Package org.openscience.cdk.formula
Class MolecularFormula
java.lang.Object
org.openscience.cdk.formula.MolecularFormula
- All Implemented Interfaces:
Cloneable
,ICDKObject
,IMolecularFormula
- Direct Known Subclasses:
DebugMolecularFormula
Class defining a molecular formula object. It maintains
a list of list
IIsotope
.
Examples:
[C5H5]-
C6H6
12C513CH6
- Author:
- miguelrojasch
- Source code:
- main
- Belongs to CDK module:
- data
- Keywords:
- molecular formula
- Created on:
- 2007-11-20
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionadd
(IMolecularFormula formula) Adds an molecularFormula to this MolecularFormula.addIsotope
(IIsotope isotope) Adds an Isotope to this MolecularFormula one time.addIsotope
(IIsotope isotope, int count) Adds an Isotope to this MolecularFormula in a number of occurrences.clone()
Clones this MolecularFormula object and its content.boolean
True, if the MolecularFormula contains the given IIsotope object and not the instance.Returns aIChemObjectBuilder
for the data classes that extend this class.Access the charge of this IMolecularFormula.int
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.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.isotopes()
Returns an Iterator for looping over all isotopes in this IMolecularFormula.protected boolean
Compare to IIsotope.void
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
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.
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Constructor Details
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MolecularFormula
public MolecularFormula()Constructs an empty MolecularFormula.
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Method Details
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add
Adds an molecularFormula to this MolecularFormula.- Specified by:
add
in interfaceIMolecularFormula
- Parameters:
formula
- The molecularFormula to be added to this chemObject- Returns:
- The IMolecularFormula
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addIsotope
Adds an Isotope to this MolecularFormula one time.- Specified by:
addIsotope
in interfaceIMolecularFormula
- Parameters:
isotope
- The isotope to be added to this MolecularFormula- Returns:
- the new molecular formula
- See Also:
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addIsotope
Adds an Isotope to this MolecularFormula in a number of occurrences.- Specified by:
addIsotope
in interfaceIMolecularFormula
- Parameters:
isotope
- The isotope to be added to this MolecularFormulacount
- The number of occurrences to add- Returns:
- the new molecular formula
- See Also:
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contains
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 interfaceIMolecularFormula
- Parameters:
isotope
- The IIsotope this MolecularFormula is searched for- Returns:
- True, if the MolecularFormula contains the given isotope object
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getCharge
Access the charge of this IMolecularFormula. If the charge has not been set the return value is null.- Specified by:
getCharge
in interfaceIMolecularFormula
- Returns:
- the charge of this IMolecularFormula
- See Also:
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getIsotopeCount
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 interfaceIMolecularFormula
- Parameters:
isotope
- The IIsotope to look for- Returns:
- The occurrence of this isotope in this IMolecularFormula
- See Also:
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getIsotopeCount
public int getIsotopeCount()Checks a set of Nodes for the number of different isotopes in the IMolecularFormula.- Specified by:
getIsotopeCount
in interfaceIMolecularFormula
- Returns:
- The the number of different isotopes in this IMolecularFormula
- See Also:
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isotopes
Returns an Iterator for looping over all isotopes in this IMolecularFormula.- Specified by:
isotopes
in interfaceIMolecularFormula
- Returns:
- An Iterator with the isotopes in this IMolecularFormula
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setCharge
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 theMolecularFormulaManipulator
:IMolecularFormula mf = MolecularFormulaManipulator.getMolecularFormula("[C6H5O]-", bldr); MolecularFormulaManipulator.adjustProtonation(mf, +1); MolecularFormulaManipulator.getString(mf); // "C6H6O"
- Specified by:
setCharge
in interfaceIMolecularFormula
- Parameters:
charge
- The partial charge- See Also:
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removeAllIsotopes
public void removeAllIsotopes()Removes all isotopes of this molecular formula.- Specified by:
removeAllIsotopes
in interfaceIMolecularFormula
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removeIsotope
Removes the given isotope from the MolecularFormula.- Specified by:
removeIsotope
in interfaceIMolecularFormula
- Parameters:
isotope
- The IIsotope to be removed
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clone
Clones this MolecularFormula object and its content. I should integrate into ChemObject.- Specified by:
clone
in interfaceIMolecularFormula
- Overrides:
clone
in classObject
- Returns:
- The cloned object
- Throws:
CloneNotSupportedException
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setProperty
Sets a property for a IChemObject. I should integrate into ChemObject.- Specified by:
setProperty
in interfaceIMolecularFormula
- Parameters:
description
- An object description of the property (most likely a unique string)property
- An object with the property itself- See Also:
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removeProperty
Removes a property for a IChemObject. I should integrate into ChemObject.- Specified by:
removeProperty
in interfaceIMolecularFormula
- Parameters:
description
- The object description of the property (most likely a unique string)- See Also:
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getProperty
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 interfaceIMolecularFormula
- 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:
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getProperty
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 interfaceIMolecularFormula
- 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:
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getProperties
Returns a Map with the IChemObject's properties.I should integrate into ChemObject.- Specified by:
getProperties
in interfaceIMolecularFormula
- Returns:
- The object's properties as an Hashtable
- See Also:
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setProperties
Sets the properties of this object.- Specified by:
setProperties
in interfaceIMolecularFormula
- Parameters:
properties
- a Hashtable specifying the property values- See Also:
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isTheSame
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 compareisotopeTwo
- The second Isotope to compare- Returns:
- True, if both isotope are the same
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getBuilder
Description copied from interface:ICDKObject
Returns aIChemObjectBuilder
for the data classes that extend this class.- Specified by:
getBuilder
in interfaceICDKObject
- Returns:
- The
IChemObjectBuilder
matching thisICDKObject
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