IsotopeFactory (cdk 2.5 API)

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:
master

Belongs to CDK module:
core

Created on:

2001-08-29

Field Summary

Fields
Modifier and Type Field and Description

static IIsotope[] EMPTY_ISOTOPE_ARRAY

protected static ILoggingTool logger

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

Constructor Summary

Constructors
Constructor and Description

IsotopeFactory()

Constructors
Constructor and Description
`IsotopeFactory()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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(IElement element)` Gets the natural mass of this element, defined as average of masses of isotopes, weighted by abundance.
`double`	`getNaturalMass(int atomicNum)` 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 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

Class IsotopeFactory

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

EMPTY_ISOTOPE_ARRAY

logger

Constructor Detail

IsotopeFactory

Method Detail

getSize

add

getIsotopes

getIsotopes

getIsotopes

getIsotopes

getIsotope

getIsotope

getMajorIsotope

getMajorIsotopeMass

getExactMass

isElement

getMajorIsotope

getElement

getElement

getElementSymbol

configure

configure

configureAtoms

getNaturalMass

getNaturalMass