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java.lang.Objectorg.jmol.smiles.SmilesAtom
public class SmilesAtom
This class represents an atom in a SmilesMolecule
.
Field Summary | |
---|---|
private int |
atomicMass
|
private SmilesBond[] |
bonds
|
private int |
bondsCount
|
private int |
charge
|
private java.lang.String |
chiralClass
|
static java.lang.String |
CHIRALITY_ALLENE
Constant used for Allene chirality. |
static java.lang.String |
CHIRALITY_OCTAHEDRAL
Constant used for Octahedral chirality. |
static java.lang.String |
CHIRALITY_SQUARE_PLANAR
Constant used for Square Planar chirality. |
static java.lang.String |
CHIRALITY_TETRAHEDRAL
Constant used for Tetrahedral chirality. |
static java.lang.String |
CHIRALITY_TRIGONAL_BIPYRAMIDAL
Constant used for Trigonal Bipyramidal chirality. |
private int |
chiralOrder
|
static java.lang.String |
DEFAULT_CHIRALITY
Constant used for default chirality. |
private int |
hydrogenCount
|
private static int |
INITIAL_BONDS
|
private int |
matchingAtom
|
private int |
number
|
private java.lang.String |
symbol
|
Constructor Summary | |
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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. |
java.lang.String |
getChiralClass()
Returns the chiral class of the atom. |
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. |
java.lang.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(java.lang.String chiralClass)
Sets the chiral class of the atom. |
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(java.lang.String symbol)
Sets the symbol of the atm. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
private int number
private java.lang.String symbol
private int atomicMass
private int charge
private int hydrogenCount
private int matchingAtom
private java.lang.String chiralClass
private int chiralOrder
private SmilesBond[] bonds
private int bondsCount
private static final int INITIAL_BONDS
public static final java.lang.String DEFAULT_CHIRALITY
public static final java.lang.String CHIRALITY_ALLENE
public static final java.lang.String CHIRALITY_OCTAHEDRAL
public static final java.lang.String CHIRALITY_SQUARE_PLANAR
public static final java.lang.String CHIRALITY_TETRAHEDRAL
public static final java.lang.String CHIRALITY_TRIGONAL_BIPYRAMIDAL
Constructor Detail |
---|
public SmilesAtom(int number)
SmilesAtom
.
number
- Atom number in the molecule.Method Detail |
---|
public void createMissingHydrogen(SmilesMolecule molecule)
SmilesMolecule
.
molecule
- Molecule containing the atom.public int getNumber()
public java.lang.String getSymbol()
public void setSymbol(java.lang.String symbol)
symbol
- Atom symbol.public int getAtomicMass()
public void setAtomicMass(int mass)
mass
- Atomic mass.public int getCharge()
public void setCharge(int charge)
charge
- Charge.public int getMatchingAtom()
public void setMatchingAtom(int atom)
atom
- Temporary: number of a matching atom in a molecule.public java.lang.String getChiralClass()
CHIRALITY_...
constants)
public void setChiralClass(java.lang.String chiralClass)
CHIRALITY_...
constants)
chiralClass
- Chiral class.public int getChiralOrder()
public void setChiralOrder(int chiralOrder)
chiralOrder
- Chiral order.public int getHydrogenCount()
public void setHydrogenCount(int count)
count
- Number of hydrogen atoms.public int getBondsCount()
public SmilesBond getBond(int number)
number
.
number
- Bond number.
public void addBond(SmilesBond bond)
bond
- Bond to add.
|
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