Package org.jmol.symmetry
Class SpaceGroup
- java.lang.Object
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- org.jmol.symmetry.SpaceGroup
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class SpaceGroup extends Object
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Field Summary
Fields Modifier and Type Field Description (package private) char
ambiguityType
private static String
ambiguousNames
(package private) char
axisChoice
private static String[]
canonicalSeitzList
(package private) String
crystalClass
(package private) boolean
doNormalize
(package private) SymmetryOperation[]
finalOperations
(package private) HallInfo
hallInfo
(package private) String
hallSymbol
(package private) String
hmSymbol
(package private) String
hmSymbolAbbr
(package private) String
hmSymbolAbbrShort
(package private) String
hmSymbolAlternative
(package private) String
hmSymbolExt
(package private) String
hmSymbolFull
private static Map<Integer,javajs.util.Lst<SpaceGroup>>
htByOpCount
(package private) int
index
private Map<String,Object>
info
(package private) String
intlTableNumber
(package private) String
intlTableNumberExt
(package private) String
intlTableNumberFull
(package private) boolean
isBilbao
(package private) boolean
isBio
(package private) boolean
isSSG
private static String
lastInfo
(package private) int
latticeOp
(package private) int
latticeParameter
(package private) String
latticeType
private int
modDim
(package private) String
name
private static int
NAME_HALL
private static int
NAME_HM
private static int
NAME_UNK
private Integer
nHallOperators
(package private) int
operationCount
(package private) SymmetryOperation[]
operations
private static SpaceGroup[]
SG
private static int
sgIndex
private static String[]
STR_SG
intlNo:options;nOps;schoenflies;hermannMauguin;Hall;BilbaoFlag(package private) char
uniqueAxis
(package private) Map<String,Integer>
xyzList
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Constructor Summary
Constructors Modifier Constructor Description private
SpaceGroup(int index, 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, String xyz0, boolean isSpecial)
private int
addOperation(String xyz0, int opId, boolean allowScaling)
(package private) int
addSymmetry(String xyz, int opId, boolean allowScaling)
(package private) int
addSymmetrySM(String xyz, javajs.util.M4 operation)
private void
buildSpaceGroup(String cifLine)
private int
checkXYZlist(String xyz)
private static SpaceGroup
createSGFromList(String name, javajs.util.Lst<?> data)
(package private) static SpaceGroup
createSpaceGroup(int desiredSpaceGroupIndex, String name, Object data, int modDim)
private static SpaceGroup
createSpaceGroupN(String name)
private static SpaceGroup[]
createSpaceGroups()
private static SpaceGroup
determineSpaceGroup(String name, float a, float b, float c, float alpha, float beta, float gamma, int lastIndex)
private static int
determineSpaceGroupIndex(String name, float a, float b, float c, float alpha, float beta, float gamma, int lastIndex)
private static SpaceGroup
determineSpaceGroupN(String name)
(package private) static SpaceGroup
determineSpaceGroupNA(String name, float[] unitCellParams)
private static SpaceGroup
determineSpaceGroupNS(String name, SpaceGroup sg)
private static char
determineUniqueAxis(float a, float b, float c, float alpha, float beta, float gamma)
private static String
dumpAll()
private static String
dumpAllSeitz()
private Object
dumpCanonicalSeitzList()
(package private) String
dumpInfo()
(package private) Object
dumpInfoObj()
private static SpaceGroup
findSpaceGroup(int opCount, String s)
private void
generateAllOperators(HallInfo h)
private void
generateOperatorsFromXyzInfo(String xyzInfo)
private static String
getCanonicalSeitz(int i)
private String
getCanonicalSeitzList()
(package private) SpaceGroup
getDerivedSpaceGroup()
private Map<String,Object>
getInfo(SymmetryInterface cellInfo)
(package private) static Object
getInfo(SpaceGroup sg, String spaceGroup, SymmetryInterface cellInfo, boolean asMap)
(package private) String
getLatticeDesignation()
(package private) 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()
(package private) int
getSiteMultiplicity(javajs.util.P3 pt, UnitCell unitCell)
private static SpaceGroup[]
getSpaceGroups()
(package private) 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(String name)
private void
setLattice(char latticeCode, boolean isCentrosymmetric)
(package private) void
setLatticeParam(int latticeParameter)
void
setName(String name)
private static String
toCap(String s, int n)
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
String name
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hallSymbol
String hallSymbol
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crystalClass
String crystalClass
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hmSymbol
String hmSymbol
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hmSymbolFull
String hmSymbolFull
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hmSymbolExt
String hmSymbolExt
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hmSymbolAbbr
String hmSymbolAbbr
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hmSymbolAlternative
String hmSymbolAlternative
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hmSymbolAbbrShort
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
String intlTableNumber
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intlTableNumberFull
String intlTableNumberFull
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intlTableNumberExt
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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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
String latticeType
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nHallOperators
private Integer nHallOperators
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canonicalSeitzList
private static 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 String ambiguousNames
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lastInfo
private static String lastInfo
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SG
private static SpaceGroup[] SG
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htByOpCount
private static Map<Integer,javajs.util.Lst<SpaceGroup>> htByOpCount
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STR_SG
private static String[] STR_SG
intlNo:options;nOps;schoenflies;hermannMauguin;Hall;BilbaoFlag
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Constructor Detail
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SpaceGroup
private SpaceGroup(int index, String cifLine, boolean doInit)
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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, String name, Object data, int modDim)
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createSGFromList
private static SpaceGroup createSGFromList(String name, javajs.util.Lst<?> data)
- Parameters:
name
-data
- Lst<SymmetryOperation> or Lst<M4>- Returns:
- a new SpaceGroup if successful or null
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addSymmetry
int addSymmetry(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
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 Object getInfo(SpaceGroup sg, String spaceGroup, SymmetryInterface cellInfo, boolean asMap)
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getInfo
private Map<String,Object> getInfo(SymmetryInterface cellInfo)
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dumpInfo
String dumpInfo()
- Returns:
- detailed information
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dumpInfoObj
Object dumpInfoObj()
- Returns:
- detailed information
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getName
String getName()
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getLatticeDesignation
String getLatticeDesignation()
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setLatticeParam
void setLatticeParam(int latticeParameter)
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dumpCanonicalSeitzList
private 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 String getCanonicalSeitzList()
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findSpaceGroup
private static SpaceGroup findSpaceGroup(int opCount, String s)
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dumpAll
private static final String dumpAll()
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dumpAllSeitz
private static final String dumpAllSeitz()
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getCanonicalSeitz
private static 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(String name)
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addOperation
private int addOperation(String xyz0, int opId, boolean allowScaling)
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checkXYZlist
private int checkXYZlist(String xyz)
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addOp
private int addOp(SymmetryOperation op, String xyz0, boolean isSpecial)
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generateOperatorsFromXyzInfo
private void generateOperatorsFromXyzInfo(String xyzInfo)
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generateAllOperators
private void generateAllOperators(HallInfo h)
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addSymmetrySM
int addSymmetrySM(String xyz, javajs.util.M4 operation)
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determineSpaceGroupN
private static final SpaceGroup determineSpaceGroupN(String name)
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determineSpaceGroupNS
private static final SpaceGroup determineSpaceGroupNS(String name, SpaceGroup sg)
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determineSpaceGroupNA
static final SpaceGroup determineSpaceGroupNA(String name, float[] unitCellParams)
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determineSpaceGroup
private static final SpaceGroup determineSpaceGroup(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(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(String cifLine)
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setHMSymbol
private void setHMSymbol(String name)
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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(String name)
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