Package org.openscience.cdk

Class Association

    • Field Detail

      • electronCount

        protected final int electronCount
        Number of electrons in the association.
        See Also:
        Constant Field Values

      • atoms

        protected IAtom[] atoms
        The atoms which take part in the association.

      • atomCount

        protected int atomCount

    • Constructor Detail

      • Association

        public Association​(IAtom atom1,
                   IAtom atom2)
        Constructs an association between two Atom's.
        Parameters:
        atom1 - An atom to be associated with another atom
        atom2 - An atom to be associated with another atom
        See Also:
        Atom

      • Association

        public Association()
        Constructs an empty association.
        See Also:
        Atom

    • Method Detail

      • setAtoms

        public void setAtoms​(IAtom[] atoms)
        Sets the array of atoms making up this Association.
        Parameters:
        atoms - An array of atoms that forms this Association
        See Also:
        getAtoms()

      • getAtomCount

        public int getAtomCount()
        Returns the number of Atoms in this Association.
        Returns:
        The number of Atoms in this Association

      • contains

        public boolean contains​(IAtom atom)
        Returns true if the given atom participates in this Association.
        Parameters:
        atom - The atom to be tested if it participates in this Association
        Returns:
        true if the atom participates in this Association

      • setAtomAt

        public void setAtomAt​(IAtom atom,
                      int position)
        Sets an Atom in this Association.
        Parameters:
        atom - The atom to be set
        position - The position in this Association where the atom is to be inserted
        See Also:
        getAtomAt(int)

      • toString

        public String toString()
        Returns a one line string representation of this Container. This method is conform RFC #9.
        Specified by:
        toString in interface IChemObject
        Overrides:
        toString in class Object
        Returns:
        The string representation of this Container

      • setElectronCount

        public void setElectronCount​(Integer electronCount)
        Sets the number of electrons in this electron container.
        Specified by:
        setElectronCount in interface IElectronContainer
        Parameters:
        electronCount - The number of electrons in this electron container.
        See Also:
        getElectronCount()

      • getListenerCount

        public int getListenerCount()
        Returns the number of ChemObjectListeners registered with this object.
        Specified by:
        getListenerCount in interface IChemObject
        Returns:
        the number of registered listeners.

      • notifyChanged

        public void notifyChanged()
        This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
        Specified by:
        notifyChanged in interface IChemObject

      • notifyChanged

        public void notifyChanged​(IChemObjectChangeEvent evt)
        This should be triggered by an method that changes the content of an object to that the registered listeners can react to it. This is a version of notifyChanged() which allows to propagate a change event while preserving the original origin.
        Specified by:
        notifyChanged in interface IChemObject
        Parameters:
        evt - A ChemObjectChangeEvent pointing to the source of where the change happend

      • 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 IChemObject
        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:
        IChemObject.getProperty(Object), IChemObject.addProperties(java.util.Map)

      • clone

        public Object clone()
             throws CloneNotSupportedException
        Clones this IChemObject. It clones the identifier, flags, properties and pointer vectors. The ChemObjectListeners are not cloned, and neither is the content of the pointer vectors.
        Specified by:
        clone in interface IChemObject
        Overrides:
        clone in class Object
        Returns:
        The cloned object
        Throws:
        CloneNotSupportedException - if the IChemObject cannot be cloned

      • compare

        public boolean compare​(Object object)
        Compares a IChemObject with this IChemObject.
        Parameters:
        object - Object of type AtomType
        Returns:
        true if the atom types are equal

      • setID

        public void setID​(String identifier)
        Sets the identifier (ID) of this object.
        Specified by:
        setID in interface IChemObject
        Parameters:
        identifier - a String representing the ID value
        See Also:
        getID()

      • setFlag

        public void setFlag​(int mask,
                    boolean value)
        Sets the value of some flag. The flag is a mask from a given CDKConstant (e.g. IChemObject.AROMATIC or IChemObject.VISITED). The flags are intrinsic internal properties and should not be used to store custom values, please use IChemObject.setProperty(Object, Object). 
        
 // set this chem object to be aromatic
 chemObject.setFlag(CDKConstants.ISAROMATIC, Boolean.TRUE);
 // ...
 // indicate we have visited this chem object
 chemObject.setFlag(CDKConstants.VISITED, Boolean.TRUE);
        Specified by:
        setFlag in interface IChemObject
        Parameters:
        mask - flag to set the value for
        value - value to assign to flag
        See Also:
        IChemObject.getFlag(int)

      • getFlag

        public boolean getFlag​(int mask)
        Returns the value of a given flag. The flag is a mask from a given CDKConstant (e.g. IChemObject.AROMATIC). 
        
 if(chemObject.getFlag(CDKConstants.ISAROMATIC)){
     // handle aromatic flag on this chem object
 }
        Specified by:
        getFlag in interface IChemObject
        Parameters:
        mask - flag to retrieve the value of
        Returns:
        true if the flag flag_type is set
        See Also:
        IChemObject.setFlag(int, boolean)

      • getFlagValue

        public Integer getFlagValue()
        Access the internal value used to store the flags. The flags are stored on a single numeric value and are set/cleared.
        Specified by:
        getFlagValue in interface IChemObject
        Returns:
        numeric representation of the flags

      • set

        public void set​(int flags)
        Description copied from interface: IChemObject
        Set the provided flags. Any on-bits in the input parameter are set on in the ChemObject.
        Specified by:
        set in interface IChemObject
        Parameters:
        flags - the flags

      • clear

        public void clear​(int flags)
        Description copied from interface: IChemObject
        Clear the provided flags. Any on-bits in the input parameter are set on in the ChemObject.
        Specified by:
        clear in interface IChemObject
        Parameters:
        flags - the flags

      • is

        public boolean is​(int flags)
        Description copied from interface: IChemObject
        Test if a flag(s) are set on this ChemObject. If multiple flags are provided they must all be set to return true. 
        
 atom.set(IS_IN_RING);
 atom.is(IS_IN_RING); // false!
 atom.is(IS_IN_RING+IS_AROMATIC); // false!
 atom.set(IS_AROMATIC);
 atom.is(IS_IN_RING+IS_AROMATIC); // true!
        Specified by:
        is in interface IChemObject
        Parameters:
        flags - the flags

      • flags

        public int flags()
        Description copied from interface: IChemObject
        Access the current value of the flags for this ChemObject.
        Specified by:
        flags in interface IChemObject
        Returns:
        the flag value (32-bit integer)

      • setProperties

        public void setProperties​(Map<Object,​Object> properties)
        Set the properties of this object to the provided map (shallow copy). Any existing properties are removed.
        Specified by:
        setProperties in interface IChemObject
        Parameters:
        properties - map key-value pairs

      • shallowCopy

        public Object shallowCopy()
        Clones this IChemObject, but preserves references to Objects.
        Returns:
        Shallow copy of this IChemObject
        See Also:
        clone()

      • setNotification

        public void setNotification​(boolean bool)
        Description copied from interface: IChemObject
        Set a flag to use or not use notification. By default it should be set to true.
        Specified by:
        setNotification in interface IChemObject
        Parameters:
        bool - if true, then notification messages are sent.
        See Also:
        IChemObject.getNotification()