ichemobjectbuilder.java

化学图形处理软件

/* $Revision: 7996 $ $Author: egonw $ $Date: 2007-02-24 17:48:55 +0100 (Sat, 24 Feb 2007) $
 *
 * Copyright (C) 2006-2007  Egon Willighagen <[e-mail]>
 *
 * Contact: [e-mail]
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 */
package org.openscience.cdk.interfaces;

import javax.vecmath.Point3d;

/**
 * A helper class to instantiate a IChemObject for a specific implementation.
 *
 * @author        egonw
 * @cdk.module    interfaces
 */
public interface IChemObjectBuilder {

    /**
     * Constructs an completely unset IAminoAcid.
     * 
     * @return IAminoAcid implementation defined for this IChemObjectBuilder
     */
	public IAminoAcid newAminoAcid();

    /**
     * Constructs an completely unset IAtom.
     * 
     * @return IAtom implementation defined for this IChemObjectBuilder
     */
	public IAtom newAtom();
	
    /**
     * Constructs an IAtom from a String containing an element symbol.
     *
     * @param   element  The IElement from which the Atom should be constructed
     * @return           IAtom implementation defined for this IChemObjectBuilder
     */
    public IAtom newAtom(IElement element);
    
    /**
     * Constructs an IAtom from a String containing an element symbol.
     *
     * @param   elementSymbol  The String describing the element for the Atom
     * @return                 IAtom implementation defined for this IChemObjectBuilder
     */
    public IAtom newAtom(String elementSymbol);
    
    /**
     * Constructs an IAtom from an Element and a Point2d.
     *
     * @param   elementSymbol   The Element
     * @param   point2d         The Point
     * @return                  IAtom implementation defined for this IChemObjectBuilder
     */
    public IAtom newAtom(String elementSymbol, javax.vecmath.Point2d point2d);

    /**
     * Constructs an IAtom from an Element and a Point3d.
     *
     * @param   elementSymbol   The symbol of the atom
     * @param   point3d         The 3D coordinates of the atom
     * @return                  IAtom implementation defined for this IChemObjectBuilder
     */
    public IAtom newAtom(String elementSymbol, javax.vecmath.Point3d point3d);

	/**
	 * Constructs an empty IAtomContainer.
	 * 
     * @return IAtomContainer implementation defined for this IChemObjectBuilder
	 */
	public IAtomContainer newAtomContainer();
    
	/**
	 * Constructs an empty IAtomContainer that will contain a certain number of
	 * atoms and electronContainers. It will set the starting array lengths to the
	 * defined values, but will not create any IAtom or IElectronContainer's.
	 *
	 * @param  atomCount               Number of atoms to be in this container
	 * @param  bondCount               Number of bonds to be in this container
	 * @param  lonePairCount           Number of lone pairs to be in this container
	 * @param  singleElectronCount     Number of single electrons to be in this
	 *                                 container
	 *                                                               
     * @return                         IAtomContainer implementation defined for
     *                                 this IChemObjectBuilder
	 */
	public IAtomContainer newAtomContainer(int atomCount, int bondCount, int lonePairCount, int singleElectronCount);
    
	/**
	 * Constructs an IAtomContainer with a copy of the atoms and electronContainers
	 * of another IAtomContainer (A shallow copy, i.e., with the same objects as in
	 * the original IAtomContainer).
	 *
	 * @param  container  An AtomContainer to copy the atoms and electronContainers from
     * @return            IAtomContainer implementation defined for this IChemObjectBuilder
	 */
	public IAtomContainer newAtomContainer(IAtomContainer container);

    /**
     * Constructs an IAtomParity.
     *
     * @param centralAtom Atom for which the parity is defined
     * @param first       First Atom of four that define the stereochemistry
     * @param second      Second Atom of four that define the stereochemistry
     * @param third       Third Atom of four that define the stereochemistry
     * @param fourth      Fourth Atom of four that define the stereochemistry
     * @param parity      +1 or -1, defining the parity
     * @return            IAtomParity implementation defined for this IChemObjectBuilder
     */
    public IAtomParity newAtomParity(IAtom centralAtom, 
        IAtom first, IAtom second, IAtom third, IAtom fourth,
        int parity);

    /**
	 * Constructor for the IAtomType object.
     *
     * @param elementSymbol  Symbol of the atom
     * @return               IAtomType implementation defined for this IChemObjectBuilder
	 */
	public IAtomType newAtomType(String elementSymbol);

	/**
	 * Constructor for the IAtomType object.
	 *
	 * @param  identifier     An id for this atom type, like C3 for sp3 carbon
	 * @param  elementSymbol  The element symbol identifying the element to which this atom type applies
     * @return                IAtomType implementation defined for this IChemObjectBuilder
	 */
	public IAtomType newAtomType(String identifier, String elementSymbol);
	
    /**
     * Constructs an IAtomType from a String containing an element symbol.
     *
     * @param   element  The IElement from which the AtomType should be constructed
     * @return           IAtomType implementation defined for this IChemObjectBuilder
     */
    public IAtomType newAtomType(IElement element);
	/**
	 * Contructs a new IBioPolymer to store the IStrands.
	 * 
     * @return  IBioPolymer implementation defined for this IChemObjectBuilder
	 */	
	public IBioPolymer newBioPolymer();
	
	/**
	 * Constructs an IPDBAtom from a IElement.
	 * 
     * @param   element  The Element for the PDBAtom
     * @return           IPDBAtom implementation defined for this IChemObjectBuilder
	 */	
	public IPDBAtom newPDBAtom(IElement element);
	
	/**
	 * Constructs an IPDBAtom from a String containing an element symbol.
	 * 
     * @param   symbol  The String describing the element for the PDBAtom
     * @return          IPDBAtom implementation defined for this IChemObjectBuilder
	 */	
	public IPDBAtom newPDBAtom(String symbol);
	
	 /**
     * Constructs an IPDBAtom from an Element and a Point3d.
     *
     * @param   elementSymbol   The symbol of the atom
     * @param   point3d         The 3D coordinates of the atom
     * @return                  IPDBAtom implementation defined for this IChemObjectBuilder
     */
    public IPDBAtom newPDBAtom(String elementSymbol, Point3d point3d);
    
    /**
	 * Contructs a new IPDBPolymer to store the IStrands.
	 * 
     * @return  IPDBPolymer implementation defined for this IChemObjectBuilder
	 */	
	public IPDBPolymer newPDBPolymer();
	
	/**
     * Constructs an IPDBStructure.
     *
     * @return IPDBStructure implementation defined for this IChemObjectBuilder
     */
    public IPDBStructure newPDBStructure();
    
	/**
     * Constructs an IPDBMonomer.
     *
     * @return IPDBMonomer implementation defined for this IChemObjectBuilder
     */
    public IPDBMonomer newPDBMonomer();

    /**
	 * Constructs an empty IBond.
	 * 
     * @return IBond implementation defined for this IChemObjectBuilder
	 */
	public IBond newBond();
	
	/**
	 * Constructs a IBond with a single bond order..
	 *
	 * @param  atom1  the first IAtom in the bond
	 * @param  atom2  the second IAtom in the bond
     * @return IBond  implementation defined for this IChemObjectBuilder
	 */
	public IBond newBond(IAtom atom1, IAtom atom2);
	
	/**
	 * Constructs a IBond with a given order.
	 *
	 * @param  atom1  the first IAtom in the bond
	 * @param  atom2  the second IAtom in the bond
	 * @param  order  the bond order
     * @return IBond  implementation defined for this IChemObjectBuilder
	 */
	public IBond newBond(IAtom atom1, IAtom atom2, double order);
	
	/**
	 * Constructs a IBond with a given order and stereo orientation from an array
	 * of atoms.
	 *
	 * @param  atom1   the first Atom in the bond
	 * @param  atom2   the second Atom in the bond
	 * @param  order   the bond order
	 * @param  stereo  a descriptor the stereochemical orientation of this bond
     * @return IBond   implementation defined for this IChemObjectBuilder
	 */
	public IBond newBond(IAtom atom1, IAtom atom2, double order, int stereo);

	/**
	 * Constructs an empty IChemFile.
	 * 
     * @return IChemFile implementation defined for this IChemObjectBuilder
	 */
	public IChemFile newChemFile();
	
	/**
	 * Constructs an new IChemModel with a null IMoleculeSet.
	 * 
     * @return IChemModel implementation defined for this IChemObjectBuilder
	 */
	public IChemModel newChemModel();
	
	/**
	 * Constructs an new IChemObject.
	 * 
     * @return IChemObject implementation defined for this IChemObjectBuilder
	 */
	public IChemObject newChemObject();
	
	/**
	 * Constructs an new IChemObject from an existing one.
	 * 
     * @return IChemObject implementation defined for this IChemObjectBuilder
	 */
	public IChemObject newChemObject(IChemObject object);

	/**
	 * Constructs an empty IChemSequence.
	 * 
     * @return IChemSequence implementation defined for this IChemObjectBuilder
	 */
	public IChemSequence newChemSequence();   
	
    /**
     * Constructs a new ICrystal with zero length cell axis.
     * 
     * @return ICrystal implementation defined for this IChemObjectBuilder
     */
    public ICrystal newCrystal();
    
    /**
     * Constructs a new ICrystal with zero length cell axis
     * and adds the atoms in the IAtomContainer as cell content.
     *
     * @param container  the IAtomContainer providing the atoms and bonds
     * @return           ICrystal implementation defined for this IChemObjectBuilder