Package org.openscience.cdk.silent

Class AdductFormula

java.lang.Object
org.openscience.cdk.silent.AdductFormula
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

  • Constructor Details

    • AdductFormula

      public AdductFormula()
      Constructs an empty AdductFormula.
      See Also:

    • 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:

  • Method Details

    • addMolecularFormula

      public void addMolecularFormula(IMolecularFormula formula)
      Adds an molecularFormula to this chemObject.
      Specified by:
      addMolecularFormula in interface IMolecularFormulaSet
      Parameters:
      formula - The molecularFormula to be added to this chemObject

    • add

      public void add(IMolecularFormulaSet formulaSet)
      Adds all molecularFormulas in the AdductFormula to this chemObject.
      Specified by:
      add in interface IMolecularFormulaSet
      Parameters:
      formulaSet - The MolecularFormulaSet

    • 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 interface IAdductFormula
      Parameters:
      isotope - The IIsotope this AdductFormula is searched for
      Returns:
      True, if the AdductFormula contains the given isotope object

    • 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 interface IAdductFormula
      Returns:
      the charge of this Adduct
      See Also:

    • 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 interface IAdductFormula
      Parameters:
      isotope - The IIsotope to look for
      Returns:
      The occurrence of this isotope in this adduct
      See Also:

    • getIsotopeCount

      public int getIsotopeCount()
      Checks a set of Nodes for the number of different isotopes in the adduct formula.
      Specified by:
      getIsotopeCount in interface IAdductFormula
      Returns:
      The the number of different isotopes in this adduct formula
      See Also:

    • isotopes

      public Iterable<IIsotope> isotopes()
      Returns an Iterator for looping over all isotopes in this adduct formula.
      Specified by:
      isotopes in interface IAdductFormula
      Returns:
      An Iterator with the isotopes in this adduct formula

    • setCharge

      public void setCharge(Integer charge)
      Deprecated.
      No use this method. The charge is defined in each IMolecularFormula.
      Specified by:
      setCharge in interface IAdductFormula
      Parameters:
      charge - The partial charge
      See Also:

    • molecularFormulas

      public Iterable<IMolecularFormula> molecularFormulas()
      Returns an Iterable for looping over all IMolecularFormula in this adduct formula.
      Specified by:
      molecularFormulas in interface IMolecularFormulaSet
      Returns:
      An Iterable with the IMolecularFormula in this adduct formula
      See Also:

    • iterator

      public Iterator<IMolecularFormula> iterator()
      Returns an Iterator for looping over all IMolecularFormula in this adduct formula.
      Specified by:
      iterator in interface Iterable<IMolecularFormula>
      Returns:
      An Iterator with the IMolecularFormula in this adduct formula

    • size

      public int size()
      Returns the number of MolecularFormulas in this AdductFormula.
      Specified by:
      size in interface IMolecularFormulaSet
      Returns:
      The number of MolecularFormulas in this AdductFormula

    • contains

      public boolean contains(IMolecularFormula formula)
      True, if the AdductFormula contains the given IMolecularFormula object.
      Specified by:
      contains in interface IMolecularFormulaSet
      Parameters:
      formula - The IMolecularFormula this AdductFormula is searched for
      Returns:
      True, if the AdductFormula contains the given IMolecularFormula object

    • getMolecularFormula

      public IMolecularFormula getMolecularFormula(int position)
      Returns the MolecularFormula at position number in the chemObject.
      Specified by:
      getMolecularFormula in interface IMolecularFormulaSet
      Parameters:
      position - The position of the IMolecularFormula to be returned.
      Returns:
      The IMolecularFormula at position number .

    • removeAllMolecularFormulas

      public void removeAllMolecularFormulas()
      Removes all IMolecularFormula from this chemObject.
      Specified by:
      removeAllMolecularFormulas in interface IMolecularFormulaSet

    • removeMolecularFormula

      public void removeMolecularFormula(IMolecularFormula formula)
      Removes an IMolecularFormula from this chemObject.
      Specified by:
      removeMolecularFormula in interface IMolecularFormulaSet
      Parameters:
      formula - The IMolecularFormula to be removed from this chemObject

    • removeMolecularFormula

      public void removeMolecularFormula(int position)
      Removes an MolecularFormula from this chemObject.
      Specified by:
      removeMolecularFormula in interface IMolecularFormulaSet
      Parameters:
      position - The position of the MolecularFormula to be removed from this chemObject

    • clone

      public Object clone() throws CloneNotSupportedException
      Clones this AdductFormula object and its content.
      Specified by:
      clone in interface IAdductFormula
      Specified by:
      clone in interface IMolecularFormulaSet
      Overrides:
      clone in class Object
      Returns:
      The cloned object
      Throws:
      CloneNotSupportedException

    • 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