Atom

java.lang.Object
- javax.vecmath.Tuple3f
- - javax.vecmath.Point3f
  - - org.jmol.util.Point3fi
    - - org.jmol.modelset.Atom

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, JmolNode
```
public final class Atom
extends Point3fi
implements JmolNode
```
See Also:
Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`(package private) char`	`alternateLocationID`
`private short`	`atomicAndIsotopeNumber`
`byte`	`atomID`
`(package private) int`	`atomSite`
`private java.util.BitSet`	`atomSymmetry`
`(package private) Bond[]`	`bonds`
`(package private) int`	`clickabilityFlags`
`(package private) short`	`colixAtom`
`private static byte`	`FLAG_MASK`
`private byte`	`formalChargeAndFlags`
`(package private) Group`	`group`
`private static byte`	`IS_HETERO_FLAG`
`short`	`madAtom`
`(package private) int`	`nBackbonesDisplayed`
`(package private) int`	`nBondsDisplayed`
`(package private) byte`	`paletteID`
`static int`	`RADIUS_MAX`
`(package private) int`	`shapeVisibilityFlags`
`private float`	`userDefinedVanDerWaalRadius`
`private byte`	`valence`
`private static byte`	`VIBRATION_VECTOR_FLAG`

Fields inherited from class org.jmol.util.Point3fi
index, modelIndex, screenDiameter, screenX, screenY, screenZ

Fields inherited from class javax.vecmath.Tuple3f
x, y, z

Constructor Summary

Constructors
Constructor and Description
`Atom(int modelIndex, int atomIndex, float x, float y, float z, float radius, java.util.BitSet atomSymmetry, int atomSite, short atomicAndIsotopeNumber, int formalCharge, boolean isHetero, char alternateLocationID)`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addDisplayedBackbone(int backboneVisibilityFlag, boolean isVisible)`
`(package private) void`	`addDisplayedBond(int stickVisibilityFlag, boolean isVisible)`
`static float`	`atomPropertyFloat(Viewer viewer, Atom atom, int tokWhat)` called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
`static int`	`atomPropertyInt(Atom atom, int tokWhat)` called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
`static java.lang.String`	`atomPropertyString(Atom atom, int tokWhat)`
`static javax.vecmath.Tuple3f`	`atomPropertyTuple(Atom atom, int tok)`
`short`	`calculateMad(Viewer viewer, RadiusData rd)`
`(package private) void`	`clearBonds()`
`void`	`delete(java.util.BitSet bsBonds)`
`(package private) void`	`deleteBond(Bond bond)`
`private void`	`deleteBond(int i)`
`boolean`	`equals(java.lang.Object obj)`
`Atom`	`findAromaticNeighbor(int notAtomIndex)`
`float`	`getADPMinMax(boolean isMax)`
`char`	`getAlternateLocationID()`
`short`	`getAtomicAndIsotopeNumber()`
`byte`	`getAtomID()`
`java.lang.String`	`getAtomName()`
`int`	`getAtomNumber()`
`int`	`getAtomSite()`
`java.util.BitSet`	`getAtomSymmetry()`
`java.lang.String`	`getAtomType()`
`int`	`getBfactor100()`
`Bond`	`getBond(Atom atomOther)`
`int`	`getBondedAtomIndex(int bondIndex)`
`float`	`getBondingRadiusFloat()`
`Bond[]`	`getBonds()`
`int`	`getCellTranslation(int cellNNN, int[] cellRange, int nOps)` Looks for a match in the cellRange list for this atom within the specified translation set select symop=0NNN for this
`(package private) Chain`	`getChain()`
`char`	`getChainID()`
`int`	`getClickabilityFlags()`
`short`	`getColix()`
`int`	`getCovalentBondCount()`
`int`	`getCovalentHydrogenCount()`
`float`	`getCovalentRadiusFloat()`
`boolean`	`getCrossLinkLeadAtomIndexes(java.util.List vReturn)`
`(package private) int`	`getCurrentBondCount()`
`float`	`getDimensionValue(int dimension)`
`JmolEdge[]`	`getEdges()`
`short`	`getElementNumber()`
`java.lang.String`	`getElementSymbol()`
`java.lang.String`	`getElementSymbol(boolean withIsotope)`
`java.lang.Object[]`	`getEllipsoid()`
`int`	`getFormalCharge()`
`private javax.vecmath.Point3f`	`getFractionalCoord(boolean asAbsolute)`
`private float`	`getFractionalCoord(char ch, boolean asAbsolute)`
`javax.vecmath.Point3f`	`getFractionalUnitCoord(boolean asCartesian)`
`private float`	`getFractionalUnitCoord(char ch)`
`float`	`getFractionalUnitDistance(javax.vecmath.Point3f pt, javax.vecmath.Point3f ptTemp1, javax.vecmath.Point3f ptTemp2)`
`Group`	`getGroup()`
`java.lang.String`	`getGroup1(char c0)`
`java.lang.String`	`getGroup3(boolean allowNull)`
`short`	`getGroupID()`
`int`	`getGroupIndex()`
`float`	`getGroupParameter(int tok)`
`java.lang.String`	`getGroupType()`
`(package private) java.lang.String`	`getIdentity(boolean allInfo)`
`(package private) java.lang.String`	`getIdentityXYZ(boolean allInfo)`
`int`	`getImplicitHydrogenCount()`
`int`	`getIndex()`
`java.lang.String`	`getInfo()`
`(package private) java.lang.String`	`getInfoXYZ(boolean useChimeFormat)`
`char`	`getInsertionCode()`
`short`	`getIsotopeNumber()`
`int`	`getModelFileIndex()`
`int`	`getModelFileNumber()`
`int`	`getModelIndex()`
`int`	`getModelNumber()`
`(package private) java.lang.String`	`getModelNumberForLabel()`
`int`	`getMoleculeNumber()`
`int`	`getMonomerIndex()`
`int`	`getNBackbonesDisplayed()`
`int`	`getOccupancy100()`
`int`	`getOffsetResidueAtom(java.lang.String name, int offset)`
`byte`	`getPaletteID()`
`float`	`getPartialCharge()`
`int`	`getPolymerIndexInModel()`
`int`	`getPolymerLength()`
`byte`	`getProteinStructureSubType()`
`java.lang.String`	`getProteinStructureTag()`
`byte`	`getProteinStructureType()`
`float`	`getRadius()`
`int`	`getRasMolRadius()`
`int`	`getResno()`
`int`	`getSelectedGroupCountWithinChain()`
`int`	`getSelectedGroupIndexWithinChain()`
`int`	`getSelectedMonomerCountWithinPolymer()`
`int`	`getSelectedMonomerIndexWithinPolymer()`
`(package private) int`	`getSeqcode()`
`(package private) java.lang.String`	`getSeqcodeString()`
`(package private) int`	`getSeqNumber()`
`int`	`getShapeVisibilityFlags()`
`int`	`getStrucNo()`
`java.lang.String`	`getStructureId()`
`int`	`getSurfaceDistance100()`
`(package private) java.lang.String`	`getSymmetryOperatorList()`
`int`	`getSymmetryTranslation(int symop, int[] cellRange, int nOps)` Given a symmetry operation number, the set of cells in the model, and the number of operations, this method returns either 0 or the cell number (555, 666) of the translated symmetry operation corresponding to this atom.
`(package private) int`	`getTargetValence()`
`int`	`getValence()`
`float`	`getVanderwaalsRadiusFloat(Viewer viewer, int iType)`
`private int`	`getVdwType(int iType)`
`float`	`getVibrationCoord(char ch)`
`javax.vecmath.Vector3f`	`getVibrationVector()`
`(package private) float`	`getVolume(Viewer viewer, int iType)`
`int`	`hashCode()`
`boolean`	`hasVibration()`
`(package private) boolean`	`isAlternateLocationMatch(java.lang.String strPattern)`
`boolean`	`isBonded(Atom atomOther)`
`boolean`	`isCarbohydrate()`
`boolean`	`isClickable()`
`boolean`	`isCrossLinked(JmolNode node)`
`(package private) boolean`	`isCursorOnTopOf(int xCursor, int yCursor, int minRadius, Atom competitor)`
`boolean`	`isDeleted()`
`boolean`	`isDna()`
`(package private) boolean`	`isGroup3(java.lang.String group3)`
`boolean`	`isHetero()`
`boolean`	`isInFrame()`
`boolean`	`isLeadAtom()`
`boolean`	`isNucleic()`
`boolean`	`isProtein()`
`boolean`	`isPurine()`
`boolean`	`isPyrimidine()`
`boolean`	`isRna()`
`boolean`	`isShapeVisible(int shapeVisibilityFlag)`
`boolean`	`isTranslucent()`
`boolean`	`isVisible(int flags)` determine if an atom or its PDB group is visible
`(package private) boolean`	`isWithinStructure(byte type)`
`void`	`setAtomicAndIsotopeNumber(int n)`
`void`	`setBonds(Bond[] bonds)`
`void`	`setClickable(int flag)`
`void`	`setColixAtom(short colixAtom)`
`(package private) void`	`setFormalCharge(int charge)`
`(package private) void`	`setFractionalCoord(int tok, float fValue, boolean asAbsolute)`
`(package private) void`	`setFractionalCoord(javax.vecmath.Point3f ptNew, boolean asAbsolute)`
`(package private) void`	`setFractionalCoord(javax.vecmath.Point3f pt, javax.vecmath.Point3f ptNew, boolean asAbsolute)`
`(package private) void`	`setGroup(Group group)`
`void`	`setGroupBits(java.util.BitSet bs)`
`void`	`setMadAtom(Viewer viewer, RadiusData rd)`
`void`	`setPaletteID(byte paletteID)`
`boolean`	`setRadius(float radius)`
`void`	`setShapeVisibility(int shapeVisibilityFlag, boolean isVisible)`
`void`	`setShapeVisibilityFlags(int flag)`
`void`	`setTranslucent(boolean isTranslucent, float translucentLevel)`
`void`	`setValence(int nBonds)`
`(package private) void`	`setVibrationVector()`
`java.lang.String`	`toString()`

Methods inherited from class javax.vecmath.Point3f
distance, distanceL1, distanceLinf, distanceSquared, project

Methods inherited from class javax.vecmath.Tuple3f
absolute, absolute, add, add, clamp, clamp, clampMax, clampMax, clampMin, clampMin, clone, epsilonEquals, equals, get, get, getX, getY, getZ, interpolate, interpolate, negate, negate, scale, scale, scaleAdd, scaleAdd, set, set, set, set, setX, setY, setZ, sub, sub

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.jmol.api.JmolNode
set

Field Detail

VIBRATION_VECTOR_FLAG
```
private static final byte VIBRATION_VECTOR_FLAG
```
See Also:
Constant Field Values

IS_HETERO_FLAG
```
private static final byte IS_HETERO_FLAG
```
See Also:
Constant Field Values

FLAG_MASK
```
private static final byte FLAG_MASK
```
See Also:
Constant Field Values

RADIUS_MAX
```
public static final int RADIUS_MAX
```
See Also:
Constant Field Values

group
```
Group group
```

atomSymmetry
```
private java.util.BitSet atomSymmetry
```

atomSite
```
int atomSite
```

userDefinedVanDerWaalRadius

private float userDefinedVanDerWaalRadius

atomicAndIsotopeNumber
```
private short atomicAndIsotopeNumber
```

formalChargeAndFlags
```
private byte formalChargeAndFlags
```

valence
```
private byte valence
```

alternateLocationID
```
char alternateLocationID
```

atomID
```
public byte atomID
```

madAtom
```
public short madAtom
```

colixAtom
```
short colixAtom
```

paletteID
```
byte paletteID
```

bonds
```
Bond[] bonds
```

nBondsDisplayed
```
int nBondsDisplayed
```

nBackbonesDisplayed
```
int nBackbonesDisplayed
```

clickabilityFlags
```
int clickabilityFlags
```

shapeVisibilityFlags
```
int shapeVisibilityFlags
```

Constructor Detail

Atom

public Atom(int modelIndex,
    int atomIndex,
    float x,
    float y,
    float z,
    float radius,
    java.util.BitSet atomSymmetry,
    int atomSite,
    short atomicAndIsotopeNumber,
    int formalCharge,
    boolean isHetero,
    char alternateLocationID)

Method Detail

getAtomID
```
public byte getAtomID()
```

getBonds
```
public Bond[] getBonds()
```

setBonds
```
public void setBonds(Bond[] bonds)
```

getNBackbonesDisplayed
```
public int getNBackbonesDisplayed()
```

setShapeVisibilityFlags

public final void setShapeVisibilityFlags(int flag)

setShapeVisibility

public final void setShapeVisibility(int shapeVisibilityFlag,
                      boolean isVisible)

isBonded

public boolean isBonded(Atom atomOther)

getBond
```
public Bond getBond(Atom atomOther)
```

addDisplayedBond

void addDisplayedBond(int stickVisibilityFlag,
                    boolean isVisible)

addDisplayedBackbone

public void addDisplayedBackbone(int backboneVisibilityFlag,
                        boolean isVisible)

deleteBond
```
void deleteBond(Bond bond)
```

deleteBond
```
private void deleteBond(int i)
```

clearBonds
```
void clearBonds()
```

getBondedAtomIndex
```
public int getBondedAtomIndex(int bondIndex)
```
Specified by:

getBondedAtomIndex in interface JmolNode

setMadAtom

public void setMadAtom(Viewer viewer,
              RadiusData rd)

calculateMad

public short calculateMad(Viewer viewer,
                 RadiusData rd)

getADPMinMax

public float getADPMinMax(boolean isMax)

getRasMolRadius
```
public int getRasMolRadius()
```

getCovalentBondCount
```
public int getCovalentBondCount()
```
Specified by:

getCovalentBondCount in interface JmolNode

getCovalentHydrogenCount
```
public int getCovalentHydrogenCount()
```
Specified by:

getCovalentHydrogenCount in interface JmolNode

getEdges
```
public JmolEdge[] getEdges()
```
Specified by:

getEdges in interface JmolNode

setColixAtom

public void setColixAtom(short colixAtom)

setPaletteID

public void setPaletteID(byte paletteID)

setTranslucent

public void setTranslucent(boolean isTranslucent,
                  float translucentLevel)

isTranslucent
```
public boolean isTranslucent()
```

getElementNumber
```
public short getElementNumber()
```
Specified by:

getElementNumber in interface JmolNode

getIsotopeNumber
```
public short getIsotopeNumber()
```
Specified by:

getIsotopeNumber in interface JmolNode

getAtomicAndIsotopeNumber
```
public short getAtomicAndIsotopeNumber()
```
Specified by:

getAtomicAndIsotopeNumber in interface JmolNode

setAtomicAndIsotopeNumber

public void setAtomicAndIsotopeNumber(int n)

getElementSymbol

public java.lang.String getElementSymbol(boolean withIsotope)

getElementSymbol

public java.lang.String getElementSymbol()

getAlternateLocationID
```
public char getAlternateLocationID()
```

isAlternateLocationMatch

boolean isAlternateLocationMatch(java.lang.String strPattern)

isHetero
```
public boolean isHetero()
```

hasVibration
```
public boolean hasVibration()
```

setFormalCharge
```
void setFormalCharge(int charge)
```

setVibrationVector
```
void setVibrationVector()
```

getFormalCharge
```
public int getFormalCharge()
```
Specified by:

getFormalCharge in interface JmolNode

getOccupancy100
```
public int getOccupancy100()
```

getBfactor100
```
public int getBfactor100()
```

setRadius

public boolean setRadius(float radius)

delete

public void delete(java.util.BitSet bsBonds)

isDeleted
```
public boolean isDeleted()
```
Specified by:

isDeleted in interface JmolNode

setValence
```
public void setValence(int nBonds)
```

getValence
```
public int getValence()
```
Specified by:

getValence in interface JmolNode

getImplicitHydrogenCount
```
public int getImplicitHydrogenCount()
```
Specified by:

getImplicitHydrogenCount in interface JmolNode

getTargetValence
```
int getTargetValence()
```

getDimensionValue

public float getDimensionValue(int dimension)

getVanderwaalsRadiusFloat

public float getVanderwaalsRadiusFloat(Viewer viewer,
                              int iType)

getVdwType
```
private int getVdwType(int iType)
```
Parameters:
iType -

Returns:
if VDW_AUTO, will return VDW_AUTO_JMOL, VDW_AUTO_RASMOL, or VDW_AUTO_BABEL based on the model type

getCovalentRadiusFloat
```
public float getCovalentRadiusFloat()
```

getBondingRadiusFloat
```
public float getBondingRadiusFloat()
```

getVolume

float getVolume(Viewer viewer,
              int iType)

getCurrentBondCount
```
int getCurrentBondCount()
```

getColix
```
public short getColix()
```

getPaletteID
```
public byte getPaletteID()
```

getRadius
```
public float getRadius()
```

getIndex
```
public int getIndex()
```
Specified by:

getIndex in interface JmolNode

getAtomSite
```
public int getAtomSite()
```
Specified by:

getAtomSite in interface JmolNode

getAtomSymmetry

public java.util.BitSet getAtomSymmetry()

setGroup
```
void setGroup(Group group)
```

getGroup
```
public Group getGroup()
```

setGroupBits
```
public void setGroupBits(java.util.BitSet bs)
```
Specified by:

setGroupBits in interface JmolNode

getAtomName
```
public java.lang.String getAtomName()
```
Specified by:

getAtomName in interface JmolNode

getAtomType
```
public java.lang.String getAtomType()
```

getAtomNumber
```
public int getAtomNumber()
```

isInFrame
```
public boolean isInFrame()
```

getShapeVisibilityFlags
```
public int getShapeVisibilityFlags()
```

isShapeVisible

public boolean isShapeVisible(int shapeVisibilityFlag)

getPartialCharge
```
public float getPartialCharge()
```

getEllipsoid

public java.lang.Object[] getEllipsoid()

getSymmetryTranslation
```
public int getSymmetryTranslation(int symop,
                         int[] cellRange,
                         int nOps)
```
Given a symmetry operation number, the set of cells in the model, and the number of operations, this method returns either 0 or the cell number (555, 666) of the translated symmetry operation corresponding to this atom. atomSymmetry is a bitset that is created in adapter.smarter.AtomSetCollection It is arranged as follows: |--overall--|---cell1---|---cell2---|---cell3---|... |012..nOps-1|012..nOps-1|012..nOp-1s|012..nOps-1|... If a bit is set, it means that the atom was created using that operator operating on the base file set and translated for that cell. If any bit is set in any of the cell blocks, then the same bit will also be set in the overall block. This allows for rapid determination of special positions and also of atom membership in any operation set. Note that it is not necessarily true that an atom is IN the designated cell, because one can load {nnn mmm 0}, and then, for example, the {-x,-y,-z} operator sends atoms from 555 to 444. Still, those atoms would be marked as cell 555 here, because no translation was carried out. That is, the numbers 444 in symop=3444 do not refer to a cell, per se. What they refer to is the file-designated operator plus a translation of {-1 -1 -1/1}.

Parameters:
symop - = 0, 1, 2, 3, ....
cellRange - = {444, 445, 446, 454, 455, 456, .... }
nOps - = 2 for x,y,z;-x,-y,-z, for example

Returns:
cell number such as 565

getCellTranslation
```
public int getCellTranslation(int cellNNN,
                     int[] cellRange,
                     int nOps)
```
Looks for a match in the cellRange list for this atom within the specified translation set select symop=0NNN for this

Parameters:
cellNNN -
cellRange -
nOps -

Returns:
matching cell number, if applicable

getSymmetryOperatorList

java.lang.String getSymmetryOperatorList()

getModelIndex
```
public int getModelIndex()
```
Specified by:

getModelIndex in interface JmolNode

getMoleculeNumber
```
public int getMoleculeNumber()
```

getFractionalCoord

private float getFractionalCoord(char ch,
                       boolean asAbsolute)

getFractionalUnitCoord

private float getFractionalUnitCoord(char ch)

getFractionalCoord

private javax.vecmath.Point3f getFractionalCoord(boolean asAbsolute)

getFractionalUnitCoord

public javax.vecmath.Point3f getFractionalUnitCoord(boolean asCartesian)

getFractionalUnitDistance

public float getFractionalUnitDistance(javax.vecmath.Point3f pt,
                              javax.vecmath.Point3f ptTemp1,
                              javax.vecmath.Point3f ptTemp2)

setFractionalCoord

void setFractionalCoord(int tok,
                      float fValue,
                      boolean asAbsolute)

setFractionalCoord

void setFractionalCoord(javax.vecmath.Point3f ptNew,
                      boolean asAbsolute)

setFractionalCoord

void setFractionalCoord(javax.vecmath.Point3f pt,
                      javax.vecmath.Point3f ptNew,
                      boolean asAbsolute)

isCursorOnTopOf

boolean isCursorOnTopOf(int xCursor,
                      int yCursor,
                      int minRadius,
                      Atom competitor)

getInfo
```
public java.lang.String getInfo()
```

getInfoXYZ

java.lang.String getInfoXYZ(boolean useChimeFormat)

getIdentityXYZ

java.lang.String getIdentityXYZ(boolean allInfo)

getIdentity

java.lang.String getIdentity(boolean allInfo)

getGroupIndex
```
public int getGroupIndex()
```

getGroup3

public java.lang.String getGroup3(boolean allowNull)

Specified by:: getGroup3 in interface JmolNode

getGroup1
```
public java.lang.String getGroup1(char c0)
```
Specified by:

getGroup1 in interface JmolNode

isGroup3

boolean isGroup3(java.lang.String group3)

isProtein
```
public boolean isProtein()
```
Specified by:

isProtein in interface JmolNode

isCarbohydrate
```
public boolean isCarbohydrate()
```

isNucleic
```
public boolean isNucleic()
```
Specified by:

isNucleic in interface JmolNode

isDna
```
public boolean isDna()
```
Specified by:

isDna in interface JmolNode

isRna
```
public boolean isRna()
```
Specified by:

isRna in interface JmolNode

isPurine
```
public boolean isPurine()
```
Specified by:

isPurine in interface JmolNode

isPyrimidine
```
public boolean isPyrimidine()
```
Specified by:

isPyrimidine in interface JmolNode

getSeqcode
```
int getSeqcode()
```

getResno
```
public int getResno()
```
Specified by:

getResno in interface JmolNode

isClickable
```
public boolean isClickable()
```

getClickabilityFlags
```
public int getClickabilityFlags()
```

setClickable
```
public void setClickable(int flag)
```

isVisible
```
public boolean isVisible(int flags)
```
determine if an atom or its PDB group is visible

Parameters:
flags - TODO

Returns:
true if the atom is in the "select visible" set

isLeadAtom
```
public boolean isLeadAtom()
```
Specified by:

isLeadAtom in interface JmolNode

getGroupParameter

public float getGroupParameter(int tok)

getChainID
```
public char getChainID()
```
Specified by:

getChainID in interface JmolNode

getSurfaceDistance100
```
public int getSurfaceDistance100()
```

getVibrationVector

public javax.vecmath.Vector3f getVibrationVector()

getVibrationCoord

public float getVibrationCoord(char ch)

getPolymerLength
```
public int getPolymerLength()
```

getPolymerIndexInModel
```
public int getPolymerIndexInModel()
```

getMonomerIndex
```
public int getMonomerIndex()
```

getSelectedGroupCountWithinChain

public int getSelectedGroupCountWithinChain()

getSelectedGroupIndexWithinChain

public int getSelectedGroupIndexWithinChain()

getSelectedMonomerCountWithinPolymer

public int getSelectedMonomerCountWithinPolymer()

getSelectedMonomerIndexWithinPolymer

public int getSelectedMonomerIndexWithinPolymer()

getChain
```
Chain getChain()
```

getModelNumberForLabel

java.lang.String getModelNumberForLabel()

getModelNumber
```
public int getModelNumber()
```

getModelFileIndex
```
public int getModelFileIndex()
```

getModelFileNumber
```
public int getModelFileNumber()
```

getGroupType
```
public java.lang.String getGroupType()
```
Specified by:

getGroupType in interface JmolNode

getProteinStructureType
```
public byte getProteinStructureType()
```

getProteinStructureSubType

public byte getProteinStructureSubType()

getStrucNo
```
public int getStrucNo()
```

getStructureId

public java.lang.String getStructureId()

getProteinStructureTag

public java.lang.String getProteinStructureTag()

getGroupID
```
public short getGroupID()
```

getSeqcodeString
```
java.lang.String getSeqcodeString()
```

getSeqNumber
```
int getSeqNumber()
```

getInsertionCode
```
public char getInsertionCode()
```

equals
```
public boolean equals(java.lang.Object obj)
```
Overrides:

equals in class javax.vecmath.Tuple3f

hashCode
```
public int hashCode()
```
Overrides:

hashCode in class javax.vecmath.Tuple3f

findAromaticNeighbor

public Atom findAromaticNeighbor(int notAtomIndex)

atomPropertyInt
```
public static int atomPropertyInt(Atom atom,
                  int tokWhat)
```
called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()

Parameters:
atom -
tokWhat -

Returns:
int value or Integer.MIN_VALUE

atomPropertyFloat
```
public static float atomPropertyFloat(Viewer viewer,
                      Atom atom,
                      int tokWhat)
```
called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()

Parameters:
viewer -
atom -
tokWhat -

Returns:
float value or value*100 (asInt=true) or throw an error if not found

atomPropertyString

public static java.lang.String atomPropertyString(Atom atom,
                                  int tokWhat)

atomPropertyTuple

public static javax.vecmath.Tuple3f atomPropertyTuple(Atom atom,
                                      int tok)

isWithinStructure
```
boolean isWithinStructure(byte type)
```

getOffsetResidueAtom

public int getOffsetResidueAtom(java.lang.String name,
                       int offset)

Specified by:: getOffsetResidueAtom in interface JmolNode

isCrossLinked
```
public boolean isCrossLinked(JmolNode node)
```
Specified by:

isCrossLinked in interface JmolNode

getCrossLinkLeadAtomIndexes
```
public boolean getCrossLinkLeadAtomIndexes(java.util.List vReturn)
```
Specified by:

getCrossLinkLeadAtomIndexes in interface JmolNode

toString
```
public java.lang.String toString()
```
Overrides:

toString in class javax.vecmath.Tuple3f

Class Atom

Field Summary

Fields inherited from class org.jmol.util.Point3fi

Fields inherited from class javax.vecmath.Tuple3f

Constructor Summary

Method Summary

Methods inherited from class javax.vecmath.Point3f

Methods inherited from class javax.vecmath.Tuple3f

Methods inherited from class java.lang.Object

Methods inherited from interface org.jmol.api.JmolNode

Field Detail

VIBRATION_VECTOR_FLAG

IS_HETERO_FLAG

FLAG_MASK

RADIUS_MAX

group

atomSymmetry

atomSite

userDefinedVanDerWaalRadius

atomicAndIsotopeNumber

formalChargeAndFlags

valence

alternateLocationID

atomID

madAtom

colixAtom

paletteID

bonds

nBondsDisplayed

nBackbonesDisplayed

clickabilityFlags

shapeVisibilityFlags

Constructor Detail

Atom

Method Detail

getAtomID

getBonds

setBonds

getNBackbonesDisplayed

setShapeVisibilityFlags

setShapeVisibility

isBonded

getBond

addDisplayedBond

addDisplayedBackbone

deleteBond

deleteBond

clearBonds

getBondedAtomIndex

setMadAtom

calculateMad

getADPMinMax

getRasMolRadius

getCovalentBondCount

getCovalentHydrogenCount

getEdges

setColixAtom

setPaletteID

setTranslucent

isTranslucent

getElementNumber

getIsotopeNumber

getAtomicAndIsotopeNumber

setAtomicAndIsotopeNumber

getElementSymbol

getElementSymbol

getAlternateLocationID

isAlternateLocationMatch

isHetero

hasVibration

setFormalCharge

setVibrationVector

getFormalCharge

getOccupancy100

getBfactor100

setRadius

delete

isDeleted

setValence

getValence