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:
main
Belongs to CDK module:
interfaces
Keywords:
molecular formula
Created on:
2007-11-20
  • Method Details

    • add

      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

      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:
    • 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:
    • 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:
    • 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

      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:
    • clone

      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:
    • 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:
    • 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:
    • 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:
    • 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

      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: