org.openscience.cdk.silent

Class AdductFormula

java.lang.Object

org.openscience.cdk.silent.AdductFormula

All Implemented Interfaces:

Cloneable, Iterable<IMolecularFormula>, IAdductFormula, ICDKObject, IMolecularFormulaSet

public class AdductFormula
extends Object
implements Iterable<IMolecularFormula>, IAdductFormula, Cloneable

Class defining an adduct object in a MolecularFormula. It maintains a list of list IMolecularFormula.

Examples:

• [C2H4O2+Na]+

Author:

miguelrojasch

Belongs to CDK module:

silent

Keywords:

molecular formula

Created on:

2007-11-20

Constructor Summary

Constructors

Constructor and Description
AdductFormula() Constructs an empty AdductFormula.
AdductFormula(IMolecularFormula formula) Constructs an AdductFormula with a copy AdductFormula of another AdductFormula (A shallow copy, i.e., with the same objects as in the original AdductFormula).

Method Summary

Methods

Modifier and Type	Method and Description
void	add(IMolecularFormulaSet formulaSet) Adds all molecularFormulas in the AdductFormula to this chemObject.
void	addMolecularFormula(IMolecularFormula formula) Adds an molecularFormula to this chemObject.
Object	clone() Clones this AdductFormula object and its content.
boolean	contains(IIsotope isotope) True, if the AdductFormula contains the given IIsotope object and not the instance.
boolean	contains(IMolecularFormula formula) True, if the AdductFormula contains the given IMolecularFormula object.
IChemObjectBuilder	getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
Integer	getCharge() Returns the partial charge of this Adduct.
int	getIsotopeCount() Checks a set of Nodes for the number of different isotopes in the adduct formula.
int	getIsotopeCount(IIsotope isotope) Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope.
IMolecularFormula	getMolecularFormula(int position) Returns the MolecularFormula at position number in the chemObject.
Iterable<IIsotope>	isotopes() Returns an Iterator for looping over all isotopes in this adduct formula.
Iterator<IMolecularFormula>	iterator() Returns an Iterator for looping over all IMolecularFormula in this adduct formula.
Iterable<IMolecularFormula>	molecularFormulas() Returns an Iterable for looping over all IMolecularFormula in this adduct formula.
void	removeAllMolecularFormulas() Removes all IMolecularFormula from this chemObject.
void	removeMolecularFormula(IMolecularFormula formula) Removes an IMolecularFormula from this chemObject.
void	removeMolecularFormula(int position) Removes an MolecularFormula from this chemObject.
void	setCharge(Integer charge) Deprecated.
int	size() Returns the number of MolecularFormulas in this AdductFormula.

Methods inherited from class java.lang.Object

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

Constructor Detail

AdductFormula

public AdductFormula()

Constructs an empty AdductFormula.

See Also:

AdductFormula(IMolecularFormula)

AdductFormula

public AdductFormula(IMolecularFormula formula)

Constructs an AdductFormula with a copy AdductFormula of another AdductFormula (A shallow copy, i.e., with the same objects as in the original AdductFormula).

Parameters:

formula - An MolecularFormula to copy from

See Also:

AdductFormula()

Method Detail

addMolecularFormula

public void addMolecularFormula(IMolecularFormula formula)

Adds an molecularFormula to this chemObject.

Specified by:

addMolecularFormula in interface IMolecularFormulaSet

Parameters:

formula - The molecularFormula to be added to this chemObject

add

public void add(IMolecularFormulaSet formulaSet)

Adds all molecularFormulas in the AdductFormula to this chemObject.

Specified by:

add in interface IMolecularFormulaSet

Parameters:

formulaSet - The MolecularFormulaSet

contains

public boolean contains(IIsotope isotope)

True, if the AdductFormula contains the given IIsotope object and not the instance. The method looks for other isotopes which has the same symbol, natural abundance and exact mass.

Specified by:

contains in interface IAdductFormula

Parameters:

isotope - The IIsotope this AdductFormula is searched for

Returns:

True, if the AdductFormula contains the given isotope object

getCharge

public Integer getCharge()

Returns the partial charge of this Adduct. If the charge has not been set the return value is Double.NaN.

Specified by:

getCharge in interface IAdductFormula

Returns:

the charge of this Adduct

See Also:

setCharge(java.lang.Integer)

getIsotopeCount

public int getIsotopeCount(IIsotope isotope)

Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope. It returns 0 if the does not exist.

Specified by:

getIsotopeCount in interface IAdductFormula

Parameters:

isotope - The IIsotope to look for

Returns:

The occurrence of this isotope in this adduct

See Also:

getIsotopeCount()

getIsotopeCount

public int getIsotopeCount()

Checks a set of Nodes for the number of different isotopes in the adduct formula.

Specified by:

getIsotopeCount in interface IAdductFormula

Returns:

The the number of different isotopes in this adduct formula

See Also:

getIsotopeCount(IIsotope)

isotopes

public Iterable<IIsotope> isotopes()

Returns an Iterator for looping over all isotopes in this adduct formula.

Specified by:

isotopes in interface IAdductFormula

Returns:

An Iterator with the isotopes in this adduct formula

setCharge

public void setCharge(Integer charge)

Deprecated.

No use this method. The charge is defined in each IMolecularFormula.

Specified by:

setCharge in interface IAdductFormula

Parameters:

charge - The partial charge

See Also:

getCharge()

molecularFormulas

public Iterable<IMolecularFormula> molecularFormulas()

Returns an Iterable for looping over all IMolecularFormula in this adduct formula.

Specified by:

molecularFormulas in interface IMolecularFormulaSet

Returns:

An Iterable with the IMolecularFormula in this adduct formula

See Also:

IMolecularFormulaSet.addMolecularFormula(IMolecularFormula)

iterator

public Iterator<IMolecularFormula> iterator()

Returns an Iterator for looping over all IMolecularFormula in this adduct formula.

Specified by:

iterator in interface Iterable<IMolecularFormula>

Returns:

An Iterator with the IMolecularFormula in this adduct formula

size

public int size()

Returns the number of MolecularFormulas in this AdductFormula.

Specified by:

size in interface IMolecularFormulaSet

Returns:

The number of MolecularFormulas in this AdductFormula

contains

public boolean contains(IMolecularFormula formula)

True, if the AdductFormula contains the given IMolecularFormula object.

Specified by:

contains in interface IMolecularFormulaSet

Parameters:

formula - The IMolecularFormula this AdductFormula is searched for

Returns:

True, if the AdductFormula contains the given IMolecularFormula object

getMolecularFormula

public IMolecularFormula getMolecularFormula(int position)

Returns the MolecularFormula at position number in the chemObject.

Specified by:

getMolecularFormula in interface IMolecularFormulaSet

Parameters:

position - The position of the IMolecularFormula to be returned.

Returns:

The IMolecularFormula at position number .

removeAllMolecularFormulas

public void removeAllMolecularFormulas()

Removes all IMolecularFormula from this chemObject.

Specified by:

removeAllMolecularFormulas in interface IMolecularFormulaSet

removeMolecularFormula

public void removeMolecularFormula(IMolecularFormula formula)

Removes an IMolecularFormula from this chemObject.

Specified by:

removeMolecularFormula in interface IMolecularFormulaSet

Parameters:

formula - The IMolecularFormula to be removed from this chemObject

removeMolecularFormula

public void removeMolecularFormula(int position)

Removes an MolecularFormula from this chemObject.

Specified by:

removeMolecularFormula in interface IMolecularFormulaSet

Parameters:

position - The position of the MolecularFormula to be removed from this chemObject

clone

public Object clone()
             throws CloneNotSupportedException

Clones this AdductFormula object and its content.

Specified by:

clone in interface IAdductFormula

Specified by:

clone in interface IMolecularFormulaSet

Overrides:

clone in class Object

Returns:

The cloned object

Throws:

CloneNotSupportedException

getBuilder

public IChemObjectBuilder getBuilder()

Description copied from interface: ICDKObject

Returns a IChemObjectBuilder for the data classes that extend this class.

Specified by:

getBuilder in interface ICDKObject

Returns:

The IChemObjectBuilder matching this ICDKObject