org.jmol.smiles
public class SmilesAtom extends Object
SmilesMolecule
.
Field Summary | |
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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 | |
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SmilesAtom(int number)
Constructs a SmilesAtom .
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Method Summary | |
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void | addBond(SmilesBond bond)
Add a bond to the atom.
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void | createMissingHydrogen(SmilesMolecule molecule)
Creates missing hydrogen atoms in a SmilesMolecule .
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int | getAtomicMass()
Returns the atomic mass of the atom.
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SmilesBond | getBond(int number)
Returns the bond at index number .
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int | getBondsCount()
Returns the number of bonds of this atom.
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int | getCharge()
Returns the charge of the atom.
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String | getChiralClass()
Returns the chiral class of the atom.
(see CHIRALITY_... constants)
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int | getChiralOrder()
Returns the chiral order of the atom.
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int | getHydrogenCount()
Returns the number of hydrogen atoms bonded with this atom.
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int | getMatchingAtom()
Returns the number of a matching atom in a molecule.
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int | getNumber()
Returns the atom number of the atom.
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String | getSymbol()
Returns the symbol of the atom.
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void | setAtomicMass(int mass)
Sets the atomic mass of the atom.
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void | setCharge(int charge)
Sets the charge of the atom.
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void | setChiralClass(String chiralClass)
Sets the chiral class of the atom.
(see CHIRALITY_... constants)
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void | setChiralOrder(int chiralOrder)
Sets the chiral order of the atom.
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void | setHydrogenCount(int count)
Sets the number of hydrogen atoms bonded with this atom.
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void | setMatchingAtom(int atom)
Sets the number of a matching atom in a molecule.
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void | setSymbol(String symbol)
Sets the symbol of the atm.
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SmilesAtom
.
Parameters: number Atom number in the molecule.
Parameters: bond Bond to add.
SmilesMolecule
.
Parameters: molecule Molecule containing the atom.
Returns: Atomic mass.
number
.
Parameters: number Bond number.
Returns: Bond.
Returns: Number of bonds.
Returns: Charge.
CHIRALITY_...
constants)
Returns: Chiral class.
Returns: Chiral order.
Returns: Number of hydrogen atoms.
Returns: matching atom.
Returns: Atom number.
Returns: Atom symbol.
Parameters: mass Atomic mass.
Parameters: charge Charge.
CHIRALITY_...
constants)
Parameters: chiralClass Chiral class.
Parameters: chiralOrder Chiral order.
Parameters: count Number of hydrogen atoms.
Parameters: atom Temporary: number of a matching atom in a molecule.
Parameters: symbol Atom symbol.