Uses of Class
com.compomics.util.experiment.biology.atoms.Atom

Packages that use Atom

Package	Description
com.compomics.util.experiment.biology.atoms	The atom classes.
com.compomics.util.experiment.biology.atoms.impl	Atoms implementations.
com.compomics.util.gui.atoms	Atoms GUI dialogs.

Uses of Atom in com.compomics.util.experiment.biology.atoms

Fields in com.compomics.util.experiment.biology.atoms declared as Atom

Modifier and Type	Field	Description
static final Atom	Atom.C	The carbon atom.
static final Atom	Atom.Ca	The Calcium atom.
static final Atom	Atom.Cl	The Chlorine atom.
static final Atom	Atom.Co	The Cobalt atom.
static final Atom	Atom.Cu	The Copper atom.
static final Atom	Atom.F	The Fluorine atom.
static final Atom	Atom.Fe	The Iron atom.
static final Atom	Atom.H	The hydrogen atom.
static final Atom	Atom.He	The helium atom.
static final Atom	Atom.I	The Iodine atom.
static final Atom	Atom.K	The Potassium atom.
static final Atom	Atom.Li	The phosphorus atom.
static final Atom	Atom.Mg	The Magnesium atom.
static final Atom	Atom.Mn	The Manganese atom.
static final Atom	Atom.N	The nitrogen atom.
static final Atom	Atom.Na	The sodium atom.
static final Atom	Atom.Ni	The Nickel atom.
static final Atom	Atom.O	The oxygen atom.
static final Atom	Atom.P	The phosphorus atom.
static final Atom	Atom.S	The sulfur atom.
static final Atom	Atom.Se	The selenium atom.
static final Atom	Atom.Zn	The Zinc atom.

Methods in com.compomics.util.experiment.biology.atoms that return Atom

Modifier and Type	Method	Description
static Atom	Atom.getAtom(String shortName)	Returns the atom corresponding to the given short name.

Methods in com.compomics.util.experiment.biology.atoms with parameters of type Atom

Modifier and Type	Method	Description
int	AtomChain.getOccurrence(Atom atom, Integer isotope)	Returns the occurrence of a given atom in the chain.
void	AtomChain.remove(Atom atom, Integer isotope)	Removes all the occurrences of the given atom.
void	AtomChain.setOccurrence(Atom atom, Integer isotope, Integer occurrence)	Sets the occurrence of a given atom.

Constructors in com.compomics.util.experiment.biology.atoms with parameters of type Atom

Modifier	Constructor	Description
	AtomImpl(Atom atom, Integer isotope)	Constructor.

Uses of Atom in com.compomics.util.experiment.biology.atoms.impl

Subclasses of Atom in com.compomics.util.experiment.biology.atoms.impl

Modifier and Type	Class	Description
class	Calcium	The calcium atom.
class	Carbon	Carbon.
class	Chlorine	The Chlorine atom.
class	Cobalt	The Cobalt atom.
class	Copper	The copper atom.
class	Fluorine	The fluorine atom.
class	Helium	The helium atom.
class	Hydrogen	The hydrogen atom.
class	Iodine	Iodine.
class	Iron	The iron atom.
class	Lithium	The Lithium atom.
class	Magnesium	The magnesium atom.
class	Manganese	The Manganese atom.
class	Nickel	The Nickel atom.
class	Nitrogen	The nitrogen atom.
class	Oxygen	The oxygen atom.
class	Phosphorus	The phosphorus atom.
class	Potassium	The potassium atom.
class	Selenium	Selenium.
class	Sodium	The sodium atom.
class	Sulfur	The sulfur atom.
class	Zinc	The zinc atom.

Uses of Atom in com.compomics.util.gui.atoms

Methods in com.compomics.util.gui.atoms that return Atom

Modifier and Type	Method	Description
Atom	AtomPanel.getAtom()	Returns the currently selected atom.

Constructors in com.compomics.util.gui.atoms with parameters of type Atom

Modifier	Constructor	Description
	AtomPanel(AtomChainDialog atomChainDialog, Atom atom, int isotope, int occurrence, int panelIndex, boolean addOnly)	Creates a new AtomPanel.