org.jmol.modelset

Class AtomCollection

public abstract class AtomCollection extends Object

Field Summary
intatomCount
String[]atomNames
Atom[]atoms
int[]atomSerials
intbfactor100Hi
intbfactor100Lo
short[]bfactor100s
BitSetbsEmpty
BitSetbsFoundRectangle
BitSetbsHidden
protected Bspfbspf
BitSetbsSurface
Object[]clientAtomReferences
Object[][]ellipsoids
Graphics3Dg3d
booleanhasBfactorRange
protected floatmaxBondingRadius
floatmaxVanderwaalsRadius
static intminimumPixelSelectionRadius
intnSurfaceAtoms
byte[]occupancies
float[]partialCharges
protected static booleanshowRebondTimes
byte[]specialAtomIDs
protected int[]surfaceDistance100s
intsurfaceDistanceMax
protected BitSet[]tainted
static byteTAINT_COORD
static byteTAINT_FORMALCHARGE
static byteTAINT_MAX
static byteTAINT_OCCUPANCY
static byteTAINT_PARTIALCHARGE
static byteTAINT_TEMPERATURE
static byteTAINT_VALENCE
static byteTAINT_VANDERWAALS
static byteTAINT_VIBRATION
static String[]userSettableValues
Vector3f[]vibrationVectors
Viewerviewer
Method Summary
voidcalcBfactorRange(BitSet bs)
voidcalcSurfaceDistances()
Point3f[]calculateSurface(BitSet bsSelected, float envelopeRadius)
voidclearBfactorRange()
voiddeleteAtoms(int firstAtomIndex, int nAtoms, BitSet bs)
protected voidfillAtomData(AtomData atomData, int mode)
BitSetfindAtomsInRectangle(Rectangle rect, BitSet bsModels)
protected voidfindMaxRadii()
protected voidfindNearestAtomIndex(int x, int y, Atom[] closest)
protected Point3f[][]getAdditionalHydrogens(BitSet atomSet, int[] nTotal)
AtomgetAtomAt(int atomIndex)
protected BitSetgetAtomBits(int tokType, Object specInfo)
general unqualified lookup of atom set type
StringgetAtomChain(int i)
shortgetAtomColix(int i)
intgetAtomCount()
protected intgetAtomCountInModel(int modelIndex)
StringgetAtomicPropertyState(int taintWhat, BitSet bsSelected)
static voidgetAtomicPropertyState(StringBuffer commands, Atom[] atoms, int atomCount, byte type, BitSet bs, String label, float[] fData)
intgetAtomIndexFromAtomNumber(int atomNumber)
int[]getAtomIndices(BitSet bs)
StringgetAtomInfo(int i, String format)
StringgetAtomInfoXYZ(int i, boolean useChimeFormat)
intgetAtomModelIndex(int i)
StringgetAtomName(int i)
String[]getAtomNames()
intgetAtomNumber(int i)
Point3fgetAtomPoint3f(int i)
floatgetAtomRadius(int i)
Atom[]getAtoms()
BitSetgetAtomsWithin(float distance, Point4f plane)
StringgetAtomSequenceCode(int i)
floatgetAtomVdwRadius(int i)
floatgetAtomX(int i)
floatgetAtomY(int i)
floatgetAtomZ(int i)
intgetBfactor100Hi()
intgetBfactor100Lo()
short[]getBFactors()
protected BitSetgetChainBits(char chain)
protected StringgetChimeInfo(int tok, BitSet bs)
BitSetgetClickableSet()
StringgetElementName(int i)
intgetElementNumber(int i)
StringgetElementSymbol(int i)
Object[]getEllipsoid(int i)
StringgetHybridizationAndAxes(int atomIndex, Vector3f z, Vector3f x, String lcaoTypeRaw, boolean hybridizationCompatible)
BitSetgetIdentifierOrNull(String identifier)
overhauled by RMH Nov 1, 2006.
floatgetMaxVanderwaalsRadius()
BitSetgetModelBitSet(BitSet atomList)
float[]getPartialCharges()
QuaterniongetQuaternion(int i, char qtype)
protected floatgetRadiusVdwJmol(Atom atom)
protected BitSetgetSeqcodeBits(int seqcode, boolean returnEmpty)
BitSetgetSpecName(String name)
BitSetgetSpecNameOrNull(String name, boolean checkStar)
intgetSurfaceDistance100(int atomIndex)
intgetSurfaceDistanceMax()
BitSetgetTaintedAtoms(byte type)
static intgetUserSettableType(String dataType)
floatgetVibrationCoord(int atomIndex, char c)
Vector3fgetVibrationVector(int atomIndex)
BitSetgetVisibleSet()
booleanisAtomHidden(int iAtom)
booleanisAtomNameMatch(Atom atom, String strPattern, boolean checkStar)
booleanisCursorOnTopOf(Atom contender, int x, int y, int radius, Atom champion)
used by Frame and AminoMonomer and NucleicMonomer -- does NOT check for clickability
protected booleanisInLatticeCell(int i, Point3f cell)
voidloadCoordinates(String data, boolean isVibrationVectors)
voidloadData(int type, String name, String dataString)
protected voidmerge(AtomCollection mergeModelSet)
booleanmodelSetHasVibrationVectors()
protected voidreleaseModelSet()
voidsetAtomCoord(BitSet bs, int tokType, Object xyzValues)
voidsetAtomCoord(int atomIndex, float x, float y, float z)
voidsetAtomCoordRelative(int atomIndex, float x, float y, float z)
protected voidsetAtomCoordRelative(BitSet atomSet, float x, float y, float z)
voidsetAtomProperty(BitSet bs, int tok, int iValue, float fValue, float[] values)
voidsetAtomVibrationVector(int atomIndex, float x, float y, float z)
protected voidsetBFactor(int atomIndex, float bfactor)
voidsetBsHidden(BitSet bs)
protected voidsetEllipsoid(int atomIndex, Object[] ellipsoid)
voidsetFormalCharges(BitSet bs, int formalCharge)
protected voidsetOccupancy(int atomIndex, int occupancy)
protected voidsetPartialCharge(int atomIndex, float partialCharge)
voidsetTaintedAtoms(BitSet bs, byte type)
protected voidsetVibrationVector(int atomIndex, float x, float y, float z)
voidsetVibrationVector(int atomIndex, int tok, float fValue)
protected voidtaint(int atomIndex, byte type)
voiduntaint(int i, byte type)

Field Detail

atomCount

int atomCount

atomNames

String[] atomNames

atoms

public Atom[] atoms

atomSerials

int[] atomSerials

bfactor100Hi

private int bfactor100Hi

bfactor100Lo

private int bfactor100Lo

bfactor100s

short[] bfactor100s

bsEmpty

final BitSet bsEmpty

bsFoundRectangle

final BitSet bsFoundRectangle

bsHidden

private BitSet bsHidden

bspf

protected Bspf bspf

bsSurface

private BitSet bsSurface

clientAtomReferences

Object[] clientAtomReferences

ellipsoids

Object[][] ellipsoids

g3d

Graphics3D g3d

hasBfactorRange

private boolean hasBfactorRange

maxBondingRadius

protected float maxBondingRadius

maxVanderwaalsRadius

private float maxVanderwaalsRadius

minimumPixelSelectionRadius

private static final int minimumPixelSelectionRadius

nSurfaceAtoms

private int nSurfaceAtoms

occupancies

byte[] occupancies

partialCharges

float[] partialCharges

showRebondTimes

protected static final boolean showRebondTimes

specialAtomIDs

byte[] specialAtomIDs

surfaceDistance100s

protected int[] surfaceDistance100s

surfaceDistanceMax

private int surfaceDistanceMax

tainted

protected BitSet[] tainted

TAINT_COORD

public static final byte TAINT_COORD

TAINT_FORMALCHARGE

private static final byte TAINT_FORMALCHARGE

TAINT_MAX

public static final byte TAINT_MAX

TAINT_OCCUPANCY

private static final byte TAINT_OCCUPANCY

TAINT_PARTIALCHARGE

private static final byte TAINT_PARTIALCHARGE

TAINT_TEMPERATURE

private static final byte TAINT_TEMPERATURE

TAINT_VALENCE

private static final byte TAINT_VALENCE

TAINT_VANDERWAALS

private static final byte TAINT_VANDERWAALS

TAINT_VIBRATION

private static final byte TAINT_VIBRATION

userSettableValues

private static final String[] userSettableValues

vibrationVectors

Vector3f[] vibrationVectors

viewer

public Viewer viewer

Method Detail

calcBfactorRange

private void calcBfactorRange(BitSet bs)

calcSurfaceDistances

private void calcSurfaceDistances()

calculateSurface

public Point3f[] calculateSurface(BitSet bsSelected, float envelopeRadius)

clearBfactorRange

public void clearBfactorRange()

deleteAtoms

public void deleteAtoms(int firstAtomIndex, int nAtoms, BitSet bs)

fillAtomData

protected void fillAtomData(AtomData atomData, int mode)

findAtomsInRectangle

public BitSet findAtomsInRectangle(Rectangle rect, BitSet bsModels)

findMaxRadii

protected void findMaxRadii()

findNearestAtomIndex

protected void findNearestAtomIndex(int x, int y, Atom[] closest)

getAdditionalHydrogens

protected Point3f[][] getAdditionalHydrogens(BitSet atomSet, int[] nTotal)

getAtomAt

public Atom getAtomAt(int atomIndex)

getAtomBits

protected BitSet getAtomBits(int tokType, Object specInfo)
general unqualified lookup of atom set type

Parameters: tokType specInfo

Returns: BitSet; or null if we mess up the type

getAtomChain

public String getAtomChain(int i)

getAtomColix

public short getAtomColix(int i)

getAtomCount

public int getAtomCount()

getAtomCountInModel

protected int getAtomCountInModel(int modelIndex)

getAtomicPropertyState

public String getAtomicPropertyState(int taintWhat, BitSet bsSelected)

getAtomicPropertyState

public static void getAtomicPropertyState(StringBuffer commands, Atom[] atoms, int atomCount, byte type, BitSet bs, String label, float[] fData)

getAtomIndexFromAtomNumber

public int getAtomIndexFromAtomNumber(int atomNumber)

getAtomIndices

public int[] getAtomIndices(BitSet bs)

getAtomInfo

public String getAtomInfo(int i, String format)

getAtomInfoXYZ

public String getAtomInfoXYZ(int i, boolean useChimeFormat)

getAtomModelIndex

public int getAtomModelIndex(int i)

getAtomName

public String getAtomName(int i)

getAtomNames

public String[] getAtomNames()

getAtomNumber

public int getAtomNumber(int i)

getAtomPoint3f

public Point3f getAtomPoint3f(int i)

getAtomRadius

public float getAtomRadius(int i)

getAtoms

public Atom[] getAtoms()

getAtomsWithin

public BitSet getAtomsWithin(float distance, Point4f plane)

getAtomSequenceCode

public String getAtomSequenceCode(int i)

getAtomVdwRadius

public float getAtomVdwRadius(int i)

getAtomX

public float getAtomX(int i)

getAtomY

public float getAtomY(int i)

getAtomZ

public float getAtomZ(int i)

getBfactor100Hi

public int getBfactor100Hi()

getBfactor100Lo

public int getBfactor100Lo()

getBFactors

public short[] getBFactors()

getChainBits

protected BitSet getChainBits(char chain)

getChimeInfo

protected String getChimeInfo(int tok, BitSet bs)

getClickableSet

public BitSet getClickableSet()

getElementName

String getElementName(int i)

getElementNumber

public int getElementNumber(int i)

getElementSymbol

public String getElementSymbol(int i)

getEllipsoid

public Object[] getEllipsoid(int i)

getHybridizationAndAxes

public String getHybridizationAndAxes(int atomIndex, Vector3f z, Vector3f x, String lcaoTypeRaw, boolean hybridizationCompatible)

getIdentifierOrNull

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

Parameters: identifier

Returns: null or bs

getMaxVanderwaalsRadius

public float getMaxVanderwaalsRadius()

getModelBitSet

public BitSet getModelBitSet(BitSet atomList)

getPartialCharges

public float[] getPartialCharges()

getQuaternion

public Quaternion getQuaternion(int i, char qtype)

getRadiusVdwJmol

protected float getRadiusVdwJmol(Atom atom)

getSeqcodeBits

protected BitSet getSeqcodeBits(int seqcode, boolean returnEmpty)

getSpecName

private BitSet getSpecName(String name)

getSpecNameOrNull

private BitSet getSpecNameOrNull(String name, boolean checkStar)

getSurfaceDistance100

int getSurfaceDistance100(int atomIndex)

getSurfaceDistanceMax

public int getSurfaceDistanceMax()

getTaintedAtoms

public BitSet getTaintedAtoms(byte type)

getUserSettableType

public static int getUserSettableType(String dataType)

getVibrationCoord

public float getVibrationCoord(int atomIndex, char c)

getVibrationVector

public Vector3f getVibrationVector(int atomIndex)

getVisibleSet

public BitSet getVisibleSet()

isAtomHidden

public boolean isAtomHidden(int iAtom)

isAtomNameMatch

boolean isAtomNameMatch(Atom atom, String strPattern, boolean checkStar)

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

isInLatticeCell

protected boolean isInLatticeCell(int i, Point3f cell)

loadCoordinates

private void loadCoordinates(String data, boolean isVibrationVectors)

loadData

public void loadData(int type, String name, String dataString)

merge

protected void merge(AtomCollection mergeModelSet)

modelSetHasVibrationVectors

public boolean modelSetHasVibrationVectors()

releaseModelSet

protected void releaseModelSet()

setAtomCoord

public void setAtomCoord(BitSet bs, int tokType, Object xyzValues)

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(BitSet atomSet, float x, float y, float z)

setAtomProperty

public void setAtomProperty(BitSet bs, int tok, int iValue, float fValue, float[] values)

setAtomVibrationVector

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

setBFactor

protected void setBFactor(int atomIndex, float bfactor)

setBsHidden

public void setBsHidden(BitSet bs)

setEllipsoid

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

setFormalCharges

public void setFormalCharges(BitSet bs, int formalCharge)

setOccupancy

protected void setOccupancy(int atomIndex, int occupancy)

setPartialCharge

protected void setPartialCharge(int atomIndex, float partialCharge)

setTaintedAtoms

public void setTaintedAtoms(BitSet bs, byte type)

setVibrationVector

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

setVibrationVector

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

taint

protected void taint(int atomIndex, byte type)

untaint

private void untaint(int i, byte type)