodesicMap
private FastBitSet geodesicMap
mapT
private FastBitSet mapT
mads
private short[] mads
atomData
private AtomData atomData
viewer
private AtomDataServer viewer
atomCount
private int atomCount
emptySet
private FastBitSet emptySet
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
modelZeroBased
private boolean modelZeroBased
disregardNeighbors
private boolean disregardNeighbors
bsMySelected
private BitSet bsMySelected
dotsConvexMaps
private FastBitSet[] dotsConvexMaps
dotsConvexMax
private int dotsConvexMax
geodesicCount
private int geodesicCount
bsSurface
private BitSet bsSurface
radiusP
private float radiusP
diameterP
private float diameterP
bsIgnore
private BitSet bsIgnore
onlySelectedDots
private boolean onlySelectedDots
isSurface
private boolean isSurface
multiModel
private boolean multiModel
currentPoints
private Point3f[] currentPoints
indexI
private int indexI
centerI
private Point3f centerI
radiusI
private float radiusI
radiiIP2
private float radiiIP2
pointT
private final Point3f pointT
centerT
private Point3f centerT
vertexTest
private final Point3f[] vertexTest
power4
private static int[] power4
neighborCount
private int neighborCount
neighborIndices
private int[] neighborIndices
neighborCenters
private Point3f[] neighborCenters
neighborPlusProbeRadii2
private float[] neighborPlusProbeRadii2
neighborRadii2
private float[] neighborRadii2
EnvelopeCalculation
public EnvelopeCalculation(AtomDataServer viewer,
int atomCount,
short[] mads,
boolean asJavaBitSet)
getDotsConvexMaps
public FastBitSet[] getDotsConvexMaps()
getDotsConvexMax
public int getDotsConvexMax()
allocDotsConvexMaps
public void allocDotsConvexMaps(int max)
getBsSurfaceClone
public BitSet getBsSurfaceClone()
setMads
public void setMads(short[] mads)
setFromBits
public void setFromBits(int index,
BitSet bs)
newSet
public void newSet()
reCalculate
public void reCalculate(BitSet bs)
calculate
public void calculate(RadiusData rd,
float maxRadius,
BitSet bsSelected,
BitSet bsIgnore,
boolean disregardNeighbors,
boolean onlySelectedDots,
boolean isSurface,
boolean multiModel)
- Parameters:
rd
- maxRadius
- bsSelected
- bsIgnore
- disregardNeighbors
- onlySelectedDots
- isSurface
- multiModel
-
getRadius
public float getRadius(int atomIndex)
getPoints
public Point3f[] getPoints()
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(FastBitSet points)
calcConvexBits
private void calcConvexBits()
getNeighbors
private AtomIndexIterator getNeighbors(AtomIndexIterator iter)
deleteAtoms
public void deleteAtoms(int firstAtomDeleted,
int nAtomsDeleted,
BitSet bsAtoms)