Package org.openscience.cdk.silent
Class AdductFormula
- java.lang.Object
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- org.openscience.cdk.silent.AdductFormula
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- All Implemented Interfaces:
Cloneable
,Iterable<IMolecularFormula>
,IAdductFormula
,ICDKObject
,IMolecularFormulaSet
public class AdductFormula extends Object implements Iterable<IMolecularFormula>, IAdductFormula, Cloneable
Class defining an adduct object in a MolecularFormula. It maintains a list of list IMolecularFormula.Examples:
[C2H4O2+Na]+
- Author:
- miguelrojasch
- Belongs to CDK module:
- silent
- Keywords:
- molecular formula
- Created on:
- 2007-11-20
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Constructor Summary
Constructors Constructor Description AdductFormula()
Constructs an empty AdductFormula.AdductFormula(IMolecularFormula formula)
Constructs an AdductFormula with a copy AdductFormula of another AdductFormula (A shallow copy, i.e., with the same objects as in the original AdductFormula).
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Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description void
add(IMolecularFormulaSet formulaSet)
Adds all molecularFormulas in the AdductFormula to this chemObject.void
addMolecularFormula(IMolecularFormula formula)
Adds an molecularFormula to this chemObject.Object
clone()
Clones this AdductFormula object and its content.boolean
contains(IIsotope isotope)
True, if the AdductFormula contains the given IIsotope object and not the instance.boolean
contains(IMolecularFormula formula)
True, if the AdductFormula contains the given IMolecularFormula object.IChemObjectBuilder
getBuilder()
Returns aIChemObjectBuilder
for the data classes that extend this class.Integer
getCharge()
Returns the partial charge of this Adduct.int
getIsotopeCount()
Checks a set of Nodes for the number of different isotopes in the adduct formula.int
getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope.IMolecularFormula
getMolecularFormula(int position)
Returns the MolecularFormula at positionnumber
in the chemObject.Iterable<IIsotope>
isotopes()
Returns an Iterator for looping over all isotopes in this adduct formula.Iterator<IMolecularFormula>
iterator()
Returns an Iterator for looping over all IMolecularFormula in this adduct formula.Iterable<IMolecularFormula>
molecularFormulas()
Returns an Iterable for looping over all IMolecularFormula in this adduct formula.void
removeAllMolecularFormulas()
Removes all IMolecularFormula from this chemObject.void
removeMolecularFormula(int position)
Removes an MolecularFormula from this chemObject.void
removeMolecularFormula(IMolecularFormula formula)
Removes an IMolecularFormula from this chemObject.void
setCharge(Integer charge)
Deprecated.int
size()
Returns the number of MolecularFormulas in this AdductFormula.-
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Constructor Detail
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AdductFormula
public AdductFormula()
Constructs an empty AdductFormula.- See Also:
AdductFormula(IMolecularFormula)
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AdductFormula
public AdductFormula(IMolecularFormula formula)
Constructs an AdductFormula with a copy AdductFormula of another AdductFormula (A shallow copy, i.e., with the same objects as in the original AdductFormula).- Parameters:
formula
- An MolecularFormula to copy from- See Also:
AdductFormula()
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Method Detail
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addMolecularFormula
public void addMolecularFormula(IMolecularFormula formula)
Adds an molecularFormula to this chemObject.- Specified by:
addMolecularFormula
in interfaceIMolecularFormulaSet
- Parameters:
formula
- The molecularFormula to be added to this chemObject
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add
public void add(IMolecularFormulaSet formulaSet)
Adds all molecularFormulas in the AdductFormula to this chemObject.- Specified by:
add
in interfaceIMolecularFormulaSet
- Parameters:
formulaSet
- The MolecularFormulaSet
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contains
public boolean contains(IIsotope isotope)
True, if the AdductFormula 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 interfaceIAdductFormula
- Parameters:
isotope
- The IIsotope this AdductFormula is searched for- Returns:
- True, if the AdductFormula contains the given isotope object
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getCharge
public Integer getCharge()
Returns the partial charge of this Adduct. If the charge has not been set the return value is Double.NaN.- Specified by:
getCharge
in interfaceIAdductFormula
- Returns:
- the charge of this Adduct
- See Also:
setCharge(java.lang.Integer)
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getIsotopeCount
public int getIsotopeCount(IIsotope isotope)
Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope. It returns 0 if the does not exist.- Specified by:
getIsotopeCount
in interfaceIAdductFormula
- Parameters:
isotope
- The IIsotope to look for- Returns:
- The occurrence of this isotope in this adduct
- See Also:
getIsotopeCount()
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getIsotopeCount
public int getIsotopeCount()
Checks a set of Nodes for the number of different isotopes in the adduct formula.- Specified by:
getIsotopeCount
in interfaceIAdductFormula
- Returns:
- The the number of different isotopes in this adduct formula
- See Also:
getIsotopeCount(IIsotope)
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isotopes
public Iterable<IIsotope> isotopes()
Returns an Iterator for looping over all isotopes in this adduct formula.- Specified by:
isotopes
in interfaceIAdductFormula
- Returns:
- An Iterator with the isotopes in this adduct formula
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setCharge
public void setCharge(Integer charge)
Deprecated.No use this method. The charge is defined in each IMolecularFormula.- Specified by:
setCharge
in interfaceIAdductFormula
- Parameters:
charge
- The partial charge- See Also:
getCharge()
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molecularFormulas
public Iterable<IMolecularFormula> molecularFormulas()
Returns an Iterable for looping over all IMolecularFormula in this adduct formula.- Specified by:
molecularFormulas
in interfaceIMolecularFormulaSet
- Returns:
- An Iterable with the IMolecularFormula in this adduct formula
- See Also:
IMolecularFormulaSet.addMolecularFormula(IMolecularFormula)
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iterator
public Iterator<IMolecularFormula> iterator()
Returns an Iterator for looping over all IMolecularFormula in this adduct formula.- Specified by:
iterator
in interfaceIterable<IMolecularFormula>
- Returns:
- An Iterator with the IMolecularFormula in this adduct formula
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size
public int size()
Returns the number of MolecularFormulas in this AdductFormula.- Specified by:
size
in interfaceIMolecularFormulaSet
- Returns:
- The number of MolecularFormulas in this AdductFormula
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contains
public boolean contains(IMolecularFormula formula)
True, if the AdductFormula contains the given IMolecularFormula object.- Specified by:
contains
in interfaceIMolecularFormulaSet
- Parameters:
formula
- The IMolecularFormula this AdductFormula is searched for- Returns:
- True, if the AdductFormula contains the given IMolecularFormula object
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getMolecularFormula
public IMolecularFormula getMolecularFormula(int position)
Returns the MolecularFormula at positionnumber
in the chemObject.- Specified by:
getMolecularFormula
in interfaceIMolecularFormulaSet
- Parameters:
position
- The position of the IMolecularFormula to be returned.- Returns:
- The IMolecularFormula at position
number
.
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removeAllMolecularFormulas
public void removeAllMolecularFormulas()
Removes all IMolecularFormula from this chemObject.- Specified by:
removeAllMolecularFormulas
in interfaceIMolecularFormulaSet
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removeMolecularFormula
public void removeMolecularFormula(IMolecularFormula formula)
Removes an IMolecularFormula from this chemObject.- Specified by:
removeMolecularFormula
in interfaceIMolecularFormulaSet
- Parameters:
formula
- The IMolecularFormula to be removed from this chemObject
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removeMolecularFormula
public void removeMolecularFormula(int position)
Removes an MolecularFormula from this chemObject.- Specified by:
removeMolecularFormula
in interfaceIMolecularFormulaSet
- Parameters:
position
- The position of the MolecularFormula to be removed from this chemObject
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clone
public Object clone() throws CloneNotSupportedException
Clones this AdductFormula object and its content.- Specified by:
clone
in interfaceIAdductFormula
- Specified by:
clone
in interfaceIMolecularFormulaSet
- Overrides:
clone
in classObject
- Returns:
- The cloned object
- Throws:
CloneNotSupportedException
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getBuilder
public IChemObjectBuilder 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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