org.openscience.cdk.silent

Class MolecularFormula

java.lang.Object

org.openscience.cdk.silent.MolecularFormula

All Implemented Interfaces:

Cloneable, ICDKObject, IMolecularFormula

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

Belongs to CDK module:

silent

Keywords:

molecular formula

Created on:

2007-11-20

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() Access the 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.
<T> T	getProperty(Object description) Returns a property for the IChemObject - the object is automatically cast to the required type.
<T> T	getProperty(Object description, Class<T> c) Access a property of the given description and cast the specified class.
Iterable<IIsotope>	isotopes() Returns an Iterator for looping over all isotopes in this IMolecularFormula.
protected boolean	isTheSame(IIsotope isotopeOne, IIsotope isotopeTwo) Compare to IIsotope.
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 charge of this IMolecularFormula, since there is no atom associated with the charge the number of a given isotope is not modified.
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, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MolecularFormula

public MolecularFormula()

Constructs an empty MolecularFormula.

Method Detail

add

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

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

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

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

public Integer getCharge()

Access the charge of this IMolecularFormula. If the charge has not been set the return value is null.

Specified by:

getCharge in interface IMolecularFormula

Returns:

the charge of this IMolecularFormula

See Also:

IMolecularFormula.setCharge(java.lang.Integer)

getIsotopeCount

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

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

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

public void setCharge(Integer charge)

Sets the charge of this IMolecularFormula, since there is no atom associated with the charge the number of a given isotope is not modified.

 // Correct usage
 IMolecularFormula phenolate = MolecularFormulaManipulator.getMolecularFormula("C6H5O", builder)
 mf.setCharge(-1);
 // MF=C6H5O-

 // Wrong! the H6 is not automatically adjust
 IMolecularFormula phenolate = MolecularFormulaManipulator.getMolecularFormula("C6H6O", builder)
 mf.setCharge(-1);
 // MF=C6H6O- (wrong)
 

If you wish to adjust the protonation of a formula try the convenience method of the MolecularFormulaManipulator:

 IMolecularFormula mf = MolecularFormulaManipulator.getMolecularFormula("[C6H5O]-", bldr);
 MolecularFormulaManipulator.adjustProtonation(mf, +1);
 MolecularFormulaManipulator.getString(mf); // "C6H6O"
 

Specified by:

setCharge in interface IMolecularFormula

Parameters:

charge - The partial charge

See Also:

IMolecularFormula.getCharge()

removeAllIsotopes

public void removeAllIsotopes()

Removes all isotopes of this molecular formula.

Specified by:

removeAllIsotopes in interface IMolecularFormula

removeIsotope

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

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

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

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

public <T> T getProperty(Object description)

Returns a property for the IChemObject - the object is automatically cast to the required type. This does however mean if the wrong type is provided then a runtime ClassCastException will be thrown.

IAtom atom = new Atom("C");
     atom.setProperty("number", 1); // set an integer property

     // access the property and automatically cast to an int
     Integer number = atom.getProperty("number");

     // if the method is in a chain or needs to be nested the type
     // can be provided
     methodAcceptingInt(atom.getProperty("number", Integer.class));

     // the type cannot be checked and so...
     String number = atom.getProperty("number"); // ClassCastException

     // if the type is provided a more meaningful error is thrown
     atom.getProperty("number", String.class); // IllegalArgumentException

 

Specified by:

getProperty in interface IMolecularFormula

Type Parameters:

T - generic return type

Parameters:

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

Returns:

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

See Also:

IMolecularFormula.setProperty(java.lang.Object, java.lang.Object), IMolecularFormula.getProperty(Object, Class), IMolecularFormula.removeProperty(java.lang.Object)

getProperty

public <T> T getProperty(Object description,
                Class<T> c)

Access a property of the given description and cast the specified class.

IAtom atom = new Atom("C");
     atom.setProperty("number", 1); // set an integer property

     // access the property and automatically cast to an int
     Integer number = atom.getProperty("number");

     // if the method is in a chain or needs to be nested the type
     // can be provided
     methodAcceptingInt(atom.getProperty("number", Integer.class));

     // the type cannot be checked and so...
     String number = atom.getProperty("number"); // ClassCastException

     // if the type is provided a more meaningful error is thrown
     atom.getProperty("number", String.class); // IllegalArgumentException

 

Specified by:

getProperty in interface IMolecularFormula

Type Parameters:

T - generic type (of provided class)

Parameters:

description - description of a property (normally a string)

c - type of the value to be returned

Returns:

the value stored for the specified description.

See Also:

IMolecularFormula.getProperty(Object), IMolecularFormula.getProperties()

getProperties

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

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()

isTheSame

protected boolean isTheSame(IIsotope isotopeOne,
                IIsotope isotopeTwo)

Compare to IIsotope. The method doesn't compare instance but if they have the same symbol, natural abundance and exact mass.

Parameters:

isotopeOne - The first Isotope to compare

isotopeTwo - The second Isotope to compare

Returns:

True, if both isotope are the same

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