org.openscience.cdk.interfaces

Interface ICrystal

All Superinterfaces:

Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener

All Known Implementing Classes:

Crystal, Crystal, DebugCrystal

public interface ICrystal
extends IAtomContainer

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 asymetric atoms. Though this is not enforced, it is assumed by all methods.

Source code:

master

Belongs to CDK module:

interfaces

Keywords:

crystal

Method Summary

Modifier and Type	Method and Description
void	add(IAtomContainer container) Adds the atoms in the AtomContainer as cell content.
void	addAtom(IAtom atom) Adds the atom to the crystal.
ICrystal	clone() Returns a deep clone of this IChemObject.
javax.vecmath.Vector3d	getA() Gets the A unit cell axes in carthesian coordinates as a three element double array.
javax.vecmath.Vector3d	getB() Gets the B unit cell axes in carthesian coordinates as a three element double array.
javax.vecmath.Vector3d	getC() Gets the C unit cell axes in carthesian 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 carthesian coordinates in a eucledian space.
void	setB(javax.vecmath.Vector3d newAxis) Sets the B unit cell axes in carthesian coordinates.
void	setC(javax.vecmath.Vector3d newAxis) Sets the C unit cell axes in carthesian coordinates.
void	setSpaceGroup(String group) Sets the space group of this crystal.
void	setZ(Integer value) Sets the number of assymmetric parts in the unit cell.

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.IChemObject

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

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

getBuilder

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

stateChanged

Method Detail

add

void add(IAtomContainer container)

Adds the atoms in the AtomContainer as cell content. Symmetry related atoms should not be added unless P1 space group is used.

Specified by:

add in interface IAtomContainer

Parameters:

container - The molecule to add

addAtom

void addAtom(IAtom atom)

Adds the atom to the crystal. Symmetry related atoms should not be added unless P1 space group is used.

Specified by:

addAtom in interface IAtomContainer

Parameters:

atom - the atom to add

setA

void setA(javax.vecmath.Vector3d newAxis)

Sets the A unit cell axes in carthesian coordinates in a eucledian space.

Parameters:

newAxis - the new A axis

See Also:

getA()

getA

javax.vecmath.Vector3d getA()

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

Returns:

a Vector3D representing the A axis

See Also:

setA(javax.vecmath.Vector3d)

setB

void setB(javax.vecmath.Vector3d newAxis)

Sets the B unit cell axes in carthesian coordinates.

Parameters:

newAxis - the new B axis

See Also:

getB()

getB

javax.vecmath.Vector3d getB()

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

Returns:

a Vector3D representing the B axis

See Also:

setB(javax.vecmath.Vector3d)

setC

void setC(javax.vecmath.Vector3d newAxis)

Sets the C unit cell axes in carthesian coordinates.

Parameters:

newAxis - the new C axis

See Also:

getC()

getC

javax.vecmath.Vector3d getC()

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

Returns:

a Vector3D representing the C axis

See Also:

setC(javax.vecmath.Vector3d)

getSpaceGroup

String getSpaceGroup()

Gets the space group of this crystal.

Returns:

the space group of this crystal structure

See Also:

setSpaceGroup(java.lang.String)

setSpaceGroup

void setSpaceGroup(String group)

Sets the space group of this crystal.

Parameters:

group - the space group of this crystal structure

See Also:

getSpaceGroup()

getZ

Integer getZ()

Gets the number of asymmetric parts in the unit cell.

Returns:

the number of assymetric parts in the unit cell

See Also:

setZ(java.lang.Integer)

setZ

void setZ(Integer value)

Sets the number of assymmetric parts in the unit cell.

Parameters:

value - the number of assymetric parts in the unit cell

See Also:

getZ()

clone

ICrystal clone()
        throws CloneNotSupportedException

Returns a deep clone of this IChemObject.

Specified by:

clone in interface IAtomContainer

Specified by:

clone in interface IChemObject

Returns:

Object the clone of this IChemObject.

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned