Package org.jmol.symmetry
Class SpaceGroup
- java.lang.Object
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- org.jmol.symmetry.SpaceGroup
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class SpaceGroup extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description (package private) char
ambiguityType
private static java.lang.String
ambiguousNames
(package private) char
axisChoice
private static java.lang.String[]
canonicalSeitzList
(package private) java.lang.String
crystalClass
(package private) boolean
doNormalize
(package private) SymmetryOperation[]
finalOperations
(package private) HallInfo
hallInfo
(package private) java.lang.String
hallSymbol
(package private) java.lang.String
hmSymbol
(package private) java.lang.String
hmSymbolAbbr
(package private) java.lang.String
hmSymbolAbbrShort
(package private) java.lang.String
hmSymbolAlternative
(package private) java.lang.String
hmSymbolExt
(package private) java.lang.String
hmSymbolFull
private static java.util.Map<java.lang.Integer,javajs.util.Lst<SpaceGroup>>
htByOpCount
(package private) int
index
(package private) java.lang.String
intlTableNumber
(package private) java.lang.String
intlTableNumberExt
(package private) java.lang.String
intlTableNumberFull
(package private) boolean
isBilbao
(package private) boolean
isBio
(package private) boolean
isSSG
private static java.lang.String
lastInfo
(package private) int
latticeOp
(package private) int
latticeParameter
(package private) java.lang.String
latticeType
private int
modDim
(package private) java.lang.String
name
private static int
NAME_HALL
private static int
NAME_HM
private static int
NAME_UNK
private java.lang.Integer
nHallOperators
(package private) int
operationCount
(package private) SymmetryOperation[]
operations
private static SpaceGroup[]
SG
private static int
sgIndex
private static java.lang.String[]
STR_SG
intlNo:options;nOps;schoenflies;hermannMauguin;Hall;BilbaoFlag(package private) char
uniqueAxis
(package private) java.util.Map<java.lang.String,java.lang.Integer>
xyzList
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Constructor Summary
Constructors Modifier Constructor Description private
SpaceGroup(int index, java.lang.String cifLine, boolean doInit)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description (package private) boolean
addLatticeVectors(javajs.util.Lst<float[]> lattvecs)
private int
addOp(SymmetryOperation op, java.lang.String xyz0, boolean isSpecial)
private int
addOperation(java.lang.String xyz0, int opId, boolean allowScaling)
(package private) int
addSymmetry(java.lang.String xyz, int opId, boolean allowScaling)
(package private) int
addSymmetrySM(java.lang.String xyz, javajs.util.M4 operation)
private void
buildSpaceGroup(java.lang.String cifLine)
private int
checkXYZlist(java.lang.String xyz)
private static SpaceGroup
createSGFromList(java.lang.String name, javajs.util.Lst<?> data)
(package private) static SpaceGroup
createSpaceGroup(int desiredSpaceGroupIndex, java.lang.String name, java.lang.Object data, int modDim)
private static SpaceGroup
createSpaceGroupN(java.lang.String name)
private static SpaceGroup[]
createSpaceGroups()
private static SpaceGroup
determineSpaceGroup(java.lang.String name, float a, float b, float c, float alpha, float beta, float gamma, int lastIndex)
private static int
determineSpaceGroupIndex(java.lang.String name, float a, float b, float c, float alpha, float beta, float gamma, int lastIndex)
private static SpaceGroup
determineSpaceGroupN(java.lang.String name)
(package private) static SpaceGroup
determineSpaceGroupNA(java.lang.String name, float[] unitCellParams)
private static SpaceGroup
determineSpaceGroupNS(java.lang.String name, SpaceGroup sg)
private static char
determineUniqueAxis(float a, float b, float c, float alpha, float beta, float gamma)
private static java.lang.String
dumpAll()
private static java.lang.String
dumpAllSeitz()
private java.lang.Object
dumpCanonicalSeitzList()
(package private) java.lang.String
dumpInfo()
(package private) java.lang.Object
dumpInfoObj()
private static SpaceGroup
findSpaceGroup(int opCount, java.lang.String s)
private void
generateAllOperators(HallInfo h)
private void
generateOperatorsFromXyzInfo(java.lang.String xyzInfo)
private static java.lang.String
getCanonicalSeitz(int i)
private java.lang.String
getCanonicalSeitzList()
(package private) SpaceGroup
getDerivedSpaceGroup()
(package private) static java.lang.Object
getInfo(SpaceGroup sg, java.lang.String spaceGroup, SymmetryInterface cellInfo, boolean asMap)
(package private) java.lang.String
getLatticeDesignation()
(package private) java.lang.String
getName()
(package private) static SpaceGroup
getNull(boolean doInit, boolean doNormalize, boolean doFinalize)
(package private) javajs.util.M4
getOperation(int i)
(package private) int
getOperationCount()
javajs.util.M4
getRawOperation(int i)
(package private) int
getSiteMultiplicity(javajs.util.P3 pt, UnitCell unitCell)
private static SpaceGroup[]
getSpaceGroups()
(package private) java.lang.String
getXyz(int i, boolean doNormalize)
private void
init(boolean addXYZ)
(package private) void
newPoint(int i, javajs.util.P3 atom1, javajs.util.P3 atom2, int transX, int transY, int transZ)
(package private) void
setFinalOperations(javajs.util.P3[] atoms, int atomIndex, int count, boolean doNormalize)
private void
setHMSymbol(java.lang.String name)
private void
setLattice(char latticeCode, boolean isCentrosymmetric)
(package private) void
setLatticeParam(int latticeParameter)
void
setName(java.lang.String name)
private static java.lang.String
toCap(java.lang.String s, int n)
java.lang.String
toString()
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Field Detail
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index
int index
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isSSG
boolean isSSG
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name
java.lang.String name
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hallSymbol
java.lang.String hallSymbol
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crystalClass
java.lang.String crystalClass
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hmSymbol
java.lang.String hmSymbol
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hmSymbolFull
java.lang.String hmSymbolFull
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hmSymbolExt
java.lang.String hmSymbolExt
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hmSymbolAbbr
java.lang.String hmSymbolAbbr
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hmSymbolAlternative
java.lang.String hmSymbolAlternative
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hmSymbolAbbrShort
java.lang.String hmSymbolAbbrShort
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ambiguityType
char ambiguityType
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uniqueAxis
char uniqueAxis
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axisChoice
char axisChoice
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intlTableNumber
java.lang.String intlTableNumber
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intlTableNumberFull
java.lang.String intlTableNumberFull
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intlTableNumberExt
java.lang.String intlTableNumberExt
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hallInfo
HallInfo hallInfo
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latticeParameter
int latticeParameter
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operations
SymmetryOperation[] operations
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finalOperations
SymmetryOperation[] finalOperations
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operationCount
int operationCount
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latticeOp
int latticeOp
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xyzList
java.util.Map<java.lang.String,java.lang.Integer> xyzList
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modDim
private int modDim
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doNormalize
boolean doNormalize
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isBio
boolean isBio
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isBilbao
boolean isBilbao
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latticeType
java.lang.String latticeType
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nHallOperators
private java.lang.Integer nHallOperators
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canonicalSeitzList
private static java.lang.String[] canonicalSeitzList
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NAME_UNK
private static final int NAME_UNK
- See Also:
- Constant Field Values
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NAME_HM
private static final int NAME_HM
- See Also:
- Constant Field Values
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NAME_HALL
private static final int NAME_HALL
- See Also:
- Constant Field Values
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sgIndex
private static int sgIndex
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ambiguousNames
private static java.lang.String ambiguousNames
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lastInfo
private static java.lang.String lastInfo
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SG
private static SpaceGroup[] SG
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htByOpCount
private static java.util.Map<java.lang.Integer,javajs.util.Lst<SpaceGroup>> htByOpCount
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STR_SG
private static java.lang.String[] STR_SG
intlNo:options;nOps;schoenflies;hermannMauguin;Hall;BilbaoFlag
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Method Detail
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getNull
static SpaceGroup getNull(boolean doInit, boolean doNormalize, boolean doFinalize)
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init
private void init(boolean addXYZ)
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createSpaceGroup
static SpaceGroup createSpaceGroup(int desiredSpaceGroupIndex, java.lang.String name, java.lang.Object data, int modDim)
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createSGFromList
private static SpaceGroup createSGFromList(java.lang.String name, javajs.util.Lst<?> data)
- Parameters:
name
-data
- Lstor Lst - Returns:
- a new SpaceGroup if successful or null
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addSymmetry
int addSymmetry(java.lang.String xyz, int opId, boolean allowScaling)
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setFinalOperations
void setFinalOperations(javajs.util.P3[] atoms, int atomIndex, int count, boolean doNormalize)
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getOperationCount
int getOperationCount()
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getOperation
javajs.util.M4 getOperation(int i)
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getXyz
java.lang.String getXyz(int i, boolean doNormalize)
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newPoint
void newPoint(int i, javajs.util.P3 atom1, javajs.util.P3 atom2, int transX, int transY, int transZ)
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getInfo
static java.lang.Object getInfo(SpaceGroup sg, java.lang.String spaceGroup, SymmetryInterface cellInfo, boolean asMap)
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dumpInfo
java.lang.String dumpInfo()
- Returns:
- detailed information
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dumpInfoObj
java.lang.Object dumpInfoObj()
- Returns:
- detailed information
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getName
java.lang.String getName()
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getLatticeDesignation
java.lang.String getLatticeDesignation()
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setLatticeParam
void setLatticeParam(int latticeParameter)
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dumpCanonicalSeitzList
private java.lang.Object dumpCanonicalSeitzList()
- Returns:
- either a String or a SpaceGroup, depending on index.
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getDerivedSpaceGroup
SpaceGroup getDerivedSpaceGroup()
- Returns:
- a known space group or null
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getCanonicalSeitzList
private java.lang.String getCanonicalSeitzList()
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findSpaceGroup
private static SpaceGroup findSpaceGroup(int opCount, java.lang.String s)
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dumpAll
private static final java.lang.String dumpAll()
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dumpAllSeitz
private static final java.lang.String dumpAllSeitz()
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getCanonicalSeitz
private static java.lang.String getCanonicalSeitz(int i)
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setLattice
private void setLattice(char latticeCode, boolean isCentrosymmetric)
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createSpaceGroupN
private static final SpaceGroup createSpaceGroupN(java.lang.String name)
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addOperation
private int addOperation(java.lang.String xyz0, int opId, boolean allowScaling)
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checkXYZlist
private int checkXYZlist(java.lang.String xyz)
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addOp
private int addOp(SymmetryOperation op, java.lang.String xyz0, boolean isSpecial)
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generateOperatorsFromXyzInfo
private void generateOperatorsFromXyzInfo(java.lang.String xyzInfo)
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generateAllOperators
private void generateAllOperators(HallInfo h)
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addSymmetrySM
int addSymmetrySM(java.lang.String xyz, javajs.util.M4 operation)
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determineSpaceGroupN
private static final SpaceGroup determineSpaceGroupN(java.lang.String name)
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determineSpaceGroupNS
private static final SpaceGroup determineSpaceGroupNS(java.lang.String name, SpaceGroup sg)
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determineSpaceGroupNA
static final SpaceGroup determineSpaceGroupNA(java.lang.String name, float[] unitCellParams)
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determineSpaceGroup
private static final SpaceGroup determineSpaceGroup(java.lang.String name, float a, float b, float c, float alpha, float beta, float gamma, int lastIndex)
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determineSpaceGroupIndex
private static final int determineSpaceGroupIndex(java.lang.String name, float a, float b, float c, float alpha, float beta, float gamma, int lastIndex)
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determineUniqueAxis
private static final char determineUniqueAxis(float a, float b, float c, float alpha, float beta, float gamma)
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buildSpaceGroup
private void buildSpaceGroup(java.lang.String cifLine)
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setHMSymbol
private void setHMSymbol(java.lang.String name)
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toCap
private static java.lang.String toCap(java.lang.String s, int n)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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getSpaceGroups
private static SpaceGroup[] getSpaceGroups()
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createSpaceGroups
private static SpaceGroup[] createSpaceGroups()
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addLatticeVectors
boolean addLatticeVectors(javajs.util.Lst<float[]> lattvecs)
- Parameters:
lattvecs
- could be magnetic centering, in which case there is an additional lattice parameter that is time reversal- Returns:
- true if successful
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getSiteMultiplicity
int getSiteMultiplicity(javajs.util.P3 pt, UnitCell unitCell)
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setName
public void setName(java.lang.String name)
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getRawOperation
public javajs.util.M4 getRawOperation(int i)
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