org.jmol.smiles
Class SmilesAtom

java.lang.Object
  org.jmol.smiles.SmilesAtom

public class SmilesAtom
extends java.lang.Object

Atom in a SmilesMolecule

Field Summary

static java.lang.String	CHIRALITY_ALLENE
static java.lang.String	CHIRALITY_OCTAHEDRAL
static java.lang.String	CHIRALITY_SQUARE_PLANAR
static java.lang.String	CHIRALITY_TETRAHEDRAL
static java.lang.String	CHIRALITY_TRIGONAL_BIPYRAMIDAL
static java.lang.String	DEFAULT_CHIRALITY

Constructor Summary

SmilesAtom(int number)
SmilesAtom constructor

Method Summary

void	addBond(SmilesBond bond)
void	createMissingHydrogen(SmilesMolecule molecule) Creates missing hydrogen
int	getAtomicMass()
SmilesBond	getBond(int number)
int	getBondsCount()
int	getCharge()
java.lang.String	getChiralClass()
int	getChiralOrder()
int	getHydrogenCount()
int	getMatchingAtom()
int	getNumber()
java.lang.String	getSymbol()
void	setAtomicMass(int mass)
void	setCharge(int charge)
void	setChiralClass(java.lang.String chiralClass)
void	setChiralOrder(int chiralOrder)
void	setHydrogenCount(int count)
void	setMatchingAtom(int atom)
void	setSymbol(java.lang.String symbol)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT_CHIRALITY

public static final java.lang.String DEFAULT_CHIRALITY

See Also:

Constant Field Values

CHIRALITY_ALLENE

public static final java.lang.String CHIRALITY_ALLENE

See Also:

Constant Field Values

CHIRALITY_OCTAHEDRAL

public static final java.lang.String CHIRALITY_OCTAHEDRAL

See Also:

Constant Field Values

CHIRALITY_SQUARE_PLANAR

public static final java.lang.String CHIRALITY_SQUARE_PLANAR

See Also:

Constant Field Values

CHIRALITY_TETRAHEDRAL

public static final java.lang.String CHIRALITY_TETRAHEDRAL

See Also:

Constant Field Values

CHIRALITY_TRIGONAL_BIPYRAMIDAL

public static final java.lang.String CHIRALITY_TRIGONAL_BIPYRAMIDAL

See Also:

Constant Field Values

Constructor Detail

SmilesAtom

public SmilesAtom(int number)

SmilesAtom constructor

Parameters:

number - Atom number in the molecule

Method Detail

createMissingHydrogen

public void createMissingHydrogen(SmilesMolecule molecule)

Creates missing hydrogen

Parameters:

molecule - Molecule containing the atom

getNumber

public int getNumber()

getSymbol

public java.lang.String getSymbol()

setSymbol

public void setSymbol(java.lang.String symbol)

getAtomicMass

public int getAtomicMass()

setAtomicMass

public void setAtomicMass(int mass)

getCharge

public int getCharge()

setCharge

public void setCharge(int charge)

getMatchingAtom

public int getMatchingAtom()

setMatchingAtom

public void setMatchingAtom(int atom)

getChiralClass

public java.lang.String getChiralClass()

setChiralClass

public void setChiralClass(java.lang.String chiralClass)

getChiralOrder

public int getChiralOrder()

setChiralOrder

public void setChiralOrder(int chiralOrder)

getHydrogenCount

public int getHydrogenCount()

setHydrogenCount

public void setHydrogenCount(int count)

getBondsCount

public int getBondsCount()

getBond

public SmilesBond getBond(int number)

addBond

public void addBond(SmilesBond bond)