Atom

java.lang.Object
- javajs.util.T3
- - javajs.util.P3
  - - org.jmol.util.Point3fi
    - - org.jmol.modelset.Atom

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javajs.api.JSONEncodable, BNode, Node
```
public class Atom
extends Point3fi
implements BNode
```
See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`char`	`altloc`
`private short`	`atomicAndIsotopeNumber`
`byte`	`atomID`
`int`	`atomSite`
`BS`	`atomSymmetry`
`Bond[]`	`bonds` MAY BE NULL
`int`	`clickabilityFlags`
`short`	`colixAtom`
`private static byte`	`FLAG_MASK`
`private byte`	`formalChargeAndFlags`
`Group`	`group`
`private static byte`	`IS_HETERO_FLAG`
`static short`	`MAD_GLOBAL`
`short`	`madAtom`
`int`	`nBackbonesDisplayed`
`private int`	`nBondsDisplayed`
`byte`	`paletteID`
`static float`	`RADIUS_GLOBAL`
`static int`	`RADIUS_MAX`
`int`	`shapeVisibilityFlags`
`private float`	`userDefinedVanDerWaalRadius`
`(package private) byte`	`valence`
`private static byte`	`VIBRATION_VECTOR_FLAG`

Fields inherited from class org.jmol.util.Point3fi
i, mi, sD, sX, sY, sZ

Fields inherited from class javajs.util.T3
x, y, z

Constructor Summary

Constructors
Constructor and Description

Atom()

Constructors
Constructor and Description
`Atom()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addDisplayedBackbone(int backboneVisibilityFlag, boolean isVisible)`
`(package private) void`	`addDisplayedBond(int stickVisibilityFlag, boolean isVisible)`
`float`	`atomPropertyFloat(Viewer vwr, int tokWhat, javajs.util.P3 ptTemp)` called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
`int`	`atomPropertyInt(int tokWhat)` called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
`java.lang.String`	`atomPropertyString(Viewer vwr, int tokWhat)`
`javajs.util.T3`	`atomPropertyTuple(Viewer vwr, int tok, javajs.util.P3 ptTemp)`
`short`	`calculateMad(Viewer vwr, RadiusData rd)`
`boolean`	`checkVisible()`
`(package private) void`	`deleteBond(Bond bond)`
`private void`	`deleteBondAt(int i)`
`void`	`deleteBonds(BS bsBonds)`
`boolean`	`equals(java.lang.Object obj)` Returns true if all of the data members of Tuple3f t1 are equal to the corresponding data members in this
`Atom`	`findAromaticNeighbor(int notAtomIndex)`
`BS`	`findAtomsLike(java.lang.String atomExpression)`
`float`	`getADPMinMax(boolean isMax)`
`int`	`getAtomicAndIsotopeNumber()`
`java.lang.String`	`getAtomName()`
`int`	`getAtomNumber()`
`int`	`getAtomSite()`
`java.lang.String`	`getAtomType()`
`int`	`getBfactor100()`
`java.lang.String`	`getBioStructureTypeName()`
`Bond`	`getBond(Atom atomOther)`
`int`	`getBondedAtomIndex(int bondIndex)`
`float`	`getBondingRadius()`
`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
`Chain`	`getChain()`
`int`	`getChainID()`
`java.lang.String`	`getChainIDStr()`
`int`	`getCovalentBondCount()`
`int`	`getCovalentHydrogenCount()`
`boolean`	`getCrossLinkLeadAtomIndexes(javajs.util.Lst<java.lang.Integer> vReturn)`
`(package private) int`	`getCurrentBondCount()`
`float`	`getDimensionValue(int dimension)`
`Edge[]`	`getEdges()`
`int`	`getElementNumber()`
`java.lang.String`	`getElementSymbol()`
`java.lang.String`	`getElementSymbolIso(boolean withIsotope)`
`int`	`getFormalCharge()`
`private float`	`getFractionalCoord(boolean fixJavaFloat, char ch, boolean asAbsolute, javajs.util.P3 pt)`
`private javajs.util.P3`	`getFractionalCoordPt(boolean fixJavaFloat, boolean asAbsolute, javajs.util.P3 pt)`
`private float`	`getFractionalUnitCoord(boolean fixJavaFloat, char ch, javajs.util.P3 pt)`
`(package private) javajs.util.P3`	`getFractionalUnitCoordPt(boolean fixJavaFloat, boolean asCartesian, javajs.util.P3 pt)`
`(package private) float`	`getFractionalUnitDistance(javajs.util.P3 pt, javajs.util.P3 ptTemp1, javajs.util.P3 ptTemp2)`
`java.lang.String`	`getGroup1(char c0)`
`java.lang.String`	`getGroup3(boolean allowNull)`
`void`	`getGroupBits(BS bs)`
`short`	`getGroupID()`
`float`	`getGroupParameter(int tok)`
`private float`	`getHydrophobicity()`
`(package private) java.lang.String`	`getIdentity(boolean allInfo)`
`(package private) java.lang.String`	`getIdentityXYZ(boolean allInfo, javajs.util.P3 pt)`
`int`	`getImplicitHydrogenCount()`
`int`	`getIndex()`
`java.lang.String`	`getInfo()`
`java.lang.String`	`getInfoXYZ(boolean fixJavaFloat, boolean useChimeFormat, javajs.util.P3 pt)`
`char`	`getInsertionCode()`
`int`	`getIsotopeNumber()`
`private float`	`getMass()`
`int`	`getModelIndex()`
`int`	`getModelNumber()`
`java.lang.String`	`getModelNumberForLabel()`
`JmolModulationSet`	`getModulation()`
`float`	`getModulationCoord(char ch)`
`(package private) int`	`getMoleculeNumber(boolean inModel)`
`int`	`getMonomerIndex()`
`int`	`getOccupancy100()`
`int`	`getOffsetResidueAtom(java.lang.String name, int offset)`
`float`	`getPartialCharge()`
`int`	`getPolymerIndexInModel()`
`int`	`getPolymerLength()`
`STR`	`getProteinStructureSubType()`
`java.lang.String`	`getProteinStructureTag()`
`STR`	`getProteinStructureType()`
`float`	`getRadius()`
`int`	`getRasMolRadius()`
`int`	`getResno()`
`int`	`getSelectedGroupCountWithinChain()`
`int`	`getSelectedGroupIndexWithinChain()`
`int`	`getSelectedMonomerCountWithinPolymer()`
`int`	`getSelectedMonomerIndexWithinPolymer()`
`(package private) int`	`getSeqcode()`
`java.lang.String`	`getSeqcodeString()`
`int`	`getSeqID()`
`int`	`getStrucNo()`
`java.lang.String`	`getStructureId()`
`int`	`getSurfaceDistance100()`
`(package private) java.lang.String`	`getSymmetryOperatorList(boolean isAll)`
`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`	`getSymOp()`
`(package private) int`	`getTargetValence()`
`java.lang.Object[]`	`getTensors()`
`(package private) SymmetryInterface`	`getUnitCell()`
`int`	`getValence()`
`float`	`getVanderwaalsRadiusFloat(Viewer vwr, VDW type)`
`private VDW`	`getVdwType(VDW type)`
`float`	`getVibrationCoord(char ch)`
`Vibration`	`getVibrationVector()`
`(package private) float`	`getVolume(Viewer vwr, VDW vType)`
`int`	`hashCode()` Returns a hash number based on the data values in this object.
`boolean`	`hasVibration()`
`(package private) boolean`	`isAltLoc(java.lang.String strPattern)`
`boolean`	`isBonded(Atom atomOther)`
`(package private) boolean`	`isCarbohydrate()`
`boolean`	`isClickable()`
`boolean`	`isCovalentlyBonded(Atom atomOther)`
`boolean`	`isCrossLinked(BNode node)`
`(package private) boolean`	`isCursorOnTopOf(int xCursor, int yCursor, int minRadius, Atom competitor)`
`boolean`	`isDeleted()`
`boolean`	`isDna()`
`boolean`	`isHetero()`
`boolean`	`isLeadAtom()`
`boolean`	`isNucleic()`
`boolean`	`isProtein()`
`boolean`	`isPurine()`
`boolean`	`isPyrimidine()`
`boolean`	`isRna()`
`boolean`	`isTranslucent()`
`boolean`	`isVisible(int flags)`
`(package private) boolean`	`isWithinStructure(STR type)`
`Atom`	`setAtom(int modelIndex, int atomIndex, javajs.util.P3 xyz, float radius, BS atomSymmetry, int atomSite, short atomicAndIsotopeNumber, int formalCharge, boolean isHetero)`
`void`	`setAtomicAndIsotopeNumber(int n)`
`void`	`setClickable(int flag)`
`void`	`setFormalCharge(int charge)`
`(package private) void`	`setFractionalCoord(int tok, float fValue, boolean asAbsolute)`
`void`	`setFractionalCoordPt(javajs.util.P3 pt, javajs.util.P3 ptNew, boolean asAbsolute)`
`(package private) void`	`setFractionalCoordTo(javajs.util.P3 ptNew, boolean asAbsolute)`
`(package private) void`	`setGroup(Group group)`
`void`	`setMadAtom(Viewer vwr, RadiusData rd)`
`boolean`	`setRadius(float radius)`
`void`	`setShapeVisibility(int flag, boolean isVisible)`
`void`	`setTranslucent(boolean isTranslucent, float translucentLevel)`
`void`	`setValence(int nBonds)`
`(package private) void`	`setVibrationVector()`
`java.lang.String`	`toString()` Returns a string that contains the values of this Tuple3f.

Methods inherited from class org.jmol.util.Point3fi
copy, set2

Methods inherited from class javajs.util.P3
getUnlikely, new3, newP

Methods inherited from class javajs.util.T3
add, add2, add3, ave, cross, distance, distanceSquared, dot, floatToIntBits0, length, lengthSquared, normalize, scale, scaleAdd2, scaleT, set, setA, setT, sub, sub2, toJSON

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

Methods inherited from interface org.jmol.util.Node
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

RADIUS_GLOBAL
```
public static final float RADIUS_GLOBAL
```
See Also:

Constant Field Values

MAD_GLOBAL
```
public static short MAD_GLOBAL
```

altloc
```
public char altloc
```

atomID
```
public byte atomID
```

atomSite
```
public int atomSite
```

group
```
public Group group
```

userDefinedVanDerWaalRadius

private float userDefinedVanDerWaalRadius

valence
```
byte valence
```

atomicAndIsotopeNumber
```
private short atomicAndIsotopeNumber
```

atomSymmetry
```
public BS atomSymmetry
```

formalChargeAndFlags
```
private byte formalChargeAndFlags
```

madAtom
```
public short madAtom
```

colixAtom
```
public short colixAtom
```

paletteID
```
public byte paletteID
```

bonds
```
public Bond[] bonds
```
MAY BE NULL

nBondsDisplayed
```
private int nBondsDisplayed
```

nBackbonesDisplayed
```
public int nBackbonesDisplayed
```

clickabilityFlags
```
public int clickabilityFlags
```

shapeVisibilityFlags
```
public int shapeVisibilityFlags
```

Constructor Detail
- Atom
```
public Atom()
```

Method Detail

setAtom

public Atom setAtom(int modelIndex,
                    int atomIndex,
                    javajs.util.P3 xyz,
                    float radius,
                    BS atomSymmetry,
                    int atomSite,
                    short atomicAndIsotopeNumber,
                    int formalCharge,
                    boolean isHetero)

Parameters:: modelIndex -; atomIndex -; xyz -; radius -; atomSymmetry -; atomSite -; atomicAndIsotopeNumber -; formalCharge -; isHetero -
Returns:: this

setShapeVisibility

public final void setShapeVisibility(int flag,
                                     boolean isVisible)

isCovalentlyBonded

public boolean isCovalentlyBonded(Atom atomOther)

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)
```

deleteBondAt
```
private void deleteBondAt(int i)
```

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

getBondedAtomIndex in interface Node

setMadAtom

public void setMadAtom(Viewer vwr,
                       RadiusData rd)

calculateMad

public short calculateMad(Viewer vwr,
                          RadiusData rd)

getADPMinMax

public float getADPMinMax(boolean isMax)

getTensors

public java.lang.Object[] getTensors()

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

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

getCovalentBondCount in interface Node

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

getCovalentHydrogenCount in interface Node

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

getEdges in interface Node

setTranslucent

public void setTranslucent(boolean isTranslucent,
                           float translucentLevel)

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

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

getElementNumber in interface Node

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

getIsotopeNumber in interface Node

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

getAtomicAndIsotopeNumber in interface Node

setAtomicAndIsotopeNumber

public void setAtomicAndIsotopeNumber(int n)

getElementSymbolIso

public java.lang.String getElementSymbolIso(boolean withIsotope)

getElementSymbol

public java.lang.String getElementSymbol()

isAltLoc

boolean isAltLoc(java.lang.String strPattern)

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

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

setFormalCharge

public void setFormalCharge(int charge)

setVibrationVector
```
void setVibrationVector()
```

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

getFormalCharge in interface Node

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

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

getHydrophobicity
```
private float getHydrophobicity()
```

setRadius

public boolean setRadius(float radius)

deleteBonds
```
public void deleteBonds(BS bsBonds)
```

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

isDeleted in interface BNode

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

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

getValence in interface Node

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

getImplicitHydrogenCount in interface Node

getTargetValence
```
int getTargetValence()
```

getDimensionValue

public float getDimensionValue(int dimension)

getVanderwaalsRadiusFloat

public float getVanderwaalsRadiusFloat(Viewer vwr,
                                       VDW type)

getVdwType
```
private VDW getVdwType(VDW type)
```
Parameters:

type -

Returns:

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

getBondingRadius
```
public float getBondingRadius()
```

getVolume

float getVolume(Viewer vwr,
                VDW vType)

getCurrentBondCount
```
int getCurrentBondCount()
```

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

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

getIndex in interface Node

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

getAtomSite in interface Node

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

getGroupBits
```
public void getGroupBits(BS bs)
```
Specified by:

getGroupBits in interface BNode

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

getAtomName in interface Node

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

getAtomType in interface Node

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

getSeqID
```
public int getSeqID()
```

isVisible
```
public boolean isVisible(int flags)
```

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

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(boolean isAll)

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

getModelIndex in interface Node

getMoleculeNumber

int getMoleculeNumber(boolean inModel)

getFractionalCoord

private float getFractionalCoord(boolean fixJavaFloat,
                                 char ch,
                                 boolean asAbsolute,
                                 javajs.util.P3 pt)

getFractionalCoordPt

private javajs.util.P3 getFractionalCoordPt(boolean fixJavaFloat,
                                            boolean asAbsolute,
                                            javajs.util.P3 pt)

getUnitCell
```
SymmetryInterface getUnitCell()
```

getFractionalUnitCoord

private float getFractionalUnitCoord(boolean fixJavaFloat,
                                     char ch,
                                     javajs.util.P3 pt)

getFractionalUnitCoordPt

javajs.util.P3 getFractionalUnitCoordPt(boolean fixJavaFloat,
                                        boolean asCartesian,
                                        javajs.util.P3 pt)

Parameters:: fixJavaFloat - ALWAYS set true for any new references to this method. False is for legacy only; asCartesian -; pt -
Returns:: unit cell coord

getFractionalUnitDistance

float getFractionalUnitDistance(javajs.util.P3 pt,
                                javajs.util.P3 ptTemp1,
                                javajs.util.P3 ptTemp2)

setFractionalCoord

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

setFractionalCoordTo

void setFractionalCoordTo(javajs.util.P3 ptNew,
                          boolean asAbsolute)

setFractionalCoordPt

public void setFractionalCoordPt(javajs.util.P3 pt,
                                 javajs.util.P3 ptNew,
                                 boolean asAbsolute)

isCursorOnTopOf

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

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

getInfoXYZ

public java.lang.String getInfoXYZ(boolean fixJavaFloat,
                                   boolean useChimeFormat,
                                   javajs.util.P3 pt)

getIdentityXYZ

java.lang.String getIdentityXYZ(boolean allInfo,
                                javajs.util.P3 pt)

getIdentity

java.lang.String getIdentity(boolean allInfo)

getGroup3

public java.lang.String getGroup3(boolean allowNull)

Specified by:: getGroup3 in interface BNode

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

getGroup1 in interface BNode

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

isProtein in interface BNode

isCarbohydrate
```
boolean isCarbohydrate()
```

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

isNucleic in interface BNode

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

isDna in interface BNode

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

isRna in interface BNode

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

isPurine in interface BNode

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

isPyrimidine in interface BNode

getSeqcode
```
int getSeqcode()
```

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

getResno in interface BNode

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

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

checkVisible
```
public boolean checkVisible()
```

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

isLeadAtom in interface BNode

getGroupParameter

public float getGroupParameter(int tok)

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

getChainID in interface BNode

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

getChainIDStr in interface BNode

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

getVibrationVector
```
public Vibration getVibrationVector()
```

getModulation

public JmolModulationSet getModulation()

getVibrationCoord

public float getVibrationCoord(char ch)

getModulationCoord

public float getModulationCoord(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
```
public Chain getChain()
```

getModelNumberForLabel

public java.lang.String getModelNumberForLabel()

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

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

getBioStructureTypeName in interface BNode

getProteinStructureType
```
public STR getProteinStructureType()
```

getProteinStructureSubType

public STR getProteinStructureSubType()

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

getStructureId

public java.lang.String getStructureId()

getProteinStructureTag

public java.lang.String getProteinStructureTag()

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

getSeqcodeString

public java.lang.String getSeqcodeString()

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

equals
```
public boolean equals(java.lang.Object obj)
```
Description copied from class: javajs.util.T3

Returns true if all of the data members of Tuple3f t1 are equal to the corresponding data members in this

Overrides:

equals in class javajs.util.T3

Parameters:

obj - the vector with which the comparison is made.

hashCode
```
public int hashCode()
```
Description copied from class: javajs.util.T3

Returns a hash number based on the data values in this object. Two different Tuple3f objects with identical data values (ie, returns true for equals(Tuple3f) ) will return the same hash number. Two vectors with different data members may return the same hash value, although this is not likely.

Overrides:

hashCode in class javajs.util.T3

findAromaticNeighbor

public Atom findAromaticNeighbor(int notAtomIndex)

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

Parameters:

tokWhat -

Returns:

int value or Integer.MIN_VALUE

getSymOp
```
int getSymOp()
```

atomPropertyFloat
```
public float atomPropertyFloat(Viewer vwr,
                               int tokWhat,
                               javajs.util.P3 ptTemp)
```
called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()

Parameters:

vwr -

tokWhat -

ptTemp -

Returns:

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

getMass
```
private float getMass()
```

atomPropertyString

public java.lang.String atomPropertyString(Viewer vwr,
                                           int tokWhat)

atomPropertyTuple

public javajs.util.T3 atomPropertyTuple(Viewer vwr,
                                        int tok,
                                        javajs.util.P3 ptTemp)

isWithinStructure
```
boolean isWithinStructure(STR type)
```

getOffsetResidueAtom

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

Specified by:: getOffsetResidueAtom in interface BNode

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

isCrossLinked in interface BNode

getCrossLinkLeadAtomIndexes

public boolean getCrossLinkLeadAtomIndexes(javajs.util.Lst<java.lang.Integer> vReturn)

Specified by:: getCrossLinkLeadAtomIndexes in interface BNode

toString
```
public java.lang.String toString()
```
Description copied from class: javajs.util.T3

Returns a string that contains the values of this Tuple3f. The form is (x,y,z).

Overrides:

toString in class javajs.util.T3

Returns:

the String representation

findAtomsLike

public BS findAtomsLike(java.lang.String atomExpression)

Specified by:: findAtomsLike in interface Node

Class Atom

Field Summary

Fields inherited from class org.jmol.util.Point3fi

Fields inherited from class javajs.util.T3

Constructor Summary

Method Summary

Methods inherited from class org.jmol.util.Point3fi

Methods inherited from class javajs.util.P3

Methods inherited from class javajs.util.T3

Methods inherited from class java.lang.Object

Methods inherited from interface org.jmol.util.Node

Field Detail

VIBRATION_VECTOR_FLAG

IS_HETERO_FLAG

FLAG_MASK

RADIUS_MAX

RADIUS_GLOBAL

MAD_GLOBAL

altloc

atomID

atomSite

group

userDefinedVanDerWaalRadius

valence

atomicAndIsotopeNumber

atomSymmetry

formalChargeAndFlags

madAtom

colixAtom

paletteID

bonds

nBondsDisplayed

nBackbonesDisplayed

clickabilityFlags

shapeVisibilityFlags

Constructor Detail

Atom

Method Detail

setAtom

setShapeVisibility

isCovalentlyBonded

isBonded

getBond

addDisplayedBond

addDisplayedBackbone

deleteBond

deleteBondAt

getBondedAtomIndex

setMadAtom

calculateMad

getADPMinMax

getTensors

getRasMolRadius

getCovalentBondCount

getCovalentHydrogenCount

getEdges

setTranslucent

isTranslucent

getElementNumber

getIsotopeNumber

getAtomicAndIsotopeNumber

setAtomicAndIsotopeNumber

getElementSymbolIso

getElementSymbol

isAltLoc

isHetero

hasVibration

setFormalCharge

setVibrationVector

getFormalCharge

getOccupancy100

getBfactor100

getHydrophobicity

setRadius

deleteBonds

isDeleted

setValence

getValence

getImplicitHydrogenCount

getTargetValence