public interface ICrystal extends IAtomContainer
The crystal is designed to store only the asymetric atoms. Though this is not enforced, it is assumed by all methods.
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.
|
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, isEmpty, lonePairs, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, singleElectrons, stereoElements
addListener, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString
getBuilder
stateChanged
void add(IAtomContainer container)
add
in interface IAtomContainer
container
- The molecule to addvoid addAtom(IAtom atom)
addAtom
in interface IAtomContainer
atom
- the atom to addvoid setA(javax.vecmath.Vector3d newAxis)
newAxis
- the new A axisgetA()
javax.vecmath.Vector3d getA()
setA(javax.vecmath.Vector3d)
void setB(javax.vecmath.Vector3d newAxis)
newAxis
- the new B axisgetB()
javax.vecmath.Vector3d getB()
setB(javax.vecmath.Vector3d)
void setC(javax.vecmath.Vector3d newAxis)
newAxis
- the new C axisgetC()
javax.vecmath.Vector3d getC()
setC(javax.vecmath.Vector3d)
String getSpaceGroup()
setSpaceGroup(java.lang.String)
void setSpaceGroup(String group)
group
- the space group of this crystal structuregetSpaceGroup()
Integer getZ()
setZ(java.lang.Integer)
void setZ(Integer value)
value
- the number of assymetric parts in the unit cellgetZ()
ICrystal clone() throws CloneNotSupportedException
IChemObject
clone
in interface IAtomContainer
clone
in interface IChemObject
CloneNotSupportedException
- if the IChemObject cannot be cloned