public abstract class Atom extends ExperimentObject
Modifier and Type | Field and Description |
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static Atom |
C
The carbon atom.
|
static Atom |
H
The hydrogen atom.
|
static Atom |
He
The helium atom.
|
static Atom |
I
The Iodine atom.
|
protected HashMap<Integer,Double> |
isotopeMap
Map of the isotope masses relative to the monoisotopic peak (+1 for
carbon 13).
|
protected String |
letter
The single letter code of the atom.
|
static Atom |
Li
The phosphorus atom.
|
protected Double |
monoisotopicMass
The monoisotopic mass.
|
static Atom |
N
The nitrogen atom.
|
static Atom |
Na
The sodium atom.
|
protected String |
name
The name of the atom.
|
static Atom |
O
The oxygen atom.
|
static Atom |
P
The phosphorus atom.
|
protected HashMap<Integer,Double> |
representativeComposition
Map of the isotope representative composition of the stable isotopes.
|
static Atom |
S
The sulfur atom.
|
static Atom |
Se
The selenium atom.
|
Constructor and Description |
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Atom() |
Modifier and Type | Method and Description |
---|---|
static Atom |
getAtom(String shortName)
Returns the atom corresponding to the given short name.
|
Double |
getDifferenceToMonoisotopic(int isotopeNumber)
Returns the mass difference between the given isotope and the
monoisotopic mass.
|
static String[] |
getImplementedAtoms(boolean includeSelect)
Returns an array of implemented atoms indicated by their short name.
|
ArrayList<Integer> |
getImplementedIsotopes()
returns an unsorted list of isotopes for which a mass is available relative to the
monoisotopic peak (+1 for carbon 13).
|
Double |
getIsotopeMass(int isotopeNumber)
Returns the mass corresponding to the given isotope number.
|
String |
getLetter()
Returns the single letter code of the atom.
|
Double |
getMonoisotopicMass()
Returns the monoisotopic mass.
|
String |
getName()
Returns the name of the atom.
|
addUrParam, getParameterKey, getUrParam
public static final Atom H
public static final Atom N
public static final Atom O
public static final Atom C
public static final Atom S
public static final Atom P
public static final Atom He
public static final Atom Li
public static final Atom Na
public static final Atom Se
public static final Atom I
protected Double monoisotopicMass
protected HashMap<Integer,Double> isotopeMap
protected HashMap<Integer,Double> representativeComposition
protected String name
protected String letter
public static String[] getImplementedAtoms(boolean includeSelect)
includeSelect
- if true, the first item is set to '- Select -'public static Atom getAtom(String shortName)
shortName
- the short name of the atompublic Double getMonoisotopicMass()
public String getName()
public String getLetter()
public ArrayList<Integer> getImplementedIsotopes()
public Double getIsotopeMass(int isotopeNumber)
isotopeNumber
- the isotope number of interest relative to the
monoisotopic peak (+1 for carbon 13).public Double getDifferenceToMonoisotopic(int isotopeNumber)
isotopeNumber
- the isotope number relative to the monoisotopic peak
(+1 for carbon 13)Copyright © 2016. All rights reserved.