/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2002-2007 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;
import java.io.Serializable;
import javax.vecmath.Vector3d;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.ICrystal;
/**
* Class representing a molecular crystal.
* The crystal is described with molecules in fractional
* coordinates and three cell axes: a,b and c.
*
* <p>The crystal is designed to store only the asymmetric atoms.
* Though this is not enforced, it is assumed by all methods.
*
* @cdk.module data
* @cdk.githash
*
* @cdk.keyword crystal
*/
public class Crystal extends AtomContainer implements Serializable, ICrystal, Cloneable
{
/**
* Determines if a de-serialized object is compatible with this class.
*
* This value must only be changed if and only if the new version
* of this class is incompatible with the old version. See Sun docs
* for <a href=http://java.sun.com/products/jdk/1.1/docs/guide/serialization/spec/version.doc.html>details</a>.
*/
private static final long serialVersionUID = 5919649450390509278L;
/** The a axis. */
private Vector3d aAxis;
/** The b axis. */
private Vector3d bAxis;
/** The c axis. */
private Vector3d cAxis;
/**
* Number of symmetry related atoms.
*/
private Integer zValue = 1;
/**
* Number of symmetry related atoms.
*/
private String spaceGroup = "P1";
/**
* Constructs a new crystal with zero length cell axis.
*/
public Crystal() {
super();
setZeroAxes();
}
/**
* Constructs a new crystal with zero length cell axis
* and adds the atoms in the AtomContainer as cell content.
*
* @param container the AtomContainer providing the atoms and bonds
*/
public Crystal(IAtomContainer container) {
super(container);
setZeroAxes();
}
/**
* Sets the A unit cell axes in Cartesian coordinates in a
* Euclidean space.
*
* @param newAxis the new A axis
*
* @see #getA
*/
public void setA(Vector3d newAxis) {
aAxis = newAxis;
notifyChanged();
}
/**
* Gets the A unit cell axes in Cartesian coordinates
* as a three element double array.
*
* @return a Vector3D representing the A axis
*
* @see #setA
*/
public Vector3d getA() {
return aAxis;
}
/**
* Sets the B unit cell axes in Cartesian coordinates.
*
* @param newAxis the new B axis
*
* @see #getB
*/
public void setB(Vector3d newAxis) {
bAxis = newAxis;
notifyChanged();
}
/**
* Gets the B unit cell axes in Cartesian coordinates
* as a three element double array.
*
* @return a Vector3D representing the B axis
*
* @see #setB
*/
public Vector3d getB() {
return bAxis;
}
/**
* Sets the C unit cell axes in Cartesian coordinates.
*
* @param newAxis the new C axis
*
* @see #getC
*/
public void setC(Vector3d newAxis) {
cAxis = newAxis;
notifyChanged();
}
/**
* Gets the C unit cell axes in Cartesian coordinates
* as a three element double array.
*
* @return a Vector3D representing the C axis
*
* @see #setC
*/
public Vector3d getC() {
return cAxis;
}
/**
* Gets the space group of this crystal.
*
* @return the space group of this crystal structure
*
* @see #setSpaceGroup
*/
public String getSpaceGroup() {
return spaceGroup;
}
/**
* Sets the space group of this crystal.
*
* @param group the space group of this crystal structure
*
* @see #getSpaceGroup
*/
public void setSpaceGroup(String group) {
spaceGroup = group;
notifyChanged();
}
/**
* Gets the number of asymmetric parts in the unit cell.
*
* @return the number of asymmetric parts in the unit cell
* @see #setZ
*/
public Integer getZ() {
return zValue;
}
/**
* Sets the number of asymmetric parts in the unit cell.
*
* @param value the number of asymmetric parts in the unit cell
* @see #getZ
*/
public void setZ(Integer value) {
this.zValue = value;
notifyChanged();
}
/**
* Makes a clone of this crystal.
*
* @return The cloned crystal.
*/
public Object clone() throws CloneNotSupportedException {
Crystal clone = (Crystal)super.clone();
// clone the axes
clone.setA(new Vector3d(this.aAxis));
clone.setB(new Vector3d(this.bAxis));
clone.setC(new Vector3d(this.cAxis));
return clone;
}
/**
* Returns a String representation of this crystal.
*/
public String toString() {
StringBuffer resultString = new StringBuffer(64);
resultString.append("Crystal(").append(hashCode());
if (getSpaceGroup() != null) {
resultString.append(", SG=").append(getSpaceGroup());
}
if (getZ() > 0) {
resultString.append(", Z=").append(getZ());
}
if (getA() != null) {
resultString.append(", a=(").append(aAxis.x).append(", ").append(aAxis.y).append(", ").append(aAxis.z);
}
if (getB() != null) {
resultString.append("), b=(").append(bAxis.x).append(", ").append(bAxis.y).append(", ").append(bAxis.z);
}
if (getC() != null) {
resultString.append("), c=(").append(cAxis.x).append(", ").append(cAxis.y).append(", ").append(cAxis.z);
}
resultString.append(", ").append(super.toString());
return resultString.toString();
}
/**
* Initializes the unit cell axes to zero length.
*/
private void setZeroAxes() {
aAxis = new Vector3d(0.0, 0.0, 0.0);
bAxis = new Vector3d(0.0, 0.0, 0.0);
cAxis = new Vector3d(0.0, 0.0, 0.0);
}
}