Uses of Class
org.expasy.mzjava.core.mol.Atom

Packages that use Atom

Package	Description
org.expasy.mzjava.core.mol
org.expasy.mzjava.glycomics.ms.spectrum
org.expasy.mzjava.proteomics.mol.modification
org.expasy.mzjava.proteomics.mol.modification.unimod
org.expasy.mzjava.proteomics.ms.spectrum

Uses of Atom in org.expasy.mzjava.core.mol

Fields in org.expasy.mzjava.core.mol declared as Atom

Modifier and Type	Field and Description
static Atom	PeriodicTable.C
static Atom	PeriodicTable.C13
static Atom	PeriodicTable.Ca
static Atom	PeriodicTable.Cu
static Atom	PeriodicTable.Fe
static Atom	PeriodicTable.H
static Atom	PeriodicTable.I
static Atom	PeriodicTable.K
static Atom	PeriodicTable.Mg
static Atom	PeriodicTable.Mn
static Atom	PeriodicTable.N
static Atom	PeriodicTable.Na
static Atom	PeriodicTable.O
static Atom	PeriodicTable.P
static Atom	PeriodicTable.S
static Atom	PeriodicTable.Zn

Fields in org.expasy.mzjava.core.mol with type parameters of type Atom

Modifier and Type	Field and Description
protected gnu.trove.map.TObjectIntMap<Atom>	Composition.atomCounterMap

Methods in org.expasy.mzjava.core.mol that return Atom

Modifier and Type	Method and Description
Atom	PeriodicTable.getAtom(AtomicSymbol atomicSymbol) Return the default isotope for the atomicSymbol
Atom	PeriodicTable.getAtom(AtomicSymbol atomicSymbol, int massNumber) Return the atom for the atomicSymbol with the number of neutrons given by massNumber
Atom	PeriodicTable.getAtom(String symbol) Parse the symbol and return the corresponding Atom.

Methods in org.expasy.mzjava.core.mol that return types with arguments of type Atom

Modifier and Type	Method and Description
Set<Atom>	Composition.getAtoms() Returns a set containing all the Atoms in this composition.
List<Atom>	PeriodicTable.getAtoms(AtomicSymbol atomicSymbol) Return all the atoms for the given symbol sorted by mass For example AtomicSymbol.C will return {C12, C13, C14}

Methods in org.expasy.mzjava.core.mol with parameters of type Atom

Modifier and Type	Method and Description
Composition.Builder	Composition.Builder.add(Atom atom, int count) Add the atom count times.
static double	MassCalculator.calculateAverageMass(Atom atom) Calculates average mass of Atom
int	Atom.compareTo(Atom o)
int	Composition.getCount(Atom atom) Counts the number of times atom occurs in this Composition

Method parameters in org.expasy.mzjava.core.mol with type arguments of type Atom

Modifier and Type	Method and Description
static String	Composition.Builder.makeFormula(gnu.trove.map.TObjectIntMap<Atom> atomCounterMap, int charge) Make the atomic formula given an atomCounterMap and charge
int	AtomicCompositionParser.parse(String content, gnu.trove.map.TObjectIntMap<Atom> composition) Parses the given string content and transmit data to builder.

Constructor parameters in org.expasy.mzjava.core.mol with type arguments of type Atom

Constructor and Description
Composition(String formula, gnu.trove.map.TObjectIntMap<Atom> atomCountMap, int charge)
Composition(gnu.trove.map.TObjectIntMap<Atom> atomCounterMap, int charge) Construct a new composition that contains the charge and the atoms in the atomCounterMap.

Uses of Atom in org.expasy.mzjava.glycomics.ms.spectrum

Methods in org.expasy.mzjava.glycomics.ms.spectrum with parameters of type Atom

Modifier and Type	Method and Description
GlycanFragAnnotation.FragBuilder	GlycanFragAnnotation.FragBuilder.addIsotope(Atom isotope) Add the isotope

Uses of Atom in org.expasy.mzjava.proteomics.mol.modification

Constructor parameters in org.expasy.mzjava.proteomics.mol.modification with type arguments of type Atom

Constructor and Description
NeutralLoss(gnu.trove.map.TObjectIntMap<Atom> atomCountMap, int charge, Set<String> sites)

Uses of Atom in org.expasy.mzjava.proteomics.mol.modification.unimod

Method parameters in org.expasy.mzjava.proteomics.mol.modification.unimod with type arguments of type Atom

Modifier and Type	Method and Description
UnimodMod.Builder	UnimodMod.Builder.setComposition(gnu.trove.map.TObjectIntMap<Atom> atomCountMap) Set the atom counter map that contains the composition

Constructor parameters in org.expasy.mzjava.proteomics.mol.modification.unimod with type arguments of type Atom

Constructor and Description
UnimodMod(int recordId, boolean approved, String psiMsName, String interimName, String fullName, gnu.trove.map.TObjectIntMap<Atom> atomCounterMap, List<String> sites, List<NeutralLoss> neutralLosses, List<NeutralLoss> precursorNeutralLosses)

Uses of Atom in org.expasy.mzjava.proteomics.ms.spectrum

Methods in org.expasy.mzjava.proteomics.ms.spectrum with parameters of type Atom

Modifier and Type	Method and Description
PepFragAnnotation.Builder	PepFragAnnotation.Builder.addIsotope(Atom isotope) Add the isotope