Package org.openscience.cdk

Class Crystal

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.AtomContainer

org.openscience.cdk.Crystal

All Implemented Interfaces:

Serializable, Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener, ICrystal

Direct Known Subclasses:

DebugCrystal

public class Crystal
extends AtomContainer
implements Serializable, ICrystal, Cloneable

Class representing a molecular crystal. The crystal is described with molecules in fractional coordinates and three cell axes: a,b and c.

The crystal is designed to store only the asymmetric atoms. Though this is not enforced, it is assumed by all methods.

See Also:

Serialized Form

Source code:

main

Belongs to CDK module:

data

Keywords:

crystal

Field Summary

Fields inherited from class org.openscience.cdk.AtomContainer

atomCount, atoms, bondCount, bonds, growArraySize, lonePairCount, lonePairs, singleElectronCount, singleElectrons, stereoElements

Constructor Summary

Constructors

Constructor	Description
Crystal()	Constructs a new crystal with zero length cell axis.
Crystal(IAtomContainer container)	Constructs a new crystal with zero length cell axis and adds the atoms in the AtomContainer as cell content.

Method Summary

Modifier and Type	Method	Description
ICrystal	clone()	Makes a clone of this crystal.
javax.vecmath.Vector3d	getA()	Gets the A unit cell axes in Cartesian coordinates as a three element double array.
javax.vecmath.Vector3d	getB()	Gets the B unit cell axes in Cartesian coordinates as a three element double array.
javax.vecmath.Vector3d	getC()	Gets the C unit cell axes in Cartesian coordinates as a three element double array.
String	getSpaceGroup()	Gets the space group of this crystal.
Integer	getZ()	Gets the number of asymmetric parts in the unit cell.
void	setA(javax.vecmath.Vector3d newAxis)	Sets the A unit cell axes in Cartesian coordinates in a Euclidean space.
void	setB(javax.vecmath.Vector3d newAxis)	Sets the B unit cell axes in Cartesian coordinates.
void	setC(javax.vecmath.Vector3d newAxis)	Sets the C unit cell axes in Cartesian coordinates.
void	setSpaceGroup(String group)	Sets the space group of this crystal.
void	setZ(Integer value)	Sets the number of asymmetric parts in the unit cell.
String	toString()	Returns a String representation of this crystal.

Methods inherited from class org.openscience.cdk.AtomContainer

add, addAtom, addBond, addBond, addBond, addElectronContainer, addLonePair, addLonePair, addSingleElectron, addSingleElectron, addStereoElement, atoms, bonds, contains, contains, contains, contains, contains, electronContainers, getAtom, getAtomCount, getAtomNumber, getBond, getBond, getBondCount, getBondNumber, getBondNumber, getBondOrderSum, getConnectedAtomsCount, getConnectedAtomsList, getConnectedBondsCount, getConnectedBondsCount, getConnectedBondsList, getConnectedElectronContainersList, getConnectedLonePairsCount, getConnectedLonePairsList, getConnectedSingleElectronsCount, getConnectedSingleElectronsList, getElectronContainer, getElectronContainerCount, getFirstAtom, getLastAtom, getLonePair, getLonePairCount, getLonePairNumber, getMaximumBondOrder, getMinimumBondOrder, getSingleElectron, getSingleElectronCount, getSingleElectronNumber, getTitle, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, singleElectrons, stateChanged, stereoElements

Methods inherited from class org.openscience.cdk.ChemObject

addListener, addProperties, compare, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.openscience.cdk.interfaces.IAtomContainer

addBond, addBond, addBond, addElectronContainer, addLonePair, addLonePair, addSingleElectron, addSingleElectron, addStereoElement, atoms, bonds, contains, contains, contains, contains, contains, electronContainers, getAtom, getAtomCount, getAtomNumber, getBond, getBond, getBondCount, getBondNumber, getBondNumber, getBondOrderSum, getConnectedAtomsCount, getConnectedAtomsList, getConnectedBondsCount, getConnectedBondsCount, getConnectedBondsList, getConnectedElectronContainersList, getConnectedLonePairsCount, getConnectedLonePairsList, getConnectedSingleElectronsCount, getConnectedSingleElectronsList, getElectronContainer, getElectronContainerCount, getFirstAtom, getLastAtom, getLonePair, getLonePairCount, getLonePairNumber, getMaximumBondOrder, getMinimumBondOrder, getSingleElectron, getSingleElectronCount, getSingleElectronNumber, getTitle, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, singleElectrons, stereoElements

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

getBuilder

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject

addListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Methods inherited from interface org.openscience.cdk.interfaces.IChemObjectListener

stateChanged

Methods inherited from interface org.openscience.cdk.interfaces.ICrystal

add, addAtom

Constructor Detail

Crystal

public Crystal()

Constructs a new crystal with zero length cell axis.

Crystal

public Crystal(IAtomContainer container)

Constructs a new crystal with zero length cell axis and adds the atoms in the AtomContainer as cell content.

Parameters:

container - the AtomContainer providing the atoms and bonds

Method Detail

setA

public void setA(javax.vecmath.Vector3d newAxis)

Sets the A unit cell axes in Cartesian coordinates in a Euclidean space.

Specified by:

setA in interface ICrystal

Parameters:

newAxis - the new A axis

See Also:

getA()

getA

public javax.vecmath.Vector3d getA()

Gets the A unit cell axes in Cartesian coordinates as a three element double array.

Specified by:

getA in interface ICrystal

Returns:

a Vector3D representing the A axis

See Also:

setA(javax.vecmath.Vector3d)

setB

public void setB(javax.vecmath.Vector3d newAxis)

Sets the B unit cell axes in Cartesian coordinates.

Specified by:

setB in interface ICrystal

Parameters:

newAxis - the new B axis

See Also:

getB()

getB

public javax.vecmath.Vector3d getB()

Gets the B unit cell axes in Cartesian coordinates as a three element double array.

Specified by:

getB in interface ICrystal

Returns:

a Vector3D representing the B axis

See Also:

setB(javax.vecmath.Vector3d)

setC

public void setC(javax.vecmath.Vector3d newAxis)

Sets the C unit cell axes in Cartesian coordinates.

Specified by:

setC in interface ICrystal

Parameters:

newAxis - the new C axis

See Also:

getC()

getC

public javax.vecmath.Vector3d getC()

Gets the C unit cell axes in Cartesian coordinates as a three element double array.

Specified by:

getC in interface ICrystal

Returns:

a Vector3D representing the C axis

See Also:

setC(javax.vecmath.Vector3d)

getSpaceGroup

public String getSpaceGroup()

Gets the space group of this crystal.

Specified by:

getSpaceGroup in interface ICrystal

Returns:

the space group of this crystal structure

See Also:

setSpaceGroup(java.lang.String)

setSpaceGroup

public void setSpaceGroup(String group)

Sets the space group of this crystal.

Specified by:

setSpaceGroup in interface ICrystal

Parameters:

group - the space group of this crystal structure

See Also:

getSpaceGroup()

getZ

public Integer getZ()

Gets the number of asymmetric parts in the unit cell.

Specified by:

getZ in interface ICrystal

Returns:

the number of asymmetric parts in the unit cell

See Also:

setZ(java.lang.Integer)

setZ

public void setZ(Integer value)

Sets the number of asymmetric parts in the unit cell.

Specified by:

setZ in interface ICrystal

Parameters:

value - the number of asymmetric parts in the unit cell

See Also:

getZ()

clone

public ICrystal clone()
               throws CloneNotSupportedException

Makes a clone of this crystal.

Specified by:

clone in interface IAtomContainer

Specified by:

clone in interface IChemObject

Specified by:

clone in interface ICrystal

Overrides:

clone in class AtomContainer

Returns:

The cloned crystal.

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned

toString

public String toString()

Returns a String representation of this crystal.

Specified by:

toString in interface IChemObject

Overrides:

toString in class AtomContainer

Returns:

a String representation of this object