org.openscience.cdk.formula

Class MolecularFormula

java.lang.Object

org.openscience.cdk.formula.MolecularFormula

All Implemented Interfaces:

Cloneable, ICDKObject, IMolecularFormula

Direct Known Subclasses:

DebugMolecularFormula

@TestClass(value="org.openscience.cdk.formula.MolecularFormulaTest")
public class MolecularFormula
extends Object
implements IMolecularFormula

Class defining a molecular formula object. It maintains a list of list IIsotope.

Examples:

• [C5H5]-
• C6H6
• 12C513CH6

Author:

miguelrojasch

Keywords:

molecular formula

Created on:

2007-11-20

Belongs to CDK module:

data

Source code:

master

Constructor Summary

Constructors

Constructor and Description
MolecularFormula() Constructs an empty MolecularFormula.

Method Summary

Methods

Modifier and Type	Method and Description
IMolecularFormula	add(IMolecularFormula formula) Adds an molecularFormula to this MolecularFormula.
IMolecularFormula	addIsotope(IIsotope isotope) Adds an Isotope to this MolecularFormula one time.
IMolecularFormula	addIsotope(IIsotope isotope, int count) Adds an Isotope to this MolecularFormula in a number of occurrences.
Object	clone() Clones this MolecularFormula object and its content.
boolean	contains(IIsotope isotope) True, if the MolecularFormula contains the given IIsotope object and not the instance.
IChemObjectBuilder	getBuilder() Returns a IChemObjectBuilder for the data classes that extend this class.
Integer	getCharge() Returns the partial charge of this IMolecularFormula.
int	getIsotopeCount() Checks a set of Nodes for the number of different isotopes in the IMolecularFormula.
int	getIsotopeCount(IIsotope isotope) Checks a set of Nodes for the occurrence of the isotope in the IMolecularFormula from a particular isotope.
Map<Object,Object>	getProperties() Returns a Map with the IChemObject's properties.I should integrate into ChemObject.
Object	getProperty(Object description) Returns a property for the IChemObject.
Iterable<IIsotope>	isotopes() Returns an Iterator for looping over all isotopes in this IMolecularFormula.
void	removeAllIsotopes() Removes all isotopes of this molecular formula.
void	removeIsotope(IIsotope isotope) Removes the given isotope from the MolecularFormula.
void	removeProperty(Object description) Removes a property for a IChemObject.
void	setCharge(Integer charge) Sets the partial charge of this IMolecularFormula.
void	setProperties(Map<Object,Object> properties) Sets the properties of this object.
void	setProperty(Object description, Object property) Sets a property for a IChemObject.

Methods inherited from class java.lang.Object

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

Constructor Detail

MolecularFormula

public MolecularFormula()

Constructs an empty MolecularFormula.

Method Detail

add

@TestMethod(value="testAdd_IMolecularFormula")
public IMolecularFormula add(IMolecularFormula formula)

Adds an molecularFormula to this MolecularFormula.

Specified by:

add in interface IMolecularFormula

Parameters:

formula - The molecularFormula to be added to this chemObject

Returns:

The IMolecularFormula

addIsotope

@TestMethod(value="addIsotope_IIsotope")
public IMolecularFormula addIsotope(IIsotope isotope)

Adds an Isotope to this MolecularFormula one time.

Specified by:

addIsotope in interface IMolecularFormula

Parameters:

isotope - The isotope to be added to this MolecularFormula

Returns:

the new molecular formula

See Also:

addIsotope(IIsotope, int)

addIsotope

@TestMethod(value="testAddIsotope_IIsotope_int")
public IMolecularFormula addIsotope(IIsotope isotope,
                                           int count)

Adds an Isotope to this MolecularFormula in a number of occurrences.

Specified by:

addIsotope in interface IMolecularFormula

Parameters:

isotope - The isotope to be added to this MolecularFormula

count - The number of occurrences to add

Returns:

the new molecular formula

See Also:

addIsotope(IIsotope)

contains

@TestMethod(value="testContains_IIsotope")
public boolean contains(IIsotope isotope)

True, if the MolecularFormula 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 IMolecularFormula

Parameters:

isotope - The IIsotope this MolecularFormula is searched for

Returns:

True, if the MolecularFormula contains the given isotope object

getCharge

@TestMethod(value="testGetCharge")
public Integer getCharge()

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

Specified by:

getCharge in interface IMolecularFormula

Returns:

the charge of this IMolecularFormula

See Also:

setCharge(java.lang.Integer)

getIsotopeCount

@TestMethod(value="testGetIsotopeCount_IIsotope")
public int getIsotopeCount(IIsotope isotope)

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

Specified by:

getIsotopeCount in interface IMolecularFormula

Parameters:

isotope - The IIsotope to look for

Returns:

The occurrence of this isotope in this IMolecularFormula

See Also:

getIsotopeCount()

getIsotopeCount

@TestMethod(value="testGetIsotopeCount")
public int getIsotopeCount()

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

Specified by:

getIsotopeCount in interface IMolecularFormula

Returns:

The the number of different isotopes in this IMolecularFormula

See Also:

getIsotopeCount(IIsotope)

isotopes

@TestMethod(value="testIsotopes")
public Iterable<IIsotope> isotopes()

Returns an Iterator for looping over all isotopes in this IMolecularFormula.

Specified by:

isotopes in interface IMolecularFormula

Returns:

An Iterator with the isotopes in this IMolecularFormula

setCharge

@TestMethod(value="testSetCharge_Integer")
public void setCharge(Integer charge)

Sets the partial charge of this IMolecularFormula.

Specified by:

setCharge in interface IMolecularFormula

Parameters:

charge - The partial charge

See Also:

getCharge()

removeAllIsotopes

@TestMethod(value="testRemoveAllIsotopes")
public void removeAllIsotopes()

Removes all isotopes of this molecular formula.

Specified by:

removeAllIsotopes in interface IMolecularFormula

removeIsotope

@TestMethod(value="testRemoveIsotope_IIsotope")
public void removeIsotope(IIsotope isotope)

Removes the given isotope from the MolecularFormula.

Specified by:

removeIsotope in interface IMolecularFormula

Parameters:

isotope - The IIsotope to be removed

clone

@TestMethod(value="testClone")
public Object clone()
             throws CloneNotSupportedException

Clones this MolecularFormula object and its content. I should integrate into ChemObject.

Specified by:

clone in interface IMolecularFormula

Overrides:

clone in class Object

Returns:

The cloned object

Throws:

CloneNotSupportedException

setProperty

@TestMethod(value="testSetProperty_Object_Object")
public void setProperty(Object description,
                               Object property)

Sets a property for a IChemObject. I should integrate into ChemObject.

Specified by:

setProperty in interface IMolecularFormula

Parameters:

description - An object description of the property (most likely a unique string)

property - An object with the property itself

See Also:

getProperty(java.lang.Object), removeProperty(java.lang.Object)

removeProperty

@TestMethod(value="testRemoveProperty_Object")
public void removeProperty(Object description)

Removes a property for a IChemObject. I should integrate into ChemObject.

Specified by:

removeProperty in interface IMolecularFormula

Parameters:

description - The object description of the property (most likely a unique string)

See Also:

setProperty(java.lang.Object, java.lang.Object), getProperty(java.lang.Object)

getProperty

@TestMethod(value="testGetProperty_Object")
public Object getProperty(Object description)

Returns a property for the IChemObject. I should integrate into ChemObject.

Specified by:

getProperty in interface IMolecularFormula

Parameters:

description - An object description of the property (most likely a unique string)

Returns:

The object containing the property. Returns null if propert is not set.

See Also:

setProperty(java.lang.Object, java.lang.Object), removeProperty(java.lang.Object)

getProperties

@TestMethod(value="testGetProperties")
public Map<Object,Object> getProperties()

Returns a Map with the IChemObject's properties.I should integrate into ChemObject.

Specified by:

getProperties in interface IMolecularFormula

Returns:

The object's properties as an Hashtable

See Also:

setProperties(java.util.Map<java.lang.Object, java.lang.Object>)

setProperties

@TestMethod(value="testSetProperties_Hashtable")
public void setProperties(Map<Object,Object> properties)

Sets the properties of this object.

Specified by:

setProperties in interface IMolecularFormula

Parameters:

properties - a Hashtable specifying the property values

See Also:

getProperties()

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