IAtom.java

/* $Revision$ $Author$ $Date$
 *
 * Copyright (C) 2006-2007  Egon Willighagen <egonw@users.sf.net>
 *
 * Contact: cdk-devel@lists.sourceforge.net
 *
 * 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.Point2d;
import javax.vecmath.Point3d;

/**
 * Represents the idea of an chemical atom.
 *
 * @cdk.module  interfaces
 *
 * @author      egonw
 * @cdk.created 2005-08-24
 * @cdk.keyword atom
 * @cdk.githash
 */
public interface IAtom extends IAtomType {
    
	/**
	 * Sets the partial charge of this atom.
	 *
	 * @param  charge  The partial charge
	 * @see    #getCharge
	 */
	public void setCharge(Double charge);

	/**
	 * Returns the partial charge of this atom.
	 *
	 * @return the charge of this atom
	 * @see    #setCharge
	 */
	public Double getCharge();

	/**
	 * Sets the implicit hydrogen count of this atom.
	 *
	 * @param  hydrogenCount  The number of hydrogen atoms bonded to this atom.
	 * @see    #getHydrogenCount
	 */
	public void setHydrogenCount(Integer hydrogenCount);

	/**
	 * Returns the implicit hydrogen count of this atom.
	 *
	 * @return    The hydrogen count of this atom.
	 * @see       #setHydrogenCount
	 */
	public Integer getHydrogenCount();

	/**
	 * Sets a point specifying the location of this
	 * atom in a 2D space.
	 *
	 * @param  point2d  A point in a 2D plane
	 * @see    #getPoint2d
	 */
	public void setPoint2d(Point2d point2d);
	
	/**
	 * Sets a point specifying the location of this
	 * atom in 3D space.
	 *
	 * @param  point3d  A point in a 3-dimensional space
	 * @see    #getPoint3d
	 */
	public void setPoint3d(Point3d point3d);
	
	/**
	 * Sets a point specifying the location of this
	 * atom in a Crystal unit cell.
	 *
	 * @param  point3d  A point in a 3d fractional unit cell space
	 * @see    #getFractionalPoint3d
	 * @see    org.openscience.cdk.Crystal
	 */
	public void setFractionalPoint3d(Point3d point3d);

	/**
	 * Sets the stereo parity for this atom.
	 *
	 * @param  stereoParity  The stereo parity for this atom
	 * @see    org.openscience.cdk.CDKConstants for predefined values.
	 * @see    #getStereoParity
	 */
	public void setStereoParity(Integer stereoParity);
	
	/**
	 * Returns a point specifying the location of this
	 * atom in a 2D space.
	 *
	 * @return    A point in a 2D plane. Null if unset.
	 * @see       #setPoint2d
	 */
	public Point2d getPoint2d();
	
	/**
	 * Returns a point specifying the location of this
	 * atom in a 3D space.
	 *
	 * @return    A point in 3-dimensional space. Null if unset.
	 * @see       #setPoint3d
	 */
	public Point3d getPoint3d();
	
	/**
	 * Returns a point specifying the location of this
	 * atom in a Crystal unit cell.
	 *
	 * @return    A point in 3d fractional unit cell space. Null if unset.
	 * @see       #setFractionalPoint3d
	 * @see       org.openscience.cdk.CDKConstants for predefined values.
	 */
	public Point3d getFractionalPoint3d();
	
	/**
	 * Returns the stereo parity of this atom. It uses the predefined values
	 * found in CDKConstants.
	 *
	 * @return    The stereo parity for this atom
	 * @see       org.openscience.cdk.CDKConstants
	 * @see       #setStereoParity
	 */
	public Integer getStereoParity();
	
}