org.openscience.cdk.interfaces

Interface IMolecularFormula

All Superinterfaces:

Cloneable, ICDKObject

All Known Implementing Classes:

DebugMolecularFormula, MolecularFormula, MolecularFormula

public interface IMolecularFormula
extends ICDKObject

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

Examples:

• [C5H5]-
• C6H6
• ¹²C₅¹³CH₆

Author:

miguelrojasch

Source code:

master

Belongs to CDK module:

interfaces

Keywords:

molecular formula

Created on:

2007-11-20

Method Summary

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.
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 Iterable 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.I should integrate into ChemObject.
void	setProperty(Object description, Object property) Sets a property for a IChemObject.

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

getBuilder

Method Detail

add

IMolecularFormula add(IMolecularFormula formula)

Adds an molecularFormula to this MolecularFormula.

Parameters:

formula - The molecularFormula to be added to this chemObject

Returns:

the new molecular formula

addIsotope

IMolecularFormula addIsotope(IIsotope isotope)

Adds an Isotope to this MolecularFormula one time.

Parameters:

isotope - The isotope to be added to this MolecularFormula

Returns:

the new molecular formula

See Also:

addIsotope(IIsotope, int)

addIsotope

IMolecularFormula addIsotope(IIsotope isotope,
                             int count)

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

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)

getIsotopeCount

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.

Parameters:

isotope - The IIsotope to look for

Returns:

The occurrence of this isotope in this IMolecularFormula

See Also:

getIsotopeCount()

isotopes

Iterable<IIsotope> isotopes()

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

Returns:

An Iterable with the isotopes in this IMolecularFormula

getIsotopeCount

int getIsotopeCount()

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

Returns:

The the number of different isotopes in this IMolecularFormula

See Also:

getIsotopeCount(IIsotope)

contains

boolean contains(IIsotope isotope)

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

Parameters:

isotope - The IIsotope this IMolecularFormula is searched for

Returns:

True, if the IMolecularFormula contains the given isotope object

removeIsotope

void removeIsotope(IIsotope isotope)

Removes the given isotope from the MolecularFormula.

Parameters:

isotope - The IIsotope to be removed

removeAllIsotopes

void removeAllIsotopes()

Removes all isotopes of this molecular formula.

setCharge

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"
 

Parameters:

charge - The partial charge

See Also:

getCharge()

getCharge

Integer getCharge()

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

Returns:

the charge of this IMolecularFormula

See Also:

setCharge(java.lang.Integer)

clone

Object clone()
      throws CloneNotSupportedException

Clones this MolecularFormula object and its content.

Returns:

The cloned object

Throws:

CloneNotSupportedException

setProperty

void setProperty(Object description,
                 Object property)

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

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

void removeProperty(Object description)

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

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

<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

 

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:

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

getProperty

<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

 

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:

getProperty(Object), getProperties()

getProperties

Map<Object,Object> getProperties()

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

Returns:

The object's properties as an Hashtable

See Also:

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

setProperties

void setProperties(Map<Object,Object> properties)

Sets the properties of this object.I should integrate into ChemObject.

Parameters:

properties - a Hashtable specifying the property values

See Also:

getProperties()