org.jmol.modelset
Class AtomCollection
java.lang.Object
org.jmol.modelset.AtomCollection
- Direct Known Subclasses:
- BondCollection
public abstract class AtomCollection
- extends java.lang.Object
Method Summary |
private void |
calcBfactorRange(java.util.BitSet bs)
|
private void |
calcSurfaceDistances()
|
javax.vecmath.Point3f[] |
calculateSurface(java.util.BitSet bsSelected,
float envelopeRadius)
|
void |
clearBfactorRange()
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protected void |
deleteModelAtoms(int firstAtomIndex,
int nAtoms,
java.util.BitSet bs)
|
protected void |
fillAtomData(AtomData atomData,
int mode)
|
java.util.BitSet |
findAtomsInRectangle(java.awt.Rectangle rect,
java.util.BitSet bsModels)
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protected void |
findMaxRadii()
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protected void |
findNearestAtomIndex(int x,
int y,
Atom[] closest)
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protected javax.vecmath.Point3f[][] |
getAdditionalHydrogens(java.util.BitSet atomSet,
int[] nTotal)
|
Atom |
getAtomAt(int atomIndex)
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protected java.util.BitSet |
getAtomBits(int tokType,
java.lang.Object specInfo)
general unqualified lookup of atom set type |
java.lang.String |
getAtomChain(int i)
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short |
getAtomColix(int i)
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int |
getAtomCount()
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float[] |
getAtomicCharges()
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java.lang.String |
getAtomicPropertyState(int taintWhat,
java.util.BitSet bsSelected)
|
static void |
getAtomicPropertyState(java.lang.StringBuffer commands,
Atom[] atoms,
int atomCount,
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)
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java.lang.String |
getAtomInfo(int i,
java.lang.String format)
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java.lang.String |
getAtomInfoXYZ(int i,
boolean useChimeFormat)
|
int |
getAtomModelIndex(int i)
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java.lang.String |
getAtomName(int i)
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java.lang.String[] |
getAtomNames()
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int |
getAtomNumber(int i)
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javax.vecmath.Point3f |
getAtomPoint3f(int i)
|
float |
getAtomRadius(int i)
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Atom[] |
getAtoms()
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java.lang.String |
getAtomSequenceCode(int i)
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java.util.BitSet |
getAtomsWithin(float distance,
javax.vecmath.Point4f plane)
|
java.lang.String[] |
getAtomTypes()
|
float |
getAtomVdwRadius(int i)
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float |
getAtomX(int i)
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float |
getAtomY(int i)
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float |
getAtomZ(int i)
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int |
getBfactor100Hi()
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int |
getBfactor100Lo()
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short[] |
getBFactors()
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protected java.util.BitSet |
getChainBits(char chain)
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protected java.lang.String |
getChimeInfo(int tok,
java.util.BitSet bs)
|
java.util.BitSet |
getClickableSet()
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(package private) java.lang.String |
getElementName(int i)
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int |
getElementNumber(int i)
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java.lang.String |
getElementSymbol(int i)
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java.lang.Object[] |
getEllipsoid(int i)
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protected boolean |
getHaveStraightness()
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java.lang.Object |
getHelixData(java.util.BitSet bs,
int tokType)
|
java.lang.String |
getHybridizationAndAxes(int atomIndex,
javax.vecmath.Vector3f z,
javax.vecmath.Vector3f x,
java.lang.String lcaoTypeRaw,
boolean hybridizationCompatible)
|
private java.util.BitSet |
getIdentifierOrNull(java.lang.String identifier)
overhauled by RMH Nov 1, 2006. |
float |
getMaxVanderwaalsRadius()
|
float[] |
getPartialCharges()
|
Quaternion |
getQuaternion(int i,
char qtype)
|
protected float |
getRadiusVdwJmol(Atom atom)
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protected java.util.BitSet |
getSeqcodeBits(int seqcode,
boolean returnEmpty)
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private java.util.BitSet |
getSpecName(java.lang.String name)
|
private java.util.BitSet |
getSpecNameOrNull(java.lang.String name,
boolean checkStar)
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(package private) int |
getSurfaceDistance100(int atomIndex)
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int |
getSurfaceDistanceMax()
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java.util.BitSet |
getTaintedAtoms(byte type)
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static int |
getUserSettableType(java.lang.String dataType)
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float |
getVibrationCoord(int atomIndex,
char c)
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javax.vecmath.Vector3f |
getVibrationVector(int atomIndex,
boolean forceNew)
|
java.util.BitSet |
getVisibleSet()
|
boolean |
isAtomHidden(int iAtom)
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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 |
protected boolean |
isInLatticeCell(int i,
javax.vecmath.Point3f cell)
|
private void |
loadCoordinates(java.lang.String data,
boolean isVibrationVectors)
|
protected void |
merge(AtomCollection mergeModelSet)
|
boolean |
modelSetHasVibrationVectors()
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protected void |
releaseModelSet()
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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 atomSet,
float x,
float y,
float z)
|
void |
setAtomCoordRelative(int atomIndex,
float x,
float y,
float z)
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void |
setAtomData(int type,
java.lang.String name,
java.lang.String dataString)
|
protected void |
setAtomName(int atomIndex,
java.lang.String name)
|
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)
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protected boolean |
setBFactor(int atomIndex,
float bfactor)
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void |
setBsHidden(java.util.BitSet bs)
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protected void |
setEllipsoid(int atomIndex,
java.lang.Object[] ellipsoid)
|
void |
setFormalCharges(java.util.BitSet bs,
int formalCharge)
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void |
setHaveStraightness(boolean TF)
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protected boolean |
setOccupancy(int atomIndex,
int occupancy)
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protected boolean |
setPartialCharge(int atomIndex,
float partialCharge)
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void |
setTaintedAtoms(java.util.BitSet bs,
byte type)
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protected void |
setVibrationVector(int atomIndex,
float x,
float y,
float z)
|
private void |
setVibrationVector(int atomIndex,
int tok,
float fValue)
|
protected void |
taint(int atomIndex,
byte type)
|
private void |
untaint(int i,
byte type)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
specialAtomIDs
byte[] specialAtomIDs
clientAtomReferences
java.lang.Object[] clientAtomReferences
vibrationVectors
javax.vecmath.Vector3f[] vibrationVectors
occupancies
byte[] occupancies
bfactor100s
short[] bfactor100s
partialCharges
float[] partialCharges
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
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
private static final byte TAINT_ELEMENT
- See Also:
- Constant Field Values
TAINT_FORMALCHARGE
private static final byte TAINT_FORMALCHARGE
- 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_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
minimumPixelSelectionRadius
private static final int minimumPixelSelectionRadius
- See Also:
- Constant Field Values
bsEmpty
private final java.util.BitSet bsEmpty
bsFoundRectangle
private final java.util.BitSet bsFoundRectangle
AtomCollection
public AtomCollection()
releaseModelSet
protected void releaseModelSet()
merge
protected void merge(AtomCollection mergeModelSet)
setHaveStraightness
public void setHaveStraightness(boolean TF)
getHaveStraightness
protected boolean getHaveStraightness()
getAtoms
public Atom[] getAtoms()
getAtomAt
public Atom getAtomAt(int atomIndex)
getAtomCount
public int getAtomCount()
modelSetHasVibrationVectors
public boolean modelSetHasVibrationVectors()
getAtomNames
public java.lang.String[] getAtomNames()
getAtomTypes
public java.lang.String[] getAtomTypes()
getPartialCharges
public float[] getPartialCharges()
getBFactors
public short[] getBFactors()
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)
getAtomX
public float getAtomX(int i)
getAtomY
public float getAtomY(int i)
getAtomZ
public float getAtomZ(int i)
getAtomPoint3f
public javax.vecmath.Point3f getAtomPoint3f(int i)
getAtomRadius
public float getAtomRadius(int i)
getAtomVdwRadius
public float getAtomVdwRadius(int i)
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)
getBfactor100Lo
public int getBfactor100Lo()
getBfactor100Hi
public int getBfactor100Hi()
getSurfaceDistanceMax
public int getSurfaceDistanceMax()
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 atomSet,
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)
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
protected void setAtomName(int atomIndex,
java.lang.String name)
setAtomType
protected void setAtomType(int atomIndex,
java.lang.String type)
setOccupancy
protected boolean setOccupancy(int atomIndex,
int occupancy)
setPartialCharge
protected boolean setPartialCharge(int atomIndex,
float partialCharge)
setBFactor
protected boolean setBFactor(int atomIndex,
float bfactor)
setEllipsoid
protected void setEllipsoid(int atomIndex,
java.lang.Object[] ellipsoid)
setAtomData
public void setAtomData(int type,
java.lang.String name,
java.lang.String dataString)
loadCoordinates
private void loadCoordinates(java.lang.String data,
boolean isVibrationVectors)
getUserSettableType
public static int getUserSettableType(java.lang.String dataType)
getTaintedAtoms
public java.util.BitSet getTaintedAtoms(byte type)
taint
protected void taint(int atomIndex,
byte type)
untaint
private void untaint(int i,
byte type)
setTaintedAtoms
public void setTaintedAtoms(java.util.BitSet bs,
byte type)
getAtomicPropertyState
public java.lang.String getAtomicPropertyState(int taintWhat,
java.util.BitSet bsSelected)
getAtomicPropertyState
public static void getAtomicPropertyState(java.lang.StringBuffer commands,
Atom[] atoms,
int atomCount,
byte type,
java.util.BitSet bs,
java.lang.String label,
float[] fData)
findNearestAtomIndex
protected void findNearestAtomIndex(int x,
int y,
Atom[] closest)
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(java.awt.Rectangle rect,
java.util.BitSet bsModels)
fillAtomData
protected void fillAtomData(AtomData atomData,
int mode)
getAdditionalHydrogens
protected javax.vecmath.Point3f[][] getAdditionalHydrogens(java.util.BitSet atomSet,
int[] nTotal)
getHybridizationAndAxes
public java.lang.String getHybridizationAndAxes(int atomIndex,
javax.vecmath.Vector3f z,
javax.vecmath.Vector3f x,
java.lang.String lcaoTypeRaw,
boolean hybridizationCompatible)
getChimeInfo
protected java.lang.String getChimeInfo(int tok,
java.util.BitSet bs)
getAtomBits
protected java.util.BitSet getAtomBits(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
isInLatticeCell
protected boolean isInLatticeCell(int i,
javax.vecmath.Point3f cell)
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 chain)
getAtomIndices
public int[] getAtomIndices(java.util.BitSet bs)
getAtomsWithin
public java.util.BitSet getAtomsWithin(float distance,
javax.vecmath.Point4f plane)
getVisibleSet
public java.util.BitSet getVisibleSet()
getClickableSet
public java.util.BitSet getClickableSet()
deleteModelAtoms
protected void deleteModelAtoms(int firstAtomIndex,
int nAtoms,
java.util.BitSet bs)