Atom

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

All Implemented Interfaces:

Serializable, Cloneable, JmolNode
```
public class Atom
extends Point3fi
implements JmolNode
```
See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`char`	`altloc`
`private short`	`atomicAndIsotopeNumber`
`byte`	`atomID`
`int`	`atomSite`
`private BS`	`atomSymmetry`
`static int`	`BACKBONE_VISIBILITY_FLAG`
`(package private) Bond[]`	`bonds`
`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`
`(package private) int`	`nBackbonesDisplayed`
`(package private) int`	`nBondsDisplayed`
`(package private) 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
index, modelIndex, 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 Static 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)`
`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 String`	`atomPropertyString(Viewer viewer, Atom atom, int tokWhat)`
`static javajs.util.T3`	`atomPropertyTuple(Atom atom, int tok)`
`short`	`calculateMad(Viewer viewer, RadiusData rd)`
`(package private) void`	`clearBonds()`
`(package private) void`	`deleteBond(Bond bond)`
`private void`	`deleteBondAt(int i)`
`void`	`deleteBonds(BS bsBonds)`
`boolean`	`equals(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(String atomExpression)`
`float`	`getADPMinMax(boolean isMax)`
`char`	`getAlternateLocationID()`
`int`	`getAtomicAndIsotopeNumber()`
`byte`	`getAtomID()`
`String`	`getAtomName()`
`int`	`getAtomNumber()`
`int`	`getAtomSite()`
`BS`	`getAtomSymmetry()`
`String`	`getAtomType()`
`int`	`getBfactor100()`
`String`	`getBioStructureTypeName()`
`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
`Chain`	`getChain()`
`int`	`getChainID()`
`String`	`getChainIDStr()`
`int`	`getClickabilityFlags()`
`short`	`getColix()`
`int`	`getCovalentBondCount()`
`int`	`getCovalentHydrogenCount()`
`private float`	`getCovalentRadiusFloat()`
`boolean`	`getCrossLinkLeadAtomIndexes(javajs.util.List<Integer> vReturn)`
`(package private) int`	`getCurrentBondCount()`
`float`	`getDimensionValue(int dimension)`
`JmolEdge[]`	`getEdges()`
`int`	`getElementNumber()`
`String`	`getElementSymbol()`
`String`	`getElementSymbolIso(boolean withIsotope)`
`int`	`getFormalCharge()`
`private float`	`getFractionalCoord(char ch, boolean asAbsolute)`
`private javajs.util.P3`	`getFractionalCoordPt(boolean asAbsolute)`
`private float`	`getFractionalUnitCoord(char ch)`
`(package private) javajs.util.P3`	`getFractionalUnitCoordPt(boolean asCartesian)`
`(package private) float`	`getFractionalUnitDistance(javajs.util.P3 pt, javajs.util.P3 ptTemp1, javajs.util.P3 ptTemp2)`
`Group`	`getGroup()`
`String`	`getGroup1(char c0)`
`String`	`getGroup3(boolean allowNull)`
`void`	`getGroupBits(BS bs)`
`short`	`getGroupID()`
`float`	`getGroupParameter(int tok)`
`private float`	`getHydrophobicity()`
`(package private) String`	`getIdentity(boolean allInfo)`
`(package private) String`	`getIdentityXYZ(boolean allInfo)`
`int`	`getImplicitHydrogenCount()`
`int`	`getIndex()`
`String`	`getInfo()`
`(package private) String`	`getInfoXYZ(boolean useChimeFormat)`
`char`	`getInsertionCode()`
`int`	`getIsotopeNumber()`
`private float`	`getMass()`
`int`	`getModelFileIndex()`
`int`	`getModelFileNumber()`
`int`	`getModelIndex()`
`int`	`getModelNumber()`
`String`	`getModelNumberForLabel()`
`(package private) int`	`getMoleculeNumber(boolean inModel)`
`int`	`getMonomerIndex()`
`int`	`getNBackbonesDisplayed()`
`int`	`getOccupancy100()`
`int`	`getOffsetResidueAtom(String name, int offset)`
`byte`	`getPaletteID()`
`float`	`getPartialCharge()`
`int`	`getPolymerIndexInModel()`
`int`	`getPolymerLength()`
`EnumStructure`	`getProteinStructureSubType()`
`String`	`getProteinStructureTag()`
`EnumStructure`	`getProteinStructureType()`
`float`	`getRadius()`
`int`	`getRasMolRadius()`
`int`	`getResno()`
`int`	`getSelectedGroupCountWithinChain()`
`int`	`getSelectedGroupIndexWithinChain()`
`int`	`getSelectedMonomerCountWithinPolymer()`
`int`	`getSelectedMonomerIndexWithinPolymer()`
`(package private) int`	`getSeqcode()`
`String`	`getSeqcodeString()`
`int`	`getShapeVisibilityFlags()`
`int`	`getStrucNo()`
`String`	`getStructureId()`
`int`	`getSurfaceDistance100()`
`(package private) 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`	`getSymOp()`
`(package private) int`	`getTargetValence()`
`Object[]`	`getTensors()`
`(package private) SymmetryInterface`	`getUnitCell()`
`int`	`getValence()`
`float`	`getVanderwaalsRadiusFloat(Viewer viewer, EnumVdw type)`
`private EnumVdw`	`getVdwType(EnumVdw type)`
`float`	`getVibrationCoord(char ch)`
`javajs.util.V3`	`getVibrationVector()`
`(package private) float`	`getVolume(Viewer viewer, EnumVdw vType)`
`int`	`hashCode()` Returns a hash number based on the data values in this object.
`boolean`	`hasVibration()`
`(package private) boolean`	`isAltLoc(String strPattern)`
`boolean`	`isBonded(Atom atomOther)`
`(package private) boolean`	`isCarbohydrate()`
`boolean`	`isClickable()`
`boolean`	`isCovalentlyBonded(Atom atomOther)`
`boolean`	`isCrossLinked(JmolNode node)`
`(package private) boolean`	`isCursorOnTopOf(int xCursor, int yCursor, int minRadius, Atom competitor)`
`boolean`	`isDeleted()`
`boolean`	`isDna()`
`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
`boolean`	`isWithinFourBonds(Atom atomOther)`
`(package private) boolean`	`isWithinStructure(EnumStructure type)`
`void`	`setAltLoc(char altLoc)`
`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`	`setAtomSymmetry(BS bsSymmetry)`
`void`	`setBonds(Bond[] bonds)`
`void`	`setClickable(int flag)`
`void`	`setColixAtom(short colixAtom)`
`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 viewer, RadiusData rd)`
`void`	`setPaletteID(byte paletteID)`
`boolean`	`setRadius(float radius)`
`void`	`setShapeVisibility(int flag, boolean isVisible)`
`void`	`setShapeVisibilityFlags(int flag)`
`void`	`setTranslucent(boolean isTranslucent, float translucentLevel)`
`void`	`setValence(int nBonds)`
`(package private) void`	`setVibrationVector()`
`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
new3, newP

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

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

Methods inherited from interface org.jmol.util.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

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
```
private BS atomSymmetry
```

formalChargeAndFlags
```
private byte formalChargeAndFlags
```

madAtom
```
public short madAtom
```

colixAtom
```
public short colixAtom
```

paletteID
```
byte paletteID
```

bonds
```
Bond[] bonds
```

nBondsDisplayed
```
int nBondsDisplayed
```

nBackbonesDisplayed
```
int nBackbonesDisplayed
```

clickabilityFlags
```
public int clickabilityFlags
```

shapeVisibilityFlags
```
public int shapeVisibilityFlags
```

BACKBONE_VISIBILITY_FLAG

public static final int BACKBONE_VISIBILITY_FLAG

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

Method Detail

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

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

bonds -- WHICH MAY BE NULL

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

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

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

setAltLoc
```
public void setAltLoc(char altLoc)
```

setShapeVisibilityFlags

public final void setShapeVisibilityFlags(int flag)

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)
```

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)

getTensors
```
public Object[] getTensors()
```

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 int getElementNumber()
```
Specified by:

getElementNumber in interface JmolNode

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

getIsotopeNumber in interface JmolNode

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

getAtomicAndIsotopeNumber in interface JmolNode

setAtomicAndIsotopeNumber

public void setAtomicAndIsotopeNumber(int n)

getElementSymbolIso

public String getElementSymbolIso(boolean withIsotope)

getElementSymbol
```
public String getElementSymbol()
```

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

isAltLoc
```
boolean isAltLoc(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 JmolNode

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 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,
                                       EnumVdw type)

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

type -

Returns:

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

getCovalentRadiusFloat

private float getCovalentRadiusFloat()

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

getVolume

float getVolume(Viewer viewer,
                EnumVdw vType)

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

setAtomSymmetry

public void setAtomSymmetry(BS bsSymmetry)

getAtomSymmetry
```
public BS getAtomSymmetry()
```

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

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

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

getGroupBits in interface JmolNode

getAtomName
```
public String getAtomName()
```
Specified by:

getAtomName in interface JmolNode

getAtomType
```
public String getAtomType()
```
Specified by:

getAtomType in interface JmolNode

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

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

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

isShapeVisible

public boolean isShapeVisible(int shapeVisibilityFlag)

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
```
String getSymmetryOperatorList()
```

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

getModelIndex in interface JmolNode

getMoleculeNumber

int getMoleculeNumber(boolean inModel)

getFractionalCoord

private float getFractionalCoord(char ch,
                                 boolean asAbsolute)

getFractionalCoordPt

private javajs.util.P3 getFractionalCoordPt(boolean asAbsolute)

getUnitCell
```
SymmetryInterface getUnitCell()
```

getFractionalUnitCoord

private float getFractionalUnitCoord(char ch)

getFractionalUnitCoordPt

javajs.util.P3 getFractionalUnitCoordPt(boolean asCartesian)

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 String getInfo()
```

getInfoXYZ

String getInfoXYZ(boolean useChimeFormat)

getIdentityXYZ

String getIdentityXYZ(boolean allInfo)

getIdentity
```
String getIdentity(boolean allInfo)
```

getGroup3
```
public String getGroup3(boolean allowNull)
```
Specified by:

getGroup3 in interface JmolNode

getGroup1
```
public String getGroup1(char c0)
```
Specified by:

getGroup1 in interface JmolNode

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

isProtein in interface JmolNode

isCarbohydrate
```
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 -

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 int getChainID()
```
Specified by:

getChainID in interface JmolNode

getChainIDStr
```
public String getChainIDStr()
```
Specified by:

getChainIDStr in interface JmolNode

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

getVibrationVector

public javajs.util.V3 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
```
public Chain getChain()
```

getModelNumberForLabel

public String getModelNumberForLabel()

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

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

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

getBioStructureTypeName
```
public String getBioStructureTypeName()
```
Specified by:

getBioStructureTypeName in interface JmolNode

getProteinStructureType

public EnumStructure getProteinStructureType()

getProteinStructureSubType

public EnumStructure getProteinStructureSubType()

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

getStructureId
```
public String getStructureId()
```

getProteinStructureTag

public String getProteinStructureTag()

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

getSeqcodeString
```
public String getSeqcodeString()
```

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

equals
```
public boolean equals(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 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

getSymOp
```
int getSymOp()
```

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

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

atomPropertyString

public static String atomPropertyString(Viewer viewer,
                                        Atom atom,
                                        int tokWhat)

atomPropertyTuple

public static javajs.util.T3 atomPropertyTuple(Atom atom,
                                               int tok)

isWithinStructure

boolean isWithinStructure(EnumStructure type)

getOffsetResidueAtom

public int getOffsetResidueAtom(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(javajs.util.List<Integer> vReturn)
```
Specified by:

getCrossLinkLeadAtomIndexes in interface JmolNode

toString
```
public 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

isWithinFourBonds

public boolean isWithinFourBonds(Atom atomOther)

findAtomsLike
```
public BS findAtomsLike(String atomExpression)
```
Specified by:

findAtomsLike in interface JmolNode

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.JmolNode

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

BACKBONE_VISIBILITY_FLAG

Constructor Detail

Atom

Method Detail

getAtomID

getBonds

setBonds

getNBackbonesDisplayed

setAtom

setAltLoc

setShapeVisibilityFlags

setShapeVisibility

isCovalentlyBonded

isBonded

getBond

addDisplayedBond

addDisplayedBackbone

deleteBond

deleteBondAt

clearBonds

getBondedAtomIndex

setMadAtom

calculateMad

getADPMinMax

getTensors

getRasMolRadius

getCovalentBondCount

getCovalentHydrogenCount

getEdges

setColixAtom

setPaletteID

setTranslucent

isTranslucent

getElementNumber

getIsotopeNumber

getAtomicAndIsotopeNumber

setAtomicAndIsotopeNumber

getElementSymbolIso

getElementSymbol

getAlternateLocationID

isAltLoc

isHetero

hasVibration

setFormalCharge

setVibrationVector