Package org.openscience.cdk.interfaces

Interface IMolecularFormula

    • Method Detail

      • add

        IMolecularFormula add​(IMolecularFormula formula)
        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(IIsotope, int)

      • 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:
        addIsotope(IIsotope)

      • 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:
        getIsotopeCount()

      • 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:
        getIsotopeCount(IIsotope)

      • 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()

      • 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:
        setCharge(java.lang.Integer)

      • 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:
        setProperty(java.lang.Object, java.lang.Object), getProperty(Object, Class), removeProperty(java.lang.Object)

      • 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:
        getProperty(Object), getProperties()

      • 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:
        getProperties()