Package org.openscience.cdk.debug

Class DebugMolecularFormula

java.lang.Object

org.openscience.cdk.formula.MolecularFormula

org.openscience.cdk.debug.DebugMolecularFormula

All Implemented Interfaces:

Cloneable, ICDKObject, IMolecularFormula

public class DebugMolecularFormula
extends MolecularFormula
implements IMolecularFormula

Debugging implementation of IMolecularFormula.

Constructor Summary

Constructors

Constructor	Description
DebugMolecularFormula()

Method Summary

Modifier and Type	Method	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.
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.
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 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 org.openscience.cdk.formula.MolecularFormula

clone, getProperty, isTheSame

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.openscience.cdk.interfaces.IMolecularFormula

clone, getProperty

Constructor Details

DebugMolecularFormula

public DebugMolecularFormula()

Method Details

add

public IMolecularFormula add(IMolecularFormula formula)

Adds an molecularFormula to this MolecularFormula.

Specified by:

add in interface IMolecularFormula

Overrides:

add in class MolecularFormula

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

Overrides:

addIsotope in class MolecularFormula

Parameters:

isotope - The isotope to be added to this MolecularFormula

Returns:

the new molecular formula

See Also:

• MolecularFormula.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

Overrides:

addIsotope in class MolecularFormula

Parameters:

isotope - The isotope to be added to this MolecularFormula

count - The number of occurrences to add

Returns:

the new molecular formula

See Also:

• MolecularFormula.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

Overrides:

contains in class MolecularFormula

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

Overrides:

getCharge in class MolecularFormula

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

Overrides:

getIsotopeCount in class MolecularFormula

Parameters:

isotope - The IIsotope to look for

Returns:

The occurrence of this isotope in this IMolecularFormula

See Also:

• MolecularFormula.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

Overrides:

getIsotopeCount in class MolecularFormula

Returns:

The the number of different isotopes in this IMolecularFormula

See Also:

• MolecularFormula.getIsotopeCount(IIsotope)

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

Overrides:

getProperties in class MolecularFormula

Returns:

The object's properties as an Hashtable

See Also:

• MolecularFormula.setProperties(java.util.Map<java.lang.Object, 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

Overrides:

getProperty in class MolecularFormula

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)

isotopes

public Iterable<IIsotope> isotopes()

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

Specified by:

isotopes in interface IMolecularFormula

Overrides:

isotopes in class MolecularFormula

Returns:

An Iterator with the isotopes in this IMolecularFormula

removeAllIsotopes

public void removeAllIsotopes()

Removes all isotopes of this molecular formula.

Specified by:

removeAllIsotopes in interface IMolecularFormula

Overrides:

removeAllIsotopes in class MolecularFormula

removeIsotope

public void removeIsotope(IIsotope isotope)

Removes the given isotope from the MolecularFormula.

Specified by:

removeIsotope in interface IMolecularFormula

Overrides:

removeIsotope in class MolecularFormula

Parameters:

isotope - The IIsotope to be removed

removeProperty

public void removeProperty(Object description)

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

Specified by:

removeProperty in interface IMolecularFormula

Overrides:

removeProperty in class MolecularFormula

Parameters:

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

See Also:

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

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

Overrides:

setCharge in class MolecularFormula

Parameters:

charge - The partial charge

See Also:

• IMolecularFormula.getCharge()

setProperties

public void setProperties(Map<Object,Object> properties)

Sets the properties of this object.

Specified by:

setProperties in interface IMolecularFormula

Overrides:

setProperties in class MolecularFormula

Parameters:

properties - a Hashtable specifying the property values

See Also:

• MolecularFormula.getProperties()

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

Overrides:

setProperty in class MolecularFormula

Parameters:

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

property - An object with the property itself

See Also:

• MolecularFormula.getProperty(java.lang.Object)
• MolecularFormula.removeProperty(java.lang.Object)

getBuilder

public IChemObjectBuilder getBuilder()

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

Specified by:

getBuilder in interface ICDKObject

Overrides:

getBuilder in class MolecularFormula

Returns:

The IChemObjectBuilder matching this ICDKObject