public final class EnvelopeCalculation extends java.lang.Object implements JmolEnvCalc
Modifier and Type | Field and Description |
---|---|
private int |
ac |
private AtomData |
atomData |
private BS |
bsIgnore |
private BS |
bsMySelected |
private BS |
bsSurface |
private BS |
bsTemp |
private javajs.util.P3 |
centerI |
private javajs.util.P3 |
centerT |
private javajs.util.P3[] |
currentPoints |
private float |
diameterP |
private boolean |
disregardNeighbors |
private BS[] |
dotsConvexMaps |
private int |
dotsConvexMax |
private static BS |
EMPTY_SET |
private int |
geodesicCount |
private BS |
geodesicMap |
private int |
indexI |
private boolean |
isSurface |
private short[] |
mads |
private BS |
mapT |
private float |
maxRadius |
private boolean |
modelZeroBased |
private boolean |
multiModel |
private javajs.util.P3[] |
neighborCenters |
private int |
neighborCount |
private int[] |
neighborIndices |
private float[] |
neighborPlusProbeRadii2 |
private float[] |
neighborRadii2 |
private boolean |
onlySelectedDots |
private javajs.util.P3 |
pointT |
private static int[] |
power4 |
private float |
radiiIP2 |
private float |
radiusI |
private float |
radiusP |
private javajs.util.P3[] |
vertexTest |
private AtomDataServer |
vwr |
Constructor and Description |
---|
EnvelopeCalculation() |
Modifier and Type | Method and Description |
---|---|
private void |
addIncompleteFaces(BS points) |
void |
allocDotsConvexMaps(int max) |
private void |
calcConvexBits() |
private void |
calcConvexMap(boolean isSurface) |
void |
calculate(RadiusData rd,
float maxRadius,
BS bsSelected,
BS bsIgnore,
boolean disregardNeighbors,
boolean onlySelectedDots,
boolean isSurface,
boolean multiModel) |
private void |
checkNewDotsArray() |
void |
deleteAtoms(int firstAtomDeleted,
int nAtomsDeleted) |
float |
getAppropriateRadius(int atomIndex) |
BS |
getBsSurfaceClone() |
BS[] |
getDotsConvexMaps() |
int |
getDotsConvexMax() |
private AtomIndexIterator |
getNeighbors(AtomIndexIterator iter) |
javajs.util.P3[] |
getPoints() |
float |
getRadius(int atomIndex) |
void |
newSet() |
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.
|
EnvelopeCalculation |
set(AtomDataServer vwr,
int ac,
short[] mads) |
private void |
setAtomI(int indexI) |
private void |
setDotsConvexMax() |
void |
setFromBits(int index,
BS bs) |
void |
setMads(short[] mads) |
private BS geodesicMap
private BS mapT
private short[] mads
private AtomData atomData
private AtomDataServer vwr
private int ac
private static BS EMPTY_SET
private float maxRadius
private boolean modelZeroBased
private boolean disregardNeighbors
private BS bsMySelected
private BS[] dotsConvexMaps
private int dotsConvexMax
private int geodesicCount
private BS bsSurface
private float radiusP
private float diameterP
private BS bsTemp
private BS bsIgnore
private boolean onlySelectedDots
private boolean isSurface
private boolean multiModel
private javajs.util.P3[] currentPoints
private int indexI
private javajs.util.P3 centerI
private float radiusI
private float radiiIP2
private final javajs.util.P3 pointT
private javajs.util.P3 centerT
private final javajs.util.P3[] vertexTest
private static int[] power4
private int neighborCount
private int[] neighborIndices
private javajs.util.P3[] neighborCenters
private float[] neighborPlusProbeRadii2
private float[] neighborRadii2
public EnvelopeCalculation set(AtomDataServer vwr, int ac, short[] mads)
set
in interface JmolEnvCalc
vwr
- ac
- mads
- public BS[] getDotsConvexMaps()
public int getDotsConvexMax()
public void allocDotsConvexMaps(int max)
public BS getBsSurfaceClone()
getBsSurfaceClone
in interface JmolEnvCalc
public void setMads(short[] mads)
public void setFromBits(int index, BS bs)
public void newSet()
public void reCalculate(BS bs, javajs.util.M3 m)
bs
- m
- public void calculate(RadiusData rd, float maxRadius, BS bsSelected, BS bsIgnore, boolean disregardNeighbors, boolean onlySelectedDots, boolean isSurface, boolean multiModel)
calculate
in interface JmolEnvCalc
rd
- maxRadius
- bsSelected
- bsIgnore
- disregardNeighbors
- onlySelectedDots
- isSurface
- multiModel
- public float getRadius(int atomIndex)
public javajs.util.P3[] getPoints()
getPoints
in interface JmolEnvCalc
private void setDotsConvexMax()
public float getAppropriateRadius(int atomIndex)
private void setAtomI(int indexI)
private void calcConvexMap(boolean isSurface)
private void addIncompleteFaces(BS points)
private void calcConvexBits()
private void checkNewDotsArray()
private AtomIndexIterator getNeighbors(AtomIndexIterator iter)
public void deleteAtoms(int firstAtomDeleted, int nAtomsDeleted)
firstAtomDeleted
- nAtomsDeleted
-