org.jmol.modelset
Class AtomCollection

java.lang.Object
  extended by org.jmol.modelset.AtomCollection
Direct Known Subclasses:
BondCollection

public abstract class AtomCollection
extends java.lang.Object


Nested Class Summary
(package private)  class AtomCollection.AtomSorter
           
 
Field Summary
private  int[] aaRet
           
private static float almost180
           
(package private)  int atomCount
           
(package private)  java.lang.String[] atomNames
           
 Atom[] atoms
           
(package private)  int[] atomSerials
           
(package private)  java.lang.String[] atomTypes
           
private  int bfactor100Hi
           
private  int bfactor100Lo
           
(package private)  short[] bfactor100s
           
private  java.util.BitSet bsEmpty
           
private  java.util.BitSet bsFoundRectangle
           
private  java.util.BitSet bsHidden
           
protected  Bspf bspf
           
private  java.util.BitSet bsSurface
           
protected  java.lang.Object[][] ellipsoids
           
protected  Graphics3D g3d
           
private  boolean hasBfactorRange
           
protected  boolean haveStraightness
           
(package private)  float[] hydrophobicities
           
(package private)  float[] ionicRadii
           
protected  float maxBondingRadius
           
private  float maxVanderwaalsRadius
           
private  int nSurfaceAtoms
           
(package private)  byte[] occupancies
           
(package private)  float[] partialCharges
           
protected  boolean preserveState
           
private static float sqrt3_2
           
protected  int[] surfaceDistance100s
           
private  int surfaceDistanceMax
           
static byte TAINT_ATOMNAME
           
static byte TAINT_ATOMNO
           
static byte TAINT_ATOMTYPE
           
static byte TAINT_COORD
           
static byte TAINT_ELEMENT
           
static byte TAINT_FORMALCHARGE
           
static byte TAINT_HYDROPHOBICITY
           
private static byte TAINT_IONICRADIUS
           
static byte TAINT_MAX
           
private static byte TAINT_OCCUPANCY
           
private static byte TAINT_PARTIALCHARGE
           
private static byte TAINT_TEMPERATURE
           
private static byte TAINT_VALENCE
           
private static byte TAINT_VANDERWAALS
           
private static byte TAINT_VIBRATION
           
protected  java.util.BitSet[] tainted
           
private static java.lang.String[] userSettableValues
           
 javax.vecmath.Vector3f[] vibrationVectors
           
 Viewer viewer
           
private static javax.vecmath.Vector3f vRef
           
 
Constructor Summary
AtomCollection()
           
 
Method Summary
private  void calcBfactorRange(java.util.BitSet bs)
           
private  void calcSurfaceDistances()
           
 javax.vecmath.Point3f[][] calculateHydrogens(java.util.BitSet bs, int[] nTotal, boolean doAll, boolean justCarbon, java.util.List<Atom> vConnect)
          get a list of potential H atom positions based on elemental valence and formal charge
 javax.vecmath.Point3f[] calculateSurface(java.util.BitSet bsSelected, float envelopeRadius)
           
 float calculateVolume(java.util.BitSet bs, EnumVdw vType)
           
 void clearBfactorRange()
           
protected  void deleteModelAtoms(int firstAtomIndex, int nAtoms, java.util.BitSet bs)
           
protected  void fillAtomData(AtomData atomData, int mode)
           
 java.util.BitSet findAtomsInRectangle(Rectangle rect, java.util.BitSet bsModels)
           
protected  void findMaxRadii()
           
protected  void findNearestAtomIndex(int x, int y, Atom[] closest, java.util.BitSet bsNot)
           
private  java.util.BitSet findNotAttached(int nAttached, int[][] angles, int[] ptrs, int nPtrs)
           
protected  java.util.BitSet getAtomBitsMaybeDeleted(int tokType, java.lang.Object specInfo)
          general unqualified lookup of atom set type
 java.lang.String getAtomChain(int i)
           
 short getAtomColix(int i)
           
 int getAtomCount()
           
 float[] getAtomicCharges()
           
 java.lang.String getAtomicPropertyState(int taintWhat, java.util.BitSet bsSelected)
           
 void getAtomicPropertyState(java.lang.StringBuffer commands, byte type, java.util.BitSet bs, java.lang.String label, float[] fData)
           
 int getAtomIndexFromAtomNumber(int atomNumber, java.util.BitSet bsVisibleFrames)
           
 int[] getAtomIndices(java.util.BitSet bs)
           
 java.lang.String getAtomInfo(int i, java.lang.String format)
           
 java.lang.String getAtomInfoXYZ(int i, boolean useChimeFormat)
           
 int getAtomModelIndex(int i)
           
 java.lang.String getAtomName(int i)
           
 int getAtomNumber(int i)
           
 javax.vecmath.Point3f getAtomPoint3f(int i)
           
 java.util.List<javax.vecmath.Point3f> getAtomPointVector(java.util.BitSet bs)
           
 float getAtomRadius(int i)
           
 java.lang.String getAtomSequenceCode(int i)
           
 java.util.BitSet getAtomsWithin(float distance, javax.vecmath.Point3f[] points, java.util.BitSet bsInclude)
           
 java.util.BitSet getAtomsWithin(float distance, javax.vecmath.Point4f plane)
           
 java.lang.String[] getAtomTypes()
           
 float getAtomVdwRadius(int i, EnumVdw type)
           
private  Atom[] getAttached(Atom atom, int nMax, boolean doSort)
           
 int getBfactor100Hi()
           
 int getBfactor100Lo()
           
 short[] getBFactors()
           
protected  java.util.BitSet getChainBits(char chainId)
           
protected  java.lang.String getChimeInfo(int tok, java.util.BitSet bs)
           
 java.util.BitSet getClickableSet()
           
(package private)  java.lang.String getElementName(int i)
           
 int getElementNumber(int i)
           
 java.lang.String getElementSymbol(int i)
           
 java.lang.Object[] getEllipsoid(int i)
           
protected  boolean getHaveStraightness()
           
 java.lang.Object getHelixData(java.util.BitSet bs, int tokType)
           
 java.lang.String getHybridizationAndAxes(int atomIndex, int atomicNumber, javax.vecmath.Vector3f z, javax.vecmath.Vector3f x, java.lang.String lcaoTypeRaw, boolean hybridizationCompatible, boolean doAlignZ)
           
private  java.lang.String getHybridizationAndAxesD(int atomIndex, javax.vecmath.Vector3f z, javax.vecmath.Vector3f x, java.lang.String lcaoType)
          dsp3 (trigonal bipyramidal, see-saw, T-shaped) or d2sp3 (square planar, square pyramidal, octahedral)
 float[] getHydrophobicity()
           
private  java.util.BitSet getIdentifierOrNull(java.lang.String identifier)
          overhauled by RMH Nov 1, 2006.
(package private)  int getImplicitHydrogenCount(Atom atom)
           
 float[] getIonicRadii()
           
 float getMaxVanderwaalsRadius()
           
 float[] getPartialCharges()
           
 Quaternion getQuaternion(int i, char qtype)
           
protected  float getRadiusVdwJmol(Atom atom)
           
protected  java.util.BitSet getSeqcodeBits(int seqcode, boolean returnEmpty)
           
private  java.util.BitSet getSpecName(java.lang.String name)
           
private  java.util.BitSet getSpecNameOrNull(java.lang.String name, boolean checkStar)
           
(package private)  int getSurfaceDistance100(int atomIndex)
           
 int getSurfaceDistanceMax()
           
 java.util.BitSet getTaintedAtoms(byte type)
           
static int getUserSettableType(java.lang.String dataType)
           
 float getVibrationCoord(int atomIndex, char c)
           
 javax.vecmath.Vector3f getVibrationVector(int atomIndex, boolean forceNew)
           
 java.util.BitSet getVisibleSet()
           
private  float getWorkingRadius(Atom atom, AtomData atomData)
           
private  boolean isAdjacentSp2(Atom atom)
           
 boolean isAtomHidden(int iAtom)
           
private  boolean isAtomNameMatch(Atom atom, java.lang.String strPattern, boolean checkStar)
           
(package private)  boolean isCursorOnTopOf(Atom contender, int x, int y, int radius, Atom champion)
          used by Frame and AminoMonomer and NucleicMonomer -- does NOT check for clickability
private  boolean isTainted(int atomIndex, byte type)
           
private  void loadCoordinates(java.lang.String data, boolean isVibrationVectors, boolean doTaint)
           
protected  void mergeAtomArrays(AtomCollection mergeModelSet)
           
 boolean modelSetHasVibrationVectors()
           
protected  void releaseModelSet()
           
 void setAtomCoord(java.util.BitSet bs, int tokType, java.lang.Object xyzValues)
           
 void setAtomCoord(int atomIndex, float x, float y, float z)
           
protected  void setAtomCoordRelative(java.util.BitSet bs, float x, float y, float z)
           
 void setAtomCoordRelative(int atomIndex, float x, float y, float z)
           
 void setAtomData(int type, java.lang.String name, java.lang.String dataString, boolean isDefault)
           
 void setAtomName(int atomIndex, java.lang.String name)
           
 boolean setAtomNumber(int atomIndex, int atomno)
           
 void setAtomProperty(java.util.BitSet bs, int tok, int iValue, float fValue, java.lang.String sValue, float[] values, java.lang.String[] list)
           
protected  void setAtomType(int atomIndex, java.lang.String type)
           
private  void setAtomVibrationVector(int atomIndex, float x, float y, float z)
           
private  void setBf(int i)
           
protected  boolean setBFactor(int atomIndex, float bfactor)
           
 void setBsHidden(java.util.BitSet bs)
           
protected  void setElement(Atom atom, int atomicNumber)
           
protected  void setEllipsoid(int atomIndex, java.lang.Object[] ellipsoid)
           
 void setFormalCharges(java.util.BitSet bs, int formalCharge)
           
 void setHaveStraightness(boolean TF)
           
protected  boolean setHydrophobicity(int atomIndex, float value)
           
protected  boolean setIonicRadius(int atomIndex, float radius)
           
protected  boolean setOccupancy(int atomIndex, int occupancy)
           
protected  boolean setPartialCharge(int atomIndex, float partialCharge)
           
 void setPreserveState(boolean TF)
           
 void setTaintedAtoms(java.util.BitSet bs, byte type)
           
protected  void setVibrationVector(int atomIndex, float x, float y, float z)
           
private  void setVibrationVector(int atomIndex, int tok, float fValue)
           
 void taint(java.util.BitSet bsAtoms, byte type)
           
protected  void taint(int atomIndex, byte type)
           
private  void untaint(int atomIndex, byte type)
           
 void unTaintAtoms(java.util.BitSet bs, byte type)
           
(package private)  void validateBspf(boolean isValid)
           
(package private)  void validateBspf(int modelIndex, boolean isValid)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

viewer

public Viewer viewer

g3d

protected Graphics3D g3d

atoms

public Atom[] atoms

atomCount

int atomCount

atomNames

java.lang.String[] atomNames

atomTypes

java.lang.String[] atomTypes

atomSerials

int[] atomSerials

vibrationVectors

public javax.vecmath.Vector3f[] vibrationVectors

occupancies

byte[] occupancies

bfactor100s

short[] bfactor100s

partialCharges

float[] partialCharges

ionicRadii

float[] ionicRadii

hydrophobicities

float[] hydrophobicities

ellipsoids

protected java.lang.Object[][] ellipsoids

surfaceDistance100s

protected int[] surfaceDistance100s

haveStraightness

protected boolean haveStraightness

bsHidden

private java.util.BitSet bsHidden

maxBondingRadius

protected float maxBondingRadius

maxVanderwaalsRadius

private float maxVanderwaalsRadius

hasBfactorRange

private boolean hasBfactorRange

bfactor100Lo

private int bfactor100Lo

bfactor100Hi

private int bfactor100Hi

surfaceDistanceMax

private int surfaceDistanceMax

bsSurface

private java.util.BitSet bsSurface

nSurfaceAtoms

private int nSurfaceAtoms

bspf

protected Bspf bspf

preserveState

protected boolean preserveState

TAINT_ATOMNAME

public static final byte TAINT_ATOMNAME
See Also:
Constant Field Values

TAINT_ATOMTYPE

public static final byte TAINT_ATOMTYPE
See Also:
Constant Field Values

TAINT_COORD

public static final byte TAINT_COORD
See Also:
Constant Field Values

TAINT_ELEMENT

public static final byte TAINT_ELEMENT
See Also:
Constant Field Values

TAINT_FORMALCHARGE

public static final byte TAINT_FORMALCHARGE
See Also:
Constant Field Values

TAINT_HYDROPHOBICITY

public static final byte TAINT_HYDROPHOBICITY
See Also:
Constant Field Values

TAINT_IONICRADIUS

private static final byte TAINT_IONICRADIUS
See Also:
Constant Field Values

TAINT_OCCUPANCY

private static final byte TAINT_OCCUPANCY
See Also:
Constant Field Values

TAINT_PARTIALCHARGE

private static final byte TAINT_PARTIALCHARGE
See Also:
Constant Field Values

TAINT_TEMPERATURE

private static final byte TAINT_TEMPERATURE
See Also:
Constant Field Values

TAINT_VALENCE

private static final byte TAINT_VALENCE
See Also:
Constant Field Values

TAINT_VANDERWAALS

private static final byte TAINT_VANDERWAALS
See Also:
Constant Field Values

TAINT_VIBRATION

private static final byte TAINT_VIBRATION
See Also:
Constant Field Values

TAINT_ATOMNO

public static final byte TAINT_ATOMNO
See Also:
Constant Field Values

TAINT_MAX

public static final byte TAINT_MAX
See Also:
Constant Field Values

userSettableValues

private static final java.lang.String[] userSettableValues

tainted

protected java.util.BitSet[] tainted

bsEmpty

private final java.util.BitSet bsEmpty

bsFoundRectangle

private final java.util.BitSet bsFoundRectangle

aaRet

private int[] aaRet

sqrt3_2

private static final float sqrt3_2

vRef

private static final javax.vecmath.Vector3f vRef

almost180

private static final float almost180
See Also:
Constant Field Values
Constructor Detail

AtomCollection

public AtomCollection()
Method Detail

releaseModelSet

protected void releaseModelSet()

mergeAtomArrays

protected void mergeAtomArrays(AtomCollection mergeModelSet)

setHaveStraightness

public void setHaveStraightness(boolean TF)

getHaveStraightness

protected boolean getHaveStraightness()

getAtomPointVector

public java.util.List<javax.vecmath.Point3f> getAtomPointVector(java.util.BitSet bs)

getAtomCount

public int getAtomCount()

modelSetHasVibrationVectors

public boolean modelSetHasVibrationVectors()

getAtomTypes

public java.lang.String[] getAtomTypes()

getPartialCharges

public float[] getPartialCharges()

getIonicRadii

public float[] getIonicRadii()

getBFactors

public short[] getBFactors()

getHydrophobicity

public float[] getHydrophobicity()

setBsHidden

public void setBsHidden(java.util.BitSet bs)

isAtomHidden

public boolean isAtomHidden(int iAtom)

getAtomInfo

public java.lang.String getAtomInfo(int i,
                                    java.lang.String format)

getAtomInfoXYZ

public java.lang.String getAtomInfoXYZ(int i,
                                       boolean useChimeFormat)

getElementSymbol

public java.lang.String getElementSymbol(int i)

getElementNumber

public int getElementNumber(int i)

getElementName

java.lang.String getElementName(int i)

getAtomName

public java.lang.String getAtomName(int i)

getAtomNumber

public int getAtomNumber(int i)

getAtomPoint3f

public javax.vecmath.Point3f getAtomPoint3f(int i)

getAtomRadius

public float getAtomRadius(int i)

getAtomVdwRadius

public float getAtomVdwRadius(int i,
                              EnumVdw type)

getAtomColix

public short getAtomColix(int i)

getAtomChain

public java.lang.String getAtomChain(int i)

getAtomSequenceCode

public java.lang.String getAtomSequenceCode(int i)

getAtomModelIndex

public int getAtomModelIndex(int i)

getEllipsoid

public java.lang.Object[] getEllipsoid(int i)

getQuaternion

public Quaternion getQuaternion(int i,
                                char qtype)

getHelixData

public java.lang.Object getHelixData(java.util.BitSet bs,
                                     int tokType)

getAtomIndexFromAtomNumber

public int getAtomIndexFromAtomNumber(int atomNumber,
                                      java.util.BitSet bsVisibleFrames)

setFormalCharges

public void setFormalCharges(java.util.BitSet bs,
                             int formalCharge)

getAtomicCharges

public float[] getAtomicCharges()

getRadiusVdwJmol

protected float getRadiusVdwJmol(Atom atom)

getMaxVanderwaalsRadius

public float getMaxVanderwaalsRadius()

findMaxRadii

protected void findMaxRadii()

clearBfactorRange

public void clearBfactorRange()

calcBfactorRange

private void calcBfactorRange(java.util.BitSet bs)

setBf

private void setBf(int i)

getBfactor100Lo

public int getBfactor100Lo()

getBfactor100Hi

public int getBfactor100Hi()

getSurfaceDistanceMax

public int getSurfaceDistanceMax()

calculateVolume

public float calculateVolume(java.util.BitSet bs,
                             EnumVdw vType)

getSurfaceDistance100

int getSurfaceDistance100(int atomIndex)

calcSurfaceDistances

private void calcSurfaceDistances()

calculateSurface

public javax.vecmath.Point3f[] calculateSurface(java.util.BitSet bsSelected,
                                                float envelopeRadius)

setAtomCoord

public void setAtomCoord(java.util.BitSet bs,
                         int tokType,
                         java.lang.Object xyzValues)

setAtomVibrationVector

private void setAtomVibrationVector(int atomIndex,
                                    float x,
                                    float y,
                                    float z)

setAtomCoord

public void setAtomCoord(int atomIndex,
                         float x,
                         float y,
                         float z)

setAtomCoordRelative

public void setAtomCoordRelative(int atomIndex,
                                 float x,
                                 float y,
                                 float z)

setAtomCoordRelative

protected void setAtomCoordRelative(java.util.BitSet bs,
                                    float x,
                                    float y,
                                    float z)

setAtomProperty

public void setAtomProperty(java.util.BitSet bs,
                            int tok,
                            int iValue,
                            float fValue,
                            java.lang.String sValue,
                            float[] values,
                            java.lang.String[] list)

setElement

protected void setElement(Atom atom,
                          int atomicNumber)

getVibrationCoord

public float getVibrationCoord(int atomIndex,
                               char c)

getVibrationVector

public javax.vecmath.Vector3f getVibrationVector(int atomIndex,
                                                 boolean forceNew)

setVibrationVector

protected void setVibrationVector(int atomIndex,
                                  float x,
                                  float y,
                                  float z)

setVibrationVector

private void setVibrationVector(int atomIndex,
                                int tok,
                                float fValue)

setAtomName

public void setAtomName(int atomIndex,
                        java.lang.String name)

setAtomType

protected void setAtomType(int atomIndex,
                           java.lang.String type)

setAtomNumber

public boolean setAtomNumber(int atomIndex,
                             int atomno)

setOccupancy

protected boolean setOccupancy(int atomIndex,
                               int occupancy)

setPartialCharge

protected boolean setPartialCharge(int atomIndex,
                                   float partialCharge)

setIonicRadius

protected boolean setIonicRadius(int atomIndex,
                                 float radius)

setBFactor

protected boolean setBFactor(int atomIndex,
                             float bfactor)

setHydrophobicity

protected boolean setHydrophobicity(int atomIndex,
                                    float value)

setEllipsoid

protected void setEllipsoid(int atomIndex,
                            java.lang.Object[] ellipsoid)

setAtomData

public void setAtomData(int type,
                        java.lang.String name,
                        java.lang.String dataString,
                        boolean isDefault)

loadCoordinates

private void loadCoordinates(java.lang.String data,
                             boolean isVibrationVectors,
                             boolean doTaint)

validateBspf

void validateBspf(boolean isValid)

validateBspf

void validateBspf(int modelIndex,
                  boolean isValid)

setPreserveState

public void setPreserveState(boolean TF)

getUserSettableType

public static int getUserSettableType(java.lang.String dataType)

isTainted

private boolean isTainted(int atomIndex,
                          byte type)

getTaintedAtoms

public java.util.BitSet getTaintedAtoms(byte type)

taint

public void taint(java.util.BitSet bsAtoms,
                  byte type)

taint

protected void taint(int atomIndex,
                     byte type)

untaint

private void untaint(int atomIndex,
                     byte type)

setTaintedAtoms

public void setTaintedAtoms(java.util.BitSet bs,
                            byte type)

unTaintAtoms

public void unTaintAtoms(java.util.BitSet bs,
                         byte type)

getAtomicPropertyState

public java.lang.String getAtomicPropertyState(int taintWhat,
                                               java.util.BitSet bsSelected)

getAtomicPropertyState

public void getAtomicPropertyState(java.lang.StringBuffer commands,
                                   byte type,
                                   java.util.BitSet bs,
                                   java.lang.String label,
                                   float[] fData)

findNearestAtomIndex

protected void findNearestAtomIndex(int x,
                                    int y,
                                    Atom[] closest,
                                    java.util.BitSet bsNot)

isCursorOnTopOf

boolean isCursorOnTopOf(Atom contender,
                        int x,
                        int y,
                        int radius,
                        Atom champion)
used by Frame and AminoMonomer and NucleicMonomer -- does NOT check for clickability

Parameters:
contender -
x -
y -
radius -
champion -
Returns:
true if user is pointing to this atom

findAtomsInRectangle

public java.util.BitSet findAtomsInRectangle(Rectangle rect,
                                             java.util.BitSet bsModels)

fillAtomData

protected void fillAtomData(AtomData atomData,
                            int mode)

getWorkingRadius

private float getWorkingRadius(Atom atom,
                               AtomData atomData)

calculateHydrogens

public javax.vecmath.Point3f[][] calculateHydrogens(java.util.BitSet bs,
                                                    int[] nTotal,
                                                    boolean doAll,
                                                    boolean justCarbon,
                                                    java.util.List<Atom> vConnect)
get a list of potential H atom positions based on elemental valence and formal charge

Parameters:
bs -
nTotal -
doAll - -- whether we add to C that already have H or not.
justCarbon -
vConnect -
Returns:
array of arrays of points added to specific atoms

isAdjacentSp2

private boolean isAdjacentSp2(Atom atom)

getImplicitHydrogenCount

int getImplicitHydrogenCount(Atom atom)

getHybridizationAndAxes

public java.lang.String getHybridizationAndAxes(int atomIndex,
                                                int atomicNumber,
                                                javax.vecmath.Vector3f z,
                                                javax.vecmath.Vector3f x,
                                                java.lang.String lcaoTypeRaw,
                                                boolean hybridizationCompatible,
                                                boolean doAlignZ)

getHybridizationAndAxesD

private java.lang.String getHybridizationAndAxesD(int atomIndex,
                                                  javax.vecmath.Vector3f z,
                                                  javax.vecmath.Vector3f x,
                                                  java.lang.String lcaoType)
dsp3 (trigonal bipyramidal, see-saw, T-shaped) or d2sp3 (square planar, square pyramidal, octahedral)

Parameters:
atomIndex -
z -
x -
lcaoType -
Returns:
valid hybridization or null

getAttached

private Atom[] getAttached(Atom atom,
                           int nMax,
                           boolean doSort)

findNotAttached

private java.util.BitSet findNotAttached(int nAttached,
                                         int[][] angles,
                                         int[] ptrs,
                                         int nPtrs)

getChimeInfo

protected java.lang.String getChimeInfo(int tok,
                                        java.util.BitSet bs)

getAtomBitsMaybeDeleted

protected java.util.BitSet getAtomBitsMaybeDeleted(int tokType,
                                                   java.lang.Object specInfo)
general unqualified lookup of atom set type

Parameters:
tokType -
specInfo -
Returns:
BitSet; or null if we mess up the type

getIdentifierOrNull

private java.util.BitSet getIdentifierOrNull(java.lang.String identifier)
overhauled by RMH Nov 1, 2006.

Parameters:
identifier -
Returns:
null or bs

getSpecName

private java.util.BitSet getSpecName(java.lang.String name)

getSpecNameOrNull

private java.util.BitSet getSpecNameOrNull(java.lang.String name,
                                           boolean checkStar)

isAtomNameMatch

private boolean isAtomNameMatch(Atom atom,
                                java.lang.String strPattern,
                                boolean checkStar)

getSeqcodeBits

protected java.util.BitSet getSeqcodeBits(int seqcode,
                                          boolean returnEmpty)

getChainBits

protected java.util.BitSet getChainBits(char chainId)

getAtomIndices

public int[] getAtomIndices(java.util.BitSet bs)

getAtomsWithin

public java.util.BitSet getAtomsWithin(float distance,
                                       javax.vecmath.Point4f plane)

getAtomsWithin

public java.util.BitSet getAtomsWithin(float distance,
                                       javax.vecmath.Point3f[] points,
                                       java.util.BitSet bsInclude)

getVisibleSet

public java.util.BitSet getVisibleSet()

getClickableSet

public java.util.BitSet getClickableSet()

deleteModelAtoms

protected void deleteModelAtoms(int firstAtomIndex,
                                int nAtoms,
                                java.util.BitSet bs)