peakml.chemistry
Class PeriodicTable

java.lang.Object
  peakml.chemistry.PeriodicTable

public abstract class PeriodicTable
extends java.lang.Object

This class stores the periodic table of elements with precise masses. At present not all the elements are available, check the enumated ints for a complete list of all the available options. The weights and other information is taken from the national institute of standardization (nist).

Next to the elements this class provides some convenience methods like a PPM calculator.

Nested Class Summary

static class	PeriodicTable.Derivative http://mass-spec.stanford.edu/assets/SUMS_common_ESI_ions.pdf http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator/
static class	PeriodicTable.Element Central class describing all the properties of an element.
static class	PeriodicTable.Isotope Central class describing all the properties of an isotope.
static class	PeriodicTable.NaturalIsotope

Field Summary

static int	ACETONITRILE The index of acetonitrile in the elements array.
static int	ADDUCT The derivative can only be an adduct
static int	ADDUCT_DEDUCT The derivative can be both an adduct as well as a deduct
static PeriodicTable.Derivative[]	adducts_positive Static, at startup initialized array of all the positive adducts kept in this class.
static int	ALUMINUM The index of the aluminum element in the elements array.
static int	ARSENIC The index of the arsenic element in the elements array.
static int	BROMIDE The index of the bromide element in the elements array.
static int	BROMINE The index of the bromine element in the elements array.
static int	CALCIUM The index of the calcium element in the elements array.
static int	CARBON The index of the carbon element in the elements array.
static int	CESIUM The index of the cesium element in the elements array.
static int	CHLORINE The index of the chlorine element in the elements array.
static int	CHROMIUM The index of the chromium element in the elements array.
static int	COBALT The index of the cobalt element in the elements array.
static int	COPPER The index of the copper element in the elements array.
static double	dalton The precise value of one dalton.
static int	DEDUCT The derivative can only be a deduct
static int	DEUTERIUM The index of the deuterium element in the elements array.
static double	electronmass The precise mass of an electron
static PeriodicTable.Element[]	elements Static, at startup initialized array of all the elements kept in this class.
static int	FLUORINE The index of the fluor element in the elements array.
static int	HYDROGEN The index of the hydrogen element in the elements array.
static int	IODINE The index of the iodine element in the elements array.
static int	IRON The index of the iron element in the elements array.
static int	LITHIUM The index of the lithium element in the elements array.
static int	MAGNESIUM The index of the magnesium element in the elements array.
static int	MANGANESE The index of the magnese element in the elements array.
static int	METHANOL The index of methanol in the elements array.
static int	MOLYBDENUM The index of the molybdenum element in the elements array.
static int	NATRIUM The index of the natrium element in the elements array.
static PeriodicTable.NaturalIsotope[]	natural_isotopes
static int	NICKEL The index of the nickel element in the elements array.
static int	NITROGEN The index of the nitrogen element in the elements array.
static int	NR_ELEMENTS The number of elements in the elements array.
static int	OXYGEN The index of the oxygen element in the elements array.
static int	PHOSPHORUS The index of the phosphorus element in the elements array.
static int	POTASSIUM The index of the potassium element in the elements array.
static double	proton The precise mass of a proton
static int	RUBIDUM The index of the rubidum element in the elements array.
static int	SELENIUM The index of the selenuum element in the elements array.
static int	SILICON The index of the silicon element in the elements array.
static int	SULFUR The index of the sulfur element in the elements array.
static int	TRITIUM The index of the tritium element in the elements array.
static int	TUNGSTEN The index of the tungsten element in the elements array.
static int	ZINC The index of the zinc element in the elements array.
static int	ZIRCONIUM The index of the zirconium element in the elements array.

Constructor Summary

PeriodicTable()

Method Summary

static PeriodicTable.Element	getElement(java.lang.String identifier) Returns the element with the given identifier (e.g.
static double	getIsotopeMassDifference(int element, int isotope) Returns the difference of the most common isotope of the given element to the given isotope.
static boolean	inRange(double realmass, double observedmass, double ppm)
static double	PPM(double mass, double nr) This method calculates the parts per million for the given mass.
static double	PPMNr(double mass, double deviation) Calculates the ppm-value for the given deviation to the given mass.

Methods inherited from class java.lang.Object

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

Field Detail

CARBON

public static final int CARBON

The index of the carbon element in the elements array.

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Constant Field Values

HYDROGEN

public static final int HYDROGEN

The index of the hydrogen element in the elements array.

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Constant Field Values

DEUTERIUM

public static final int DEUTERIUM

The index of the deuterium element in the elements array.

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Constant Field Values

TRITIUM

public static final int TRITIUM

The index of the tritium element in the elements array.

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Constant Field Values

FLUORINE

public static final int FLUORINE

The index of the fluor element in the elements array.

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Constant Field Values

NITROGEN

public static final int NITROGEN

The index of the nitrogen element in the elements array.

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Constant Field Values

OXYGEN

public static final int OXYGEN

The index of the oxygen element in the elements array.

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Constant Field Values

PHOSPHORUS

public static final int PHOSPHORUS

The index of the phosphorus element in the elements array.

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Constant Field Values

CHLORINE

public static final int CHLORINE

The index of the chlorine element in the elements array.

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Constant Field Values

SULFUR

public static final int SULFUR

The index of the sulfur element in the elements array.

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Constant Field Values

NATRIUM

public static final int NATRIUM

The index of the natrium element in the elements array.

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Constant Field Values

POTASSIUM

public static final int POTASSIUM

The index of the potassium element in the elements array.

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Constant Field Values

COPPER

public static final int COPPER

The index of the copper element in the elements array.

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Constant Field Values

CALCIUM

public static final int CALCIUM

The index of the calcium element in the elements array.

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Constant Field Values

SELENIUM

public static final int SELENIUM

The index of the selenuum element in the elements array.

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Constant Field Values

LITHIUM

public static final int LITHIUM

The index of the lithium element in the elements array.

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Constant Field Values

BROMIDE

public static final int BROMIDE

The index of the bromide element in the elements array.

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Constant Field Values

MAGNESIUM

public static final int MAGNESIUM

The index of the magnesium element in the elements array.

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Constant Field Values

IODINE

public static final int IODINE

The index of the iodine element in the elements array.

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Constant Field Values

IRON

public static final int IRON

The index of the iron element in the elements array.

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Constant Field Values

MANGANESE

public static final int MANGANESE

The index of the magnese element in the elements array.

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Constant Field Values

ZINC

public static final int ZINC

The index of the zinc element in the elements array.

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Constant Field Values

COBALT

public static final int COBALT

The index of the cobalt element in the elements array.

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Constant Field Values

NICKEL

public static final int NICKEL

The index of the nickel element in the elements array.

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Constant Field Values

TUNGSTEN

public static final int TUNGSTEN

The index of the tungsten element in the elements array.

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Constant Field Values

BROMINE

public static final int BROMINE

The index of the bromine element in the elements array.

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Constant Field Values

SILICON

public static final int SILICON

The index of the silicon element in the elements array.

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Constant Field Values

CESIUM

public static final int CESIUM

The index of the cesium element in the elements array.

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Constant Field Values

ARSENIC

public static final int ARSENIC

The index of the arsenic element in the elements array.

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Constant Field Values

CHROMIUM

public static final int CHROMIUM

The index of the chromium element in the elements array.

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Constant Field Values

ALUMINUM

public static final int ALUMINUM

The index of the aluminum element in the elements array.

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Constant Field Values

MOLYBDENUM

public static final int MOLYBDENUM

The index of the molybdenum element in the elements array.

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Constant Field Values

RUBIDUM

public static final int RUBIDUM

The index of the rubidum element in the elements array.

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Constant Field Values

ZIRCONIUM

public static final int ZIRCONIUM

The index of the zirconium element in the elements array.

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Constant Field Values

METHANOL

public static final int METHANOL

The index of methanol in the elements array.

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Constant Field Values

ACETONITRILE

public static final int ACETONITRILE

The index of acetonitrile in the elements array.

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Constant Field Values

NR_ELEMENTS

public static final int NR_ELEMENTS

The number of elements in the elements array.

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Constant Field Values

elements

public static final PeriodicTable.Element[] elements

Static, at startup initialized array of all the elements kept in this class. The index of the elements can be located with the static integers. For each element general properties like its valency is recorded. Next to this all the isotopes are recorded, which can be found in mass ascending order.

natural_isotopes

public static final PeriodicTable.NaturalIsotope[] natural_isotopes

ADDUCT

public static final int ADDUCT

The derivative can only be an adduct

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Constant Field Values

DEDUCT

public static final int DEDUCT

The derivative can only be a deduct

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Constant Field Values

ADDUCT_DEDUCT

public static final int ADDUCT_DEDUCT

The derivative can be both an adduct as well as a deduct

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Constant Field Values

adducts_positive

public static final PeriodicTable.Derivative[] adducts_positive

Static, at startup initialized array of all the positive adducts kept in this class. The index of the adducts can be located with the static integers. For each adduct properties like the mass difference are recorded. http://maltese.dbs.aber.ac.uk:8888/hrmet/search/disprules.php

dalton

public static final double dalton

The precise value of one dalton.

electronmass

public static final double electronmass

The precise mass of an electron

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Constant Field Values

proton

public static final double proton

The precise mass of a proton

Constructor Detail

PeriodicTable

public PeriodicTable()

Method Detail

getElement

public static PeriodicTable.Element getElement(java.lang.String identifier)

Returns the element with the given identifier (e.g. carbon is identified with C). When the element is not stored in the class null is returned.

Returns:

The element with the given identifier.

getIsotopeMassDifference

public static double getIsotopeMassDifference(int element,
                                              int isotope)

Returns the difference of the most common isotope of the given element to the given isotope. When the element does not exist or the element does not have the indicated isotope -1 is returned.

Parameters:

element - The index of the element.

isotope - The index of the isotope.

Returns:

The mass difference between the most common isotope and the given isotope.

PPM

public static double PPM(double mass,
                         double nr)

This method calculates the parts per million for the given mass. Parts per million ("ppm") denotes one particle of a given substance for every 999,999 other particles. This is roughly equivalent to one drop of ink in a 150 liter (40 gallon) drum of water, or one second per 280 hours. One part in 106 — a precision of 0.0001%.

The higher the given mass the bigger the returned value.

Parameters:

mass - The mass to be used as reference

nr - The number of PPM (e.g. 1 PPM, 3 PPM, etc.)

Returns:

The parts per million value.

PPMNr

public static double PPMNr(double mass,
                           double deviation)

Calculates the ppm-value for the given deviation to the given mass. See PPM(double, double) for more information.

Parameters:

mass - The mass to be used as reference

deviation - The deviation to the given mass

inRange

public static boolean inRange(double realmass,
                              double observedmass,
                              double ppm)