ambit2.descriptors

Class IsotopeFactory

java.lang.Object

ambit2.descriptors.IsotopeFactory

public class IsotopeFactory
extends Object

Used to store and return data of a particular isotope. As this class is a singleton class, one gets an instance with:

 IsotopeFactory ifac = IsotopFactory.getInstance(new IChemObject().getBuilder());
 

Data about the isotopes are read from the file org.openscience.cdk.config.isotopes.xml in the cdk-standard module. Part of the data in this file was collected from the website webelements.org.

The use of this class is exemplified as follows. To get information about the major isotope of hydrogen, one can use this code:

   IsotopeFactory factory = IsotopeFactory.getInstance(SilentChemObjectBuilder.getInstance());
   Isotope major = factory.getMajorIsotope("H");
 

Author:

steinbeck

Method Summary

Modifier and Type	Method and Description
org.openscience.cdk.interfaces.IAtom	configure(org.openscience.cdk.interfaces.IAtom atom) Configures an atom.
org.openscience.cdk.interfaces.IAtom	configure(org.openscience.cdk.interfaces.IAtom atom, org.openscience.cdk.interfaces.IIsotope isotope) Configures an atom to have all the data of the given isotope.
void	configureAtoms(org.openscience.cdk.interfaces.IAtomContainer container) Configures atoms in an AtomContainer to carry all the correct data according to their element type.
org.openscience.cdk.interfaces.IElement	getElement(int atomicNumber) Returns an element according to a given atomic number.
org.openscience.cdk.interfaces.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.
static IsotopeFactory	getInstance(org.openscience.cdk.interfaces.IChemObjectBuilder builder) Returns an IsotopeFactory instance.
org.openscience.cdk.interfaces.IIsotope[]	getIsotopes(String symbol) Gets an array of all isotopes known to the IsotopeFactory for the given element symbol.
org.openscience.cdk.interfaces.IIsotope	getMajorIsotope(int atomicNumber) Returns the most abundant (major) isotope with a given atomic number.
org.openscience.cdk.interfaces.IIsotope	getMajorIsotope(String symbol) Returns the most abundant (major) isotope whose symbol equals element.
double	getNaturalMass(org.openscience.cdk.interfaces.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

Method Detail

getInstance

public static IsotopeFactory getInstance(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
                                  throws IOException

Returns an IsotopeFactory instance.

Parameters:

builder - ChemObjectBuilder used to construct the Isotope's

Returns:

The instance value

Throws:

IOException - Description of the Exception

getSize

public int getSize()

Returns the number of isotopes defined by this class.

Returns:

The size value

getIsotopes

public org.openscience.cdk.interfaces.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

getMajorIsotope

public org.openscience.cdk.interfaces.IIsotope getMajorIsotope(int atomicNumber)

Returns the most abundant (major) isotope with a given atomic number.

The isotope's abundancy is for atoms with atomic number 60 and smaller defined as a number that is proportional to the 100 of the most abundant isotope. For atoms with higher atomic numbers, the abundancy is defined as a percentage.

Parameters:

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

Returns:

The isotope corresponding to the given atomic number

See Also:

getMajorIsotope(String symbol)

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 org.openscience.cdk.interfaces.IIsotope getMajorIsotope(String symbol)

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

Parameters:

symbol - Description of the Parameter

Returns:

The Major Isotope value

getElement

public org.openscience.cdk.interfaces.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 org.openscience.cdk.interfaces.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 org.openscience.cdk.interfaces.IAtom configure(org.openscience.cdk.interfaces.IAtom atom)

Configures an atom. Finds the correct element type by looking at the atoms element symbol.

Parameters:

atom - The atom to be configured

Returns:

The configured atom

configure

public org.openscience.cdk.interfaces.IAtom configure(org.openscience.cdk.interfaces.IAtom atom,
                                                      org.openscience.cdk.interfaces.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(org.openscience.cdk.interfaces.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(org.openscience.cdk.interfaces.IElement element)

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

Parameters:

element - Description of the Parameter

Returns:

The natural mass value