public class Crystal extends AtomContainer implements Serializable, ICrystal, Cloneable
The crystal is designed to store only the asymmetric atoms. Though this is not enforced, it is assumed by all methods.
atomCount, atoms, bondCount, bonds, growArraySize, lonePairCount, lonePairs, singleElectronCount, singleElectrons, stereoElements
Constructor and Description |
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Crystal()
Constructs a new crystal with zero length cell axis.
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Crystal(IAtomContainer container)
Constructs a new crystal with zero length cell axis
and adds the atoms in the AtomContainer as cell content.
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Modifier and Type | Method and Description |
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ICrystal |
clone()
Makes a clone of this crystal.
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javax.vecmath.Vector3d |
getA()
Gets the A unit cell axes in Cartesian coordinates
as a three element double array.
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javax.vecmath.Vector3d |
getB()
Gets the B unit cell axes in Cartesian coordinates
as a three element double array.
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javax.vecmath.Vector3d |
getC()
Gets the C unit cell axes in Cartesian coordinates
as a three element double array.
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String |
getSpaceGroup()
Gets the space group of this crystal.
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Integer |
getZ()
Gets the number of asymmetric parts in the unit cell.
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void |
setA(javax.vecmath.Vector3d newAxis)
Sets the A unit cell axes in Cartesian coordinates in a
Euclidean space.
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void |
setB(javax.vecmath.Vector3d newAxis)
Sets the B unit cell axes in Cartesian coordinates.
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void |
setC(javax.vecmath.Vector3d newAxis)
Sets the C unit cell axes in Cartesian coordinates.
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void |
setSpaceGroup(String group)
Sets the space group of this crystal.
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void |
setZ(Integer value)
Sets the number of asymmetric parts in the unit cell.
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String |
toString()
Returns a String representation of this crystal.
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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
addListener, addProperties, compare, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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
addListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty
getBuilder
stateChanged
public Crystal()
public Crystal(IAtomContainer container)
container
- the AtomContainer providing the atoms and bondspublic void setA(javax.vecmath.Vector3d newAxis)
public javax.vecmath.Vector3d getA()
getA
in interface ICrystal
setA(javax.vecmath.Vector3d)
public void setB(javax.vecmath.Vector3d newAxis)
public javax.vecmath.Vector3d getB()
getB
in interface ICrystal
setB(javax.vecmath.Vector3d)
public void setC(javax.vecmath.Vector3d newAxis)
public javax.vecmath.Vector3d getC()
getC
in interface ICrystal
setC(javax.vecmath.Vector3d)
public String getSpaceGroup()
getSpaceGroup
in interface ICrystal
setSpaceGroup(java.lang.String)
public void setSpaceGroup(String group)
setSpaceGroup
in interface ICrystal
group
- the space group of this crystal structuregetSpaceGroup()
public Integer getZ()
getZ
in interface ICrystal
setZ(java.lang.Integer)
public void setZ(Integer value)
public ICrystal clone() throws CloneNotSupportedException
clone
in interface IAtomContainer
clone
in interface IChemObject
clone
in interface ICrystal
clone
in class AtomContainer
CloneNotSupportedException
- if the IChemObject cannot be clonedpublic String toString()
toString
in interface IChemObject
toString
in class AtomContainer
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