java.lang.Object
- javajs.util.T3
- - javajs.util.P3
  - - org.jmol.smiles.SmilesAtom

All Implemented Interfaces:

java.io.Serializable, javajs.api.JSONEncodable, Node
```
public class SmilesAtom
extends javajs.util.P3
implements Node
```
This class represents an atom in a SmilesMolecule.

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field	Description
`(package private) boolean`	`aromaticAmbiguous`
`(package private) float`	`atomClass`
`private int`	`atomicMass`
`(package private) int`	`atomNumber`
`(package private) int`	`atomSite`
`(package private) java.lang.String`	`atomType`
`(package private) java.lang.String`	`bioAtomName`
`(package private) char`	`bioType`
`(package private) int`	`bondCount`
`(package private) SmilesBond[]`	`bonds`
`private int`	`charge`
`(package private) int`	`component`
`(package private) int`	`connectivity`
`private int`	`covalentHydrogenCount`
`(package private) int`	`degree`
`(package private) boolean`	`elementDefined`
`(package private) int`	`elementNumber`
`(package private) int`	`explicitHydrogenCount`
`(package private) boolean`	`hasSubpattern`
`(package private) boolean`	`hasSymbol`
`(package private) int`	`implicitHydrogenCount`
`(package private) int`	`index`
`(package private) int`	`iNested`
`(package private) char`	`insCode`
`(package private) boolean`	`isAND`
`(package private) boolean`	`isAromatic`
`(package private) boolean`	`isBioAtom`
`(package private) boolean`	`isBioAtomWild`
`(package private) boolean`	`isBioResidue`
`(package private) boolean`	`isFirst`	true if this atom is the first SMILES atom or first after a .
`(package private) boolean`	`isLeadAtom`
`private boolean`	`isTopoAtom`
`(package private) int`	`jmolIndex`
`(package private) int`	`mapIndex`
`(package private) int`	`matchingComponent`
`private int`	`matchingIndex`
`private Node`	`matchingNode`
`private int`	`missingHydrogenCount`
`(package private) int`	`nonhydrogenDegree`
`(package private) boolean`	`not`
`(package private) int`	`notBondedIndex`
`(package private) boolean`	`notCrossLinked`
`(package private) int`	`nSubAtoms`
`(package private) SmilesAtom`	`parent`
`(package private) java.lang.String`	`pattern`
`(package private) int`	`primitiveType`
`(package private) java.lang.String`	`referance`
`(package private) java.lang.String`	`residueChar`
`(package private) java.lang.String`	`residueName`
`(package private) int`	`residueNumber`
`(package private) int`	`ringConnectivity`
`(package private) int`	`ringMembership`
`(package private) int`	`ringSize`
`(package private) boolean`	`selected`
`(package private) SmilesStereo`	`stereo`
`(package private) SmilesAtom[]`	`subAtoms`
`(package private) java.lang.String`	`symbol`
`(package private) static java.lang.String`	`UNBRACKETED_SET`
`(package private) int`	`valence`

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

Constructor Summary

Constructors
Constructor Description

SmilesAtom()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`(package private) void`	`addBond(SmilesBond bond)`	Add a bond to the atom.
`(package private) SmilesAtom`	`addSubAtom(SmilesAtom sAtom, boolean isAND)`
`(package private) static boolean`	`allowSmilesUnbracketed(java.lang.String xx)`
`BS`	`findAtomsLike(java.lang.String substring)`
`int`	`getAtomicAndIsotopeNumber()`
`int`	`getAtomicMass()`	Returns the atomic mass of the atom.
`(package private) static java.lang.String`	`getAtomLabel(int atomicNumber, int isotopeNumber, int valence, int charge, float osclass, int nH, boolean isAromatic, java.lang.String stereo)`	called from SmilesGenerator
`java.lang.String`	`getAtomName()`
`int`	`getAtomNumber()`	Returns the Jmol atom number
`int`	`getAtomSite()`
`java.lang.String`	`getAtomType()`
`char`	`getBioSmilesType()`
`java.lang.String`	`getBioStructureTypeName()`
`SmilesBond`	`getBond(int number)`	Returns the bond at index `number`.
`int`	`getBondCount()`
`int`	`getBondedAtomIndex(int j)`
`(package private) SmilesBond`	`getBondNotTo(SmilesAtom atom, boolean allowH)`
`(package private) SmilesBond`	`getBondTo(SmilesAtom atom)`	if atom is null, return bond TO this atom (bond.atom2 == this) otherwise, return bond connecting this atom with that atom
`int`	`getChainID()`
`java.lang.String`	`getChainIDStr()`
`int`	`getCharge()`	Returns the charge of the atom.
`int`	`getChiralClass()`
`int`	`getCovalentBondCount()`	Returns the number of bonds of this atom.
`int`	`getCovalentBondCountPlusMissingH()`	includes actual + missing
`int`	`getCovalentHydrogenCount()`
`boolean`	`getCrossLinkVector(javajs.util.Lst<java.lang.Integer> vLinks, boolean crosslinkCovalent, boolean crosslinkHBond)`
`(package private) static int`	`getDefaultCount(int elementNumber, boolean isAromatic)`
`Edge[]`	`getEdges()`
`int`	`getElementNumber()`	Returns the atomic number of the element or 0
`int`	`getExplicitHydrogenCount()`
`float`	`getFloatProperty(java.lang.String property)`
`int`	`getFormalCharge()`
`java.lang.String`	`getGroup1(char c0)`
`java.lang.String`	`getGroup3(boolean allowNull)`
`void`	`getGroupBits(BS bs)`
`int`	`getImplicitHydrogenCount()`	can be > 0 for PDB model with no H atoms or for SMILES string CCC
`int`	`getIndex()`	Returns the atom index of the atom.
`char`	`getInsertionCode()`
`int`	`getIsotopeNumber()`
`Node`	`getMatchingAtom()`	Returns the matching atom or null.
`int`	`getMatchingAtomIndex()`	Returns the number of a matching atom in a molecule.
`int`	`getMatchingBondedAtom(int i)`
`int`	`getModelIndex()`
`int`	`getMoleculeNumber(boolean inModel)`
`int`	`getOffsetResidueAtom(java.lang.String name, int offset)`
`int`	`getResno()`
`int`	`getTotalHydrogenCount()`
`int`	`getTotalValence()`
`int`	`getValence()`
`boolean`	`isCrossLinked(Node node)`
`boolean`	`isDefined()`
`boolean`	`isDeleted()`
`boolean`	`isLeadAtom()`
`boolean`	`isNucleic()`
`boolean`	`isPurine()`
`boolean`	`isPyrimidine()`
`void`	`setAtomicMass(int mass)`	Sets the atomic mass of the atom.
`(package private) void`	`setAtomName(java.lang.String name)`
`(package private) void`	`setBioAtom(char bioType)`
`void`	`setBondArray()`
`void`	`setBonds(SmilesBond[] bonds)`
`void`	`setCharge(int charge)`	Sets the charge of the atom.
`void`	`setConnectivity(int connectivity)`
`void`	`setDegree(int degree)`
`void`	`setExplicitHydrogenCount(int count)`	Sets the number of explicit hydrogen atoms bonded with this atom.
`boolean`	`setHydrogenCount()`	Finalizes the hydrogen count hydrogens in a `SmilesMolecule`.
`void`	`setImplicitHydrogenCount(int count)`	Sets the number of implicit hydrogen atoms bonded with this atom.
`SmilesAtom`	`setIndex(int index)`	Constructs a `SmilesAtom`.
`void`	`setMatchingAtom(Node jmolAtom, int index)`	Sets the number of a matching atom in a molecule.
`void`	`setNonhydrogenDegree(int degree)`
`void`	`setRingConnectivity(int rc)`
`void`	`setRingMembership(int rm)`
`void`	`setRingSize(int rs)`
`boolean`	`setSymbol(java.lang.String symbol)`	Sets the symbol of the atm.
`SmilesAtom`	`setTopoAtom(int iComponent, int ptAtom, java.lang.String symbol, int charge)`
`void`	`setValence(int valence)`
`java.lang.String`	`toString()`	Returns a string that contains the values of this Tuple3f.

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, equals, hashCode, 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
  - UNBRACKETED_SET
```
static final java.lang.String UNBRACKETED_SET
```
    See Also:
    
    Constant Field Values
  - pattern
```
java.lang.String pattern
```
  - primitiveType
```
int primitiveType
```
  - isAND
```
boolean isAND
```
  - subAtoms
```
SmilesAtom[] subAtoms
```
  - nSubAtoms
```
int nSubAtoms
```
  - index
```
int index
```
  - referance
```
java.lang.String referance
```
  - residueName
```
java.lang.String residueName
```
  - residueChar
```
java.lang.String residueChar
```
  - insCode
```
char insCode
```
  - isBioAtom
```
boolean isBioAtom
```
  - isBioResidue
```
boolean isBioResidue
```
  - isBioAtomWild
```
boolean isBioAtomWild
```
  - bioType
```
char bioType
```
  - isLeadAtom
```
boolean isLeadAtom
```
  - notBondedIndex
```
int notBondedIndex
```
  - notCrossLinked
```
boolean notCrossLinked
```
  - aromaticAmbiguous
```
boolean aromaticAmbiguous
```
  - covalentHydrogenCount
```
private int covalentHydrogenCount
```
  - not
```
boolean not
```
  - selected
```
boolean selected
```
  - hasSymbol
```
boolean hasSymbol
```
  - elementDefined
```
boolean elementDefined
```
  - atomType
```
java.lang.String atomType
```
  - bioAtomName
```
java.lang.String bioAtomName
```
  - isFirst
```
boolean isFirst
```
    true if this atom is the first SMILES atom or first after a . with no connector
  - jmolIndex
```
int jmolIndex
```
  - elementNumber
```
int elementNumber
```
  - atomNumber
```
int atomNumber
```
  - residueNumber
```
int residueNumber
```
  - explicitHydrogenCount
```
int explicitHydrogenCount
```
  - implicitHydrogenCount
```
int implicitHydrogenCount
```
  - parent
```
SmilesAtom parent
```
  - bonds
```
SmilesBond[] bonds
```
  - bondCount
```
int bondCount
```
  - iNested
```
int iNested
```
  - isAromatic
```
boolean isAromatic
```
  - atomicMass
```
private int atomicMass
```
  - charge
```
private int charge
```
  - matchingIndex
```
private int matchingIndex
```
  - stereo
```
SmilesStereo stereo
```
  - component
```
int component
```
  - matchingComponent
```
int matchingComponent
```
  - atomSite
```
int atomSite
```
  - degree
```
int degree
```
  - nonhydrogenDegree
```
int nonhydrogenDegree
```
  - valence
```
int valence
```
  - connectivity
```
int connectivity
```
  - ringMembership
```
int ringMembership
```
  - ringSize
```
int ringSize
```
  - ringConnectivity
```
int ringConnectivity
```
  - matchingNode
```
private Node matchingNode
```
  - hasSubpattern
```
boolean hasSubpattern
```
  - mapIndex
```
int mapIndex
```
  - atomClass
```
float atomClass
```
  - symbol
```
java.lang.String symbol
```
  - isTopoAtom
```
private boolean isTopoAtom
```
  - missingHydrogenCount
```
private int missingHydrogenCount
```
- Constructor Detail
  - SmilesAtom
```
SmilesAtom()
```
- Method Detail
  - allowSmilesUnbracketed
```
static boolean allowSmilesUnbracketed(java.lang.String xx)
```
  - getAtomType
```
public java.lang.String getAtomType()
```
    Specified by:
    
    getAtomType in interface Node
  - getChiralClass
```
public int getChiralClass()
```
  - isDefined
```
public boolean isDefined()
```
  - setBioAtom
```
void setBioAtom(char bioType)
```
  - setAtomName
```
void setAtomName(java.lang.String name)
```
  - setBonds
```
public void setBonds(SmilesBond[] bonds)
```
  - addSubAtom
```
SmilesAtom addSubAtom(SmilesAtom sAtom,
                      boolean isAND)
```
  - setIndex
```
public SmilesAtom setIndex(int index)
```
    Constructs a SmilesAtom.
    
    Parameters:
    
    index - Atom number in the molecule.
    
    Returns:
    
    this
  - setTopoAtom
```
public SmilesAtom setTopoAtom(int iComponent,
                              int ptAtom,
                              java.lang.String symbol,
                              int charge)
```
  - setHydrogenCount
```
public boolean setHydrogenCount()
```
    Finalizes the hydrogen count hydrogens in a SmilesMolecule. "missing" here means the number of atoms not present in the SMILES string for unbracketed atoms or the number of hydrogen atoms "CC" being really CH3CH3 or explicitly mentioned in the bracketed atom, "[CH2]". These hydrogen atoms are not part of the topological model constructed and need to be accounted for.
    
    Returns:
    
    false if inappropriate
  - getDefaultCount
```
static int getDefaultCount(int elementNumber,
                           boolean isAromatic)
```
  - getIndex
```
public int getIndex()
```
    Returns the atom index of the atom.
    
    Specified by:
    
    getIndex in interface Node
    
    Returns:
    
    Atom index.
  - setSymbol
```
public boolean setSymbol(java.lang.String symbol)
```
    Sets the symbol of the atm.
    
    Parameters:
    
    symbol - Atom symbol.
    
    Returns:
    
    false if invalid symbol
  - getElementNumber
```
public int getElementNumber()
```
    Returns the atomic number of the element or 0
    
    Specified by:
    
    getElementNumber in interface Node
    
    Returns:
    
    atomicNumber
  - getAtomicMass
```
public int getAtomicMass()
```
    Returns the atomic mass of the atom.
    
    Returns:
    
    Atomic mass.
  - getAtomNumber
```
public int getAtomNumber()
```
    Returns the Jmol atom number
    
    Specified by:
    
    getAtomNumber in interface Node
  - setAtomicMass
```
public void setAtomicMass(int mass)
```
    Sets the atomic mass of the atom.
    
    Parameters:
    
    mass - Atomic mass.
  - getCharge
```
public int getCharge()
```
    Returns the charge of the atom.
    
    Returns:
    
    Charge.
  - setCharge
```
public void setCharge(int charge)
```
    Sets the charge of the atom.
    
    Parameters:
    
    charge - Charge.
  - getMatchingAtomIndex
```
public int getMatchingAtomIndex()
```
    Returns the number of a matching atom in a molecule. This value is temporary, it is used during the pattern matching algorithm.
    
    Returns:
    
    matching atom index
  - getMatchingAtom
```
public Node getMatchingAtom()
```
    Returns the matching atom or null.
    
    Returns:
    
    matching atom
  - setMatchingAtom
```
public void setMatchingAtom(Node jmolAtom,
                            int index)
```
    Sets the number of a matching atom in a molecule. This value is temporary, it is used during the pattern matching algorithm.
    
    Parameters:
    
    jmolAtom -
    
    index - Temporary: number of a matching atom in a molecule.
  - setExplicitHydrogenCount
```
public void setExplicitHydrogenCount(int count)
```
    Sets the number of explicit hydrogen atoms bonded with this atom.
    
    Parameters:
    
    count - Number of hydrogen atoms.
  - setImplicitHydrogenCount
```
public void setImplicitHydrogenCount(int count)
```
    Sets the number of implicit hydrogen atoms bonded with this atom.
    
    Parameters:
    
    count - Number of hydrogen atoms.
  - setDegree
```
public void setDegree(int degree)
```
  - setNonhydrogenDegree
```
public void setNonhydrogenDegree(int degree)
```
  - setValence
```
public void setValence(int valence)
```
  - setConnectivity
```
public void setConnectivity(int connectivity)
```
  - setRingMembership
```
public void setRingMembership(int rm)
```
  - setRingSize
```
public void setRingSize(int rs)
```
  - setRingConnectivity
```
public void setRingConnectivity(int rc)
```
  - getModelIndex
```
public int getModelIndex()
```
    Specified by:
    
    getModelIndex in interface Node
  - getMoleculeNumber
```
public int getMoleculeNumber(boolean inModel)
```
    Specified by:
    
    getMoleculeNumber in interface Node
  - getAtomSite
```
public int getAtomSite()
```
    Specified by:
    
    getAtomSite in interface Node
  - getFormalCharge
```
public int getFormalCharge()
```
    Specified by:
    
    getFormalCharge in interface Node
  - getIsotopeNumber
```
public int getIsotopeNumber()
```
    Specified by:
    
    getIsotopeNumber in interface Node
  - getAtomicAndIsotopeNumber
```
public int getAtomicAndIsotopeNumber()
```
    Specified by:
    
    getAtomicAndIsotopeNumber in interface Node
  - getAtomName
```
public java.lang.String getAtomName()
```
    Specified by:
    
    getAtomName in interface Node
  - 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
  - addBond
```
void addBond(SmilesBond bond)
```
    Add a bond to the atom.
    
    Parameters:
    
    bond - Bond to add.
  - setBondArray
```
public void setBondArray()
```
  - getEdges
```
public Edge[] getEdges()
```
    Specified by:
    
    getEdges in interface Node
  - getBond
```
public SmilesBond getBond(int number)
```
    Returns the bond at index number.
    
    Parameters:
    
    number - Bond number.
    
    Returns:
    
    Bond.
  - getCovalentBondCount
```
public int getCovalentBondCount()
```
    Returns the number of bonds of this atom.
    
    Specified by:
    
    getCovalentBondCount in interface Node
    
    Returns:
    
    Number of bonds.
  - getBondCount
```
public int getBondCount()
```
    Specified by:
    
    getBondCount in interface Node
  - getCovalentBondCountPlusMissingH
```
public int getCovalentBondCountPlusMissingH()
```
    Description copied from interface: Node
    
    includes actual + missing
    
    Specified by:
    
    getCovalentBondCountPlusMissingH in interface Node
    
    Returns:
    
    actual + missing
  - getTotalHydrogenCount
```
public int getTotalHydrogenCount()
```
    Specified by:
    
    getTotalHydrogenCount 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
  - getExplicitHydrogenCount
```
public int getExplicitHydrogenCount()
```
  - getMatchingBondedAtom
```
public int getMatchingBondedAtom(int i)
```
  - getBondedAtomIndex
```
public int getBondedAtomIndex(int j)
```
    Specified by:
    
    getBondedAtomIndex in interface Node
  - getCovalentHydrogenCount
```
public int getCovalentHydrogenCount()
```
    Specified by:
    
    getCovalentHydrogenCount in interface Node
  - getValence
```
public int getValence()
```
    Specified by:
    
    getValence in interface Node
  - getTotalValence
```
public int getTotalValence()
```
    Specified by:
    
    getTotalValence in interface Node
  - getBondTo
```
SmilesBond getBondTo(SmilesAtom atom)
```
    if atom is null, return bond TO this atom (bond.atom2 == this) otherwise, return bond connecting this atom with that atom
    
    Parameters:
    
    atom -
    
    Returns:
    
    bond
  - getBondNotTo
```
SmilesBond getBondNotTo(SmilesAtom atom,
                        boolean allowH)
```
  - isLeadAtom
```
public boolean isLeadAtom()
```
    Specified by:
    
    isLeadAtom in interface Node
  - getOffsetResidueAtom
```
public int getOffsetResidueAtom(java.lang.String name,
                                int offset)
```
    Specified by:
    
    getOffsetResidueAtom in interface Node
  - getGroupBits
```
public void getGroupBits(BS bs)
```
    Specified by:
    
    getGroupBits 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> vLinks,
                                  boolean crosslinkCovalent,
                                  boolean crosslinkHBond)
```
    Specified by:
    
    getCrossLinkVector in interface Node
  - getBioStructureTypeName
```
public java.lang.String getBioStructureTypeName()
```
    Specified by:
    
    getBioStructureTypeName in interface Node
  - getInsertionCode
```
public char getInsertionCode()
```
    Specified by:
    
    getInsertionCode in interface Node
  - getResno
```
public int getResno()
```
    Specified by:
    
    getResno 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
  - getAtomLabel
```
static java.lang.String getAtomLabel(int atomicNumber,
                                     int isotopeNumber,
                                     int valence,
                                     int charge,
                                     float osclass,
                                     int nH,
                                     boolean isAromatic,
                                     java.lang.String stereo)
```
    called from SmilesGenerator
    
    Parameters:
    
    atomicNumber -
    
    isotopeNumber -
    
    valence - set -1 to force brackets
    
    charge -
    
    osclass - OpenSMILES value
    
    nH -
    
    isAromatic -
    
    stereo -
    
    Returns:
    
    label
  - getBioSmilesType
```
public char getBioSmilesType()
```
    Specified by:
    
    getBioSmilesType in interface Node
  - isNucleic
```
public boolean isNucleic()
```
  - isPurine
```
public boolean isPurine()
```
    Specified by:
    
    isPurine in interface Node
  - isPyrimidine
```
public boolean isPyrimidine()
```
    Specified by:
    
    isPyrimidine in interface Node
  - isDeleted
```
public boolean isDeleted()
```
    Specified by:
    
    isDeleted in interface Node
  - findAtomsLike
```
public BS findAtomsLike(java.lang.String substring)
```
    Specified by:
    
    findAtomsLike 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
  - getFloatProperty
```
public float getFloatProperty(java.lang.String property)
```
    Specified by:
    
    getFloatProperty in interface Node
    
    Parameters:
    
    property - "property_xxxx"
    
    Returns:
    
    value or Float.NaN

Class SmilesAtom

Field Summary

Fields inherited from class javajs.util.T3

Constructor Summary

Method Summary

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

UNBRACKETED_SET

pattern

primitiveType

isAND

subAtoms

nSubAtoms

index

referance

residueName

residueChar

insCode

isBioAtom

isBioResidue

isBioAtomWild

bioType

isLeadAtom

notBondedIndex

notCrossLinked

aromaticAmbiguous

covalentHydrogenCount

not

selected

hasSymbol

elementDefined

atomType

bioAtomName

isFirst

jmolIndex

elementNumber

atomNumber

residueNumber

explicitHydrogenCount

implicitHydrogenCount

parent

bonds

bondCount

iNested

isAromatic

atomicMass

charge

matchingIndex

stereo

component

matchingComponent

atomSite

degree

nonhydrogenDegree

valence

connectivity

ringMembership

ringSize

ringConnectivity

matchingNode

hasSubpattern

mapIndex

atomClass

symbol

isTopoAtom

missingHydrogenCount

Constructor Detail

SmilesAtom

Method Detail

allowSmilesUnbracketed

getAtomType

getChiralClass

isDefined

setBioAtom

setAtomName

setBonds

addSubAtom