Package org.openscience.cdk.config

Class IsotopeFactory

java.lang.Object

org.openscience.cdk.config.IsotopeFactory

Direct Known Subclasses:

Isotopes, XMLIsotopeFactory

public abstract class IsotopeFactory
extends Object

Used to store and return data of a particular isotope. The classes Isotopes extends this class and is to be used to get isotope information.

Author:

steinbeck

Source code:

main

Belongs to CDK module:

core

Created on:

2001-08-29

Field Summary

Fields

Modifier and Type	Field	Description
static IIsotope[]	EMPTY_ISOTOPE_ARRAY
protected static ILoggingTool	logger

Constructor Summary

Constructors

Constructor	Description
IsotopeFactory()

Method Summary

Modifier and Type	Method	Description
protected void	add(IIsotope isotope)	Protected methods only to be used by classes extending this class to add an IIsotope.
IAtom	configure(IAtom atom)	Configures an atom.
IAtom	configure(IAtom atom, IIsotope isotope)	Configures an atom to have all the data of the given isotope.
void	configureAtoms(IAtomContainer container)	Configures atoms in an AtomContainer to carry all the correct data according to their element type.
IElement	getElement(int atomicNumber)	Returns an element according to a given atomic number.
IElement	getElement(String symbol)	Returns an Element with a given element symbol.
String	getElementSymbol(int atomicNumber)	Returns the symbol matching the element with the given atomic number.
double	getExactMass(Integer atomicNumber, Integer massNumber)	Get the exact mass of a specified isotope for an atom.
IIsotope	getIsotope(String symbol, double exactMass, double tolerance)	Get an isotope based on the element symbol and exact mass.
IIsotope	getIsotope(String symbol, int massNumber)	Get isotope based on element symbol and mass number.
IIsotope[]	getIsotopes()	Gets a array of all isotopes known to the IsotopeFactory.
IIsotope[]	getIsotopes(double exactMass, double difference)	Gets an array of all isotopes matching the searched exact mass within a certain difference.
IIsotope[]	getIsotopes(int elem)	Gets an array of all isotopes known to the IsotopeFactory for the given element symbol.
IIsotope[]	getIsotopes(String symbol)	Gets an array of all isotopes known to the IsotopeFactory for the given element symbol.
IIsotope	getMajorIsotope(int elem)	Returns the most abundant (major) isotope with a given atomic number.
IIsotope	getMajorIsotope(String symbol)	Returns the most abundant (major) isotope whose symbol equals element.
double	getMajorIsotopeMass(int elem)	Get the mass of the most abundant (major) isotope, if there is no major isotopes 2*elem is returned.
double	getNaturalMass(int atomicNum)	Gets the natural mass of this element, defined as average of masses of isotopes, weighted by abundance.
double	getNaturalMass(IElement element)	Gets the natural mass of this element, defined as average of masses of isotopes, weighted by abundance.
int	getSize()	Returns the number of isotopes defined by this class.
boolean	isElement(String elementName)	Checks whether the given element exists.

Methods inherited from class java.lang.Object

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

Field Detail

EMPTY_ISOTOPE_ARRAY

public static final IIsotope[] EMPTY_ISOTOPE_ARRAY

logger

protected static final ILoggingTool logger

Constructor Detail

IsotopeFactory

public IsotopeFactory()

Method Detail

getSize

public int getSize()

Returns the number of isotopes defined by this class.

Returns:

The size value

add

protected void add(IIsotope isotope)

Protected methods only to be used by classes extending this class to add an IIsotope.

getIsotopes

public IIsotope[] getIsotopes(int elem)

Gets an array of all isotopes known to the IsotopeFactory for the given element symbol.

Parameters:

elem - atomic number

Returns:

An array of isotopes that matches the given element symbol

getIsotopes

public IIsotope[] getIsotopes(String symbol)

Gets an array of all isotopes known to the IsotopeFactory for the given element symbol.

Parameters:

symbol - An element symbol to search for

Returns:

An array of isotopes that matches the given element symbol

getIsotopes

public IIsotope[] getIsotopes()

Gets a array of all isotopes known to the IsotopeFactory.

Returns:

An array of all isotopes

getIsotopes

public IIsotope[] getIsotopes(double exactMass,
                              double difference)

Gets an array of all isotopes matching the searched exact mass within a certain difference.

Parameters:

exactMass - search mass

difference - mass the isotope is allowed to differ from the search mass

Returns:

An array of all isotopes

getIsotope

public IIsotope getIsotope(String symbol,
                           int massNumber)

Get isotope based on element symbol and mass number.

Parameters:

symbol - the element symbol

massNumber - the mass number

Returns:

the corresponding isotope

getIsotope

public IIsotope getIsotope(String symbol,
                           double exactMass,
                           double tolerance)

Get an isotope based on the element symbol and exact mass.

Parameters:

symbol - the element symbol

exactMass - the mass number

tolerance - allowed difference from provided exact mass

Returns:

the corresponding isotope

getMajorIsotope

public IIsotope getMajorIsotope(int elem)

Returns the most abundant (major) isotope with a given atomic number. Note that some high mass elements do not have a major isotopes (0% abundance) and this method will return null for those.

Parameters:

elem - The atomicNumber for which an isotope is to be returned

Returns:

The isotope corresponding to the given atomic number

See Also:

getMajorIsotope(String symbol)

getMajorIsotopeMass

public double getMajorIsotopeMass(int elem)

Get the mass of the most abundant (major) isotope, if there is no major isotopes 2*elem is returned.

Parameters:

elem - the atomic number

Returns:

the major isotope mass

getExactMass

public double getExactMass(Integer atomicNumber,
                           Integer massNumber)

Get the exact mass of a specified isotope for an atom. If there is no isotope with that mass number then it is returned.

Parameters:

atomicNumber - atomic number

massNumber - the mass number

Returns:

the exact mass

isElement

public boolean isElement(String elementName)

Checks whether the given element exists.

Parameters:

elementName - The element name to test

Returns:

True is the element exists, false otherwise

getMajorIsotope

public IIsotope getMajorIsotope(String symbol)

Returns the most abundant (major) isotope whose symbol equals element.

Parameters:

symbol - the symbol of the element in question

Returns:

The Major Isotope value

getElement

public IElement getElement(String symbol)

Returns an Element with a given element symbol.

Parameters:

symbol - The element symbol for the requested element

Returns:

The configured element

getElement

public IElement getElement(int atomicNumber)

Returns an element according to a given atomic number.

Parameters:

atomicNumber - The elements atomic number

Returns:

The Element

getElementSymbol

public String getElementSymbol(int atomicNumber)

Returns the symbol matching the element with the given atomic number.

Parameters:

atomicNumber - The elements atomic number

Returns:

The symbol of the Element

configure

public IAtom configure(IAtom atom)

Configures an atom. Finds the correct element type by looking at the atoms element symbol. If the element symbol is not recognised, it will throw an IllegalArgumentException.

Parameters:

atom - The atom to be configured

Returns:

The configured atom

configure

public IAtom configure(IAtom atom,
                       IIsotope isotope)

Configures an atom to have all the data of the given isotope.

Parameters:

atom - The atom to be configure

isotope - The isotope to read the data from

Returns:

The configured atom

configureAtoms

public void configureAtoms(IAtomContainer container)

Configures atoms in an AtomContainer to carry all the correct data according to their element type.

Parameters:

container - The AtomContainer to be configured

getNaturalMass

public double getNaturalMass(int atomicNum)

Gets the natural mass of this element, defined as average of masses of isotopes, weighted by abundance.

Parameters:

atomicNum - the element in question

Returns:

The natural mass value

getNaturalMass

public double getNaturalMass(IElement element)

Gets the natural mass of this element, defined as average of masses of isotopes, weighted by abundance.

Parameters:

element - the element in question

Returns:

The natural mass value