org.jmol.smiles

Class SmilesAtom

public class SmilesAtom extends Object

This class represents an atom in a SmilesMolecule.

Field Summary
int	atomicMass
SmilesBond[]	bonds
int	bondsCount
int	charge
String	chiralClass
int	chiralOrder
static String	CHIRALITY_ALLENE Constant used for Allene chirality.
static String	CHIRALITY_OCTAHEDRAL Constant used for Octahedral chirality.
static String	CHIRALITY_SQUARE_PLANAR Constant used for Square Planar chirality.
static String	CHIRALITY_TETRAHEDRAL Constant used for Tetrahedral chirality.
static String	CHIRALITY_TRIGONAL_BIPYRAMIDAL Constant used for Trigonal Bipyramidal chirality.
static String	DEFAULT_CHIRALITY Constant used for default chirality.
int	hydrogenCount
static int	INITIAL_BONDS
int	matchingAtom
int	number
String	symbol

Constructor Summary
	SmilesAtom(int number) Constructs a `SmilesAtom`.

Method Summary
void	addBond(SmilesBond bond) Add a bond to the atom.
void	createMissingHydrogen(SmilesMolecule molecule) Creates missing hydrogen atoms in a `SmilesMolecule`.
int	getAtomicMass() Returns the atomic mass of the atom.
SmilesBond	getBond(int number) Returns the bond at index `number`.
int	getBondsCount() Returns the number of bonds of this atom.
int	getCharge() Returns the charge of the atom.
String	getChiralClass() Returns the chiral class of the atom. (see `CHIRALITY_...` constants)
int	getChiralOrder() Returns the chiral order of the atom.
int	getHydrogenCount() Returns the number of hydrogen atoms bonded with this atom.
int	getMatchingAtom() Returns the number of a matching atom in a molecule.
int	getNumber() Returns the atom number of the atom.
String	getSymbol() Returns the symbol of the atom.
void	setAtomicMass(int mass) Sets the atomic mass of the atom.
void	setCharge(int charge) Sets the charge of the atom.
void	setChiralClass(String chiralClass) Sets the chiral class of the atom. (see `CHIRALITY_...` constants)
void	setChiralOrder(int chiralOrder) Sets the chiral order of the atom.
void	setHydrogenCount(int count) Sets the number of hydrogen atoms bonded with this atom.
void	setMatchingAtom(int atom) Sets the number of a matching atom in a molecule.
void	setSymbol(String symbol) Sets the symbol of the atm.

Field Detail

atomicMass

private int atomicMass

bonds

private SmilesBond[] bonds

bondsCount

private int bondsCount

charge

private int charge

chiralClass

private String chiralClass

chiralOrder

private int chiralOrder

CHIRALITY_ALLENE

public static final String CHIRALITY_ALLENE

Constant used for Allene chirality.

CHIRALITY_OCTAHEDRAL

public static final String CHIRALITY_OCTAHEDRAL

Constant used for Octahedral chirality.

CHIRALITY_SQUARE_PLANAR

public static final String CHIRALITY_SQUARE_PLANAR

Constant used for Square Planar chirality.

CHIRALITY_TETRAHEDRAL

public static final String CHIRALITY_TETRAHEDRAL

Constant used for Tetrahedral chirality.

CHIRALITY_TRIGONAL_BIPYRAMIDAL

public static final String CHIRALITY_TRIGONAL_BIPYRAMIDAL

Constant used for Trigonal Bipyramidal chirality.

DEFAULT_CHIRALITY

public static final String DEFAULT_CHIRALITY

Constant used for default chirality.

hydrogenCount

private int hydrogenCount

INITIAL_BONDS

private static final int INITIAL_BONDS

matchingAtom

private int matchingAtom

number

private int number

symbol

private String symbol

Constructor Detail

SmilesAtom

public SmilesAtom(int number)

Constructs a SmilesAtom.

Parameters: number Atom number in the molecule.

Method Detail

addBond

public void addBond(SmilesBond bond)

Add a bond to the atom.

Parameters: bond Bond to add.

createMissingHydrogen

public void createMissingHydrogen(SmilesMolecule molecule)

Creates missing hydrogen atoms in a SmilesMolecule.

Parameters: molecule Molecule containing the atom.

getAtomicMass

public int getAtomicMass()

Returns the atomic mass of the atom.

Returns: Atomic mass.

getBond

public SmilesBond getBond(int number)

Returns the bond at index number.

Parameters: number Bond number.

Returns: Bond.

getBondsCount

public int getBondsCount()

Returns the number of bonds of this atom.

Returns: Number of bonds.

getCharge

public int getCharge()

Returns the charge of the atom.

Returns: Charge.

getChiralClass

public String getChiralClass()

Returns the chiral class of the atom. (see CHIRALITY_... constants)

Returns: Chiral class.

getChiralOrder

public int getChiralOrder()

Returns the chiral order of the atom.

Returns: Chiral order.

getHydrogenCount

public int getHydrogenCount()

Returns the number of hydrogen atoms bonded with this atom.

Returns: Number of hydrogen atoms.

getMatchingAtom

public int getMatchingAtom()

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.

getNumber

public int getNumber()

Returns the atom number of the atom.

Returns: Atom number.

getSymbol

public String getSymbol()

Returns the symbol of the atom.

Returns: Atom symbol.

setAtomicMass

public void setAtomicMass(int mass)

Sets the atomic mass of the atom.

Parameters: mass Atomic mass.

setCharge

public void setCharge(int charge)

Sets the charge of the atom.

Parameters: charge Charge.

setChiralClass

public void setChiralClass(String chiralClass)

Sets the chiral class of the atom. (see CHIRALITY_... constants)

Parameters: chiralClass Chiral class.

setChiralOrder

public void setChiralOrder(int chiralOrder)

Sets the chiral order of the atom.

Parameters: chiralOrder Chiral order.

setHydrogenCount

public void setHydrogenCount(int count)

Sets the number of hydrogen atoms bonded with this atom.

Parameters: count Number of hydrogen atoms.

setMatchingAtom

public void setMatchingAtom(int atom)

Sets the number of a matching atom in a molecule. This value is temporary, it is used during the pattern matching algorithm.

Parameters: atom Temporary: number of a matching atom in a molecule.

setSymbol

public void setSymbol(String symbol)

Sets the symbol of the atm.

Parameters: symbol Atom symbol.