ichemobjectbuilder.java

化学图形处理软件

     */
    public ICrystal newCrystal(IAtomContainer container);

    /**
     * Constructs an empty IElectronContainer.
     * 
     * @return IElectronContainer implementation defined for this IChemObjectBuilder
     */
    public IElectronContainer newElectronContainer();

    /**
     * Constructs an empty IElement.
     * 
     * @return IElement implementation defined for this IChemObjectBuilder
     */
    public IElement newElement();

    /**
     * Constructs an empty IElement from an existing IElement.
     * 
     * @param   element  The IElement from which the Element should be constructed
     * @return IElement implementation defined for this IChemObjectBuilder
     */
    public IElement newElement(IElement element);

    /**
     * Constructs an IElement with a given element symbol.
     *
     * @param  symbol The element symbol that this element should have.
     * @return        IElement implementation defined for this IChemObjectBuilder
     */
    public IElement newElement(String symbol);

    /**
     * Constructs an IElement with a given element symbol, 
     * atomic number and atomic mass.
     *
     * @param   symbol       The element symbol of this element.
     * @param   atomicNumber The atomicNumber of this element.
     * @return               IElement implementation defined for this IChemObjectBuilder
     */
    public IElement newElement(String symbol, int atomicNumber);

	/**
	 * Constructor for the IIsotope object.
	 *
	 * @param  elementSymbol  The element symbol, "O" for oxygen, etc.
     * @return                IIsotope implementation defined for this IChemObjectBuilder
	 */
	public IIsotope newIsotope(String elementSymbol);
	
	/**
	 * Constructs an IIsotope object from an existing IIsotope.
	 *
     * @param   element  The IElement from which the Isotope should be constructed
     * @return          IIsotope implementation defined for this IChemObjectBuilder
	 */
	public IIsotope newIsotope(IElement element);
	
	/**
	 * Constructor for the IIsotope object.
	 *
	 * @param  atomicNumber   The atomic number of the isotope
	 * @param  elementSymbol  The element symbol, "O" for oxygen, etc.
	 * @param  massNumber     The atomic mass of the isotope, 16 for oxygen, e.g.
	 * @param  exactMass      The exact mass of the isotope, be a little more explicit here :-)
	 * @param  abundance      The natural abundance of the isotope
     * @return                IIsotope implementation defined for this IChemObjectBuilder
	 */
	public IIsotope newIsotope(int atomicNumber, String elementSymbol, 
			int massNumber, double exactMass, double abundance);

	/**
	 * Constructor for the IIsotope object.
	 *
	 * @param  atomicNumber   The atomic number of the isotope, 8 for oxygen
	 * @param  elementSymbol  The element symbol, "O" for oxygen, etc.
	 * @param  exactMass      The exact mass of the isotope, be a little more explicit here :-)
	 * @param  abundance      The natural abundance of the isotope
     * @return                IIsotope implementation defined for this IChemObjectBuilder
	 */
	public IIsotope newIsotope(int atomicNumber, String elementSymbol, 
			double exactMass, double abundance);

	/**
	 * Constructor for the IIsotope object.
	 *
	 * @param  elementSymbol  The element symbol, "O" for oxygen, etc.
	 * @param  massNumber     The atomic mass of the isotope, 16 for oxygen, e.g.
     * @return                IIsotope implementation defined for this IChemObjectBuilder
	 */
	public IIsotope newIsotope(String elementSymbol, int massNumber);
	
    /**
     * Constructs an unconnected ILonePair.
     * 
     * @return  ILonePair implementation defined for this IChemObjectBuilder
     */
    public ILonePair newLonePair();

    /**
     * Constructs an ILonePair on an IAtom.
     *
     * @param atom  IAtom to which this lone pair is connected
     * @return      ILonePair implementation defined for this IChemObjectBuilder
     */
    public ILonePair newLonePair(IAtom atom);
	
    /**
	 * Creates a directional IMapping between IChemObject's.
	 * 
	 * @param objectOne object which is being mapped 
	 * @param objectTwo object to which is being mapped
     * @return          IMapping implementation defined for this IChemObjectBuilder
	 */
	public IMapping newMapping(IChemObject objectOne, IChemObject objectTwo);
    
	/**
	 * Creates an IMolecule without any IAtoms and IBonds.
	 * 
     * @return IMolecule implementation defined for this IChemObjectBuilder
	 */
	public IMolecule newMolecule();

	/**
	 * Constructor for the IMolecule object. The parameters define the
     * initial capacity of the arrays.
	 *
	 * @param  atomCount               init capacity of IAtom array
	 * @param  electronContainerCount  init capacity of IElectronContainer array
     * @return                         IMolecule implementation defined for this IChemObjectBuilder
	 */
	public IMolecule newMolecule(int atomCount, int bondCount, int lonePairCount, int singleElectronCount);

	/**
	 * Constructs an IMolecule with
	 * a shallow copy of the atoms and bonds of an IAtomContainer.
	 *
	 * @param   container  An IMolecule to copy the atoms and bonds from
     * @return             IMolecule implementation defined for this IChemObjectBuilder
	 */
	public IMolecule newMolecule(IAtomContainer container);
	
	/**
	 * Contructs a new IMonomer.
	 * 
     * @return IMonomer implementation defined for this IChemObjectBuilder
	 */	
	public IMonomer newMonomer ();
	
	/**
	 * Contructs a new IPolymer to store the IMonomers.
	 * 
     * @return IPolymer implementation defined for this IChemObjectBuilder
	 */	
	public IPolymer newPolymer();

    /**
     * Constructs an empty, forward IReaction.
     * 
     * @return IReaction implementation defined for this IChemObjectBuilder
     */
    public IReaction newReaction();
    
	/**
	 * Constructs an empty IRing.
	 * 
     * @return IRing implementation defined for this IChemObjectBuilder
	 */
	public IRing newRing();
	
	/**
	 * Constructs a IRing from an IAtomContainer.
	 * 
	 * @param  container IAtomContainer to create the IRing from
     * @return           IRing implementation defined for this IChemObjectBuilder
	 */
	public IRing newRing(IAtomContainer container);
	
	/**
	 * Constructs a ring that will have a certain number of atoms of the given elements.
	 *
	 * @param  ringSize      The number of atoms and bonds the ring will have
	 * @param  elementSymbol The element of the atoms the ring will have
     * @return               IRing implementation defined for this IChemObjectBuilder
	 */
	public IRing newRing(int ringSize, String elementSymbol);

	/**
	 * Constructs an empty IRing that will have a certain size.
	 *
	 * @param  ringSize The size (number of atoms) the ring will have
     * @return          IRing implementation defined for this IChemObjectBuilder
	 */
	public IRing newRing(int ringSize);
		
	/**
	 * Constructs an empty IRingSet.
	 * 
     * @return IRingSet implementation defined for this IChemObjectBuilder
	 */
	public IRingSet newRingSet();
	
	/**  
	 * Constructs an empty IAtomContainerSet.
	 * 
     * @return IAtomContainerSet implementation defined for this IChemObjectBuilder
	 */
	public IAtomContainerSet newAtomContainerSet();
	
	/**  
	 * Constructs an empty IMoleculeSet.
	 * 
     * @return IMoleculeSet implementation defined for this IChemObjectBuilder
	 */
	public IMoleculeSet newMoleculeSet();
	
	/**
	 * Constructs an empty IReactionSet.
	 * 
     * @return IReactionSet implementation defined for this IChemObjectBuilder
	 */
	public IReactionSet newReactionSet();
	
    /**
     * Constructs an single electron orbital with an associated IAtom.
     * 
     * @return ISingleElectron implementation defined for this IChemObjectBuilder
     */
    public ISingleElectron newSingleElectron();
    
    /**
     * Constructs an single electron orbital on an IAtom.
     *
     * @param atom The atom to which the single electron belongs.
     * @return     ISingleElectron implementation defined for this IChemObjectBuilder
     */
    public ISingleElectron newSingleElectron(IAtom atom);   

	/**
	 * Contructs a new IStrand.
	 * 
     * @return IStrand implementation defined for this IChemObjectBuilder
	 */	
	public IStrand newStrand();

    /**
     * Constructs an empty IPseudoAtom.
     * 
     * @return IPseudoAtom implementation defined for this IChemObjectBuilder
     */
    public IPseudoAtom newPseudoAtom();
    
    /**
     * Constructs an IPseudoAtom from a label.
     *
     * @param   label  The String describing the PseudoAtom
     * @return IPseudoAtom implementation defined for this IChemObjectBuilder
     */
    public IPseudoAtom newPseudoAtom(String label);

    /**
     * Constructs an IPseudoAtom from an existing IAtom object.
     *
     * @param   element  The IElement from which the PseudoAtom should be constructed
     * @return           IPseudoAtom implementation defined for this IChemObjectBuilder
     */
    public IPseudoAtom newPseudoAtom(IElement element);

    /**
     * Constructs an IPseudoAtom from a label and a Point3d.
     *
     * @param   label   The String describing the IPseudoAtom
     * @param   point3d The 3D coordinates of the IPseudoAtom
     * @return          IPseudoAtom implementation defined for this IChemObjectBuilder
     */
    public IPseudoAtom newPseudoAtom(String label, javax.vecmath.Point3d point3d);

    /**
     * Constructs an IPseudoAtom from a label and a Point2d.
     *
     * @param   label   The String describing the IPseudoAtom
     * @param   point2d The 2D coordinates of the IPseudoAtom
     * @return          IPseudoAtom implementation defined for this IChemObjectBuilder
     */
    public IPseudoAtom newPseudoAtom(String label, javax.vecmath.Point2d point2d);
		
}