org.expasy.mzjava.core.mol

Class MassCalculator

java.lang.Object

org.expasy.mzjava.core.mol.MassCalculator

Direct Known Subclasses:

AAMassCalculator

public abstract class MassCalculator
extends Object

Version:

1.0

Author:

Oliver Horlacher

Field Summary

Fields

Modifier and Type	Field and Description
static double	PROTON_MASS

Constructor Summary

Constructors

Constructor and Description
MassCalculator()

Method Summary

Methods

Modifier and Type	Method and Description
static double	calcIsotopeDelta(Composition composition)
static double	calculateAverageMass(Atom atom) Calculates average mass of Atom
static double	calculateAverageMass(Composition composition) Calculates the sum of the average mass of each Atom in this Composition.
abstract double	calculateMz(double molecularWeight, int charge, IonType ionType) Calculate the m/z for the given neutral molecular weight.
abstract double	calculateNeutralMolecularMass(double mz, int charge) Calculate the neutral molecular weight given a m/z, charge and mass of the charge carrying particle.
abstract double	calculateNeutralMolecularMass(Peak peak)
abstract double	getDeltaMass(IonType ionType)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

PROTON_MASS

public static final double PROTON_MASS

Constructor Detail

MassCalculator

public MassCalculator()

Method Detail

getDeltaMass

public abstract double getDeltaMass(IonType ionType)

calculateNeutralMolecularMass

public abstract double calculateNeutralMolecularMass(double mz,
                                   int charge)

Calculate the neutral molecular weight given a m/z, charge and mass of the charge carrying particle.

Parameters:

mz - the m/z

charge - the charge

Returns:

the neutral molecular weight

calculateNeutralMolecularMass

public abstract double calculateNeutralMolecularMass(Peak peak)

calculateMz

public abstract double calculateMz(double molecularWeight,
                 int charge,
                 IonType ionType)

Calculate the m/z for the given neutral molecular weight.

Parameters:

molecularWeight - the neutral molecular weight

charge - the charge

Returns:

the corresponding m/z

calcIsotopeDelta

public static double calcIsotopeDelta(Composition composition)

calculateAverageMass

public static double calculateAverageMass(Atom atom)

Calculates average mass of Atom

Returns:

the average mass of the given atom.

calculateAverageMass

public static double calculateAverageMass(Composition composition)

Calculates the sum of the average mass of each Atom in this Composition.

Returns:

the average mass for this composition