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, Node, SimpleNode
```
public class Atom
extends Point3fi
implements Node
```
See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field	Description
`char`	`altloc`
`static int`	`ATOM_INFRAME`
`static int`	`ATOM_INFRAME_NOTHIDDEN`
`static int`	`ATOM_NOFLAGS`
`static int`	`ATOM_NOTHIDDEN`
`static int`	`ATOM_SHAPE_VIS_MASK`
`static int`	`ATOM_VISIBLE`
`static int`	`ATOM_VISSET`
`private short`	`atomicAndIsotopeNumber`
`byte`	`atomID`
`int`	`atomSite`
`javajs.util.BS`	`atomSymmetry`
`Bond[]`	`bonds`	MAY BE NULL
`private static int`	`CHARGE_OFFSET`
`private static int`	`CIP_CHIRALITY_MASK`
`private static int`	`CIP_CHIRALITY_OFFSET`
`private static int`	`CIP_CHIRALITY_RULE_MASK`
`private static int`	`CIP_CHIRALITY_RULE_OFFSET`
`private static int`	`CIP_MASK`
`int`	`clickabilityFlags`
`short`	`colixAtom`
`private static int`	`FLAG_MASK`
`private int`	`formalChargeAndFlags`
`Group`	`group`
`private static int`	`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 int`	`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 Description

Atom()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`(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()`
`void`	`delete(javajs.util.BS bsBonds)`
`(package private) void`	`deleteBond(Bond bond)`
`private void`	`deleteBondAt(int i)`
`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)`
`javajs.util.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()`
`char`	`getBioSmilesType()`
`java.lang.String`	`getBioStructureTypeName()`
`Bond`	`getBond(Atom atomOther)`
`int`	`getBondCount()`	Get the total number of bonds, including hydrogen bonds.
`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
`int`	`getChainID()`
`java.lang.String`	`getChainIDStr()`
`java.lang.String`	`getCIPChirality(boolean doCalculate)`	Determine R/S chirality at this position; non-H atoms only; cached in formalChargeAndFlags
`int`	`getCIPChiralityCode()`
`java.lang.String`	`getCIPChiralityRule()`
`int`	`getCovalentBondCount()`	Get the total number of covalent bonds, thus not including hydrogen bonds.
`int`	`getCovalentBondCountPlusMissingH()`	includes actual + missing
`int`	`getCovalentHydrogenCount()`
`boolean`	`getCrossLinkVector(javajs.util.Lst<java.lang.Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond)`	Used by SMILES to get vector of cross-links
`(package private) int`	`getCurrentBondCount()`
`float`	`getDimensionValue(int dimension)`
`Edge[]`	`getEdges()`	Get the bond array, including hydrogen bonds.
`int`	`getElementNumber()`
`java.lang.String`	`getElementSymbol()`
`java.lang.String`	`getElementSymbolIso(boolean withIsotope)`
`float`	`getFloatProperty(java.lang.String property)`
`int`	`getFormalCharge()`
`private float`	`getFractionalCoord(boolean fixJavaFloat, char ch, boolean ignoreOffset, javajs.util.P3 pt)`
`javajs.util.P3`	`getFractionalCoordPt(boolean fixJavaFloat, boolean ignoreOffset, 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.T3 pt, javajs.util.T3 ptTemp1, javajs.util.T3 ptTemp2)`
`java.lang.String`	`getGroup1(char c0)`
`java.lang.String`	`getGroup3(boolean allowNull)`
`void`	`getGroupBits(javajs.util.BS bs)`
`float`	`getHydrophobicity()`
`(package private) java.lang.String`	`getIdentity(boolean allInfo)`
`java.lang.String`	`getIdentityXYZ(boolean allInfo, javajs.util.P3 pt)`
`int`	`getImplicitHydrogenCount()`	can be > 0 for PDB model with no H atoms or for SMILES string CCC
`int`	`getIndex()`
`java.lang.String`	`getInfo()`
`char`	`getInsertionCode()`
`int`	`getIsotopeNumber()`
`float`	`getMass()`
`int`	`getModelIndex()`	SMILES only
`int`	`getModelNumber()`
`java.lang.String`	`getModelNumberForLabel()`
`JmolModulationSet`	`getModulation()`
`int`	`getMoleculeNumber(boolean inModel)`
`int`	`getNominalMass()`
`int`	`getOccupancy100()`
`int`	`getOffsetResidueAtom(java.lang.String name, int offset)`
`float`	`getPartialCharge()`
`float`	`getRadius()`
`int`	`getRasMolRadius()`
`int`	`getResno()`
`int`	`getSeqID()`
`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()`
`int`	`getTotalHydrogenCount()`
`int`	`getTotalValence()`
`(package private) SymmetryInterface`	`getUnitCell()`
`java.lang.String`	`getUnitID(int flags)`
`int`	`getValence()`	return the total bond order for this atom
`float`	`getVanderwaalsRadiusFloat(Viewer vwr, VDW type)`
`private VDW`	`getVdwType(VDW type)`
`float`	`getVib(char ch)`
`Vibration`	`getVibrationVector()`
`(package private) float`	`getVolume(Viewer vwr, VDW vType)`
`javajs.util.P3`	`getXYZ()`
`int`	`hashCode()`	Returns a hash number based on the data values in this object.
`boolean`	`hasVibration()`
`boolean`	`isBonded(Atom atomOther)`
`boolean`	`isClickable()`
`boolean`	`isCovalentlyBonded(Atom atomOther)`
`boolean`	`isCrossLinked(Node node)`
`(package private) boolean`	`isCursorOnTopOf(int xCursor, int yCursor, int minRadius, Atom competitor)`
`boolean`	`isDeleted()`
`boolean`	`isHetero()`
`boolean`	`isLeadAtom()`
`boolean`	`isOccupied()`
`boolean`	`isPurine()`
`boolean`	`isPyrimidine()`
`boolean`	`isVisible(int flags)`
`boolean`	`modelIsRawPDB()`
`Atom`	`setAtom(int modelIndex, int atomIndex, javajs.util.P3 xyz, float radius, javajs.util.BS atomSymmetry, int atomSite, short atomicAndIsotopeNumber, int formalCharge, boolean isHetero)`
`void`	`setAtomicAndIsotopeNumber(int n)`
`void`	`setCIPChirality(int c)`
`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)`
`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

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

Methods inherited from class javajs.util.T3
add, add2, add3, ave, cross, distance, distanceSquared, dot, floatToIntBits, 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
  - ATOM_INFRAME
```
public static final int ATOM_INFRAME
```
    See Also:
    
    Constant Field Values
  - ATOM_VISSET
```
public static final int ATOM_VISSET
```
    See Also:
    
    Constant Field Values
  - ATOM_VISIBLE
```
public static final int ATOM_VISIBLE
```
    See Also:
    
    Constant Field Values
  - ATOM_NOTHIDDEN
```
public static final int ATOM_NOTHIDDEN
```
    See Also:
    
    Constant Field Values
  - ATOM_NOFLAGS
```
public static final int ATOM_NOFLAGS
```
    See Also:
    
    Constant Field Values
  - ATOM_INFRAME_NOTHIDDEN
```
public static final int ATOM_INFRAME_NOTHIDDEN
```
    See Also:
    
    Constant Field Values
  - ATOM_SHAPE_VIS_MASK
```
public static final int ATOM_SHAPE_VIS_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 javajs.util.BS atomSymmetry
```
  - formalChargeAndFlags
```
private int formalChargeAndFlags
```
  - CHARGE_OFFSET
```
private static final int CHARGE_OFFSET
```
    See Also:
    
    Constant Field Values
  - FLAG_MASK
```
private static final int FLAG_MASK
```
    See Also:
    
    Constant Field Values
  - VIBRATION_VECTOR_FLAG
```
private static final int VIBRATION_VECTOR_FLAG
```
    See Also:
    
    Constant Field Values
  - IS_HETERO_FLAG
```
private static final int IS_HETERO_FLAG
```
    See Also:
    
    Constant Field Values
  - CIP_CHIRALITY_OFFSET
```
private static final int CIP_CHIRALITY_OFFSET
```
    See Also:
    
    Constant Field Values
  - CIP_CHIRALITY_MASK
```
private static final int CIP_CHIRALITY_MASK
```
    See Also:
    
    Constant Field Values
  - CIP_CHIRALITY_RULE_OFFSET
```
private static final int CIP_CHIRALITY_RULE_OFFSET
```
    See Also:
    
    Constant Field Values
  - CIP_CHIRALITY_RULE_MASK
```
private static final int CIP_CHIRALITY_RULE_MASK
```
    See Also:
    
    Constant Field Values
  - CIP_MASK
```
private static final int CIP_MASK
```
    See Also:
    
    Constant Field Values
  - 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,
                    javajs.util.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)
```
  - 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()
```
  - getEdges
```
public Edge[] getEdges()
```
    Description copied from interface: SimpleNode
    
    Get the bond array, including hydrogen bonds.
    
    Specified by:
    
    getEdges in interface Node
    
    Specified by:
    
    getEdges in interface SimpleNode
    
    Returns:
    
    number of bonds
  - getBondCount
```
public int getBondCount()
```
    Description copied from interface: SimpleNode
    
    Get the total number of bonds, including hydrogen bonds.
    
    Specified by:
    
    getBondCount in interface SimpleNode
    
    Returns:
    
    number of bonds
  - setTranslucent
```
public void setTranslucent(boolean isTranslucent,
                           float translucentLevel)
```
  - getElementNumber
```
public int getElementNumber()
```
    Specified by:
    
    getElementNumber in interface Node
    
    Specified by:
    
    getElementNumber in interface SimpleNode
    
    Returns:
    
    the atomic number for this aotm
  - getIsotopeNumber
```
public int getIsotopeNumber()
```
    Specified by:
    
    getIsotopeNumber in interface Node
    
    Specified by:
    
    getIsotopeNumber in interface SimpleNode
  - 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()
```
  - isHetero
```
public boolean isHetero()
```
  - hasVibration
```
public boolean hasVibration()
```
  - setFormalCharge
```
public void setFormalCharge(int charge)
```
    Parameters:
    
    charge - from -3 to 7
  - setVibrationVector
```
void setVibrationVector()
```
  - getFormalCharge
```
public int getFormalCharge()
```
    Specified by:
    
    getFormalCharge in interface Node
    
    Specified by:
    
    getFormalCharge in interface SimpleNode
    
    Returns:
    
    the formal charge for this atom
  - getOccupancy100
```
public int getOccupancy100()
```
  - isOccupied
```
public boolean isOccupied()
```
  - getBfactor100
```
public int getBfactor100()
```
  - getHydrophobicity
```
public float getHydrophobicity()
```
  - setRadius
```
public boolean setRadius(float radius)
```
  - delete
```
public void delete(javajs.util.BS bsBonds)
```
  - isDeleted
```
public boolean isDeleted()
```
    Specified by:
    
    isDeleted in interface Node
  - setValence
```
public void setValence(int nBonds)
```
  - getValence
```
public int getValence()
```
    return the total bond order for this atom
    
    Specified by:
    
    getValence in interface Node
    
    Specified by:
    
    getValence in interface SimpleNode
    
    Returns:
    
    the sum of the bond orders for this atom
  - getCovalentBondCount
```
public int getCovalentBondCount()
```
    Description copied from interface: SimpleNode
    
    Get the total number of covalent bonds, thus not including hydrogen bonds.
    
    Specified by:
    
    getCovalentBondCount in interface Node
    
    Specified by:
    
    getCovalentBondCount in interface SimpleNode
    
    Returns:
    
    number of bonds
  - getCovalentHydrogenCount
```
public int getCovalentHydrogenCount()
```
    Specified by:
    
    getCovalentHydrogenCount in interface Node
  - getImplicitHydrogenCount
```
public int getImplicitHydrogenCount()
```
    Description copied from interface: Node
    
    can be > 0 for PDB model with no H atoms or for SMILES string CCC
    
    Specified by:
    
    getImplicitHydrogenCount in interface Node
    
    Returns:
    
    number of missing H atoms
  - getTotalHydrogenCount
```
public int getTotalHydrogenCount()
```
    Specified by:
    
    getTotalHydrogenCount in interface Node
  - getTotalValence
```
public int getTotalValence()
```
    Specified by:
    
    getTotalValence in interface Node
  - getCovalentBondCountPlusMissingH
```
public int getCovalentBondCountPlusMissingH()
```
    Description copied from interface: Node
    
    includes actual + missing
    
    Specified by:
    
    getCovalentBondCountPlusMissingH in interface Node
    
    Returns:
    
    actual + missing
  - 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
    
    Specified by:
    
    getIndex in interface SimpleNode
    
    Returns:
    
    the unique ID number associated with this atom (which in Jmol is its position in the atoms[] array
  - getAtomSite
```
public int getAtomSite()
```
    Specified by:
    
    getAtomSite in interface Node
  - getGroupBits
```
public void getGroupBits(javajs.util.BS bs)
```
    Specified by:
    
    getGroupBits in interface Node
  - getAtomName
```
public java.lang.String getAtomName()
```
    Specified by:
    
    getAtomName in interface Node
    
    Specified by:
    
    getAtomName in interface SimpleNode
  - getAtomType
```
public java.lang.String getAtomType()
```
    Specified by:
    
    getAtomType in interface Node
  - getAtomNumber
```
public int getAtomNumber()
```
    Specified by:
    
    getAtomNumber in interface Node
  - 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()
```
    SMILES only
    
    Specified by:
    
    getModelIndex in interface Node
  - getMoleculeNumber
```
public int getMoleculeNumber(boolean inModel)
```
    Specified by:
    
    getMoleculeNumber in interface Node
  - getFractionalCoord
```
private float getFractionalCoord(boolean fixJavaFloat,
                                 char ch,
                                 boolean ignoreOffset,
                                 javajs.util.P3 pt)
```
  - getXYZ
```
public javajs.util.P3 getXYZ()
```
    Specified by:
    
    getXYZ in interface Node
    
    Specified by:
    
    getXYZ in interface SimpleNode
    
    Returns:
    
    the position of this atom
  - getFractionalCoordPt
```
public javajs.util.P3 getFractionalCoordPt(boolean fixJavaFloat,
                                           boolean ignoreOffset,
                                           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.T3 pt,
                                javajs.util.T3 ptTemp1,
                                javajs.util.T3 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()
```
  - getIdentityXYZ
```
public 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 Node
  - getGroup1
```
public java.lang.String getGroup1(char c0)
```
    Specified by:
    
    getGroup1 in interface Node
  - getBioSmilesType
```
public char getBioSmilesType()
```
    Specified by:
    
    getBioSmilesType in interface Node
  - isPurine
```
public boolean isPurine()
```
    Specified by:
    
    isPurine in interface Node
  - isPyrimidine
```
public boolean isPyrimidine()
```
    Specified by:
    
    isPyrimidine in interface Node
  - getResno
```
public int getResno()
```
    Specified by:
    
    getResno in interface Node
  - isClickable
```
public boolean isClickable()
```
  - setClickable
```
public void setClickable(int flag)
```
  - checkVisible
```
public boolean checkVisible()
```
  - isLeadAtom
```
public boolean isLeadAtom()
```
    Specified by:
    
    isLeadAtom in interface Node
  - getChainID
```
public int getChainID()
```
    Specified by:
    
    getChainID in interface Node
  - getChainIDStr
```
public java.lang.String getChainIDStr()
```
    Specified by:
    
    getChainIDStr in interface Node
  - getSurfaceDistance100
```
public int getSurfaceDistance100()
```
  - getVibrationVector
```
public Vibration getVibrationVector()
```
  - getModulation
```
public JmolModulationSet getModulation()
```
  - getModelNumberForLabel
```
public java.lang.String getModelNumberForLabel()
```
  - getModelNumber
```
public int getModelNumber()
```
  - getBioStructureTypeName
```
public java.lang.String getBioStructureTypeName()
```
    Specified by:
    
    getBioStructureTypeName in interface Node
  - 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
  - getVib
```
public float getVib(char ch)
```
  - getNominalMass
```
public int getNominalMass()
```
  - getMass
```
public float getMass()
```
    Specified by:
    
    getMass in interface Node
    
    Specified by:
    
    getMass in interface SimpleNode
    
    Returns:
    
    the mass or, if specified, the mass number
  - atomPropertyString
```
public java.lang.String atomPropertyString(Viewer vwr,
                                           int tokWhat)
```
  - getCIPChirality
```
public java.lang.String getCIPChirality(boolean doCalculate)
```
    Determine R/S chirality at this position; non-H atoms only; cached in formalChargeAndFlags
    
    Specified by:
    
    getCIPChirality in interface Node
    
    Parameters:
    
    doCalculate -
    
    Returns:
    
    one of "", "R", "S", "E", "Z", "r", "s", "?"
  - getCIPChiralityRule
```
public java.lang.String getCIPChiralityRule()
```
  - setCIPChirality
```
public void setCIPChirality(int c)
```
    Specified by:
    
    setCIPChirality in interface Node
    
    Specified by:
    
    setCIPChirality in interface SimpleNode
    
    Parameters:
    
    c - [0:unknown; 3:none; 1: R; 2: S; 5: Z; 6: E; 9: M, 10: P, +r,s
  - getCIPChiralityCode
```
public int getCIPChiralityCode()
```
    Specified by:
    
    getCIPChiralityCode in interface Node
  - getInsertionCode
```
public char getInsertionCode()
```
    Specified by:
    
    getInsertionCode in interface Node
  - atomPropertyTuple
```
public javajs.util.T3 atomPropertyTuple(Viewer vwr,
                                        int tok,
                                        javajs.util.P3 ptTemp)
```
  - getOffsetResidueAtom
```
public int getOffsetResidueAtom(java.lang.String name,
                                int offset)
```
    Specified by:
    
    getOffsetResidueAtom in interface Node
  - isCrossLinked
```
public boolean isCrossLinked(Node node)
```
    Specified by:
    
    isCrossLinked in interface Node
  - getCrossLinkVector
```
public boolean getCrossLinkVector(javajs.util.Lst<java.lang.Integer> vReturn,
                                  boolean crosslinkCovalent,
                                  boolean crosslinkHBond)
```
    Used by SMILES to get vector of cross-links
    
    Specified by:
    
    getCrossLinkVector in interface Node
  - 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 javajs.util.BS findAtomsLike(java.lang.String atomExpression)
```
    Specified by:
    
    findAtomsLike in interface Node
  - getUnitID
```
public java.lang.String getUnitID(int flags)
```
  - getFloatProperty
```
public float getFloatProperty(java.lang.String property)
```
    Specified by:
    
    getFloatProperty in interface Node
    
    Parameters:
    
    property - "property_xxxx"
    
    Returns:
    
    value or Float.NaN
  - modelIsRawPDB
```
public boolean modelIsRawPDB()
```
    Specified by:
    
    modelIsRawPDB 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

ATOM_INFRAME

ATOM_VISSET

ATOM_VISIBLE

ATOM_NOTHIDDEN

ATOM_NOFLAGS

ATOM_INFRAME_NOTHIDDEN

ATOM_SHAPE_VIS_MASK

RADIUS_MAX

RADIUS_GLOBAL

MAD_GLOBAL

altloc

atomID

atomSite

group

userDefinedVanDerWaalRadius

valence

atomicAndIsotopeNumber

atomSymmetry

formalChargeAndFlags

CHARGE_OFFSET

FLAG_MASK

VIBRATION_VECTOR_FLAG

IS_HETERO_FLAG

CIP_CHIRALITY_OFFSET

CIP_CHIRALITY_MASK

CIP_CHIRALITY_RULE_OFFSET

CIP_CHIRALITY_RULE_MASK

CIP_MASK

madAtom

colixAtom

paletteID

bonds

nBondsDisplayed

nBackbonesDisplayed

clickabilityFlags

shapeVisibilityFlags

Constructor Detail

Atom

Method Detail

setAtom

setShapeVisibility

isCovalentlyBonded

isBonded

getBond

addDisplayedBond

deleteBond

deleteBondAt

getBondedAtomIndex

setMadAtom

calculateMad

getADPMinMax

getTensors

getRasMolRadius

getEdges

getBondCount

setTranslucent

getElementNumber

getIsotopeNumber

getAtomicAndIsotopeNumber

setAtomicAndIsotopeNumber

getElementSymbolIso

getElementSymbol

isHetero

hasVibration

setFormalCharge

setVibrationVector

getFormalCharge

getOccupancy100