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
public class MolecularFormula extends Object implements IMolecularFormula
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

  • Constructor Details

    • MolecularFormula

      public MolecularFormula()
      Constructs an empty MolecularFormula.

  • Method Details

    • add

      public IMolecularFormula add(IMolecularFormula formula)
      Adds an molecularFormula to this MolecularFormula.
      Specified by:
      add in interface IMolecularFormula
      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
      Parameters:
      isotope - The isotope to be added to this MolecularFormula
      Returns:
      the new molecular formula
      See Also:

    • 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
      Parameters:
      isotope - The isotope to be added to this MolecularFormula
      count - The number of occurrences to add
      Returns:
      the new molecular formula
      See Also:

    • 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
      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
      Returns:
      the charge of this IMolecularFormula
      See Also:

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

    • getIsotopeCount

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

    • isotopes

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

    • 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
      Parameters:
      charge - The partial charge
      See Also:

    • removeAllIsotopes

      public void removeAllIsotopes()
      Removes all isotopes of this molecular formula.
      Specified by:
      removeAllIsotopes in interface IMolecularFormula

    • removeIsotope

      public void removeIsotope(IIsotope isotope)
      Removes the given isotope from the MolecularFormula.
      Specified by:
      removeIsotope in interface IMolecularFormula
      Parameters:
      isotope - The IIsotope to be removed

    • clone

      public Object clone() throws CloneNotSupportedException
      Clones this MolecularFormula object and its content. I should integrate into ChemObject.
      Specified by:
      clone in interface IMolecularFormula
      Overrides:
      clone in class Object
      Returns:
      The cloned object
      Throws:
      CloneNotSupportedException

    • 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
      Parameters:
      description - An object description of the property (most likely a unique string)
      property - An object with the property itself
      See Also:

    • removeProperty

      public void removeProperty(Object description)
      Removes a property for a IChemObject. I should integrate into ChemObject.
      Specified by:
      removeProperty in interface IMolecularFormula
      Parameters:
      description - The object description of the property (most likely a unique string)
      See Also:

    • 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
      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:

    • getProperty

      public <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
      Specified by:
      getProperty in interface IMolecularFormula
      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:

    • 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
      Returns:
      The object's properties as an Hashtable
      See Also:

    • setProperties

      public void setProperties(Map<Object,Object> properties)
      Sets the properties of this object.
      Specified by:
      setProperties in interface IMolecularFormula
      Parameters:
      properties - a Hashtable specifying the property values
      See Also:

    • isTheSame

      protected boolean isTheSame(IIsotope isotopeOne, IIsotope isotopeTwo)
      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 compare
      isotopeTwo - The second Isotope to compare
      Returns:
      True, if both isotope are the same

    • 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